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Chustecki JM, Johnston IG. Collective mitochondrial dynamics resolve conflicting cellular tensions: From plants to general principles. Semin Cell Dev Biol 2024; 156:253-265. [PMID: 38043948 DOI: 10.1016/j.semcdb.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 12/05/2023]
Abstract
Mitochondria play diverse and essential roles in eukaryotic cells, and plants are no exception. Plant mitochondria have several differences from their metazoan and fungal cousins: they often exist in a fragmented state, move rapidly on actin rather than microtubules, have many plant-specific metabolic features and roles, and usually contain only a subset of the complete mtDNA genome, which itself undergoes frequent recombination. This arrangement means that exchange and complementation is essential for plant mitochondria, and recent work has begun to reveal how their collective dynamics and resultant "social networks" of encounters support this exchange, connecting plant mitochondria in time rather than in space. This review will argue that this social network perspective can be extended to a "societal network", where mitochondrial dynamics are an essential part of the interacting cellular society of organelles and biomolecules. Evidence is emerging that mitochondrial dynamics allow optimal resolutions to competing cellular priorities; we will survey this evidence and review potential future research directions, highlighting that plant mitochondria can help reveal and test principles that apply across other kingdoms of life. In parallel with this fundamental cell biology, we also highlight the translational "One Health" importance of plant mitochondrial behaviour - which is exploited in the production of a vast amount of crops consumed worldwide - and the potential for multi-objective optimisation to understand and rationally re-engineer the evolved resolutions to these tensions.
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Affiliation(s)
- Joanna M Chustecki
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway; Computational Biology Unit, University of Bergen, Bergen, Norway.
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2
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Johnston IG. Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells. MOLECULAR PLANT 2019; 12:764-783. [PMID: 30445187 DOI: 10.1016/j.molp.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.
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Affiliation(s)
- Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK; Birmingham Institute for Forest Research, University of Birmingham, Birmingham, UK.
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3
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Divlianksy I, Hale ER, Segall M, Glebov LB. Achromatic complex holograms for laser mode conversion. OPTICS EXPRESS 2019; 27:225-239. [PMID: 30645370 DOI: 10.1364/oe.27.000225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
While conventional complex phase masks are chromatic, we present an achromatic holographic phase mask capable of performing optical beam transformations in a spectral range exceeding 1000 nm. The system consists of a holographic phase mask fabricated by encoding the desired phase profiles into volume Bragg gratings, inserted in between two surface gratings. This device automatically adjusts each spectral component diffracted by the surface grating to the Bragg angle of the volume Bragg grating and equalizes phase incursion for all diffracted wavelengths. Transverse mode conversion is demonstrated and compared with theory for multiple narrow line laser sources operating from 488 to 1550 nm and for a broadband femtosecond source.
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4
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The Photoconvertible Fluorescent Protein Dendra2 Tag as a Tool to Investigate Intracellular Protein Dynamics. Methods Mol Biol 2019; 1992:201-214. [PMID: 31148040 DOI: 10.1007/978-1-4939-9469-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Fluorescence proteins changing spectral properties after exposure to light with a specific wavelength have recently become outstanding aids in the study of intracellular protein dynamics. Herein we show using Arabidopsis SYNAPTOTAGMIN 1 as a model protein that the Dendra2 green to red photoconvertible protein tag in combination with confocal scanning laser microscopy is a useful tool to study membrane protein intracellular dynamics.
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5
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Kwok SJJ, Jo Y, Lin HH, Choi M, Yun SH. Millisecond cellular labelling in situ with two-photon photoconversion. BIOMEDICAL OPTICS EXPRESS 2018; 9:3067-3077. [PMID: 29984083 PMCID: PMC6033565 DOI: 10.1364/boe.9.003067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/23/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
In situ labeling of cells within living biological tissues using photoconversion has provided valuable information on cellular physiology in their natural environments. However, current photoconvertible probes typically require seconds to minutes of light exposure, limiting their uses in rapid biological processes such as intracellular diffusion and circulating cells. Here, we report that two-photon photoconversion of cyanine-based dyes offers unprecedentedly rapid photoconversion down to millisecond timescales per cell. We demonstrate potential biological applications including measuring intracellular diffusion kinetics in a spinal nerve, labeling of rapidly flowing cells in a microfluidic channel, and photoconversion of a circulating cell in vivo.
