1
|
Qamar S, Baba AI, Verger S, Andersson M. Segmentation and characterization of macerated fibers and vessels using deep learning. PLANT METHODS 2024; 20:126. [PMID: 39143615 DOI: 10.1186/s13007-024-01244-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024]
Abstract
PURPOSE Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells' shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. RESULTS In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a mAP 0.5 - 0.95 of 78 %. To assess the model's robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. CONCLUSION By leveraging YOLOv8's advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.
Collapse
Affiliation(s)
- Saqib Qamar
- Department of Physics, Umeå University, Umeå, 90187, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, 90187, Sweden
- Department of Intelligent System, Robotics, Perception, and Learning (RPL), KTH Royal Institute of Technology, Stockholm, 100 44, Sweden
| | - Abu Imran Baba
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, 90183, Sweden
| | - Stéphane Verger
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, 90187, Sweden.
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, 90183, Sweden.
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, 90187, Sweden.
| | - Magnus Andersson
- Department of Physics, Umeå University, Umeå, 90187, Sweden.
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, 90187, Sweden.
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
| |
Collapse
|
2
|
Kong S, Zhu M, Pan D, Lane B, Smith RS, Roeder AHK. Tradeoff between speed and robustness in primordium initiation mediated by auxin-CUC1 interaction. Nat Commun 2024; 15:5911. [PMID: 39003301 PMCID: PMC11246466 DOI: 10.1038/s41467-024-50172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we find that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases the intensity of auxin maxima and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we find that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validate experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.
Collapse
Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Mingyuan Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - David Pan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Brendan Lane
- Department of Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Richard S Smith
- Department of Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
3
|
Kong S, Zhu M, Pan D, Lane B, Smith RS, Roeder AHK. Tradeoff Between Speed and Robustness in Primordium Initiation Mediated by Auxin-CUC1 Interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.569401. [PMID: 38076982 PMCID: PMC10705432 DOI: 10.1101/2023.11.30.569401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we found that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases auxin maxima intensity and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we found that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validated experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.
Collapse
Affiliation(s)
- Shuyao Kong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Mingyuan Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Present address: Department of Biology, Duke University, Durham, NC 27708, USA
| | - David Pan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Brendan Lane
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Richard S. Smith
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adrienne H. K. Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Lead Contact
| |
Collapse
|
4
|
Chernova T, Ageeva M, Ivanov O, Lev-Yadun S, Gorshkova T. Characterization of the fiber-like cortical cells in moss gametophytes. PLANTA 2024; 259:92. [PMID: 38504021 DOI: 10.1007/s00425-024-04367-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024]
Abstract
MAIN CONCLUSION Fiber-like cells with thickened cell walls of specific structure and polymer composition that includes (1 → 4)-β-galactans develop in the outer stem cortex of several moss species gametophytes. The early land plants evolved several specialized cell types and tissues that did not exist in their aquatic ancestors. Of these, water-conducting elements and reproductive organs have received most of the research attention. The evolution of tissues specialized to fulfill a mechanical function is by far less studied despite their wide distribution in land plants. For vascular plants following a homoiohydric trajectory, the evolutionary emergence of mechanical tissues is mainly discussed starting with the fern-like plants with their hypodermal sterome or sclerified fibers that have xylan and lignin-based cell walls. However, mechanical challenges were also faced by bryophytes, which lack lignified cell-walls. To characterize mechanical tissues in the bryophyte lineage, following a poikilohydric trajectory, we used six wild moss species (Polytrichum juniperinum, Dicranum sp., Rhodobryum roseum, Eurhynchiadelphus sp., Climacium dendroides, and Hylocomium splendens) and analyzed the structure and composition of their cell walls. In all of them, the outer stem cortex of the leafy gametophytic generation had fiber-like cells with a thickened but non-lignified cell wall. Such cells have a spindle-like shape with pointed tips. The additional thick cell wall layer in those fiber-like cells is composed of sublayers with structural evidence for different cellulose microfibril orientation, and with specific polymer composition that includes (1 → 4)-β-galactans. Thus, the basic cellular characters of the cells that provide mechanical support in vascular plant taxa (elongated cell shape, location at the periphery of a primary organ, the thickened cell wall and its peculiar composition and structure) also exist in mosses.
