Works (68)
Updated: April 22nd, 2024 05:37
2024 article
A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters
Fernandez-Moreno, J.-P., Yaschenko, A. E., Neubauer, M., Marchi, A. J., Zhao, C., Ascencio-Ibanez, J. T., … Stepanova, A. N. (2024, February 21). PLANT BIOTECHNOLOGY JOURNAL, Vol. 2.
author keywords: repetitive DNA sequence; GoldenBraid; cis-element; sequence stuffer; hormone-responsive promoter; ethylene reporter
TL;DR:
Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes.
(via Semantic Scholar)
doi.org (publisher)
Sources: ORCID, Web Of Science
Added: February 22, 2024
2024 article
Arabidopsis as a model for translational research
Yaschenko, A. E., Alonso, J. M., & Stepanova, A. N. (2024, February 27). PLANT CELL, Vol. 2.
TL;DR:
It is envisioned that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 1, 2024
2022 review
Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 68.
author keywords: Tissue specificity; Gene expression; Synthetic biology; Transcription; factor; Epigenetics; Single cell; Transcriptomics; Logic gate; Promoter; Cis-regulatory element
MeSH headings : Computational Biology; Gene Expression; Gene Regulatory Networks / genetics; Plants / genetics; Plants / metabolism; Promoter Regions, Genetic / genetics; Synthetic Biology; Transcription Factors / metabolism
TL;DR:
Synthetic biology shows great promise not only as a means of testing candidate DNA motifs but also for establishing the general rules of nature driving promoter architecture and for the rational design of genetic circuits in research and agriculture to confer tissue-specific expression to genes or molecular pathways of interest.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: June 12, 2022
2022 journal article
To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses
PLANTS-BASEL, 11(1).
author keywords: ethylene; abiotic stress; hormone crosstalk; growth and defense tradeoff
TL;DR:
The crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses is described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: December 24, 2021
2021 journal article
Auxin Interactions with Other Hormones in Plant Development
Cold Spring Harbor Perspectives in Biology, 13(10), a039990.
MeSH headings : Indoleacetic Acids / metabolism; Plant Development; Plant Growth Regulators / metabolism
TL;DR:
A glimpse into the complexity of hormone interactions that involve auxin is provided, underscoring how patchy current understanding of this crosstalk is.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, Crossref
Added: April 27, 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
4. Quality Education
(Web of Science)
Sources: Web Of Science, ORCID
Added: February 9, 2022
2021 article
Editorial overview: Toward deciphering the molecular basis of plant phenotypic plasticity
Qiao, H., & Stepanova, A. N. (2021, October). CURRENT OPINION IN PLANT BIOLOGY, Vol. 63.
MeSH headings : Adaptation, Physiological; Plants / genetics
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: Web Of Science, ORCID
Added: November 15, 2021
2021 journal article
Leveraging synthetic biology approaches in plant hormone research
Current Opinion in Plant Biology.
MeSH headings : Biotechnology; Plant Growth Regulators; Plants / genetics; Synthetic Biology
TL;DR:
First examples of successful tool development and their applications in the area of plant hormone research are emerging, paving the way for new cadres to enter this promising field of science.
(via Semantic Scholar)
Source: ORCID
Added: January 20, 2021
2021 review
Leveraging synthetic biology approaches in plant hormone research
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 60.
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: June 28, 2021
2021 article
Plant Biology Research: What Is Next?
Stepanova, A. N. (2021, September 30). FRONTIERS IN PLANT SCIENCE, Vol. 12.
author keywords: plant biology; plant physiology; synthetic biology; translational research; data reproducibility
TL;DR:
I present my personal perspective on what the immediate questions and the biggest longer-term issues in plant science are, and suggest some themes and directions for future research in plant biology.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: November 8, 2021
2020 journal article
An Improved Recombineering Toolset for Plants
The Plant Cell.
MeSH headings : Arabidopsis / genetics; Chromosomes, Artificial, Bacterial; Gene Editing / methods; Genes, Reporter; Genetic Engineering / methods; Plants / genetics; Plants, Genetically Modified / genetics; Recombination, Genetic
TL;DR:
A scalable recombinase-mediated cassette exchange system to facilitate the transfer of the desired sequences from a bacterial artificial chromosome clone to a transformation-compatible binary vector is developed, expanding the use of the recombineering approaches beyond Arabidopsis (Arabidopsis thaliana).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: ORCID
Added: January 11, 2020
2020 journal article
Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 34(6).
MeSH headings : Arabidopsis / chemistry; Arabidopsis / genetics; Arabidopsis Proteins / genetics; Indoleacetic Acids / analysis; Indoles / analysis; Mutation; Oximes / analysis; Oxygenases / genetics; Seedlings / chemistry; Seedlings / genetics; Spectrometry, Mass, Electrospray Ionization / methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods
TL;DR:
IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations and was shown to be an appropriate sampling surface for IR-MALDESI mass spectrometry imaging of Arabidopsis seedlings.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: March 10, 2020
2020 journal article
Monitoring Ethylene in Plants: Genetically Encoded Reporters and Biosensors
Small Methods.
author keywords: biosensors; ethylene; hormones; reporters; signaling
TL;DR:
This manuscript focuses on the different approaches employed by plant biologists to monitor ethylene biosynthesis and action in plants, with a special emphasis made on genetically encoded sensors.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2020 journal article
Structure–Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes
Plant Physiology, 183(3), 1110–1125.