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Affiliation(s)
- Sheldon J J Kwok
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yongjae Jo
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 16419, South Korea
| | - Harvey H Lin
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
| | - Myunghwan Choi
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon 16419, South Korea
| | - Seok-Hyun Yun
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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6
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Li S, Ling X, Lin Y, Qin A, Gao M, Tang BZ. In situ generation of photoactivatable aggregation-induced emission probes for organelle-specific imaging. Chem Sci 2018; 9:5730-5735. [PMID: 30079182 PMCID: PMC6050595 DOI: 10.1039/c8sc01887a] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/31/2018] [Indexed: 01/08/2023] Open
Abstract
Photoactivatable fluorescent probes are ideal tools for organelle study with a significant advantage of high spatiotemporal resolution. However, conventional photo-caged fluorophores for organelle-specific imaging suffer from several drawbacks, such as aggregation-caused quenching (ACQ), instability under ambient light, low photoactivation efficiency, and toxic photo-cleavage byproducts. Herein, we propose a strategy for in situ generation of photoactivatable aggregation-induced emission (AIE) probes of 2-(2-hydroxyphenyl)-benzothiazolines from easily available disulfide and thiol substrates through tandem S-S bond reduction and intramolecular cyclization reaction. Because the photoactivatable AIE probes can be in situ generated in a quantitative yield, they can be directly used for bio-imaging without complicated separation steps. Under both one- and NIR two-photon irradiation, excellent spatiotemporal resolution and high photoactivation efficiency were achieved for specific imaging of lipid droplets and lysosomes, respectively. Based on their in situ generation and adjustable organelle-targeting ability, the photoactivatable AIE probes could become an easy-to-use imaging tool in the study of the biological functions of organelles.
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Affiliation(s)
- Shiwu Li
- Guangdong Innovative Research Team , Center for Aggregation-Induced Emission , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China.,School of Medicine , South China University of Technology , Guangzhou 510006 , China
| | - Xia Ling
- Guangdong Innovative Research Team , Center for Aggregation-Induced Emission , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China
| | - Yuhan Lin
- Guangdong Innovative Research Team , Center for Aggregation-Induced Emission , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China
| | - Anjun Qin
- Guangdong Innovative Research Team , Center for Aggregation-Induced Emission , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China
| | - Meng Gao
- National Engineering Research Center for Tissue Restoration and Reconstruction , South China University of Technology , Guangzhou 510006 , China .
| | - Ben Zhong Tang
- Guangdong Innovative Research Team , Center for Aggregation-Induced Emission , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China.,Department of Chemistry , Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , The Hong Kong University of Science & Technology , Clear Water Bay , Kowloon , Hong Kong , China .
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7
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Mazzoni-Putman SM, Stepanova AN. A Plant Biologist's Toolbox to Study Translation. FRONTIERS IN PLANT SCIENCE 2018; 9:873. [PMID: 30013583 PMCID: PMC6036148 DOI: 10.3389/fpls.2018.00873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/04/2018] [Indexed: 05/03/2023]
Abstract
Across a broad range of species and biological questions, more and more studies are incorporating translation data to better assess how gene regulation occurs at the level of protein synthesis. The inclusion of translation data improves upon, and has been shown to be more accurate than, transcriptional studies alone. However, there are many different techniques available to measure translation and it can be difficult, especially for young or aspiring scientists, to determine which methods are best applied in specific situations. We have assembled this review in order to enhance the understanding and promote the utilization of translational methods in plant biology. We cover a broad range of methods to measure changes in global translation (e.g., radiolabeling, polysome profiling, or puromycylation), translation of single genes (e.g., fluorescent reporter constructs, toeprinting, or ribosome density mapping), sequencing-based methods to uncover the entire translatome (e.g., Ribo-seq or translating ribosome affinity purification), and mass spectrometry-based methods to identify changes in the proteome (e.g., stable isotope labeling by amino acids in cell culture or bioorthogonal noncanonical amino acid tagging). The benefits and limitations of each method are discussed with a particular note of how applications from other model systems might be extended for use in plants. In order to make this burgeoning field more accessible to students and newer scientists, our review includes an extensive glossary to define key terms.
