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  • 1
    Article
    Article
    Receptor-like kinases shape the plant
    2009
    ISSN: 1465-7392 
    Details
    Language: English
    In: Nature cell biology, 2009-10, Vol.11 (10), p.1166-1173
    Description: To generate the various tissues and organs that build up the adult body, plants and animals require organized formative cell divisions and correct cell specification. In plants, these processes are controlled mainly by phytohormones and transcriptional networks. Recently, ligand-receptor-like kinase signalling pathways have been revealed as additional potentially crucial regulators of cell specification in plants. We review here the importance of such signalling cascades for plant growth and development, and we discuss, where possible, similarities to well-investigated cascades in animals.
    Subject(s): Plant Proteins - genetics ; Plants - metabolism ; Plants - genetics ; Receptor Protein-Tyrosine Kinases - genetics ; Models, Biological ; Plant Growth Regulators - genetics ; Plant Proteins - metabolism ; Signal Transduction - genetics ; Plant Growth Regulators - metabolism ; Receptor Protein-Tyrosine Kinases - metabolism ; Physiological aspects ; Protein tyrosine kinase ; Cellular signal transduction ; Genetic aspects ; Research ; Plant physiology ; Index Medicus
    ISSN: 1465-7392
    E-ISSN: 1476-4679
    DOI: 10.1038/ncb1009-1166
    Source: Academic Search Ultimate
    Source: Nature Journals Online
    Source: Alma/SFX Local Collection
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 2
    Article
    Article
    Auxin regulates aquaporin function to facilitate lateral root emergence
    2012
    ISSN: 1465-7392 
    Details
    Language: English
    In: Nature cell biology, 2012-10, Vol.14 (10), p.991-998
    Description: Aquaporins are membrane channels that facilitate water movement across cell membranes. In plants, aquaporins contribute to water relations. Here, we establish a new link between aquaporin-dependent tissue hydraulics and auxin-regulated root development in Arabidopsis thaliana. We report that most aquaporin genes are repressed during lateral root formation and by exogenous auxin treatment. Auxin reduces root hydraulic conductivity both at the cell and whole-organ levels. The highly expressed aquaporin PIP2;1 is progressively excluded from the site of the auxin response maximum in lateral root primordia (LRP) whilst being maintained at their base and underlying vascular tissues. Modelling predicts that the positive and negative perturbations of PIP2;1 expression alter water flow into LRP, thereby slowing lateral root emergence (LRE). Consistent with this mechanism, pip2;1 mutants and PIP2;1-overexpressing lines exhibit delayed LRE. We conclude that auxin promotes LRE by regulating the spatial and temporal distribution of aquaporin-dependent root tissue water transport.
    Subject(s): Indoleacetic Acids - metabolism ; Arabidopsis - growth & development ; Gene Silencing ; Plant Roots - genetics ; Aquaporins - genetics ; Arabidopsis - genetics ; Arabidopsis Proteins - metabolism ; Transcription Factors - metabolism ; Models, Biological ; Aquaporins - physiology ; Gene Expression Regulation, Plant ; Biological Transport - genetics ; Biological Transport - physiology ; Mutation ; Plant Roots - growth & development ; Water - physiology ; Arabidopsis thaliana ; Auxin ; Aquaporins ; Physiological aspects ; Development ; Plants ; Health aspects ; Index Medicus ; Water ; Arabidopsis ; Life Sciences ; Arabidopsis Proteins ; Plant Roots ; Biological Transport ; Transcription Factors ; Vegetal Biology ; Indoleacetic Acids
    ISSN: 1465-7392
    E-ISSN: 1476-4679
    DOI: 10.1038/ncb2573
    Source: Academic Search Ultimate
    Source: Alma/SFX Local Collection
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
    URL: https://hal.archives-ouvertes.fr/hal-00777292$$DView record in HAL
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  • 3
    Article
    Article
    Auxin fluxes through plasmodesmata modify root-tip auxin distribution
    2020
    ISSN: 0950-1991 
    Details
    Language: English
    In: Development (Cambridge), 2020-03-30, Vol.147 (6), p.dev181669
    Description: Auxin is a key signal regulating plant growth and development. It is well established that auxin dynamics depend on the spatial distribution of efflux and influx carriers on the cell membranes. In this study, we employ a systems approach to characterise an alternative symplastic pathway for auxin mobilisation via plasmodesmata, which function as intercellular pores linking the cytoplasm of adjacent cells. To investigate the role of plasmodesmata in auxin patterning, we developed a multicellular model of the root tip. We tested the model predictions using the DII-VENUS auxin response reporter, comparing the predicted and observed DII-VENUS distributions using genetic and chemical perturbations designed to affect both carrier-mediated and plasmodesmatal auxin fluxes. The model revealed that carrier-mediated transport alone cannot explain the experimentally determined auxin distribution in the root tip. In contrast, a composite model that incorporates both carrier-mediated and plasmodesmatal auxin fluxes re-capitulates the root-tip auxin distribution. We found that auxin fluxes through plasmodesmata enable auxin reflux and increase total root-tip auxin. We conclude that auxin fluxes through plasmodesmata modify the auxin distribution created by efflux and influx carriers.