MeSH headings : Alleles; Arabidopsis / genetics; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Binding Sites; Carbon-Sulfur Lyases / chemistry; Carbon-Sulfur Lyases / genetics; Carbon-Sulfur Lyases / metabolism; Cotyledon / genetics; Genetic Complementation Test; Genetic Loci; Heterozygote; Models, Molecular; Mutation / genetics; Phenotype; Plants, Genetically Modified; Protein Multimerization; Structure-Activity Relationship
TL;DR:
This work identified an allelic series of fertile, hypomorphic Arabidopsis (Arabidopsis thaliana) mutants for the essential glucosinolate biosynthetic gene ROOTY (RTY) that exhibit a range of phenotypic defects characteristic of enhanced auxin production and underscores the importance of employing true null mutants in genetic complementation studies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: ORCID
Added: July 2, 2020
2019 article
An improved plant toolset for high-throughput recombineering
Brumos, J., Zhao, C., Gong, Y., Soriano, D., Patel, A. P., Perez-Amador, M. A., … Alonso, J. M. (2019, June 3). (Vol. 6). Vol. 6.
TL;DR:
A recombineering-based tagging system that brings together the convenience of the classical transgenic approaches and the high degree of confidence in the obtained results provided by the direct chromosomal tagging achievable by genome editing strategies is developed.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2019 journal article
Epigenetic silencing of a multifunctional plant stress regulator
ELIFE, 8.
MeSH headings : Arabidopsis / physiology; Arabidopsis Proteins / biosynthesis; Arabidopsis Proteins / metabolism; Epigenesis, Genetic; Ethylenes / metabolism; Gene Expression Regulation, Plant; Nuclear Proteins / metabolism; Receptors, Cell Surface / biosynthesis; Signal Transduction; Transcription Factors / metabolism
TL;DR:
A chromatin-dependent regulatory mechanism at EIN2 requiring two genes is identified, which safeguards the expression of an essential multifunctional plant stress regulator.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID
Added: September 30, 2019
2019 article
From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration
Stepanova, A. N., & Alonso, J. M. (2019, July). PLANT CELL, Vol. 31, pp. 1393–1394.
MeSH headings : Ethylenes / metabolism; Gene Expression Regulation, Plant; Indoleacetic Acids / metabolism; Models, Biological; Plant Proteins / metabolism; Plant Roots / metabolism; Signal Transduction
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: July 29, 2019
2019 article
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Perkins, P., Mazzoni-Putman, S., Stepanova, A., Alonso, J., & Heber, S. (2019, June 6). BMC GENOMICS, Vol. 20.
author keywords: Ribo-seq; Next-generation sequencing; Data analysis; Web application
MeSH headings : Computer Graphics; Genomics / methods; High-Throughput Nucleotide Sequencing / methods; Humans; Protein Biosynthesis; Quality Control; RNA, Messenger / genetics; RNA, Messenger / metabolism; Ribosomes / metabolism; Sequence Analysis, RNA; Software; Transcriptome; Web Browser
TL;DR:
RiboStreamR is presented, a comprehensive Ribo-seq quality control (QC) platform in the form of an R Shiny web application that provides visualization and analysis tools for various Ribe-seq QC metrics, including read length distribution, read periodicity, and translational efficiency.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: July 1, 2019
2018 review
A Plant Biologist's Toolbox to Study Translation
[Review of ]. FRONTIERS IN PLANT SCIENCE, 9.
author keywords: translation; ribosome; Ribo-seq; TRAP; polysome profiling; toeprinting; reporter; amino acid tagging
TL;DR:
A review of translational methods in plant biology covering a broad range of methods to measure changes in global translation, with a particular note of how applications from other model systems might be extended for use in plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2018 journal article
A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
Nature Communications, 9(1).
Contributors: R. Bhosale *, J. Giri *, B. Pandey *, R. Giehl *, A. Hartmann*, R. Traini*, J. Truskina*, N. Leftley *
MeSH headings : Arabidopsis / drug effects; 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, Plant; Gravitropism / physiology; Indoleacetic Acids / metabolism; Organogenesis, Plant / drug effects; Organogenesis, Plant / genetics; Phosphates / deficiency; Phosphates / pharmacology; Plant Growth Regulators / metabolism; Plant Roots / drug effects; Plant Roots / genetics; Plant Roots / growth & development; Plant Roots / metabolism; Plants, Genetically Modified; Stress, Physiological; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is reported that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P, and auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Crossref
Added: December 19, 2019
2018 journal article
Author Correction: A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
Nature Communications, 9(1), 1818.
Contributors: R. Bhosale *, J. Giri *, B. Pandey *, R. Giehl *, A. Hartmann*, R. Traini*, J. Truskina*, N. Leftley *
TL;DR:
The original version of this Article omitted the following from the Acknowledgements: ‘The authors also thank DBT-CREST BT/HRD/03/01/2002’.
(via Semantic Scholar)
Sources: ORCID, Crossref
Added: December 19, 2019
2018 journal article
Local Auxin Biosynthesis Is a Key Regulator of Plant Development
DEVELOPMENTAL CELL, 47(3), 306-+.
Contributors: J. Brumos n, L. Robles n, J. Yun n, T. Vu n, S. Jackson n, J. Alonso n, n
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Biological Transport; Ethylenes / metabolism; Flowers / metabolism; Gene Expression Regulation, Plant / genetics; Indoleacetic Acids / metabolism; Meristem / embryology; Meristem / metabolism; Morphogenesis; Oxygenases; Plant Development / genetics; Plant Growth Regulators / genetics; Plant Growth Regulators / metabolism; Plant Roots / embryology; Plant Roots / genetics; Plant Roots / metabolism; Spatio-Temporal Analysis
TL;DR:
This study systematically addressed the role of local auxin biosynthesis in plant development and responses to the stress phytohormone ethylene by manipulating spatiotemporal patterns of WEI8 and revealed that local auxIn biosynthesis and transport act synergistically and are individually dispensable for root meristem maintenance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: November 26, 2018
2017 journal article
Editorial: Relevance of translational regulation on plant growth and environmental responses
Frontiers in Plant Science, 8.
