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Bora L, Lombrea A, Batrina SL, Buda VO, Esanu OM, Pasca O, Dehelean CA, Dinu S, Diaconeasa Z, Danciu C. A Systematic Review of Cardio-Metabolic Properties of Lonicera caerulea L. Antioxidants (Basel) 2024; 13:694. [PMID: 38929133 PMCID: PMC11201247 DOI: 10.3390/antiox13060694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/26/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
In the light of growing concerns faced by Western societies due to aging, natality decline, and epidemic of cardio-metabolic diseases, both preventable and treatable, new and effective strategical interventions are urgently needed in order to decrease their socio-economical encumbrance. The recent focus of research has been redirected towards investigating the potential of haskap (Lonicera caerulea L.) as a novel functional food or superfruit. Therefore, our present review aims to highlight the latest scientific proofs regarding the potential of Lonicera caerulea L. (LC), a perennial fruit-bearing plant rich in polyphenols, in reversing cardio-metabolic dysfunctions. In this regard, a systematic search on two databases (PubMed and Google Scholar) from 1 January 2016 to 1 December 2023 was performed, the keyword combination being Lonicera caerulea L. AND the searched pharmacological action, with the inclusion criteria consisting of in extenso original articles, written in English. The health-enhancing characteristics of haskap berries have been examined through in vitro and in vivo studies from the 35 included original papers. Positive effects regarding cardiovascular diseases and metabolic syndrome have been assigned to the antioxidant activity, hypolipidemic and hypoglycemic effects, as well as to the hepatoprotective and vasoprotective potential. Latest advances regarding LCF mechanisms of action are detailed within this review as well. All these cutting-edge data suggest that this vegetal product would be a good candidate for further clinical studies.
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Affiliation(s)
- Larisa Bora
- Department of Pharmacognosy, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (L.B.); (A.L.); (C.D.)
- Research and Processing Center for Medicinal and Aromatic Plants, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Adelina Lombrea
- Department of Pharmacognosy, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (L.B.); (A.L.); (C.D.)
- Research and Processing Center for Medicinal and Aromatic Plants, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
| | - Stefan Laurentiu Batrina
- Department of Crop Science, Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | - Valentina Oana Buda
- Research and Processing Center for Medicinal and Aromatic Plants, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
- Discipline of Clinical Pharmacy, Communication in Pharmacy, Pharmaceutical Care, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Oana-Maria Esanu
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (O.-M.E.); (O.P.)
| | - Oana Pasca
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (O.-M.E.); (O.P.)
| | - Cristina Adriana Dehelean
- Research and Processing Center for Medicinal and Aromatic Plants, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
- Department of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania
| | - Stefania Dinu
- Department of Pedodontics, Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 9 No., Revolutiei Bv., 300041 Timisoara, Romania;
- Pediatric Dentistry Research Center, Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 9 No., Revolutiei Bv., 300041 Timisoara, Romania
| | - Zorita Diaconeasa
- Department of Food Science and Technology, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine, Calea Manastur, 3-5, 400372 Cluj-Napoca, Romania;
| | - Corina Danciu
- Department of Pharmacognosy, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; (L.B.); (A.L.); (C.D.)
- Research and Processing Center for Medicinal and Aromatic Plants, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;
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Gayathiri E, Prakash P, Pandiaraj S, Ramasubburayan R, Gaur A, Sekar M, Viswanathan D, Govindasamy R. Investigating the ecological implications of nanomaterials: Unveiling plants' notable responses to nano-pollution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108261. [PMID: 38096734 DOI: 10.1016/j.plaphy.2023.108261] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 02/15/2024]
Abstract
The rapid advancement of nanotechnology has led to unprecedented innovations; however, it is crucial to analyze its environmental impacts carefully. This review thoroughly examines the complex relationship between plants and nanomaterials, highlighting their significant impact on ecological sustainability and ecosystem well-being. This study investigated the response of plants to nano-pollution stress, revealing the complex regulation of defense-related genes and proteins, and highlighting the sophisticated defense mechanisms in nature. Phytohormones play a crucial role in the complex molecular communication network that regulates plant responses to exposure to nanomaterials. The interaction between plants and nano-pollution influences plants' complex defense strategies. This reveals the interconnectedness of systems of nature. Nevertheless, these findings have implications beyond the plant domain. The incorporation of hyperaccumulator plants into pollution mitigation strategies has the potential to create more environmentally sustainable urban landscapes and improve overall environmental resilience. By utilizing these exceptional plants, we can create a future in which cities serve as centers of both innovation and ecological balance. Further investigation is necessary to explore the long-term presence of nanoparticles in the environment, their ability to induce genetic changes in plants over multiple generations, and their overall impact on ecosystems. In conclusion, this review summarizes significant scientific discoveries with broad implications beyond the confines of laboratories. This highlights the importance of understanding the interactions between plants and nanomaterials within the wider scope of environmental health. By considering these insights, we initiated a path towards the responsible utilization of nanomaterials, environmentally friendly management of pollution, and interdisciplinary exploration. We have the responsibility to balance scientific advancement and environmental preservation to create a sustainable future that combines nature's wisdom with human innovation.
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Affiliation(s)
- Ekambaram Gayathiri
- Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous), Chennai 600042, Tamil Nadu India
| | - Palanisamy Prakash
- Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, Tamil Nadu, India
| | - Saravanan Pandiaraj
- Department of Self-Development Skills, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ramasamy Ramasubburayan
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Arti Gaur
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Vadodara-390025, Gujarat, India
| | - Malathy Sekar
- Department of Botany, PG and Research Department of Botany Government Arts College for Men, (autonomous), Nandanam, Chennai 35, Tamilnadu, India
| | - Dhivya Viswanathan
- Centre for Nanobioscience, Department of Orthodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai-600077, Tamilnadu, India
| | - Rajakumar Govindasamy
- Centre for Nanobioscience, Department of Orthodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai-600077, Tamilnadu, India.
