Accurate and versatile 3D segmentation of plant tissues at cellular resolution

eLife, Journal Year: 2020, Volume and Issue: 9

Published: July 29, 2020

Quantitative analysis of plant and animal morphogenesis requires accurate segmentation individual cells in volumetric images growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image now starting emerge. Here, we present PlantSeg, a pipeline for tissues into cells. PlantSeg employs convolutional neural network predict cell boundaries graph partitioning segment based on predictions. was trained fixed live organs imaged confocal light sheet microscopes. delivers results generalizes well across different tissues, scales, acquisition settings even non samples. We diverse developmental contexts. is free open-source, both command line user-friendly graphical interface.

Language: Английский

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How Mechanical Forces Shape Plant Organs

Current Biology, Journal Year: 2021, Volume and Issue: 31(3), P. R143 - R159

Published: Feb. 1, 2021

Language: Английский

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Plant growth: the What, the How, and the Why

New Phytologist, Journal Year: 2021, Volume and Issue: 232(1), P. 25 - 41

Published: July 10, 2021

Growth is a widely used term in plant science and ecology, but it can have different meanings depending on the context spatiotemporal scale of analysis. At meristem level, growth associated with production cells initiation new organs. organ or over short time periods, often synonymously tissue expansion, while longer periods increase biomass common metric. even larger temporal spatial scales, mostly described as net primary production. Here, we first address question 'what growth?'. We propose general framework to distinguish between facets growth, corresponding physiological processes, environmental drivers mathematical formalisms. Based these definitions, then review how be measured analysed at organisational, scales. conclude by discussing why gaining better understanding essential disentangle genetic effects phenotype, uncover causalities around source sink limitations growth.

Language: Английский

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Using positional information to provide context for biological image analysis with MorphoGraphX 2.0

eLife, Journal Year: 2022, Volume and Issue: 11

Published: May 5, 2022

Positional information is a central concept in developmental biology. In developing organs, positional can be idealized as local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers plausible mechanism for the integration of molecular networks operating individual cells into spatially coordinated multicellular responses necessary organization emergent forms. Understanding how cues guide morphogenesis requires quantification gene expression and growth dynamics context their underlying systems. Here, we present recent advances MorphoGraphX software (Barbier de Reuille et al., 2015⁠) implement generalized framework to annotate organs with These systems introduce an organ-centric spatial microscopy data, allowing quantified compared thought control them.

Language: Английский

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The mechanics of plant morphogenesis

Science, Journal Year: 2023, Volume and Issue: 379(6631)

Published: Feb. 2, 2023

Understanding the mechanism by which patterned gene activity leads to mechanical deformation of cells and tissues create complex forms is a major challenge for developmental biology. Plants offer advantages addressing this problem because their do not migrate or rearrange during morphogenesis, simplifies analysis. We synthesize results from experimental analysis computational modeling show how interactions between cellulose fibers translate through wall, cell, tissue levels generate plant shapes. Genes can modify properties stresses at each level, though values pattern differ one level next. The dynamic network provides elastic resistance while allowing growth fiber sliding, enables morphogenesis maintaining strength.

Language: Английский

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Cell-cycle-linked growth reprogramming encodes developmental time into leaf morphogenesis

Current Biology, Journal Year: 2024, Volume and Issue: 34(3), P. 541 - 556.e15

Published: Jan. 21, 2024

How is time encoded into organ growth and morphogenesis? We address this question by investigating heteroblasty, where leaf development form are modified with progressing plant age. By combining morphometric analyses, fate-mapping through live-imaging, computational genetics, we identify age-dependent changes in cell-cycle-associated histogenesis that underpin heteroblasty. show juvenile leaves, cell proliferation competence rapidly released a "proliferation burst" coupled fast growth, whereas adult proliferative sustained for longer at slower rate. These effects mediated the SPL9 transcription factor response to inputs from both shoot age individual maturation along proximodistal axis. acts activating CyclinD3 family genes, which sufficient bypass requirement control of shape heteroblastic reprogramming cellular growth. In conclusion, have identified mechanism bridges across cell, tissue, whole-organism scales linking geometry.