Contributors: A. Ferrando *, M. Castellano *, P. Lisón *, D. Leister *, n & J. Hanson *
author keywords: mRNA translation; translation factors; post-transcriptional regulation; translatome; organellar gene expression
TL;DR:
The paper’s aim was to demonstrate the importance of translational regulation on plant growth and environmental Responses and the role that language plays in the development of knowledge and policy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
12. Responsible Consumption and Production
(Web of Science)
13. Climate Action
(Web of Science)
Source: ORCID
Added: December 19, 2019
2017 journal article
The triple response assay and its use to characterize ethylene mutants in Arabidopsis
Ethylene Signaling: Methods and Protocols, 1573, 163–209.
Source: NC State University Libraries
Added: August 6, 2018
2017 chapter
The triple response assay and its use to characterize ethylene mutants in arabidopsis
In Methods in Molecular Biology (Vol. 1573, pp. 163–209).
Contributors: C. Merchante * & n
author keywords: Phytohormone; Ethylene; ACC; Triple response; Arabidopsis; Seedlings; Germination; Hypocotyl; Root; Apical hook; Mutants
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Biological Assay / methods; Ethylenes / metabolism; Ethylenes / pharmacology; Gene Expression Regulation, Plant / drug effects; Germination / drug effects; Germination / genetics; Mutation; Phenotype; Plant Growth Regulators / metabolism; Plant Growth Regulators / pharmacology; Seedlings / drug effects; Seedlings / genetics; Seedlings / metabolism
TL;DR:
A simple protocol for assaying the triple response in Arabidopsis is described, which can also be employed in many other dicot species, with minor modifications to account for species-specific differences in germination.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: ORCID
Added: December 19, 2019
2017 journal article
Translation regulation in plants: an interesting past, an exciting present and a promising future
PLANT JOURNAL, 90(4), 628–653.
Contributors: C. Merchante *, n & J. Alonso n
author keywords: translation; upstream open reading frames; internal ribosomal entry sites; gene-specific translation; global regulation of translation; RNA-binding protein
MeSH headings : Gene Expression Regulation / genetics; Gene Expression Regulation / physiology; Open Reading Frames / genetics; Plants / genetics; Plants / metabolism; Protein Biosynthesis / genetics; Protein Biosynthesis / physiology; RNA, Plant / genetics; RNA, Plant / metabolism; Ribosomes / genetics; Ribosomes / metabolism
TL;DR:
The use of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2016 article
Auxin catabolism unplugged: Role of IAA oxidation in auxin homeostasis
Stepanova, A. N., & Alonso, J. M. (2016, September 27). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 113, pp. 10742–10744.
Contributors: n & J. Alonso n
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Genes, Plant; Homeostasis; Indoleacetic Acids / metabolism
TL;DR:
The recent identification of a rice 2-oxoglutarate-dependent-Fe(II) dioxygenase, originally linked to male fertility in rice and capable of oxidizing IAA into oxIAA, has opened new avenues for addressing the physiological significance of auxin catabolism in plant growth and 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, ORCID
Added: August 6, 2018
2016 article
Cutting Out the Middle Man in Light-Hormone Interactions
Stepanova, A. N., & Alonso, J. M. (2016, December 5). DEVELOPMENTAL CELL, Vol. 39, pp. 524–526.
Contributors: n & J. Alonso n
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Ethylenes / metabolism; Gene Expression Regulation, Plant; Nuclear Proteins / genetics; Transcription Factors / genetics
TL;DR:
Findings provide a paradigm for crosstalk between light and hormone signaling pathways in red-light-activated phytochrome B by bringing the F-box proteins EBF1 and 2 to the complex.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2016 journal article
Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana
IEEE Transactions on Nanobioscience, 15(2), 150–159.
Contributors: Q. Hu n, C. Merchante *, n , J. Alonso n & S. Heber n
author keywords: Arabidopsis thaliana; classification; ribosome foot-printing; semi-supervised learning; stacking; translation; uORF
MeSH headings : Algorithms; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cluster Analysis; Genome, Plant; Open Reading Frames / genetics; Protein Footprinting / methods; RNA, Plant; Ribosomes / genetics; Ribosomes / metabolism; Sequence Analysis, RNA; Supervised Machine Learning
TL;DR:
This paper uses ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana and hypothesizes that uORF translation is a complex process that might be regulated by multiple factors.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
Sources: ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain
PLANT PHYSIOLOGY, 171(1), 42–61.
Contributors: G. Villarino n, Q. Hu n, S. Manrique *, M. Flores-Vergara n, B. Sehra n, L. Robles n, J. Brumos n, n
MeSH headings : Arabidopsis / anatomy & histology; Arabidopsis / genetics; Arabidopsis Proteins / genetics; Arabidopsis Proteins / isolation & purification; Base Sequence; Chloral Hydrate; DNA, Antisense; Flowers / genetics; Gene Expression Regulation, Plant; Genome, Plant; In Situ Hybridization; Indoleacetic Acids / pharmacology; MADS Domain Proteins / genetics; MADS Domain Proteins / isolation & purification; Meristem / genetics; Meristem / growth & development; Meristem / metabolism; Microscopy, Confocal; Ovule / cytology; Ovule / growth & development; Ovule / metabolism; Protein Isoforms; Protoplasts; RNA, Plant / chemistry; RNA, Plant / isolation & purification; Seeds / growth & development; Sequence Alignment; Transcription Factors; Transcriptional Activation; Transcriptome
TL;DR:
A novel approach to analyze the transcriptional signature of the medial domain of the Arabidopsis gynoecium, highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development and identifying additional genes including novel isoforms, cis-natural antisense transcripts, and a previously unrecognized member of the REPRODUCTIVE MERISTEM family of transcriptional regulators that are potential novel regulators of medial domain 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, ORCID
Added: August 6, 2018
2015 chapter
A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana
In Bioinformatics Research and Applications (Vol. 9096, pp. 138–149).