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Vennapusa AR, Nimmakayala P, Zaman-Allah MA, Ratnakumar P. Editorial: Physiological, molecular and genetic perspectives of environmental stress response in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1213762. [PMID: 37396640 PMCID: PMC10313185 DOI: 10.3389/fpls.2023.1213762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023]
Affiliation(s)
- Amaranatha R. Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE, United States
| | - Padma Nimmakayala
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, Dunbar, WV, United States
| | | | - Pasala Ratnakumar
- Indian Council of Agricultural Research (ICAR) Indian Institute of Oilseeds Research (IIOR), Hyderabad, India
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Inzé D, Nelissen H. The translatability of genetic networks from model to crop species: lessons from the past and perspectives for the future. THE NEW PHYTOLOGIST 2022; 236:43-48. [PMID: 35801919 DOI: 10.1111/nph.18364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/11/2022] [Indexed: 05/25/2023]
Abstract
Comparative analyses of growth-regulatory mechanisms between Arabidopsis and maize revealed that even when the gene space is conserved, the translation of knowledge from model species to crops is not trivial. Based on these insights, we formulate future opportunities to improve the interpretation of curiosity-driven research towards crop improvement.
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Affiliation(s)
- Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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Spinach-based RNA mimicking GFP in plant cells. Funct Integr Genomics 2022; 22:423-428. [PMID: 35267109 PMCID: PMC9197860 DOI: 10.1007/s10142-022-00835-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 12/23/2022]
Abstract
Spinach RNA-mimicking GFP (S-RMG) has been successfully used to monitor cellular RNAs including microRNAs in bacterium, yeast, and human cells. However, S-RMG has not been established in plants. In this study, we found that like bacterial, yeast, and human cellular tRNAs, plant tRNAs such as tRNALys can protect and/or stabilize the Spinach RNA aptamer interaction with the fluorophore DFHBI enabling detectable levels of green fluorescence to be emitted. The tRNALys-Spinach-tRNALys, once delivered into "chloroplast-free" onion epidermal cells can emit strong green fluorescence in the presence of DFHBI. Our results demonstrate for the first time that Spinach-based RNA visualization has the potential for in vivo monitoring of RNAs in plant cells.
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Mo X, Cai X, Hui Q, Sun H, Yu R, Bu R, Yan B, Ou Q, Li Q, He S, Jiang C. Whole genome sequencing and metabolomics analyses reveal the biosynthesis of nerol in a multi-stress-tolerant Meyerozyma guilliermondii GXDK6. Microb Cell Fact 2021; 20:4. [PMID: 33413399 PMCID: PMC7789178 DOI: 10.1186/s12934-020-01490-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Nerol (C10H18O), an acyclic monoterpene, naturally presents in plant essential oils, and is used widely in food, cosmetics and pharmaceuticals as the valuable fragrance. Meanwhile, chemical synthesis is the only strategy for large-scale production of nerol, and the disadvantages of chemical synthesis greatly limit the production and its application. These defects drive the interests of researchers shift to the production of nerol by eco-friendly methods known as biosynthesis methods. However, the main technical bottleneck restricting the biosynthesis of nerol is the lacking of corresponding natural aroma-producing microorganisms. RESULTS In this study, a novel multi-stress-tolerant probiotics Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified by whole genome sequencing and metabolomics technology. GXDK6 showed a broad pH tolerance in the range of 2.5-10.0. The species also showed salt tolerance with up to 12% NaCl and up to 18% of KCl or MgCl2. GXDK6 exhibited heavy-metal Mn2+ tolerance of up to 5494 ppm. GXDK6 could also ferment with a total of 21 kinds of single organic matter as the carbon source, and produce abundant aromatic metabolites. Results from the gas chromatography-mass spectrometry indicated the production of 8-14 types of aromatic metabolites (isopentanol, nerol, geraniol, phenylethanol, isobutanol, etc.) when GXDK6 was fermented up to 72 h with glucose, sucrose, fructose, or xylose as the single carbon source. Among them, nerol was found to be a novel aromatic metabolite from GXDK6 fermentation, and its biosynthesis mechanism had also been further revealed. CONCLUSION A novel aroma-producing M. guilliermondii GXDK6 was identified successfully by whole genome sequencing and metabolomics technology. GXDK6 showed high multi-stress-tolerant properties with acid-base, salty, and heavy-metal environments. The aroma-producing mechanism of nerol in GXDK6 had also been revealed. These findings indicated the aroma-producing M. guilliermondii GXDK6 with multi-stress-tolerant properties has great potential value in the fermentation industry.
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Affiliation(s)
- Xueyan Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xinghua Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Qinyan Hui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Huijie Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ran Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ru Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Bing Yan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China
| | - Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Quanwen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Sheng He
- Guangxi Birth Defects Prevention and Control Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530033, China.
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China.