Collapse
Affiliation(s)
- Tatyana Chernova
- The Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia.
| | - Marina Ageeva
- Microscopy Cabinet, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Oleg Ivanov
- P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Simcha Lev-Yadun
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa-Oranim, 36006, Tivon, Israel
| | - Tatyana Gorshkova
- The Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| |
Collapse
|
5
|
Petrova A, Ageeva M, Kozlova L. Root growth of monocotyledons and dicotyledons is limited by different tissues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1462-1476. [PMID: 37646760 DOI: 10.1111/tpj.16440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Plant growth and morphogenesis are determined by the mechanical properties of its cell walls. Using atomic force microscopy, we have characterized the dynamics of cell wall elasticity in different tissues in developing roots of several plant species. The elongation growth zone of roots of all species studied was distinguished by a reduced modulus of elasticity of most cell walls compared to the meristem or late elongation zone. Within the individual developmental zones of roots, there were also significant differences in the elasticity of the cell walls of the different tissues, thus identifying the tissues that limit root growth in the different species. In cereals, this is mainly the inner cortex, whereas in dicotyledons this function is performed by the outer tissues-rhizodermis and cortex. These differences result in a different behaviour of the roots of these species during longitudinal dissection. Modelling of longitudinal root dissection using measured properties confirmed the difference shown. Thus, the morphogenesis of monocotyledonous and dicotyledonous roots relies on different tissues as growth limiting, which should be taken into account when analyzing the localization of associated molecular events. At the same time, no matrix polysaccharide was found whose immunolabelling in type I or type II cell walls would predict their mechanical properties. However, assessment of the degree of anisotropy of cortical microtubules showed a striking correlation with the elasticity of the corresponding cell walls in all species studied.
Collapse
Affiliation(s)
- Anna Petrova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Marina Ageeva
- Microscopy Cabinet, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Liudmila Kozlova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
- Mechanics and Civil Engineering Laboratory, University of Montpellier, 860 Rue de St - Priest, 34090, Montpellier, France
| |
Collapse
|
6
|
Jobert F, Yadav S, Robert S. Auxin as an architect of the pectin matrix. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6933-6949. [PMID: 37166384 PMCID: PMC10690733 DOI: 10.1093/jxb/erad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.
Collapse
Affiliation(s)
- François Jobert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
- CRRBM, Université de Picardie Jules Verne, 80000, Amiens, France
| | - Sandeep Yadav
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Stéphanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| |
Collapse
|
7
|
Medina MC, Sousa-Baena MS, Van Sluys MA, Demarco D. Laticifer growth pattern is guided by cytoskeleton organization. FRONTIERS IN PLANT SCIENCE 2022; 13:971235. [PMID: 36262651 PMCID: PMC9574190 DOI: 10.3389/fpls.2022.971235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Laticifers are secretory structures that produce latex, forming a specialized defense system against herbivory. Studies using anatomical approaches to investigate laticifer growth patterns have described their origin; however, their mode of growth, i.e., whether growth is intrusive or diffuse, remains unclear. Studies investigating how cytoskeleton filaments may influence laticifer shape establishment and growth patterns are lacking. In this study, we combined microtubule immunostaining and developmental anatomy to investigate the growth patterns in different types of laticifers. Standard anatomical methods were used to study laticifer development. Microtubules were labelled through immunolocalization of α-tubulin in three types of laticifers from three different plant species: nonanastomosing (Urvillea ulmacea), anastomosing unbranched with partial degradation of terminal cell walls (Ipomoea nil), and anastomosing branched laticifers with early and complete degradation of terminal cell walls (Asclepias curassavica). In both nonanastomosing and anastomosing laticifers, as well as in differentiating meristematic cells, parenchyma cells and idioblasts, microtubules were perpendicularly aligned to the cell growth axis. The analyses of laticifer microtubule orientation revealed an arrangement that corresponds to those cells that grow diffusely within the plant body. Nonanastomosing and anastomosing laticifers, branched or not, have a pattern which indicates diffuse growth. This innovative study on secretory structures represents a major advance in the knowledge of laticifers and their growth mode.
Collapse
Affiliation(s)
| | | | | | - Diego Demarco
- *Correspondence: Maria Camila Medina, ; Diego Demarco,
| |
Collapse
|
8
|
Riddled with holes: Understanding air space formation in plant leaves. PLoS Biol 2021; 19:e3001475. [PMID: 34871299 PMCID: PMC8675916 DOI: 10.1371/journal.pbio.3001475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/16/2021] [Indexed: 11/19/2022] Open
Abstract
Plants use energy from sunlight to transform carbon dioxide from the air into complex organic molecules, ultimately producing much of the food we eat. To make this complex chemistry more efficient, plant leaves are intricately constructed in 3 dimensions: They are flat to maximise light capture and contain extensive internal air spaces to increase gas exchange for photosynthesis. Many years of work has built up an understanding of how leaves form flat blades, but the molecular mechanisms that control air space formation are poorly understood. Here, I review our current understanding of air space formation and outline how recent advances can be harnessed to answer key questions and take the field forward. Increasing our understanding of plant air spaces will not only allow us to understand a fundamental aspect of plant development, but also unlock the potential to engineer the internal structure of crops to make them more efficient at photosynthesis with lower water requirements and more resilient in the face of a changing environment. Leaves are interwoven with large air spaces to increase the efficiency of photosynthesis; however, how these air spaces form and how different patterns have evolved is almost unknown. This Unsolved Mystery article discusses the existing evidence and poses new avenues of research to answer this question.
Collapse
|