Contributors: Q. Hu n, C. Merchante n, n , J. Alonso n & S. Heber n
author keywords: uORF; Translation; Ribosome footprinting; Stacking; Classification; Arabidopsis thaliana
TL;DR:
This paper uses ribosome footprinting together with a stacking-based classification approach to identify translated uORFs in Arabidopsis thaliana, resulting in a set of 5360 potentially translated u ORFs in 2051 genes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
Sources: ORCID, Crossref
Added: December 19, 2019
2015 journal article
A recombineering-based gene tagging system for Arabidopsis
Methods in Molecular Biology (Clifton, N.J.), 1227, 233–243.
Contributors: J. Alonso n & n
author keywords: Recombineering; Arabidopsis; Fluorescent protein; Lambda RED
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Bacteriophage lambda / genetics; Bacteriophage lambda / metabolism; Chromosomes, Artificial, Bacterial / chemistry; Chromosomes, Artificial, Bacterial / metabolism; Cloning, Molecular; Electroporation; Escherichia coli / genetics; Escherichia coli / metabolism; Genetic Engineering / methods; Genetic Vectors / chemistry; Genetic Vectors / metabolism; Homologous Recombination; Mutagenesis
TL;DR:
In this chapter, the experimental procedures involved in recombineering-based tagging of an Arabidopsis gene contained in a plant transformation-ready bacterial artificial chromosome (TAC) are described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, NC State University Libraries
Added: August 6, 2018
2015 conference paper
A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana
Bioinformatics research and applications (isbra 2015), 9096, 138–149.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2
CELL, 163(3), 684–697.
Contributors: C. Merchante n, J. Brumos n, J. Yun n, Q. Hu n, K. Spencer n, P. Enríquez n, B. Binder *, S. Heber n , n , J. Alonso n
MeSH headings : 3' Untranslated Regions; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; DNA-Binding Proteins; Ethylenes / metabolism; F-Box Proteins / genetics; Gene Expression Regulation, Plant; Nuclear Proteins / metabolism; Protein Biosynthesis; RNA, Messenger / metabolism; Receptors, Cell Surface / metabolism; Ribosomes / metabolism; Signal Transduction; Transcription Factors / metabolism
TL;DR:
Characterization of one of the targets of this translation regulatory machinery, the ethylene signaling component EBF2, indicates that the signaling molecule EIN2 and the nonsense-mediated decay proteins UPFs play a central role in this ethylene-induced translational response.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2015 conference paper
Mining transcript features related to translation in Arabidopsis using LASSO and random forest
2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2015.
Contributors: Q. Hu n, C. Merchante n, n , J. Alonso n & S. Heber n
TL;DR:
It is found that the contribution of features may be different for transcripts belonging to different functional groups, suggesting that transcripts might employ different mechanisms for the regulation of translation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2015 journal article
Plant functional genomics methods and protocols second edition preface
Plant Functional Genomics: Methods and Protocols, 2nd Edition, 1284, V-.
Source: NC State University Libraries
Added: August 6, 2018
2015 book
Plant functional genomics: Methods and protocols
In J. M. Alonso & A. N. Stepanova (Eds.), Plant Functional Genomics: Methods and Protocols: Second Edition (2nd ed., pp. 1–526).
TL;DR:
This chapter describes an approach to map chromatin features in specifi c cell types of Arabidopsis thaliana using nuclei purifi cation from individual cell types with the INTACT method followed by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq).
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 book
Arabidopsis transformation with large bacterial artificial chromosomes
In Methods in Molecular Biology (Vol. 1062, pp. 271–283).
Contributors: J. Alonso n & n
MeSH headings : Agrobacterium / genetics; Arabidopsis / genetics; Base Sequence; Chromosomes, Artificial, Bacterial / genetics; DNA Primers / genetics; DNA, Bacterial / genetics; Escherichia coli; Genome, Plant; Plants, Genetically Modified / genetics; Polymerase Chain Reaction; Transformation, Genetic
TL;DR:
This chapter describes the experimental procedures and extra cautionary measures involved in the identification of the clone containing the gene of interest, its transfer from E. coli to Agrobacterium, and the generation, verification, and analysis of the corresponding transgenic plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: ORCID
Added: December 19, 2019
2014 journal article
Genetic aspects of auxin biosynthesis and its regulation
PHYSIOLOGIA PLANTARUM, 151(1), 3–12.
Contributors: J. Brumos n, J. Alonso n & n
MeSH headings : Arabidopsis / enzymology; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Indoleacetic Acids / metabolism; Mixed Function Oxygenases / genetics; Mixed Function Oxygenases / metabolism; Plants / enzymology; Plants / genetics; Plants / metabolism; Tryptophan Transaminase / genetics; Tryptophan Transaminase / metabolism
TL;DR:
A genetic perspective is taken to describe the current view of auxin biosynthesis and its regulation in plants, focusing primarily on 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, ORCID
Added: August 6, 2018
2013 journal article
Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity
NATURE COMMUNICATIONS, 4.