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Dynamics and Endocytosis of Flot1 in Arabidopsis Require CPI1 Function. Int J Mol Sci 2020; 21:ijms21051552. [PMID: 32106431 PMCID: PMC7084554 DOI: 10.3390/ijms21051552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/15/2023] Open
Abstract
Membrane microdomains are nano-scale domains (10–200 nm) enriched in sterols and sphingolipids. They have many important biological functions, including vesicle transport, endocytosis, and pathogen invasion. A previous study reported that the membrane microdomain-associated protein Flotillin1 (Flot1) was involved in plant development in Arabidopsis thaliana; however, whether sterols affect the plant immunity conveyed by Flot1 is unknown. Here, we showed that the root length in sterol-deficient cyclopropylsterol isomerase 1 (cpi1-1) mutants expressing Flot1 was significantly shorter than in control seedlings. The cotyledon epidermal cells in cpi1-1 mutants expressing Flot1 were smaller than in controls. Moreover, variable-angle total internal reflection fluorescence microscopy (VA-TIRFM) and single-particle tracking (SPT) analysis demonstrated that the long-distance Flot1-GFP movement was decreased significantly in cpi1-1 mutants compared with the control seedlings. Meanwhile, the value of the diffusion coefficient Ĝ was dramatically decreased in cpi1-1 mutants after flagelin22 (flg22) treatment compared with the control seedlings, indicating that sterols affect the lateral mobility of Flot1-GFP within the plasma membrane. Importantly, using confocal microscopy, we determined that the endocytosis of Flot1-GFP was decreased in cpi1-1 mutants, which was confirmed by fluorescence cross spectroscopy (FCS) analysis. Hence, these results demonstrate that sterol composition plays a critical role in the plant defense responses of Flot1.
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Borah P, Das A, Milner MJ, Ali A, Bentley AR, Pandey R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes (Basel) 2018; 9:E459. [PMID: 30223541 PMCID: PMC6162444 DOI: 10.3390/genes9090459] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.
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Affiliation(s)
- Priyanka Borah
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Antara Das
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Matthew J Milner
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Arif Ali
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Alison R Bentley
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
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Understanding Forest Health with Remote Sensing, Part III: Requirements for a Scalable Multi-Source Forest Health Monitoring Network Based on Data Science Approaches. REMOTE SENSING 2018. [DOI: 10.3390/rs10071120] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Forest ecosystems fulfill a whole host of ecosystem functions that are essential for life on our planet. However, an unprecedented level of anthropogenic influences is reducing the resilience and stability of our forest ecosystems as well as their ecosystem functions. The relationships between drivers, stress, and ecosystem functions in forest ecosystems are complex, multi-faceted, and often non-linear, and yet forest managers, decision makers, and politicians need to be able to make rapid decisions that are data-driven and based on short and long-term monitoring information, complex modeling, and analysis approaches. A huge number of long-standing and standardized forest health inventory approaches already exist, and are increasingly integrating remote-sensing based monitoring approaches. Unfortunately, these approaches in monitoring, data storage, analysis, prognosis, and assessment still do not satisfy the future requirements of information and digital knowledge processing of the 21st century. Therefore, this paper discusses and presents in detail five sets of requirements, including their relevance, necessity, and the possible solutions that would be necessary for establishing a feasible multi-source forest health monitoring network for the 21st century. Namely, these requirements are: (1) understanding the effects of multiple stressors on forest health; (2) using remote sensing (RS) approaches to monitor forest health; (3) coupling different monitoring approaches; (4) using data science as a bridge between complex and multidimensional big forest health (FH) data; and (5) a future multi-source forest health monitoring network. It became apparent that no existing monitoring approach, technique, model, or platform is sufficient on its own to monitor, model, forecast, or assess forest health and its resilience. In order to advance the development of a multi-source forest health monitoring network, we argue that in order to gain a better understanding of forest health in our complex world, it would be conducive to implement the concepts of data science with the components: (i) digitalization; (ii) standardization with metadata management after the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles; (iii) Semantic Web; (iv) proof, trust, and uncertainties; (v) tools for data science analysis; and (vi) easy tools for scientists, data managers, and stakeholders for decision-making support.
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Abstract
This review discusses the important concept of cotton fiber friction at both the macro- and nanoscale. First, the technological importance of fiber friction and its role in fiber breakage during fiber processing is discussed. Next, previous studies on frictional properties of cotton fibers are reviewed and different experimental procedures to measure friction between fibers or against another surface are evaluated. Friction models developed to explain friction process during various experimental procedures are considered and their limitations are discussed. Since interpretation of friction processes at the macroscale can be challenging (mainly due to difficulties in analyzing the multiple asperities in contact), a separate section is devoted to surveying studies on the emerging field of single-asperity friction experiments with atomic force microscope (AFM). Special attention is given to studies on nanoscale frictional characteristics of rough viscoelastic surfaces (e.g., plant cuticular biopolymers and cotton fibers). Due to the close relationship between friction and adhesion hysteresis at the nanoscale, adhesion studies with AFM on viscoelastic surfaces are also reviewed. Lastly, recommendations are made for future research in the field of frictional properties of cotton fibers.
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Wang L, Xue Y, Xing J, Song K, Lin J. Exploring the Spatiotemporal Organization of Membrane Proteins in Living Plant Cells. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:525-551. [PMID: 29489393 DOI: 10.1146/annurev-arplant-042817-040233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plasma membrane proteins have important roles in transport and signal transduction. Deciphering the spatiotemporal organization of these proteins provides crucial information for elucidating the links between the behaviors of different molecules. However, monitoring membrane proteins without disrupting their membrane environment remains difficult. Over the past decade, many studies have developed single-molecule techniques, opening avenues for probing the stoichiometry and interactions of membrane proteins in their native environment by providing nanometer-scale spatial information and nanosecond-scale temporal information. In this review, we assess recent progress in the development of labeling and imaging technology for membrane protein analysis. We focus in particular on several single-molecule techniques for quantifying the dynamics and assembly of membrane proteins. Finally, we provide examples of how these new techniques are advancing our understanding of the complex biological functions of membrane proteins.
