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Kaur H, Teulon JM, Godon C, Desnos T, Chen SWW, Pellequer JL. Correlation between plant cell wall stiffening and root extension arrest phenotype in the combined abiotic stress of Fe and Al. PLANT, CELL & ENVIRONMENT 2024; 47:574-584. [PMID: 37876357 DOI: 10.1111/pce.14744] [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: 02/21/2023] [Revised: 10/01/2023] [Accepted: 10/15/2023] [Indexed: 10/26/2023]
Abstract
The plasticity and growth of plant cell walls (CWs) remain poorly understood at the molecular level. In this work, we used atomic force microscopy (AFM) to observe elastic responses of the root transition zone of 4-day-old Arabidopsis thaliana wild-type and almt1-mutant seedlings grown under Fe or Al stresses. Elastic parameters were deduced from force-distance curve measurements using the trimechanic-3PCS framework. The presence of single metal species Fe2+ or Al3+ at 10 µM exerts no noticeable effect on the root growth compared with the control conditions. On the contrary, a mix of both the metal ions produced a strong root-extension arrest concomitant with significant increase of CW stiffness. Raising the concentration of either Fe2+ or Al3+ to 20 µM, no root-extension arrest was observed; nevertheless, an increase in root stiffness occurred. In the presence of both the metal ions at 10 µM, root-extension arrest was not observed in the almt1 mutant, which substantially abolishes the ability to exude malate. Our results indicate that the combination of Fe2+ and Al3+ with exuded malate is crucial for both CW stiffening and root-extension arrest. However, stiffness increase induced by single Fe2+ or Al3+ is not sufficient for arresting root growth in our experimental conditions.
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Affiliation(s)
| | | | - Christian Godon
- Aix Marseille Université, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, Cadarache, France
| | - Thierry Desnos
- Aix Marseille Université, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, Cadarache, France
| | - Shu-Wen W Chen
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Rue Cyprien Jullin, Vinay, France
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López-Alonso J, Eroles M, Janel S, Berardi M, Pellequer JL, Dupres V, Lafont F, Rico F. PyFMLab: Open-source software for atomic force microscopy microrheology data analysis. OPEN RESEARCH EUROPE 2023; 3:187. [PMID: 39118808 PMCID: PMC11308986 DOI: 10.12688/openreseurope.16550.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 08/10/2024]
Abstract
Background Atomic force microscopy (AFM) is one of the main techniques used to characterize the mechanical properties of soft biological samples and biomaterials at the nanoscale. Despite efforts made by the AFM community to promote open-source data analysis tools, standardization continues to be a significant concern in a field that requires common analysis procedures. AFM-based mechanical measurements involve applying a controlled force to the sample and measure the resulting deformation in the so-called force-distance curves. These may include simple approach and retract or oscillatory cycles at various frequencies (microrheology). To extract quantitative parameters, such as the elastic modulus, from these measurements, AFM measurements are processed using data analysis software. Although open tools exist and allow obtaining the mechanical properties of the sample, most of them only include standard elastic models and do not allow the processing of microrheology data. In this work, we have developed an open-source software package (called PyFMLab, as of python force microscopy laboratory) capable of determining the viscoelastic properties of samples from both conventional force-distance curves and microrheology measurements. Methods PyFMLab has been written in Python, which provides an accessible syntax and sufficient computational efficiency. The software features were divided into separate, self-contained libraries to enhance code organization and modularity and to improve readability, maintainability, testability, and reusability. To validate PyFMLab, two AFM datasets, one composed of simple force curves and another including oscillatory measurements, were collected on HeLa cells. Results The viscoelastic parameters obtained on the two datasets analysed using PyFMLab were validated against data processing proprietary software and against validated MATLAB routines developed before obtaining equivalent results. Conclusions Its open-source nature and versatility makes PyFMLab an open-source solution that paves the way for standardized viscoelastic characterization of biological samples from both force-distance curves and microrheology measurements.