Contributors: S. Pietra *, A. Gustavsson*, C. Kiefer*, L. Kalmbach *, P. Hörstedt*, Y. Ikeda *, n , J. Alonso n, M. Grebe *
MeSH headings : Alleles; Amino Acid Sequence; Arabidopsis / cytology; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Sequence; Cell Division / physiology; Cell Polarity / physiology; Chromosomes, Plant; Gene Expression Regulation, Plant / physiology; Intracellular Signaling Peptides and Proteins / genetics; Intracellular Signaling Peptides and Proteins / metabolism; Microtubule-Associated Proteins / genetics; Microtubule-Associated Proteins / metabolism; Phylogeny
TL;DR:
It is demonstrated in Arabidopsis thaliana that the SABRE protein is important for mediating cell and planar polarity by stabilizing the orientation of microtubules during cell division and cell elongation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 conference paper
Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants
2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013.
Contributors: K. Merchante n, Q. Hu n, n , J. Eonso & S. Heber n
TL;DR:
The goal of this project is to develop genomic tools for the qualitative and quantitative characterization of the plant translatome, and it is hoped ribosome footprinting will allow researchers to correlate precisely mRNA features with translation efficiency, and open the way to investigate globally the mechanism of protein synthesis and its regulation at an unprecedented level of detail.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2013 review
Ethylene signaling: simple ligand, complex regulation
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 16(5), 554–560.
Contributors: C. Merchante n, J. Alonso n & n
MeSH headings : Arabidopsis / genetics; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Ethylenes / metabolism; Gene Expression Regulation, Plant; Gene Regulatory Networks; Models, Biological; Plant Growth Regulators / metabolism; Protein Kinases / genetics; Protein Kinases / metabolism; Receptors, Cell Surface / genetics; Receptors, Cell Surface / metabolism; Signal Transduction
TL;DR:
This review describes the most current outlook on ethylene signal transduction and emphasizes the latest discoveries in the ethylene field that shed light on the mechanistic mode of action of the central pathway components CTR1 and EIN2, as well as on the post-transcriptional regulatory steps that modulate the signaling flow through the pathway.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition
BIOCHEMICAL JOURNAL, 450(1), 37–46.
Contributors: J. Kopycki*, E. Wieduwild*, J. Kohlschmidt*, W. Brandt *, n , J. Alonso n, M. Pedras *, S. Abel *, C. Grubb*
author keywords: glucosinolate; glycosyltransferase; ordered binding; product inhibition; UDP-glycosyltransferase (UGT)
MeSH headings : Arabidopsis / enzymology; Arabidopsis / genetics; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / metabolism; Genome, Plant; Glucosyltransferases / chemistry; Glucosyltransferases / metabolism; Kinetics; Leucine / genetics; Leucine / metabolism; Models, Molecular; Mutation; Phenotype; Plants, Genetically Modified; Serine / genetics; Serine / metabolism; Substrate Specificity; Uridine Diphosphate Glucose / metabolism
TL;DR:
It is found that mutation of the highly conserved Ser284 to leucine [wei9-1 (weak ethylene insensitive)] caused only very mild morphological and metabolic phenotypes, in dramatic contrast with knockout mutants, indicating that steady state glucosinolate levels are actively regulated even in unchallenged plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Local Auxin Sources Orient the Apical-Basal Axis in Arabidopsis Embryos
CURRENT BIOLOGY, 23(24), 2506–2512.
Contributors: H. Robert *, P. Grones *, n , L. Robles n, A. Lokerse*, J. Alonso n, D. Weijers *, J. Friml *
MeSH headings : Arabidopsis / embryology; Arabidopsis Proteins / metabolism; Body Patterning / drug effects; Indoleacetic Acids / metabolism; Indoleacetic Acids / pharmacology; Membrane Transport Proteins / metabolism; Plant Growth Regulators / metabolism; Plant Growth Regulators / pharmacology; Plant Growth Regulators / physiology; Protein Transport; Seeds / drug effects; Seeds / growth & development
TL;DR:
The tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Molecular Mechanisms of EthyleneAuxin Interaction
MOLECULAR PLANT, 6(6), 1734–1737.
Contributors: L. Robles n, n & J. Alonso n
MeSH headings : Ethylenes / metabolism; Indoleacetic Acids / metabolism; Plant Growth Regulators / metabolism; RNA Processing, Post-Transcriptional; Transcription, Genetic
TL;DR:
This work has uncovered how these molecules are sensed by the plant cell and how they trigger signaling cascades that relay information to the nucleus, ultimately culminating in a transcriptional cascade.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2011 journal article
A Small-Molecule Screen Identifies l-Kynurenine as a Competitive Inhibitor of TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth in Arabidopsis
The Plant Cell, 23(11), 3944–3960.
Contributors: W. He*, J. Brumos n, H. Li *, Y. Ji*, M. Ke*, X. Gong*, Q. Zeng*, W. Li *
MeSH headings : Arabidopsis / drug effects; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Cell Nucleus / metabolism; DNA-Binding Proteins; Enzyme Inhibitors / pharmacology; Ethylenes / metabolism; Ethylenes / pharmacology; F-Box Proteins / metabolism; Indoleacetic Acids / metabolism; Indoleacetic Acids / pharmacology; Kynurenine / chemistry; Kynurenine / metabolism; Kynurenine / pharmacology; Models, Molecular; Nuclear Proteins / metabolism; Plant Roots / drug effects; Plant Roots / growth & development; Plant Roots / metabolism; Small Molecule Libraries; Transcription Factors / metabolism; Tryptophan Transaminase / antagonists & inhibitors; Tryptophan Transaminase / genetics; Tryptophan Transaminase / metabolism
TL;DR:
This work identifies a small molecule, l-kynurenine (Kyn), which effectively inhibited ethylene responses in Arabidopsis thaliana root tissues and describes a previously undiscovered positive feedback loop between auxin biosynthesis and ethylene signaling pathways 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, ORCID, Crossref
Added: August 6, 2018
2011 journal article
A recombineering-based gene tagging system for Arabidopsis
PLANT JOURNAL, 66(4), 712–723.