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Affiliation(s)
- Li Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Yiqun Xue
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingjing Xing
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kai Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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12
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Stanley CE, Shrivastava J, Brugman R, Heinzelmann E, van Swaay D, Grossmann G. Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels. THE NEW PHYTOLOGIST 2018; 217:1357-1369. [PMID: 29125191 DOI: 10.1111/nph.14887] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Roots grow in highly dynamic and heterogeneous environments. Biological activity as well as uneven nutrient availability or localized stress factors result in diverse microenvironments. Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip, a microfluidic platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from investigating physiology, root hair development and calcium signalling upon selective exposure to environmental stresses to tracing molecular uptake, performing selective drug treatments and localized inoculations with microbes. Using the dual-flow-RootChip, we revealed cell-autonomous adaption of root hair development under asymmetric phosphate (Pi) perfusion, with unexpected repression in root hair growth on the side exposed to low Pi and rapid tip-growth upregulation when Pi concentrations increased. The asymmetric root environment further resulted in an asymmetric gene expression of RSL4, a key transcriptional regulator of root hair growth. Our findings demonstrate that roots possess the capability to locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional levels. Being able to generate asymmetric microenvironments for roots will help further elucidate decision-making processes in root-environment interactions.
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Affiliation(s)
- Claire E Stanley
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Jagriti Shrivastava
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
- Hartmut Hoffmann-Berling International Graduate School of Heidelberg Molecular Life Sciences (HBIGS), Universität Heidelberg, 69120, Heidelberg, Germany
| | - Rik Brugman
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Elisa Heinzelmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Dirk van Swaay
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Guido Grossmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
- CellNetworks-Cluster of Excellence, Universität Heidelberg, 69120, Heidelberg, Germany
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13
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Lv X, Jing Y, Xiao J, Zhang Y, Zhu Y, Julian R, Lin J. Membrane microdomains and the cytoskeleton constrain AtHIR1 dynamics and facilitate the formation of an AtHIR1-associated immune complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:3-16. [PMID: 28081290 DOI: 10.1111/tpj.13480] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 01/04/2017] [Indexed: 05/20/2023]
Abstract
Arabidopsis hypersensitive-induced reaction (AtHIR) proteins function in plant innate immunity. However, the underlying mechanisms by which AtHIRs participate in plant immunity remain elusive. Here, using VA-TIRFM and FLIM-FRET, we revealed that AtHIR1 is present in membrane microdomains and co-localizes with the membrane microdomain marker REM1.3. Single-particle tracking analysis revealed that membrane microdomains and the cytoskeleton, especially microtubules, restrict the lateral mobility of AtHIR1 at the plasma membrane and facilitate its oligomerization. Furthermore, protein proximity index measurements, fluorescence cross-correlation spectroscopy, and biochemical experiments demonstrated that the formation of the AtHIR1 complex upon pathogen perception requires intact microdomains and cytoskeleton. Taken together, these findings suggest that microdomains and the cytoskeleton constrain AtHIR1 dynamics, promote AtHIR1 oligomerization, and increase the efficiency of the interactions of AtHIR1 with components of the AtHIR1 complex in response to pathogens, thus providing valuable insight into the mechanisms of defense-related responses in plants.
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Affiliation(s)
- Xueqin Lv
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jianwei Xiao
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Yingfang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Russell Julian
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Jinxing Lin
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
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14
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Understanding Forest Health with Remote Sensing-Part II—A Review of Approaches and Data Models. REMOTE SENSING 2017. [DOI: 10.3390/rs9020129] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Li B, Bhandari DR, Römpp A, Spengler B. High-resolution MALDI mass spectrometry imaging of gallotannins and monoterpene glucosides in the root of Paeonia lactiflora. Sci Rep 2016; 6:36074. [PMID: 27796322 PMCID: PMC5086847 DOI: 10.1038/srep36074] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/10/2016] [Indexed: 01/01/2023] Open
Abstract
High-resolution atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI) at 10 μm pixel size was performed to unravel the spatio-chemical distribution of major secondary metabolites in the root of Paeonia lactiflora. The spatial distributions of two major classes of bioactive components, gallotannins and monoterpene glucosides, were investigated and visualized at the cellular level in tissue sections of P. lactiflora roots. Accordingly, other primary and secondary metabolites were imaged, including amino acids, carbohydrates, lipids and monoterpenes, indicating the capability of untargeted localization of metabolites by using high-resolution MSI platform. The employed AP-SMALDI MSI system provides significant technological advancement in the visualization of individual molecular species at the cellular level. In contrast to previous histochemical studies of tannins using unspecific staining reagents, individual gallotannin species were accurately localized and unequivocally discriminated from other phenolic components in the root tissues. High-quality ion images were obtained, providing significant clues for understanding the biosynthetic pathway of gallotannins and monoterpene glucosides and possibly helping to decipher the role of tannins in xylem cells differentiation and in the defence mechanisms of plants, as well as to investigate the interrelationship between tannins and lignins.