    Subject(s): Index Medicus
    ISSN: 0950-1991
    E-ISSN: 1477-9129
    DOI: 10.1242/dev.181669
    Source: HighWire Press (Free Journals)
    Source: Company of Biologists
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 4
    Article
    Article
    Inference of the Arabidopsis Lateral Root Gene Regulatory Network Suggests a Bifurcation Mechanism That Defines Primordia Flanking and Central Zones
    2015
    ISSN: 1040-4651 
    Details
    Language: English
    In: The Plant cell, 2015-05-01, Vol.27 (5), p.1368-1388
    Description: A large number of genes involved in lateral root (LR) organogenesis have been identified over the last decade using forward and reverse genetic approaches in . Nevertheless, how these genes interact to form a LR regulatory network largely remains to be elucidated. In this study, we developed a time-delay correlation algorithm (TDCor) to infer the gene regulatory network (GRN) controlling LR primordium initiation and patterning in Arabidopsis from a time-series transcriptomic data set. The predicted network topology links the very early-activated genes involved in LR initiation to later expressed cell identity markers through a multistep genetic cascade exhibiting both positive and negative feedback loops. The predictions were tested for the key transcriptional regulator AUXIN RESPONSE FACTOR7 node, and over 70% of its targets were validated experimentally. Intriguingly, the predicted GRN revealed a mutual inhibition between the ARF7 and ARF5 modules that would control an early bifurcation between two cell fates. Analyses of the expression pattern of ARF7 and ARF5 targets suggest that this patterning mechanism controls flanking and central zone specification in Arabidopsis LR primordia.
    Subject(s): Datasets ; Transcription factors ; Transcriptomics ; Genes ; Fezzes ; Plant roots ; Auxins ; Gene expression regulation ; LARGE-SCALE BIOLOGY ARTICLE ; Plants ; Plant cells ; Arabidopsis Proteins - genetics ; Gene Regulatory Networks - genetics ; Arabidopsis - growth & development ; Arabidopsis - cytology ; Transcriptome ; Plant Roots - genetics ; Plant Roots - cytology ; Transcription Factors - genetics ; DNA-Binding Proteins - genetics ; Arabidopsis - genetics ; Cell Differentiation - genetics ; Algorithms ; Time Factors ; Plants, Genetically Modified ; Gene Expression Regulation, Plant ; Mutation ; Plant Roots - growth & development ; Arabidopsis thaliana ; Genetic aspects ; Gene expression ; Observations ; Index Medicus ; Life Sciences ; Botanics ; Vegetal Biology ; Biochemistry, Molecular Biology ; Large-Scale Biology
    ISSN: 1040-4651
    E-ISSN: 1532-298X
    DOI: 10.1105/tpc.114.132993
    Source: American Society of Plant Biologists
    Source: HighWire Press (Free Journals)
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
    URL: https://hal.archives-ouvertes.fr/hal-03172195$$DView record in HAL
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  • 5
    Article
    Article
    A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
    2018
    ISSN: 2041-1723 
    Details
    Language: English
    In: Nature communications, 2018-04-12, Vol.9 (1), p.1409-1409
    Description: Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
    Subject(s): Arabidopsis Proteins - genetics ; Arabidopsis - drug effects ; Basic Helix-Loop-Helix Transcription Factors - genetics ; Organogenesis, Plant - genetics ; Plant Roots - metabolism ; Indoleacetic Acids - metabolism ; Arabidopsis - growth & development ; Stress, Physiological ; Plant Roots - genetics ; Transcription Factors - genetics ; Arabidopsis - metabolism ; Plant Roots - drug effects ; Arabidopsis - genetics ; Arabidopsis Proteins - metabolism ; Transcription Factors - metabolism ; Basic Helix-Loop-Helix Transcription Factors - metabolism ; Gravitropism - physiology ; Plants, Genetically Modified ; Gene Expression Regulation, Plant ; Organogenesis, Plant - drug effects ; Phosphates - deficiency ; Plant Growth Regulators - metabolism ; Phosphates - pharmacology ; Plant Roots - growth & development ; Index Medicus ; Life Sciences ; Botanics ; Vegetal Biology
    ISSN: 2041-1723
    E-ISSN: 2041-1723
    DOI: 10.1038/s41467-018-03851-3
    Source: Nature Open Access
    Source: PubMed Central
    Source: Directory of Open Access Journals
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
    URL: https://hal.archives-ouvertes.fr/hal-02386622$$DView record in HAL
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  • 6
    Article
    Article