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8
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Aouacheria A, Baghdiguian S, Lamb HM, Huska JD, Pineda FJ, Hardwick JM. Connecting mitochondrial dynamics and life-or-death events via Bcl-2 family proteins. Neurochem Int 2017; 109:141-161. [PMID: 28461171 DOI: 10.1016/j.neuint.2017.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/17/2017] [Indexed: 12/12/2022]
Abstract
The morphology of a population of mitochondria is the result of several interacting dynamical phenomena, including fission, fusion, movement, elimination and biogenesis. Each of these phenomena is controlled by underlying molecular machinery, and when defective can cause disease. New understanding of the relationships between form and function of mitochondria in health and disease is beginning to be unraveled on several fronts. Studies in mammals and model organisms have revealed that mitochondrial morphology, dynamics and function appear to be subject to regulation by the same proteins that regulate apoptotic cell death. One protein family that influences mitochondrial dynamics in both healthy and dying cells is the Bcl-2 protein family. Connecting mitochondrial dynamics with life-death pathway forks may arise from the intersection of Bcl-2 family proteins with the proteins and lipids that determine mitochondrial shape and function. Bcl-2 family proteins also have multifaceted influences on cells and mitochondria, including calcium handling, autophagy and energetics, as well as the subcellular localization of mitochondrial organelles to neuronal synapses. The remarkable range of physical or functional interactions by Bcl-2 family proteins is challenging to assimilate into a cohesive understanding. Most of their effects may be distinct from their direct roles in apoptotic cell death and are particularly apparent in the nervous system. Dual roles in mitochondrial dynamics and cell death extend beyond BCL-2 family proteins. In this review, we discuss many processes that govern mitochondrial structure and function in health and disease, and how Bcl-2 family proteins integrate into some of these processes.
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Affiliation(s)
- Abdel Aouacheria
- Institute of Evolutionary Sciences of Montpellier (ISEM), CNRS UMR 5554, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Stephen Baghdiguian
- Institute of Evolutionary Sciences of Montpellier (ISEM), CNRS UMR 5554, University of Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Heather M Lamb
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA
| | - Jason D Huska
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA
| | - Fernando J Pineda
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins University, Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe St., Baltimore, MD 21205, USA.
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9
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Dalmasso G, Marin Zapata PA, Brady NR, Hamacher-Brady A. Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity. PLoS One 2017; 12:e0168198. [PMID: 28060865 PMCID: PMC5217980 DOI: 10.1371/journal.pone.0168198] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 11/28/2016] [Indexed: 12/25/2022] Open
Abstract
Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity.
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Affiliation(s)
- Giovanni Dalmasso
- Lysosomal Systems Biology, German Cancer Research Center (DKFZ) and BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Paula Andrea Marin Zapata
- Lysosomal Systems Biology, German Cancer Research Center (DKFZ) and BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Nathan Ryan Brady
- Systems Biology of Cell Death Mechanisms, German Cancer Research Center (DKFZ) and BioQuant, University of Heidelberg, Heidelberg, Germany
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail: (NRB); (AH-B)
| | - Anne Hamacher-Brady
- Lysosomal Systems Biology, German Cancer Research Center (DKFZ) and BioQuant, University of Heidelberg, Heidelberg, Germany
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail: (NRB); (AH-B)
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10
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Two-photon excited photoconversion of cyanine-based dyes. Sci Rep 2016; 6:23866. [PMID: 27029524 PMCID: PMC4814926 DOI: 10.1038/srep23866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 12/02/2022] Open
Abstract
The advent of phototransformable fluorescent proteins has led to significant advances in optical imaging, including the unambiguous tracking of cells over large spatiotemporal scales. However, these proteins typically require activating light in the UV-blue spectrum, which limits their in vivo applicability due to poor light penetration and associated phototoxicity on cells and tissue. We report that cyanine-based, organic dyes can be efficiently photoconverted by nonlinear excitation at the near infrared (NIR) window. Photoconversion likely involves singlet-oxygen mediated photochemical cleavage, yielding blue-shifted fluorescent products. Using SYTO62, a biocompatible and cell-permeable dye, we demonstrate photoconversion in a variety of cell lines, including depth-resolved labeling of cells in 3D culture. Two-photon photoconversion of cyanine-based dyes offer several advantages over existing photoconvertible proteins, including use of minimally toxic NIR light, labeling without need for genetic intervention, rapid kinetics, remote subsurface targeting, and long persistence of photoconverted signal. These findings are expected to be useful for applications involving rapid labeling of cells deep in tissue.