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Affiliation(s)
- Bin Li
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Dhaka Ram Bhandari
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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16
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Gemperline E, Keller C, Jayaraman D, Maeda J, Sussman MR, Ané JM, Li L. Examination of Endogenous Peptides in Medicago truncatula Using Mass Spectrometry Imaging. J Proteome Res 2016; 15:4403-4411. [PMID: 27726374 DOI: 10.1021/acs.jproteome.6b00471] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plant science is an important, rapidly developing area of study. Within plant science, one area of study that has grown tremendously with recent technological advances, such as mass spectrometry, is the field of plant-omics; however, plant peptidomics is relatively underdeveloped in comparison with proteomics and metabolomics. Endogenous plant peptides can act as signaling molecules and have been shown to affect cell division, development, nodulation, reproduction, symbiotic associations, and defense reactions. There is a growing need to uncover the role of endogenous peptides on a molecular level. Mass spectrometric imaging (MSI) is a valuable tool for biological analyses as it allows for the detection of thousands of analytes in a single experiment and also displays spatial information for the detected analytes. Despite the prediction of a large number of plant peptides, their detection and imaging with spatial localization and chemical specificity is currently lacking. Here we analyzed the endogenous peptides and proteins in Medicago truncatula using matrix-assisted laser desorption/ionization (MALDI)-MSI. Hundreds of endogenous peptides and protein fragments were imaged, with interesting peptide spatial distribution changes observed between plants in different developmental stages.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dhileepkumar Jayaraman
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Junko Maeda
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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17
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Abstract
Plant-omics is rapidly becoming an important field of study in the scientific community due to the urgent need to address many of the most important questions facing humanity today with regard to agriculture, medicine, biofuels, environmental decontamination, ecological sustainability, etc. High-performance mass spectrometry is a dominant tool for interrogating the metabolomes, peptidomes, and proteomes of a diversity of plant species under various conditions, revealing key insights into the functions and mechanisms of plant biochemistry.
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Affiliation(s)
- Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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18
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Dong B, Yang X, Zhu S, Bassham DC, Fang N. Stochastic Optical Reconstruction Microscopy Imaging of Microtubule Arrays in Intact Arabidopsis thaliana Seedling Roots. Sci Rep 2015; 5:15694. [PMID: 26503365 PMCID: PMC4621606 DOI: 10.1038/srep15694] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/30/2015] [Indexed: 12/19/2022] Open
Abstract
Super-resolution fluorescence microscopy has generated tremendous success in revealing detailed subcellular structures in animal cells. However, its application to plant cell biology remains extremely limited due to numerous technical challenges, including the generally high fluorescence background of plant cells and the presence of the cell wall. In the current study, stochastic optical reconstruction microscopy (STORM) imaging of intact Arabidopsis thaliana seedling roots with a spatial resolution of 20-40 nm was demonstrated. Using the super-resolution images, the spatial organization of cortical microtubules in different parts of a whole Arabidopsis root tip was analyzed quantitatively, and the results show the dramatic differences in the density and spatial organization of cortical microtubules in cells of different differentiation stages or types. The method developed can be applied to plant cell biological processes, including imaging of additional elements of the cytoskeleton, organelle substructure, and membrane domains.
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Affiliation(s)
- Bin Dong
- Ames Laboratory, US Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Xiaochen Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Shaobin Zhu
- Ames Laboratory, US Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Ning Fang
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302
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19
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Festa M, Lagostena L, Carpaneto A. Using the plant vacuole as a biological system to investigate the functional properties of exogenous channels and transporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:607-12. [PMID: 26431786 DOI: 10.1016/j.bbamem.2015.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/31/2015] [Accepted: 09/25/2015] [Indexed: 01/15/2023]
Abstract
Plant cells possess a large intracellular compartment that animal cells do not, the central vacuole, which has been investigated for a long time. The central vacuole can occupy up to 90% of the cellular volume and, differently from intracellular organelles from animal cells such as lysosomes or endosomes, it is easy to isolate. Because of its large dimension (up to 40 μm diameter) it can be successfully studied using the classical patch-clamp technique. Following the idea that the vacuolar membrane could be used as a convenient model to characterize the functional properties of channel-forming peptides, we verified that the phytotoxic lipodepsipeptide Syringopeptin 25A from Pseudomonas syringae pv syringae was able to form ionic pores in sugar beet vacuoles and we performed a detailed biophysical analysis. Recently, we extended the use of plant vacuoles to the expression and functional characterization of animal intracellular transporters, namely rat CLC-7, and channels, i.e. human TPC2. Since endo-lysosomal transporters and channels are still largely unexplored, principally because their intracellular localization renders them difficult to study, we believe that this novel approach will prove to be a powerful system for the investigation of the molecular mechanisms of exogenous transporters and channels. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- M Festa
- Institute of Biophysics (IBF), CNR, Via De Marini 6, 16149 Genova, Italy
| | - L Lagostena
- Institute of Biophysics (IBF), CNR, Via De Marini 6, 16149 Genova, Italy
| | - A Carpaneto
- Institute of Biophysics (IBF), CNR, Via De Marini 6, 16149 Genova, Italy.
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20
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Pieruschka R, Lawson T. Phenotyping in Plants. Preface. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5385-7. [PMID: 26512383 PMCID: PMC4585426 DOI: 10.1093/jxb/erv395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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21
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Urbanek MO, Galka-Marciniak P, Olejniczak M, Krzyzosiak WJ. RNA imaging in living cells - methods and applications. RNA Biol 2015; 11:1083-95. [PMID: 25483044 PMCID: PMC4615301 DOI: 10.4161/rna.35506] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Numerous types of transcripts perform multiple functions in cells, and these functions are mainly facilitated by the interactions of the RNA with various proteins and other RNAs. Insight into the dynamics of RNA biosynthesis, processing and cellular activities is highly desirable because this knowledge will deepen our understanding of cell physiology and help explain the mechanisms of RNA-mediated pathologies. In this review, we discuss the live RNA imaging systems that have been developed to date. We highlight information on the design of these systems, briefly discuss their advantages and limitations and provide examples of their numerous applications in various organisms and cell types. We present a detailed examination of one application of RNA imaging systems: this application aims to explain the role of mutant transcripts in human disease pathogenesis caused by triplet repeat expansions. Thus, this review introduces live RNA imaging systems and provides a glimpse into their various applications.