Contributors: R. Zhou n, L. Benavente n, n & J. Alonso n
author keywords: Arabidopsis; recombineering; Aux; IAA; gene tagging; fluorescent; proteins
MeSH headings : Agrobacterium tumefaciens / genetics; Agrobacterium tumefaciens / metabolism; Arabidopsis / genetics; Arabidopsis / metabolism; Chromosomes, Artificial, Bacterial / genetics; DNA Primers / genetics; Escherichia coli; Gene Expression Profiling / methods; Genetic Engineering / methods; Genetic Vectors; Green Fluorescent Proteins / metabolism; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; Point Mutation; Recombination, Genetic
TL;DR:
It is suggested that recombineering-based gene tagging should be the gold standard for gene expression studies in Arabidopsis because it has several advantages compared to other classical strategies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2011 article
Bypassing Transcription: A Shortcut in Cytokinin-Auxin Interactions
Stepanova, A. N., & Alonso, J. M. (2011, October 18). DEVELOPMENTAL CELL, Vol. 21, pp. 608–610.
Contributors: n & J. Alonso n
TL;DR:
A transcription-independent molecular mechanism of interaction between auxin and cytokinin in the regulation of plant meristem function is uncovered by modulating endocytic trafficking of PIN1, which controls auxin flux and, therefore, auxin 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, ORCID
Added: August 6, 2018
2011 journal article
The Arabidopsis YUCCA1 Flavin Monooxygenase Functions in the Indole-3-Pyruvic Acid Branch of Auxin Biosynthesis
PLANT CELL, 23(11), 3961–3973.
Contributors: n , J. Yun n, L. Robles n, O. Novak *, W. He*, H. Guo *, K. Ljung *, J. Alonso n
MeSH headings : Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cytochrome P-450 Enzyme System / genetics; Cytochrome P-450 Enzyme System / metabolism; Gene Knockdown Techniques; Indoleacetic Acids / metabolism; Indoles / metabolism; Oxygenases / genetics; Oxygenases / metabolism; Tryptophan Transaminase / genetics; Tryptophan Transaminase / metabolism
TL;DR:
Results strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2009 review
Ethylene signaling and response: where different regulatory modules meet
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 12(5), 548–555.
Contributors: n & J. Alonso n
MeSH headings : Ethylenes / metabolism; Gene Expression Regulation, Plant; Indoleacetic Acids / metabolism; Plant Development; Plant Growth Regulators / metabolism; Plant Proteins / metabolism; Plants / metabolism; Receptors, Cell Surface / metabolism; Signal Transduction
TL;DR:
Tissue-specific regulation of auxin biosynthesis, transport, and response by ethylene is emerging as a key element in this signal integration process.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2009 journal article
Local auxin biosynthesis modulates gradient-directed planar polarity in Arabidopsis
NATURE CELL BIOLOGY, 11(6), 731–U70.
Contributors: Y. Ikeda *, S. Men *, U. Fischer*, n , J. Alonso n, K. Ljung *, M. Grebe *
MeSH headings : Animals; Arabidopsis / anatomy & histology; Arabidopsis / metabolism; Arabidopsis Proteins / biosynthesis; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Polarity; Genes, Reporter; Morphogenesis / physiology; Mutation; Plant Roots / cytology; Plant Roots / growth & development; Plants, Genetically Modified; Protein Kinases / genetics; Protein Kinases / metabolism; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / metabolism
TL;DR:
It is demonstrated that the Raf-like kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) acts as a concentration-dependent repressor of a biosynthesis-dependent auxin gradient that modulates planar polarity in the root tip that contributes to gradient homeostasis during long-range coordination of cellular morphogenesis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2008 journal article
TAA1-Mediated Auxin Biosynthesis Is Essential for Hormone Crosstalk and Plant Development
Cell, 133(1), 177–191.
Contributors: n , J. Robertson-Hoyt n, J. Yun n, L. Benavente n, D. Xie n , K. Doležal *, A. Schlereth*, G. Jürgens *, J. Alonso n
MeSH headings : Amino Acid Sequence; Arabidopsis / drug effects; Arabidopsis / embryology; Arabidopsis / genetics; Arabidopsis / metabolism; Biosynthetic Pathways; Ethylenes / pharmacology; Indoleacetic Acids / metabolism; Indoles / metabolism; Molecular Sequence Data; Mutation; Plant Roots / drug effects; Seedlings / metabolism; Sequence Alignment; Tryptophan Transaminase / chemistry; Tryptophan Transaminase / genetics; Tryptophan Transaminase / metabolism
TL;DR:
By characterizing the Arabidopsis wei8 mutant, it is found that a small family of genes mediates tissue-specific responses to ethylene, and the IPA route of auxin production is key to generating robust auxin gradients in response to environmental and developmental cues.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2007 journal article
Multilevel interactions between ethylene and auxin in Arabidopsis roots
PLANT CELL, 19(7), 2169–2185.
