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Hériché M, Arnould C, Wipf D, Courty PE. Imaging plant tissues: advances and promising clearing practices. TRENDS IN PLANT SCIENCE 2022; 27:601-615. [PMID: 35339361 DOI: 10.1016/j.tplants.2021.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.
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Affiliation(s)
- Mathilde Hériché
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France.
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2
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Sivaguru M, Saw JJ, Wilson EM, Lieske JC, Krambeck AE, Williams JC, Romero MF, Fouke KW, Curtis MW, Kear-Scott JL, Chia N, Fouke BW. Human kidney stones: a natural record of universal biomineralization. Nat Rev Urol 2021; 18:404-432. [PMID: 34031587 DOI: 10.1038/s41585-021-00469-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 02/04/2023]
Abstract
GeoBioMed - a new transdisciplinary approach that integrates the fields of geology, biology and medicine - reveals that kidney stones composed of calcium-rich minerals precipitate from a continuum of repeated events of crystallization, dissolution and recrystallization that result from the same fundamental natural processes that have governed billions of years of biomineralization on Earth. This contextual change in our understanding of renal stone formation opens fundamentally new avenues of human kidney stone investigation that include analyses of crystalline structure and stratigraphy, diagenetic phase transitions, and paragenetic sequences across broad length scales from hundreds of nanometres to centimetres (five Powers of 10). This paradigm shift has also enabled the development of a new kidney stone classification scheme according to thermodynamic energetics and crystalline architecture. Evidence suggests that ≥50% of the total volume of individual stones have undergone repeated in vivo dissolution and recrystallization. Amorphous calcium phosphate and hydroxyapatite spherules coalesce to form planar concentric zoning and sector zones that indicate disequilibrium precipitation. In addition, calcium oxalate dihydrate and calcium oxalate monohydrate crystal aggregates exhibit high-frequency organic-matter-rich and mineral-rich nanolayering that is orders of magnitude higher than layering observed in analogous coral reef, Roman aqueduct, cave, deep subsurface and hot-spring deposits. This higher frequency nanolayering represents the unique microenvironment of the kidney in which potent crystallization promoters and inhibitors are working in opposition. These GeoBioMed insights identify previously unexplored strategies for development and testing of new clinical therapies for the prevention and treatment of kidney stones.
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Affiliation(s)
- Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Jessica J Saw
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Elena M Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Amy E Krambeck
- Department of Urology, Mayo Clinic, Rochester, MN, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James C Williams
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael F Romero
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Kyle W Fouke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - Matthew W Curtis
- Carl Zeiss Microscopy LLC, One North Broadway, White Plains, NY, USA
| | | | - Nicholas Chia
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bruce W Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl Zeiss Labs@Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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3
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Yuan J, Wang X, Zhou H, Li Y, Zhang J, Yu S, Wang M, Hao M, Zhao Q, Liu L, Li M, Li J. Comparison of Sample Preparation Techniques for Inspection of Leaf Epidermises Using Light Microscopy and Scanning Electronic Microscopy. FRONTIERS IN PLANT SCIENCE 2020; 11:133. [PMID: 32158456 PMCID: PMC7052180 DOI: 10.3389/fpls.2020.00133] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/28/2020] [Indexed: 05/17/2023]
Abstract
The micro-morphology of leaf epidermises is valuable for the study of leaf development and function, as well as the classification of plant species. There have been few studies comparing different preparation and imaging methods for visualizing the leaf epidermis. Here, four specimen preparation methods were used to investigate the leaf epidermis morphology of Arabidopsis, radish, cucumber, wheat, rice, and maize, under an inverted basic light microscope (LM), a laser scanning confocal microscope (LSCM), or a scanning electron microscope (SEM). Optical microscope specimens were obtained using either the direct isolation method or the chloral hydrate-based clearing method. SEM images were obtained using a standard stage for conventional dehydrated samples or a Coolstage for fresh tissue. Different parts of epidermis peels were well focused under the LM. Investigation of samples cleared by chloral hydrate is convenient and autofluorescence of cell walls can be detected in rice. The resolution of images of conventional SEM leaf samples was generally higher than the Coolstage images at the same magnification, whereas local collapse and shrinkage were observed in leaves with high water content when using the conventional method. However, stomatal apparatuses of Arabidopsis, cucumber, radish, and maize deformed and showed poor appearance when using the Coolstage. Moreover, we usually used glutaraldehyde as an SEM fixative when using t-butanol for freeze-drying, though methanol is considered a better fixative in recent studies. In addition, fresh samples were not stable on the Coolstage. Thus, we compared four different t-butanol freeze-drying methods and two Coolstage methods. The dimension and morphology of tissues were compared using the six different methods. The results indicate that methanol fixative obviously reduced shrinkage of SEM samples compared with glutaraldehyde and formaldehyde alcohol acetic acid (FAA) fixatives. The use of methanol and a graded series of steps improved the preservation of samples. Preparing samples with optimal cutting temperature compound and observing at -30°C helped to increase the stability of Coolstage samples. In summary, our results provide an overview of the shortcomings and merits of four different methods, and might provide some information about choosing an optimal method for visualizing epidermal morphology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mingjun Li