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11
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Sano Y, Watanabe W, Matsunaga S. Chromophore-assisted laser inactivation--towards a spatiotemporal-functional analysis of proteins, and the ablation of chromatin, organelle and cell function. J Cell Sci 2014; 127:1621-9. [PMID: 24737873 DOI: 10.1242/jcs.144527] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromophore-assisted laser or light inactivation (CALI) has been employed as a promising technique to achieve spatiotemporal knockdown or loss-of-function of target molecules in situ. CALI is performed using photosensitizers as generators of reactive oxygen species (ROS). There are two CALI approaches that use either transgenic tags with chemical photosensitizers, or genetically encoded fluorescent protein fusions. Using spatially restricted microscopy illumination, CALI can address questions regarding, for example, protein isoforms, subcellular localization or phase-specific analyses of multifunctional proteins that other knockdown approaches, such as RNA interference or treatment with chemicals, cannot. Furthermore, rescue experiments can clarify the phenotypic capabilities of CALI after the depletion of endogenous targets. CALI can also provide information about individual events that are involved in the function of a target protein and highlight them in multifactorial events. Beyond functional analysis of proteins, CALI of nuclear proteins can be performed to induce cell cycle arrest, chromatin- or locus-specific DNA damage. Even at organelle level - such as in mitochondria, the plasma membrane or lysosomes - CALI can trigger cell death. Moreover, CALI has emerged as an optogenetic tool to switch off signaling pathways, including the optical depletion of individual neurons. In this Commentary, we review recent applications of CALI and discuss the utility and effective use of CALI to address open questions in cell biology.
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Affiliation(s)
- Yukimi Sano
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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12
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Langhans M, Meckel T. Single-molecule detection and tracking in plants. PROTOPLASMA 2014; 251:277-91. [PMID: 24385216 DOI: 10.1007/s00709-013-0601-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/12/2013] [Indexed: 05/07/2023]
Abstract
Combining optical properties with a limited choice of fluorophores turns single-molecule imaging in plants into a challenging task. This explains why the technique, despite its success in the field of animal cell biology, is far from being routinely applied in plant cell research. The same challenges, however, also apply to the application of single-molecule microscopy to any intact tissue or multicellular 3D cell culture. As recent and upcoming progress in fluorescence microscopy will permit single-molecule detection in the context of multicellular systems, plant tissue imaging will experience a huge benefit from this progress. In this review, we address every step of a single-molecule experiment, highlight the critical aspects of each and elaborate on optimizations and developments required for improvements. We relate each step to recent achievements, which have so far been conducted exclusively on the root epidermis of Arabidopsis thaliana seedlings with inclined illumination and show examples of single-molecule measurements using different cells or illumination schemes.
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Affiliation(s)
- Markus Langhans
- Membrane Dynamics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 3-5, 64287, Darmstadt, Germany
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13
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Wolf H, Barisas BG, Dietz KJ, Seidel T. Kaede for detection of protein oligomerization. MOLECULAR PLANT 2013; 6:1453-62. [PMID: 23430050 DOI: 10.1093/mp/sst039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Photoconvertible fluorescent proteins such as Kaede are routinely used for tracking proteins, organelles, and whole cells. Kaede was the first identified photoconvertible fluorescent protein and has since become the most commonly used photoconvertible fluorescent protein in vertebrates. Kaede can be irreversibly converted from a green to a red fluorescent form upon UV/blue light irradiation and fluorescence of each form can be isolated separately by appropriate filter sets. Spectral properties of the Kaede forms allow Förster resonance energy transfer (FRET) from the green form as donor to the red form as acceptor. As a sample containing oligomerized Kaede-containing proteins is exposed to UV or blue light, FRET first increases as green Kaede is converted to red and then decreases as the green donor becomes depleted. Thus, FRET information is potentially obtained from a number of independent measurements taken as photoconversion proceeds. We demonstrate here the application of this approach to detect homo-aggregation and conformational dynamics of plant protein constructs. Structural alterations of 2-cys peroxiredoxin–Kaede were successfully detected depending on the redox state in living plant cells. Photoconversion was performed gradually and donor emission, acceptor emission, and FRET-derived sensitized acceptor emission were measured at each step of conversion. Since photoconvertible proteins have not been routinely used in plants, two plasmids have been designed to facilitate plant applications. The plasmids allow either transient expression of Kaede-containing protein constructs in plant cells or Gateway cloning and stable transformation of plants.