Contributors: n , J. Yun n, A. Likhacheva n & J. Alonso n
MeSH headings : Arabidopsis / drug effects; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Binding Sites; DNA-Binding Proteins / metabolism; Ethylenes / metabolism; Ethylenes / pharmacology; Gene Expression Profiling; Genes, Plant; Genes, Reporter; Glucuronidase / metabolism; Indoleacetic Acids / metabolism; Models, Biological; Mutation / genetics; Nuclear Proteins / metabolism; Oligonucleotide Array Sequence Analysis; Plant Roots / drug effects; Plant Roots / enzymology; Plant Roots / growth & development; Plant Roots / metabolism; Promoter Regions, Genetic / genetics; Reverse Transcriptase Polymerase Chain Reaction; Transcription Factors / metabolism
TL;DR:
Analysis of the morphological effects of ethylene and auxin in a variety of mutant backgrounds indicates that auxin biosynthesis, transport, signaling, and response are required for the ethylene-induced growth inhibition in roots but not in hypocotyls of dark-grown seedlings, and suggests a simple mechanistic model for the interaction between these two hormones in roots.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018
2006 journal article
PCR-based screening for insertional mutants.
Methods in Molecular Biology (Clifton, N.J.), 323, 163–172. http://www.scopus.com/inward/record.url?eid=2-s2.0-33745265233&partnerID=MN8TOARS
Source: ORCID
Added: December 19, 2019
2005 journal article
A link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis
PLANT CELL, 17(8), 2230–2242.
Contributors: n , J. Hoyt n, A. Hamilton n & J. Alonso n
MeSH headings : Anthranilate Synthase / genetics; Anthranilate Synthase / metabolism; Arabidopsis / genetics; Ethylenes / metabolism; Indoleacetic Acids / physiology; Mutation; Nitrogenous Group Transferases / genetics; Nitrogenous Group Transferases / metabolism; Plant Growth Regulators / physiology; Plant Roots / genetics; Plant Roots / physiology
TL;DR:
It is shown that ethylene-triggered inhibition of root growth, one of the classical effects of ethylene in Arabidopsis thaliana seedlings, is mediated by the action of the WEAK ETHYLENE INSENSITIVE2/ANTHRANILATE SYNTHASE α1 and ASA1 genes that encode α- and β-subunits of a rate-limiting enzyme of Trp biosynthesis, anthranilate synthase.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2005 journal article
Arabidopsis ethylene signaling pathway.
Science's STKE : Signal Transduction Knowledge Environment, 2005(276). http://www.scopus.com/inward/record.url?eid=2-s2.0-33644876995&partnerID=MN8TOARS
Source: ORCID
Added: December 19, 2019
2005 journal article
Ethylene signaling pathway.
Science's STKE : Signal Transduction Knowledge Environment, 2005(276). http://www.scopus.com/inward/record.url?eid=2-s2.0-33644877967&partnerID=MN8TOARS
Source: ORCID
Added: December 19, 2019
2005 journal article
Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs
Physiologia Plantarum, 123(2), 195–206.
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2005 journal article
Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs
Physiologia Plantarum, 123(2), 195–206.
Contributors: n & J. Alonso n
TL;DR:
A relatively well-characterized ethylene signalling and response pathway, together with numerous evidences of its interactions with other signalling/response pathways, provide an excellent example to illustrate the current knowledge and perspective on how signal integration occurs in plants.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2004 journal article
Convergence of signaling pathways in the control of differential cell growth in Arabidopsis
Developmental Cell, 7(2), 193–204.
Contributors: H. Li *, P. Johnson*, * , J. Alonso * & J. Ecker *
MeSH headings : ADP-Ribosylation Factors / genetics; Alleles; Arabidopsis / genetics; Arabidopsis / physiology; Cell Division; Cloning, Molecular; Ethylenes / pharmacology; Gene Expression Regulation, Plant; Immunoblotting; In Situ Hybridization; Indoleacetic Acids / metabolism; Models, Biological; Models, Genetic; Mutagenesis; Mutation; Phenotype; Plant Proteins / physiology; Plants, Genetically Modified; Plasmids / metabolism; RNA / metabolism; Saccharomyces cerevisiae Proteins; Signal Transduction; Time Factors; Transcription, Genetic
TL;DR:
It is demonstrated that both ethylene and light signals affect differential cell growth by acting through HLS1 to modulate the auxin response factors, pinpointing HLS 1 as a key integrator of the signaling pathways that control hypocotyl bending.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2004 journal article
Short-term growth responses to ethylene in arabidopsis seedlings are EIN3/EIL1 independent
PLANT PHYSIOLOGY, 136(2), 2921–2927.
Contributors: B. Binder n, L. Mortimore n, n , J. Ecker n & A. Bleecker n
MeSH headings : Adaptation, Physiological; Arabidopsis / drug effects; Arabidopsis / growth & development; Arabidopsis Proteins / physiology; Cyclopropanes / pharmacology; DNA-Binding Proteins; Dose-Response Relationship, Drug; Ethylenes / antagonists & inhibitors; Ethylenes / pharmacology; Gene Expression Regulation, Plant; Nuclear Proteins / physiology; Plant Growth Regulators / physiology; Receptors, Cell Surface / physiology; Seedlings / drug effects; Seedlings / growth & development; Time Factors; Transcription Factors / physiology
TL;DR:
A modified signal transduction model is proposed that accounts for the two phases of growth inhibition by ethylene for the hypocotyls of etiolated Arabidopsis seedlings.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2004 journal article
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Nucleus / metabolism; DNA-Binding Proteins; Ethylenes / metabolism; Models, Biological; Mutation; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Plant Proteins / chemistry; Plant Proteins / metabolism; Plants / genetics; Plants / metabolism; Receptors, Cell Surface / chemistry; Receptors, Cell Surface / metabolism; SKP Cullin F-Box Protein Ligases / metabolism; Signal Transduction; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
This work describes the four main modules that constitute this signaling pathway: a phosphotransfer relay, an EIN2-based unit, a ubiquitin-mediated protein degradation component, and a transcriptional cascade.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2003 journal article
Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis
Proceedings of the National Academy of Sciences of the United States of America, 100(5), 2992–2997.