    Volumetric Segmentation of Cell Cycle Markers in Confocal Images Using Machine Learning and Deep Learning
    2020
    ISSN: 1664-462X 
    Details
    Language: English
    In: Frontiers in plant science, 2020-08-28, Vol.11, p.1275-1275
    Description: Understanding plant growth processes is important for many aspects of biology and food security. Automating the observations of plant development—a process referred to as plant phenotyping—is increasingly important in the plant sciences, and is often a bottleneck. Automated tools are required to analyze the data in microscopy images depicting plant growth, either locating or counting regions of cellular features in images. In this paper, we present to the plant community an introduction to and exploration of two machine learning approaches to address the problem of marker localization in confocal microscopy. First, a comparative study is conducted on the classification accuracy of common conventional machine learning algorithms, as a means to highlight challenges with these methods. Second, a 3D (volumetric) deep learning approach is developed and presented, including consideration of appropriate loss functions and training data. A qualitative and quantitative analysis of all the results produced is performed. Evaluation of all approaches is performed on an unseen time-series sequence comprising several individual 3D volumes, capturing plant growth. The comparative analysis shows that the deep learning approach produces more accurate and robust results than traditional machine learning. To accompany the paper, we are releasing the 4D point annotation tool used to generate the annotations, in the form of a plugin for the popular ImageJ (FIJI) software. Network models and example datasets will also be available online.
    Subject(s): annotation ; deep learning ; software ; machine learning ; plant analysis procedures ; phenotyping
    ISSN: 1664-462X
    E-ISSN: 1664-462X
    DOI: 10.3389/fpls.2020.01275
    Source: PubMed Central
    Source: Directory of Open Access Journals
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 7
    Article
    Article
    The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana
    2015
    ISSN: 2041-1723 
    Details
    Language: English
    In: Nature communications, 2015-07-06, Vol.6 (1), p.7641-7641
    Description: The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence.
    Subject(s): Arabidopsis Proteins - genetics ; Indoleacetic Acids - metabolism ; Oxidoreductases - metabolism ; Arabidopsis - growth & development ; Oxidoreductases - genetics ; Transcriptome ; Transcription Factors - genetics ; Arabidopsis Proteins - metabolism ; Plant Roots - physiology ; Transcription Factors - metabolism ; Time Factors ; Gene Expression Regulation, Plant - physiology ; Gravitropism ; Mutation ; Circadian Clocks - physiology ; Index Medicus ; Life Sciences ; Science & Technology - Other Topics
    ISSN: 2041-1723
    E-ISSN: 2041-1723
    DOI: 10.1038/ncomms8641
    Source: Nature Open Access
    Source: PubMed Central
    Source: Directory of Open Access Journals
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
    URL: https://hal.umontpellier.fr/hal-03170953$$DView record in HAL
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  • 8
    Article
    Article
    From jellyfish to biosensors: the use of fluorescent proteins in plants
    2013
    ISSN: 0214-6282 
    Details
    Language: English
    In: The International journal of developmental biology, 2013, Vol.57 (6-7-8), p.525-533
    Description: The milestone discovery of green fluorescent protein (GFP) from the jellyfish Aequorea victoria, its optimisation for efficient use in plantae, and subsequent improvements in techniques for fluorescent detection and quantification have changed plant molecular biology research dramatically. Using fluorescent protein tags allows the temporal and spatial monitoring of dynamic expression patterns at tissue, cellular and subcellular scales. Genetically-encoded fluorescence has become the basis for applications such as cell-type specific transcriptomics, monitoring cell fate and identity during development of individual organs or embryos, and visualising protein-protein interactions in vivo. In this article, we will give an overview of currently available fluorescent proteins, their applications in plant research, the techniques used to analyse them and, using the recent development of an auxin sensor as an example, discuss the design principles and prospects for the next generation of fluorescent plant biosensors.