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Affiliation(s)
- Martyna O Urbanek
- a Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Poznan , Poland
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22
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Abstract
Advances in microscopy techniques applied to living cells have dramatically transformed our view of the actin cytoskeleton as a framework for cellular processes. Conventional fluorescence imaging and static analyses are useful for quantifying cellular architecture and the network of filaments that support vesicle trafficking, organelle movement, and response to biotic stress. However, new imaging techniques have revealed remarkably dynamic features of individual actin filaments and the mechanisms that underpin their construction and turnover. In this review, we briefly summarize knowledge about actin and actin-binding proteins in plant systems. We focus on the quantitative properties of the turnover of individual actin filaments, highlight actin-binding proteins that participate in actin dynamics, and summarize the current genetic evidence that has been used to dissect specific aspects of the stochastic dynamics model. Finally, we describe some signaling pathways in which recent data implicate changes in actin filament dynamics and the associated cytoplasmic responses.
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Affiliation(s)
- Jiejie Li
- Department of Biological Sciences and
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23
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Rousseau D, Chéné Y, Belin E, Semaan G, Trigui G, Boudehri K, Franconi F, Chapeau-Blondeau F. Multiscale imaging of plants: current approaches and challenges. PLANT METHODS 2015; 11:6. [PMID: 25694791 PMCID: PMC4331374 DOI: 10.1186/s13007-015-0050-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/25/2015] [Indexed: 05/18/2023]
Abstract
We review a set of recent multiscale imaging techniques, producing high-resolution images of interest for plant sciences. These techniques are promising because they match the multiscale structure of plants. However, the use of such high-resolution images is challenging in the perspective of their application to high-throughput phenotyping on large populations of plants, because of the memory cost for their data storage and the computational cost for their processing to extract information. We discuss how this renews the interest for multiscale image processing tools such as wavelets, fractals and recent variants to analyse such high-resolution images.
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Affiliation(s)
- David Rousseau
- />Université de Lyon, Laboratoire CREATIS, CNRS, UMR5220, INSERM, U1044, Université Lyon 1, INSA-Lyon, Villeurbanne France
| | - Yann Chéné
- />Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d’Angers, 62 avenue Notre Dame du Lac, Angers, 49000 France
| | - Etienne Belin
- />Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d’Angers, 62 avenue Notre Dame du Lac, Angers, 49000 France
| | - Georges Semaan
- />Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d’Angers, 62 avenue Notre Dame du Lac, Angers, 49000 France
| | - Ghassen Trigui
- />GEVES, Station Nationale d’Essais de Semences (SNES), rue Georges Morel, Beaucouzé, 49071 France
| | - Karima Boudehri
- />GEVES, Station Nationale d’Essais de Semences (SNES), rue Georges Morel, Beaucouzé, 49071 France
| | - Florence Franconi
- />La Plateforme d’Ingénierie et Analyses Moléculaires (PIAM), Université d’Angers, Angers, 49000 France
| | - François Chapeau-Blondeau
- />Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d’Angers, 62 avenue Notre Dame du Lac, Angers, 49000 France
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24
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Lerche MH, Jensen PR, Karlsson M, Meier S. NMR insights into the inner workings of living cells. Anal Chem 2014; 87:119-32. [PMID: 25084065 DOI: 10.1021/ac501467x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mathilde H Lerche
- Albeda Research , Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
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25
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Sizmur T, Lind KR, Benomar S, VanEvery H, Cademartiri L. A simple and versatile 2-dimensional platform to study plant germination and growth under controlled humidity. PLoS One 2014; 9:e96730. [PMID: 24806462 PMCID: PMC4013031 DOI: 10.1371/journal.pone.0096730] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/10/2014] [Indexed: 11/25/2022] Open
Abstract
We describe a simple, inexpensive, but remarkably versatile and controlled growth environment for the observation of plant germination and seedling root growth on a flat, horizontal surface over periods of weeks. The setup provides to each plant a controlled humidity (between 56% and 91% RH), and contact with both nutrients and atmosphere. The flat and horizontal geometry of the surface supporting the roots eliminates the gravitropic bias on their development and facilitates the imaging of the entire root system. Experiments can be setup under sterile conditions and then transferred to a non-sterile environment. The system can be assembled in 1-2 minutes, costs approximately 8.78$ per plant, is almost entirely reusable (0.43$ per experiment in disposables), and is easily scalable to a variety of plants. We demonstrate the performance of the system by germinating, growing, and imaging Wheat (Triticum aestivum), Corn (Zea mays), and Wisconsin Fast Plants (Brassica rapa). Germination rates were close to those expected for optimal conditions.
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Affiliation(s)
- Tom Sizmur
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa, United States of America
| | - Kara R. Lind
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Saida Benomar
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa, United States of America
| | - Hannah VanEvery
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical & Biological Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Ludovico Cademartiri
- Department of Materials Science & Engineering, Iowa State University, Ames, Iowa, United States of America
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical & Biological Engineering, Iowa State University, Ames, Iowa, United States of America
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26
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Ellinger D, Voigt CA. The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration. FRONTIERS IN PLANT SCIENCE 2014; 5:270. [PMID: 24995012 PMCID: PMC4061529 DOI: 10.3389/fpls.2014.00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 05/25/2014] [Indexed: 05/08/2023]
Abstract
Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant-pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant-pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein-protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host-pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.