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Affiliation(s)
- Heike Wolf
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld University, D-33501 Bielefeld, Germany
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14
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Arterial and venous progenitors of the major axial vessels originate at distinct locations. Dev Cell 2013; 25:196-206. [PMID: 23639444 DOI: 10.1016/j.devcel.2013.03.017] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 01/14/2013] [Accepted: 03/25/2013] [Indexed: 12/21/2022]
Abstract
Currently, it remains controversial how vascular endothelial progenitor cells (angioblasts) establish their arterial or venous fates. We show using zebrafish that the arterial progenitors of the major axial vessels originate earlier and closer to the midline than the venous progenitors. Both medial and lateral progenitor populations migrate to distinct arterial and venous positions and not into a common precursor vessel as previously suggested. Overexpression of VEGF or Hedgehog (Hh) homologs results in the partially randomized distribution of arterial and venous progenitors within the axial vessels. We further demonstrate that the function of the Etv2 transcription factor is required at earlier stages for arterial development than for venous. Our results argue that the medial angioblasts undergo arterial differentiation because they receive higher concentration of Vegf and Hh morphogens than the lateral angioblasts. We propose a revised model of arterial-venous differentiation that explains how angioblasts choose between an arterial and venous fate.
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15
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Peter M, Bathellier B, Fontinha B, Pliota P, Haubensak W, Rumpel S. Transgenic mouse models enabling photolabeling of individual neurons in vivo. PLoS One 2013; 8:e62132. [PMID: 23626779 PMCID: PMC3633923 DOI: 10.1371/journal.pone.0062132] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 03/19/2013] [Indexed: 01/26/2023] Open
Abstract
One of the biggest tasks in neuroscience is to explain activity patterns of individual neurons during behavior by their cellular characteristics and their connectivity within the neuronal network. To greatly facilitate linking in vivo experiments with a more detailed molecular or physiological analysis in vitro, we have generated and characterized genetically modified mice expressing photoactivatable GFP (PA-GFP) that allow conditional photolabeling of individual neurons. Repeated photolabeling at the soma reveals basic morphological features due to diffusion of activated PA-GFP into the dendrites. Neurons photolabeled in vivo can be re-identified in acute brain slices and targeted for electrophysiological recordings. We demonstrate the advantages of PA-GFP expressing mice by the correlation of in vivo firing rates of individual neurons with their expression levels of the immediate early gene c-fos. Generally, the mouse models described in this study enable the combination of various analytical approaches to characterize living cells, also beyond the neurosciences.
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Affiliation(s)
- Manuel Peter
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Brice Bathellier
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Bruno Fontinha
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Pinelopi Pliota
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Wulf Haubensak
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Simon Rumpel
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- * E-mail:
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16
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Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MM, Arriaga EA. Bioanalysis of eukaryotic organelles. Chem Rev 2013; 113:2733-811. [PMID: 23570618 PMCID: PMC3676536 DOI: 10.1021/cr300354g] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chad P. Satori
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Michelle M. Henderson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Elyse A. Krautkramer
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Vratislav Kostal
- Tescan, Libusina trida 21, Brno, 623 00, Czech Republic
- Institute of Analytical Chemistry ASCR, Veveri 97, Brno, 602 00, Czech Republic
| | - Mark M. Distefano
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
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17
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Chen T, Wang X, von Wangenheim D, Zheng M, Šamaj J, Ji W, Lin J. Probing and tracking organelles in living plant cells. PROTOPLASMA 2012; 249 Suppl 2:S157-S167. [PMID: 22183127 DOI: 10.1007/s00709-011-0364-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 12/06/2011] [Indexed: 05/31/2023]
Abstract
Intracellular organelle movements and positioning play pivotal roles in enabling plants to proliferate life efficiently and to survive diverse environmental stresses. The elaborate dissection of organelle dynamics and their underlying mechanisms (e.g., the role of the cytoskeleton in organelle movements) largely depends on the advancement and efficiency of organelle tracking systems. Here, we provide an overview of some recently developed tools for labeling and tracking organelle dynamics in living plant cells.