    Subject(s): Life Sciences ; Vegetal Biology
    ISSN: 0214-6282
    DOI: 10.1387/ijdb.130208dw
    Source: Alma/SFX Local Collection
    URL: https://hal.inrae.fr/hal-02651400$$DView record in HAL
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  • 9
    Article
    Article
    The influence of cytokinin–auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
    2011
    ISSN: 0022-5193 
    Details
    Language: English
    In: Journal of theoretical biology, 2011, Vol.283 (1), p.152-167
    Description: Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations. ► We model the cross-talk between auxin and cytokinin during root development. ► We analyse the response of their signalling network to mutations and hormonal perturbations. ► We show that some elements of the network respond differently in these two cases. ► We show that an analysis based on hormonal ratio may be misleading. ► We conclude that this mathematical model can stimulate further experimental work.
    Subject(s): Lateral root development ; Cytokinin–auxin cross-regulation ; Mathematical modelling ; Cytokinins - genetics ; Meristem - cytology ; Arabidopsis Proteins - genetics ; Indoleacetic Acids - metabolism ; Arabidopsis - growth & development ; Arabidopsis - cytology ; Plant Roots - cytology ; Gene Regulatory Networks - physiology ; Meristem - growth & development ; Arabidopsis - genetics ; Meristem - genetics ; Gene Expression Regulation, Plant - physiology ; Cytokinins - physiology ; Signal Transduction - physiology ; Models, Genetic ; Mutation ; Nuclear Proteins - genetics ; Plant Roots - growth & development ; Gene Expression Regulation, Developmental - physiology ; Arabidopsis thaliana ; Hormones ; Universities and colleges ; Gene mutations ; Analysis ; Stem cells ; Index Medicus
    ISSN: 0022-5193
    E-ISSN: 1095-8541
    DOI: 10.1016/j.jtbi.2011.05.011
    Source: Backfile Package - All of Back Files EBS [ALLOFBCKF]
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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  • 10
    Article
    Article
    Branching Out in Roots: Uncovering Form, Function, and Regulation
    2014
    ISSN: 0032-0889 
    Details
    Language: English
    In: Plant physiology (Bethesda), 2014-10-01, Vol.166 (2), p.538-550
    Description: Root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. To date, research on root branching has focused on lateral root development in young seedlings. However, many other programs of postembryonic root organogénesis exist in angiosperms. In cereal crops, the majority of the mature root system is composed of several classes of adventitious roots that include crown roots and brace roots. In this Update, we initially describe the diversity of postembryonic root forms. Next, we review recent advances in our understanding of the genes, signals, and mechanisms regulating lateral root and adventitious root branching in the plant models Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). While many common signals, regulatory components, and mechanisms have been identified that control the initiation, morphogenesis, and emergence of new lateral and adventitious root organs, much more remains to be done. We conclude by discussing the challenges and opportunities facing root branching research.
    Subject(s): Branching ; Root systems ; Plant roots ; Corn ; Auxins ; Update on Root Branching ; Plants ; Adventitious roots ; Root initiation ; Plant cells ; Rice ; Morphogenesis ; Plant Roots - physiology ; Arabidopsis - physiology ; Edible Grain - growth & development ; Arabidopsis - growth & development ; Terminology as Topic ; Edible Grain - physiology ; Plant Roots - growth & development ; Arabidopsis thaliana ; Physiological aspects ; Roots (Botany) ; Growth ; Index Medicus
    ISSN: 0032-0889
    E-ISSN: 1532-2548
    DOI: 10.1104/pp.114.245423
    Source: American Society of Plant Biologists
    Source: HighWire Press (Free Journals)
    Source: Hellenic Academic Libraries Link
    Source: PubMed Central
    Source: © ProQuest LLC All rights reserved〈img src="https://exlibris-pub.s3.amazonaws.com/PQ_Logo.jpg" style="vertical-align:middle;margin-left:7px"〉
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