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Affiliation(s)
| | - Christian A. Voigt
- *Correspondence: Christian A. Voigt, Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany e-mail:
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27
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Taran NY, Gonchar OM, Lopatko KG, Batsmanova LM, Patyka MV, Volkogon MV. The effect of colloidal solution of molybdenum nanoparticles on the microbial composition in rhizosphere of Cicer arietinum L. NANOSCALE RESEARCH LETTERS 2014; 9:289. [PMID: 25024677 PMCID: PMC4085230 DOI: 10.1186/1556-276x-9-289] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/23/2014] [Indexed: 05/11/2023]
Abstract
UNLABELLED The use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops due to the active penetration of nanoelements into the plant cells. Microbiological examination of rhizosphere soil have revealed that combined use of colloidal solution of nanoparticles of molybdenum (CSNM, 8 mg/l), and microbial preparation for pre-sowing inoculation of chickpea seeds stimulates the development of 'agronomically valuable' microflora. It was shown that combined seed treatment with colloidal solution of Mo nanoparticles with microbial preparation have stimulated nodule formation per plant by four times compared to controls. Single treatment with CSNM increased the number of nodules by two times, while the treatment of microbial preparation have not significantly affected the number of nodules per plant. PACS Colloids, 82.70.Dd; Ecology, 87.23.-n.
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Affiliation(s)
- Natalia Yu Taran
- Institute of Biology, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv 01601, Ukraine
| | - Olena M Gonchar
- National University of Life and Environmental Sciences of Ukraine, 12 Heroiv Oborony, Kyiv 03041, Ukraine
| | - Kostyantyn G Lopatko
- National University of Life and Environmental Sciences of Ukraine, 12 Heroiv Oborony, Kyiv 03041, Ukraine
| | - Lyudmila M Batsmanova
- Institute of Biology, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv 01601, Ukraine
| | - Mykola V Patyka
- National University of Life and Environmental Sciences of Ukraine, 12 Heroiv Oborony, Kyiv 03041, Ukraine
| | - Mykola V Volkogon
- Institute of Biology, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv 01601, Ukraine
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28
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Voo SS, Lange BM. Sample preparation for single cell transcriptomics: essential oil glands in Citrus fruit peel as an example. Methods Mol Biol 2014; 1153:203-212. [PMID: 24777799 DOI: 10.1007/978-1-4939-0606-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Many plant natural products are synthesized in specialized cells and tissues. To learn more about metabolism in these cells, they have to be studied in isolation. Here, we describe a protocol for the isolation of epithelial cells that surround secretory cavities in Citrus fruit peel. Cells isolated using laser microdissection are suitable for RNA isolation and downstream transcriptome analyses.
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Affiliation(s)
- Siau Sie Voo
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, Clark Hall, Room 341, Pullman, WA, 99164-6340, USA
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29
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Henty-Ridilla JL, Li J, Blanchoin L, Staiger CJ. Actin dynamics in the cortical array of plant cells. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:678-87. [PMID: 24246228 DOI: 10.1016/j.pbi.2013.10.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 05/03/2023]
Abstract
The actin cytoskeleton changes in organization and dynamics as cellular functions are reprogrammed following responses to diverse stimuli, hormones, and developmental cues. How this is choreographed and what molecular players are involved in actin remodeling continues to be an area of intense scrutiny. Advances in imaging modalities and fluorescent fusion protein reporters have illuminated the strikingly dynamic behavior of single actin filaments at high spatial and temporal resolutions. This led to a model for the stochastic dynamic turnover of actin filaments and predicted the actions and responsibilities of several key actin-binding proteins. Recently, aspects of this model have been tested using powerful genetic strategies in both Arabidopsis and Physcomitrella. Collectively, the latest data emphasize the importance of filament severing activities and regulation of barbed-end availability as key facets of plant actin filament turnover.
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30
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Deswal R, Gupta R, Dogra V, Singh R, Abat JK, Sarkar A, Mishra Y, Rai V, Sreenivasulu Y, Amalraj RS, Raorane M, Chaudhary RP, Kohli A, Giri AP, Chakraborty N, Zargar SM, Agrawal VP, Agrawal GK, Job D, Renaut J, Rakwal R. Plant proteomics in India and Nepal: current status and challenges ahead. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:461-477. [PMID: 24431515 PMCID: PMC3781272 DOI: 10.1007/s12298-013-0198-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.