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Affiliation(s)
- Tong Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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18
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Abstract
This chapter describes methods for studying membrane traffic and organelle biogenesis in Caenorhabditis elegans. These processes have traditionally been studied with yeast or mammalian cells, but C. elegans is emerging as an attractive alternative model system for cell biologists. C. elegans is well known for the ease of manipulation through classic and molecular genetic techniques. In addition, C. elegans is transparent, so fluorescent proteins can be observed in live animals. These properties have aided the development of functional assays for tracking cell biological processes in situ. Localization results obtained with fluorescent proteins can be validated with immunofluorescence and with biochemical methods, such as subcellular fractionation, adapted from methods developed for other organisms. C. elegans thus combines powerful genetics with a range of cell biological techniques to study subcellular processes in a tractable multicellular organism.
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Affiliation(s)
- Hanna Fares
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
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19
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Abstract
The ability to differentially label single cells has important implications in developmental biology. For instance, determining how hematopoietic, lymphatic, and blood vessel lineages arise in developing embryos requires fate mapping and lineage tracing of undifferentiated precursor cells. Recently, photoactivatable proteins which include: Eos1, 2, PAmCherry3, Kaede4-7, pKindling8, and KikGR9, 10 have received wide interest as cell tracing probes. The fluorescence spectrum of these photosensitive proteins can be easily converted with UV excitation, allowing a population of cells to be distinguished from adjacent ones. However, the photoefficiency of the activated protein may limit long-term cell tracking11. As an alternative to photoactivatable proteins, caged fluorescein-dextran has been widely used in embryo model systems7, 12-14. Traditionally, to uncage fluorescein-dextran, UV excitation from a fluorescence lamp house or a single photon UV laser has been used; however, such sources limit the spatial resolution of photoactivation. Here we report a protocol to fate map, lineage trace, and detect single labeled cells. Single cells in embryos injected with caged fluorescein-dextran are photoactivated with near-infrared laser pulses produced from a titanium sapphire femtosecond laser. This laser is customary in all two-photon confocal microscopes such as the LSM 510 META NLO microscope used in this paper. Since biological tissue is transparent to near-infrared irradiation15, the laser pulses can be focused deep within the embryo without uncaging cells above or below the selected focal plane. Therefore, non-linear two-photon absorption is induced only at the geometric focus to uncage fluorescein-dextran in a single cell. To detect the cell containing uncaged fluorescein-dextran, we describe a simple immunohistochemistry protocol16 to rapidly visualize the activated cell. The activation and detection protocol presented in this paper is versatile and can be applied to any model system. Note: The reagents used in this protocol can be found in the table appended at the end of the article.
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Affiliation(s)
- Vikram Kohli
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, USA
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20
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Isobe K, Hashimoto H, Suda A, Kannari F, Kawano H, Mizuno H, Miyawaki A, Midorikawa K. Measurement of two-photon excitation spectrum used to photoconvert a fluorescent protein (Kaede) by nonlinear Fourier-transform spectroscopy. BIOMEDICAL OPTICS EXPRESS 2010; 1:687-693. [PMID: 21258500 PMCID: PMC3017996 DOI: 10.1364/boe.1.000687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/11/2010] [Accepted: 08/18/2010] [Indexed: 05/03/2023]
Abstract
We demonstrate the measurement of two-photon excitation (TPE) spectra, used not only for fluorescence but also for photoconversion in green-to-red photoconvertible Kaede, using nonlinear Fourier-transform spectroscopy. It was found that in unphotoconverted Kaede, the TPE spectrum for photoconversion is much different to that for green-fluorescence. This is similar to the difference between the one-photon excitation of photoconversion in the neutral form and that of green-fluorescence in the ionized form.