Contributors: J. Alonso *, * , R. Solano *, E. Wisman*, S. Ferrari*, F. Ausubel *, J. Ecker *
MeSH headings : Alleles; Arabidopsis / genetics; Arabidopsis / metabolism; Botrytis / growth & development; Botrytis / pathogenicity; Ethylenes / pharmacology; Gene Expression Regulation, Plant / drug effects; Genes, Dominant; Genetic Complementation Test; Genetic Techniques; Genotype; Mitosporic Fungi / growth & development; Mitosporic Fungi / pathogenicity; Models, Genetic; Mutagenesis, Site-Directed; Mutation; Plant Diseases / genetics; Plant Diseases / microbiology; Plant Growth Regulators / pharmacology; Polymerase Chain Reaction; Signal Transduction
TL;DR:
Genetic mapping studies indicate that wei2 and wei3 correspond to previously unidentified ethylene pathway genes that may control cell-elongation processes functioning at the intersection of the ethylene and auxin response pathways.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2003 journal article
Genome-wide insertional mutagenesis of Arabidopsis thaliana
Science, 301(5633), 653–657.
Contributors: J. Alonso *, * , T. Leisse*, C. Kim *, H. Chen *, P. Shinn*, D. Stevenson*, J. Zimmerman*
MeSH headings : 3' Untranslated Regions; 5' Untranslated Regions; Alleles; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Composition; Chromosomes, Plant / genetics; DNA, Bacterial / genetics; DNA, Plant / chemistry; DNA, Plant / genetics; Ethylenes / pharmacology; Exons; Expressed Sequence Tags; Gene Expression; Gene Expression Profiling; Gene Expression Regulation, Plant / drug effects; Genes, Plant; Genome, Plant; Introns; Mutagenesis, Insertional; Mutation; Oligonucleotide Array Sequence Analysis; Promoter Regions, Genetic; Recombination, Genetic; Rhizobium / genetics
TL;DR:
Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels, and insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
2003 chapter
T-DNA mutagenesis in Arabidopsis
In Plant functional genomics.
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; DNA, Bacterial / genetics; Genetic Techniques; Indicators and Reagents; Mutagenesis, Insertional / methods; Rhizobium / genetics; Transformation, Genetic
TL;DR:
A simple yet robustArabidopsis transformation procedure that can be used to generate large numbers of insertional mutants in Arabidopsis thaliana is described and transformation efficiencies of up to 5% can be achieved.
(via Semantic Scholar)
Source: NC State University Libraries
Added: August 6, 2018
2003 journal article
T-DNA mutagenesis in Arabidopsis.
Methods in Molecular Biology (Clifton, N.J.), 236, 177–188. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542548233&partnerID=MN8TOARS
Source: ORCID
Added: December 19, 2019
2000 journal article
Ethylene signaling: From mutants to molecules
Current Opinion in Plant Biology, 3(5), 353–360.
Contributors: * & J. Ecker *
MeSH headings : Arabidopsis / physiology; Ethylenes / metabolism; Mutation; Plant Growth Regulators / metabolism; Signal Transduction
TL;DR:
The first discovery of ethylene responsiveness in an animal species implied a more universal role for ethylene than previously thought and major components in the ethylene signaling pathway in plants have been identified and characterized.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: December 19, 2019
1998 journal article
Nuclear events in ethylene signaling: A transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1
Genes and Development, 12(23), 3703–3714.
Contributors: R. Solano*, * , Q. Chao* & J. Ecker *
author keywords: plants; Arabidopsis; EIN3; ERF1; transcription
MeSH headings : Amino Acid Sequence; Arabidopsis; Arabidopsis Proteins; Cell Nucleus / metabolism; Cloning, Molecular; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Dimerization; Ethylenes / metabolism; Gene Expression Regulation, Plant; Models, Genetic; Molecular Sequence Data; Nuclear Proteins / metabolism; Plant Growth Regulators / metabolism; Promoter Regions, Genetic; Response Elements; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Signal Transduction; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
It is shown that EIN3 and EILs comprise a family of novel sequence-specific DNA-binding proteins that regulate gene expression by binding directly to a primary ethylene response element related to the tomato E4-element.
(via Semantic Scholar)
Source: ORCID
Added: December 19, 2019
Employment
Updated: June 3rd, 2019 15:48
2019 - present
North Carolina State University Raleigh, NC, US
Associate Professor
Plant and Microbial Biology
2014 - 2019
North Carolina State University Raleigh, NC, US
Assistant Professor
Plant and Microbial Biology
2009 - 2013
North Carolina State University Raleigh, NC, US
Research Assistant Professor
Genetics
2003 - 2009
North Carolina State University Raleigh, NC, US
Research Associate
Genetics
2001 - 2003
North Carolina State University Raleigh, NC, US
Postdoctoral fellow
Genetics
Education
Updated: October 11th, 2019 13:37
1995 - 2001
University of Pennsylvania Philadelphia, PA, US
PhD
Biology
1993 - 1995
University of Nevada Reno Reno, NV, US
BS
Biology
1990 - 1995
N. I. Lobachevsky State University of Nizhny Novgorod Nizhny Novgorod, RU
BS/MS
Biology
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