Language: Английский

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Microtubule-Mediated Wall Anisotropy Contributes to Leaf Blade Flattening

Current Biology, Journal Year: 2020, Volume and Issue: 30(20), P. 3972 - 3985.e6

Published: Sept. 10, 2020

Plant organs can adopt a wide range of shapes, resulting from highly directional cell growth and divisions. We focus here on leaves leaf-like in Arabidopsis tomato, characterized by the formation thin, flat laminae. Combining experimental approaches with 3D mechanical modeling, we provide evidence that leaf shape depends cortical microtubule mediated cellulose deposition along main predicted stress orientations, particular, adaxial-abaxial axis internal walls. This behavior be explained feedback has potential to sustain even amplify preexisting degree flatness, which turn genes involved control organ polarity margin formation.

Language: Английский

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A WOX/Auxin Biosynthesis Module Controls Growth to Shape Leaf Form

Current Biology, Journal Year: 2020, Volume and Issue: 30(24), P. 4857 - 4868.e6

Published: Oct. 8, 2020

A key challenge in biology is to understand how the regional control of cell growth gives rise final organ forms. Plant leaves must coordinate along both proximodistal and mediolateral axes produce their shape. However, cell-level mechanisms controlling this coordination remain largely unclear. Here, we show that, A. thaliana, WOX5, one WUSCHEL-RELATED HOMEOBOX (WOX) family homeobox genes, acts redundantly with WOX1 WOX3 (PRESSED FLOWER [PRS]) leaf Through genetics hormone measurements, find that these WOXs act part through YUCCA (YUC) auxin biosynthetic gene expression margin. The requirement for WOX-mediated YUC patterning shape cannot be bypassed by epidermal YUC, indicating precise domain biosynthesis important form. Using time-lapse analysis, demonstrate organizes a gradient promotes lateral consequently characteristic ellipsoid thaliana We also provide evidence WOX proteins differentiation inhibiting proximally blade promoting it distally. This regulation allows sustained enables attain its In conclusion, WOX/auxin regulatory module shapes form coordinating axes.

Language: Английский

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Of floral fortune: tinkering with the grain yield potential of cereal crops

New Phytologist, Journal Year: 2019, Volume and Issue: 225(5), P. 1873 - 1882

Published: Sept. 11, 2019

Summary Enhancing the yield potential and stability of small‐grain cereals, such as wheat ( Triticum sp.), rice Oryza sativa ), barley Hordeum vulgare is a priority for global food security. Over last several decades, plant breeders have increased grain mainly by increasing number grains produced in each inflorescence. This trait determined spikelets per spike fertile florets spikelet. Recent genetic genomic advances cereal grass species identified molecular determinants facilitated exchange information across genera. In this review, we focus on basis inflorescence architecture Triticeae crops, highlighting recent insights that helped to improve by, example, reducing preprogrammed abortion floral organs. The accumulating development can be harnessed enhance comparative reconstruction rational design boost crops.

Language: Английский

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A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

eLife, Journal Year: 2021, Volume and Issue: 10

Published: Jan. 6, 2021

A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from molecular control gene expression to cellular coordination a tissue. Using machine-learning-based digital image analysis, we generated three-dimensional atlas ovule development Arabidopsis thaliana , enabling quantitative spatio-temporal analysis and patterns with cell tissue resolution. We discovered novel morphological manifestations polarity, new mode layer formation, previously unrecognized subepidermal populations initiate curvature. The data suggest an irregular build-up WUSCHEL primordium functions for INNER NO OUTER restricting nucellar proliferation organization interior chalaza. Our work demonstrates analytical power representation when studying organ complex architecture eventually consists 1900 cells.

Language: Английский

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