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Affiliation(s)
- Keisuke Isobe
- Laser Technology Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroshi Hashimoto
- Laser Technology Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Akira Suda
- Laser Technology Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Fumihiko Kannari
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Hiroyuki Kawano
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideaki Mizuno
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumi Midorikawa
- Laser Technology Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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21
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Brown SC, Bolte S, Gaudin M, Pereira C, Marion J, Soler MN, Satiat-Jeunemaitre B. Exploring plant endomembrane dynamics using the photoconvertible protein Kaede. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:696-711. [PMID: 20545892 DOI: 10.1111/j.1365-313x.2010.04272.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Photoactivatable and photoconvertible fluorescent proteins capable of pronounced light-induced spectral changes are a powerful addition to the fluorescent protein toolbox of the cell biologist. They permit specific tracking of one subcellular structure (organelle or cell subdomain) within a differentially labelled population. They also enable pulse-chase analysis of protein traffic. The Kaede gene codes for a tetrameric protein found in the stony coral Trachyphyllia geoffroyi, which emits green fluorescence that irreversibly shifts to red following radiation with UV or violet light. We report here the use of Kaede to explore the plant secretory pathway. Kaede versions of the Golgi marker sialyl-transferase (ST-Kaede) and of the vacuolar pathway marker cardosin A (cardA-Kaede) were engineered. Several optical devices enabling photoconversion and observation of Kaede using these two constructs were assessed to optimize Kaede-based imaging protocols. Photoconverted ST-Kaede red-labelled organelles can be followed within neighbouring populations of non-converted green Golgi stacks, by their gradual development of orange/yellow coloration from de novo synthesis of Golgi proteins (green). Results highlight some aspects on the dynamics of the plant Golgi. For plant bio-imaging, the photoconvertible Kaede offers a powerful tool to track the dynamic behaviour of designated subpopulations of Golgi within living cells, while visualizing the de novo formation of proteins and structures, such as a Golgi stack.
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Affiliation(s)
- Spencer C Brown
- Laboratoire Dynamique de la Compartimentation Cellulaire, CNRS, Institut des Sciences du Végétal, Centre de recherche de Gif (FRC3115), 91198, Gif-sur-Yvette Cedex, France
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22
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Kohli V, Elezzabi AY. Prospects and developments in cell and embryo laser nanosurgery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 1:11-25. [PMID: 20049775 DOI: 10.1002/wnan.29] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recently, there has been increasing interest in the application of femtosecond (fs) laser pulses to the study of cells, tissues and embryos. This review explores the developments that have occurred within the last several years in the fields of cell and embryo nanosurgery. Each of the individual studies presented in this review clearly demonstrates the nondestructiveness of fs laser pulses, which are used to alter both cellular and subcellular sites within simple cells and more complicated multicompartmental embryos. The ability to manipulate these model systems noninvasively makes applied fs laser pulses an invaluable tool for developmental biologists, geneticists, cryobiologists, and zoologists. We are beginning to see the integration of this tool into life sciences, establishing its status among molecular and genetic cell manipulation methods. More importantly, several studies demonstrating the versatility of applied fs laser pulses have established new collaborations among physicists, engineers, and biologists with the common intent of solving biological problems.
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Affiliation(s)
- Vikram Kohli
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Abdulhakem Y Elezzabi
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
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23
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Bereiter-Hahn J, Jendrach M. Mitochondrial dynamics. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 284:1-65. [PMID: 20875628 DOI: 10.1016/s1937-6448(10)84001-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial dynamics is a key feature for the interaction of mitochondria with other organelles within a cell and also for the maintenance of their own integrity. Four types of mitochondrial dynamics are discussed: Movement within a cell and interactions with the cytoskeleton, fusion and fission events which establish coherence within the chondriome, the dynamic behavior of cristae and their components, and finally, formation and disintegration of mitochondria (mitophagy). Due to these essential functions, disturbed mitochondrial dynamics are inevitably connected to a variety of diseases. Localized ATP gradients, local control of calcium-based messaging, production of reactive oxygen species, and involvement of other metabolic chains, that is, lipid and steroid synthesis, underline that physiology not only results from biochemical reactions but, in addition, resides on the appropriate morphology and topography. These events and their molecular basis have been established recently and are the topic of this review.