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Affiliation(s)
- Javier López-Alonso
- Universite de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017, CILL—Center of Infection and Immunity of Lille, Lille, F-59000, France
| | - Mar Eroles
- Aix-Marseille Univ., CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, 13009, France
| | - Sébastien Janel
- Universite de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017, CILL—Center of Infection and Immunity of Lille, Lille, F-59000, France
| | - Massimiliano Berardi
- LaserLab, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands
- Optics 11 B.V, Amsterdam, 1101BM, The Netherlands
| | | | - Vincent Dupres
- Universite de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017, CILL—Center of Infection and Immunity of Lille, Lille, F-59000, France
| | - Frank Lafont
- Universite de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017, CILL—Center of Infection and Immunity of Lille, Lille, F-59000, France
| | - Felix Rico
- Aix-Marseille Univ., CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, 13009, France
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Kaur H, Teulon JM, Foucher AE, Fenel D, Chen SWW, Godon C, Desnos T, Pellequer JL. Measuring external primary cell wall elasticity of seedling roots using atomic force microscopy. STAR Protoc 2023; 4:102265. [PMID: 37200196 DOI: 10.1016/j.xpro.2023.102265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 05/20/2023] Open
Abstract
Stiffness plays a central action in plant cell extension. Here, we present a protocol to detect changes in stiffness on the external epidermal cell wall of living plant roots using atomic force microscopy (AFM). We provide generalized instructions for collecting force-distance curves and analysis of stiffness using contact-based mechanical model. With this protocol, and some initial training in AFM, a user is able to perform indentation experiments on 4- and 5-day-old Arabidopsis thaliana and determine stiffness properties. For complete details on the use and execution of this protocol, please refer to Godon et al.1.
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Affiliation(s)
| | | | | | - Daphna Fenel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Shu-Wen W Chen
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France; Rue Cyprien Jullin, 38470 Vinay, France
| | - Christian Godon
- Aix Marseille Université, CNRS, CEA, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13115 Saint-Paul lez-Durance, France
| | - Thierry Desnos
- Aix Marseille Université, CNRS, CEA, Institut de Biosciences et Biotechnologies Aix-Marseille, Equipe Bioénergies et Microalgues, CEA Cadarache, 13115 Saint-Paul-lez-Durance, France.
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Kontomaris SV, Stylianou A, Georgakopoulos A, Malamou A. 3D AFM Nanomechanical Characterization of Biological Materials. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:395. [PMID: 36770357 PMCID: PMC9920073 DOI: 10.3390/nano13030395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Atomic Force Microscopy (AFM) is a powerful tool enabling the mechanical characterization of biological materials at the nanoscale. Since biological materials are highly heterogeneous, their mechanical characterization is still considered to be a challenging procedure. In this paper, a new approach that leads to a 3-dimensional (3D) nanomechanical characterization is presented based on the average Young's modulus and the AFM indentation method. The proposed method can contribute to the clarification of the variability of the mechanical properties of biological samples in the 3-dimensional space (variability at the x-y plane and depth-dependent behavior). The method was applied to agarose gels, fibroblasts, and breast cancer cells. Moreover, new mathematical methods towards a quantitative mechanical characterization are also proposed. The presented approach is a step forward to a more accurate and complete characterization of biological materials and could contribute to an accurate user-independent diagnosis of various diseases such as cancer in the future.
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Affiliation(s)
- Stylianos Vasileios Kontomaris
- BioNanoTec Ltd., 2043 Nicosia, Cyprus
- Faculty of Engineering and Architecture, Metropolitan College, 15125 Athens, Greece
| | - Andreas Stylianou
- School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | - Anastasios Georgakopoulos
- School of Electrical and Computer Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - Anna Malamou
- School of Electrical and Computer Engineering, National Technical University of Athens, 15780 Athens, Greece
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Kontomaris SV, Stylianou A, Chliveros G, Malamou A. Determining Spatial Variability of Elastic Properties for Biological Samples Using AFM. MICROMACHINES 2023; 14:mi14010182. [PMID: 36677243 PMCID: PMC9862197 DOI: 10.3390/mi14010182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/26/2022] [Accepted: 01/09/2023] [Indexed: 05/29/2023]
Abstract
Measuring the mechanical properties (i.e., elasticity in terms of Young's modulus) of biological samples using Atomic Force Microscopy (AFM) indentation at the nanoscale has opened new horizons in studying and detecting various pathological conditions at early stages, including cancer and osteoarthritis. It is expected that AFM techniques will play a key role in the future in disease diagnosis and modeling using rigorous mathematical criteria (i.e., automated user-independent diagnosis). In this review, AFM techniques and mathematical models for determining the spatial variability of elastic properties of biological materials at the nanoscale are presented and discussed. Significant issues concerning the rationality of the elastic half-space assumption, the possibility of monitoring the depth-dependent mechanical properties, and the construction of 3D Young's modulus maps are also presented.
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Affiliation(s)
- Stylianos Vasileios Kontomaris
- BioNanoTec Ltd., Nicosia 2043, Cyprus
- Faculty of Engineering and Architecture, Metropolitan College, 15125 Athens, Greece
| | - Andreas Stylianou
- School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
| | - Georgios Chliveros
- Faculty of Engineering and Architecture, Metropolitan College, 15125 Athens, Greece
| | - Anna Malamou
- School of Electrical and Computer Engineering, National Technical University of Athens, 15780 Athens, Greece
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