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junhua Li
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs, College of Life Sciences, Henan Normal University, Xinxiang, China
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Wijesinghe RE, Lee SY, Ravichandran NK, Shirazi MF, Kim P, Jung HY, Jeon M, Kim J. Biophotonic approach for the characterization of initial bitter-rot progression on apple specimens using optical coherence tomography assessments. Sci Rep 2018; 8:15816. [PMID: 30361556 PMCID: PMC6202396 DOI: 10.1038/s41598-018-33791-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/04/2018] [Indexed: 12/23/2022] Open
Abstract
The tremendous advances achieved in the biophotonics technologies have intensified the necessity for non-invasive modalities that can characterize diverse biological materials with increased sensitivity and resolution. Optical coherence tomography (OCT) is one of the techniques that has been applied for biological applications in medicine and agriculture to identify structural properties. Herein, we report the successful incorporation of OCT for the identification of morphological changes that occur as a result of the bitter rot disease, through continuous detection of structural changes. Detailed inner morphological structural changes occurring in fruit specimens were precisely analyzed as a function of the disease incubation period using OCT. The conducted histological correlation and quantitative three-dimensional evaluations provide a robust platform for further discoveries related to plant materials. The results highlight the initial identification of bitter rot progression on apple specimens owing to the non-invasive inspection capability of OCT. Therefore, we expect that the proposed method will enable immediate sensitivity improvements in the inspection of plant diseases for postharvest utility.
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Affiliation(s)
- Ruchire Eranga Wijesinghe
- School of Electronics Engineering, College of IT Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea
- Department of Biomedical Engineering, College of Engineering, Kyungil University, 50, Gamasil-gil, Hayang-eup, Gyeongsan-si, Gyeongsangbuk-do, 38428, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea
| | - Naresh Kumar Ravichandran
- School of Electronics Engineering, College of IT Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea
| | - Muhammad Faizan Shirazi
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, A-1090, Vienna, Austria
| | - Pilun Kim
- School of Electronics Engineering, College of IT Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea
- Institute of Biomedical Engineering, School of Medicine, Kyungpook National University, 680, Gukchaebosang-ro, Jung-gu, Daegu, 41944, Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea
| | - Mansik Jeon
- School of Electronics Engineering, College of IT Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea.
| | - Jeehyun Kim
- School of Electronics Engineering, College of IT Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Korea
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Garcia A, Huang D, Righolt A, Righolt C, Kalaw MC, Mathur S, McAvoy E, Anderson J, Luedke A, Itorralba J, Mai S. Super-resolution structure of DNA significantly differs in buccal cells of controls and Alzheimer's patients. J Cell Physiol 2017; 232:2387-2395. [PMID: 27996096 PMCID: PMC5485033 DOI: 10.1002/jcp.25751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/01/2023]
Abstract
The advent of super-resolution microscopy allowed for new insights into cellular and physiological processes of normal and diseased cells. In this study, we report for the first time on the super-resolved DNA structure of buccal cells from patients with Alzheimer's disease (AD) versus age- and gender-matched healthy, non-caregiver controls. In this super-resolution study cohort of 74 participants, buccal cells were collected and their spatial DNA organization in the nucleus examined by 3D Structured Illumination Microscopy (3D-SIM). Quantitation of the super-resolution DNA structure revealed that the nuclear super-resolution DNA structure of individuals with AD significantly differs from that of their controls (p < 0.05) with an overall increase in the measured DNA-free/poor spaces. This represents a significant increase in the interchromatin compartment. We also find that the DNA structure of AD significantly differs in mild, moderate, and severe disease with respect to the DNA-containing and DNA-free/poor spaces. We conclude that whole genome remodeling is a feature of buccal cells in AD.
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Affiliation(s)
- Angeles Garcia
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - David Huang
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Amanda Righolt
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Christiaan Righolt
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Maria Carmela Kalaw
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Shubha Mathur
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Elizabeth McAvoy
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - James Anderson
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Angela Luedke
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Justine Itorralba
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Sabine Mai
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
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