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Affiliation(s)
- Jürgen Bereiter-Hahn
- Center of Excellence Macromolecular Complexes, Institute for Cell Biology and Neurosciences, Goethe University, Frankfurt am Main, Germany
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24
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Lanzanò L, Sui L, Costanzo E, Gulino M, Scordino A, Tudisco S, Musumeci F. Time-resolved spectral measurements of delayed luminescence from a single soybean seed: effects of thermal damage and correlation with germination performance. LUMINESCENCE 2009; 24:409-15. [PMID: 19424957 DOI: 10.1002/bio.1127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Delayed luminescence from a single dry soybean seed was investigated in both spectral and time domains, under different excitation wavelengths. Emission spectra were collected, under 337 nm laser excitation, from native and artificially deteriorated seeds and the time-dependence of different spectral components was analyzed in detail. The single seed viability was evaluated through observation of germination properties after imbibition and compared with different parameters related to the luminescence kinetics. The significant correlation found between single seed delayed luminescence parameters and germination capability strongly validates the connection of this phenomenon with the functional state of the system and suggests the development of a non-invasive technique for seed quality determination.
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Affiliation(s)
- Luca Lanzanò
- Dipartimento di Metodologie Fisiche e Chimiche per l'Ingegneria, University of Catania, Catania, Italy.
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25
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Zhao Y, Zhang Y, Liu X, Lv X, Zhou W, Luo Q, Zeng S. Photostimulation of astrocytes with femtosecond laser pulses. OPTICS EXPRESS 2009; 17:1291-1298. [PMID: 19188957 DOI: 10.1364/oe.17.001291] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The involvement of astrocytes in brain functions rather than support has been identified and widely concerned. However the lack of an effective stimulation of astrocytes hampers our understanding of their essential roles. Here, we employed 800-nm near infrared (NIR) femtosecond laser to induce Ca2+ wave in astrocytes. It was demonstrated that photostimulation of astrocytes with femtosecond laser pulses is efficient with the advantages of non-contact, non-disruptiveness, reproducibility, and high spatiotemporal precision. Photostimulation of astrocytes would facilitate investigations on information processing in neuronal circuits by providing effective way to excite astrocytes.
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Affiliation(s)
- Yuan Zhao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Department of Biomedical Engineering, Huazhong University of Science & Technology, Wuhan, China
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26
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Watanabe W, Matsunaga S, Higashi T, Fukui K, Itoh K. In vivo manipulation of fluorescently labeled organelles in living cells by multiphoton excitation. JOURNAL OF BIOMEDICAL OPTICS 2008; 13:031213. [PMID: 18601537 DOI: 10.1117/1.2939401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Femtosecond laser pulses in the near-infrared region have potential applications in the imaging and manipulation of intracellular organelles. We report on the manipulation of intracellular organelles by two-photon excitation. The dynamics of green fluorescent protein (GFP)-histone are investigated by two-photon fluorescence recovery after photobleaching (FRAP). Intracellular ablation of fluorescently labeled organelles in living cells is performed by focusing femtosecond laser pulses. We report on the selective marking of individual organelles by using two-photon conversion of a photoconvertible fluorescent protein.
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Affiliation(s)
- Wataru Watanabe
- National Institute of Advanced Industrial Science and Technology, Photonics Research Institute, 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan.
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27
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Costanzo E, Gulino M, Lanzanò L, Musumeci F, Scordino A, Tudisco S, Sui L. Single seed viability checked by delayed luminescence. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2008; 37:235-8. [PMID: 17952430 DOI: 10.1007/s00249-007-0221-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 09/12/2007] [Accepted: 09/14/2007] [Indexed: 11/25/2022]
Abstract
Time resolved spectral components of delayed luminescence (DL) from single dry soybean seeds were measured using a device with single photon sensitivity. The seeds were aged by a thermal treatment to change their viability. A correlation was observed between the seeds viability and some DL parameters, i.e. the total number of photons emitted and the relative decay probability of excited states. This relevant result confirms the close connection between the state of biological systems and their DL, and it can allow the development of a quick selection technique for single dry seeds, a goal impossible up today.
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Affiliation(s)
- Evelina Costanzo
- Dipartimento di Fisica e Astronomia, University of Catania, Catania, Italy
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