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Affiliation(s)
- Renu Deswal
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Ravi Gupta
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Vivek Dogra
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Raksha Singh
- />Department of Plant Molecular Biology, College of Life Science, Sejong University, Seoul, Republic of Korea
| | - Jasmeet Kaur Abat
- />Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Abhijit Sarkar
- />Department of Botany, Banaras Hindu University, Varanasi, India
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Yogesh Mishra
- />Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Vandana Rai
- />National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
| | - Yelam Sreenivasulu
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Ramesh Sundar Amalraj
- />Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, India
| | - Manish Raorane
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ram Prasad Chaudhary
- />Central Department of Botany, and Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Ajay Kohli
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ashok Prabhakar Giri
- />Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
| | | | - Sajad Majeed Zargar
- />School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, 180009 Jammu and Kashmir India
| | | | - Ganesh Kumar Agrawal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Dominique Job
- />CNRS/Bayer Crop Science (UMR 5240) Joint Laboratory, Lyon, France
| | - Jenny Renaut
- />Department of Environment and Agrobiotechnologies, Centre de Recherche Public-Gabriel Lippmann, Belvaux, GD Luxembourg
| | - Randeep Rakwal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
- />Organization for Educational Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
- />Department of Anatomy I, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555 Japan
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Fan L, Hao H, Xue Y, Zhang L, Song K, Ding Z, Botella MA, Wang H, Lin J. Dynamic analysis of Arabidopsis AP2 σ subunit reveals a key role in clathrin-mediated endocytosis and plant development. Development 2013; 140:3826-37. [DOI: 10.1242/dev.095711] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clathrin-mediated endocytosis, which depends on the AP2 complex, plays an essential role in many cellular and developmental processes in mammalian cells. However, the function of the AP2 complex in plants remains largely unexplored. Here, we show in Arabidopsis that the AP2 σ subunit mutant (ap2 σ) displays various developmental defects that are similar to those of mutants defective in auxin transport and/or signaling, including single, trumpet-shaped and triple cotyledons, impaired vascular pattern, reduced vegetative growth, defective silique development and drastically reduced fertility. We demonstrate that AP2 σ is closely associated and physically interacts with the clathrin light chain (CLC) in vivo using fluorescence cross-correlation spectroscopy (FCCS), protein proximity analyses and co-immunoprecipitation assays. Using variable-angle total internal reflection fluorescence microscopy (VA-TIRFM), we show that AP2 σ-mCherry spots colocalize with CLC-EGFP at the plasma membrane, and that AP2 σ-mCherry fluorescence appears and disappears before CLC-EGFP fluorescence. The density and turnover rate of the CLC-EGFP spots are significantly reduced in the ap2 σ mutant. The internalization and recycling of the endocytic tracer FM4-64 and the auxin efflux carrier protein PIN1 are also significantly reduced in the ap2 σ mutant. Further, the polar localization of PIN1-GFP is significantly disrupted during embryogenesis in the ap2 σ mutant. Taken together, our results support an essential role of AP2 σ in the assembly of a functional AP2 complex in plants, which is required for clathrin-mediated endocytosis, polar auxin transport and plant growth regulation.
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Affiliation(s)
- Lusheng Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaiqing Hao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yiqun Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Kai Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaojun Ding
- School of Life Sciences, Shandong University, Jinan 250100, China
| | - Miguel A. Botella
- Departamento de Biología Celular, Genética y Fisiología, Universidad de Málaga, 29071 Malaga, Spain
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104, USA
| | - Jinxing Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Abreu IA, Farinha AP, Negrão S, Gonçalves N, Fonseca C, Rodrigues M, Batista R, Saibo NJM, Oliveira MM. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013; 93:145-68. [PMID: 23886779 DOI: 10.1016/j.jprot.2013.07.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/20/2022]
Abstract
Plant breeders need new and more precise tools to accelerate breeding programs that address the increasing needs for food, feed, energy and raw materials, while facing a changing environment in which high salinity and drought have major impacts on crop losses worldwide. This review covers the achievements and bottlenecks in the identification and validation of proteins with relevance in abiotic stress tolerance, also mentioning the unexpected consequences of the stress in allergen expression. While addressing the key pathways regulating abiotic stress plant adaptation, comprehensive data is presented on the proteins confirmed as relevant to confer tolerance. Promising candidates still to be confirmed are also highlighted, as well as the specific protein families and protein modifications for which detection and characterization is still a challenge. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Isabel A Abreu
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Laboratory (GPlantS Lab), Av. da República, 2780-157 Oeiras, Portugal; iBET, Apartado 12, 2781-901 Oeiras, Portugal
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Shadiac N, Nagarajan Y, Waters S, Hrmova M. Close allies in membrane protein research: Cell-free synthesis and nanotechnology. Mol Membr Biol 2013; 30:229-45. [DOI: 10.3109/09687688.2012.762125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Vigani G, Morandini P, Murgia I. Searching iron sensors in plants by exploring the link among 2'-OG-dependent dioxygenases, the iron deficiency response and metabolic adjustments occurring under iron deficiency. FRONTIERS IN PLANT SCIENCE 2013; 4:169. [PMID: 23755060 PMCID: PMC3668137 DOI: 10.3389/fpls.2013.00169] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/13/2013] [Indexed: 05/18/2023]
Abstract
Knowledge accumulated on the regulation of iron (Fe) homeostasis, its intracellular trafficking and transport across various cellular compartments and organs in plants; storage proteins, transporters and transcription factors involved in Fe metabolism have been analyzed in detail in recent years. However, the key sensor(s) of cellular plant "Fe status" triggering the long-distance shoot-root signaling and leading to the root Fe deficiency responses is (are) still unknown. Local Fe sensing is also a major task for roots, for adjusting the internal Fe requirements to external Fe availability: how such sensing is achieved and how it leads to metabolic adjustments in case of nutrient shortage, is mostly unknown. Two proteins belonging to the 2'-OG-dependent dioxygenases family accumulate several folds in Fe-deficient Arabidopsis roots. Such proteins require Fe(II) as enzymatic cofactor; one of their subgroups, the HIF-P4H (hypoxia-inducible factor-prolyl 4-hydroxylase), is an effective oxygen sensor in animal cells. We envisage here the possibility that some members of the 2'-OG dioxygenase family may be involved in the Fe deficiency response and in the metabolic adjustments to Fe deficiency or even in sensing Fe, in plant cells.
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Affiliation(s)
- Gianpiero Vigani
- Dipartimento di Scienze Agrarie ed Ambientali-Produzioni, Territorio, Agroenergia, Università degli Studi di MilanoMilano, Italy
| | - Piero Morandini
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilano, Italy
| | - Irene Murgia
- Dipartimento di Bioscienze, Università degli Studi di MilanoMilano, Italy
- *Correspondence: Irene Murgia, Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy e-mail:
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Shaw SL, Ehrhardt DW. Smaller, faster, brighter: advances in optical imaging of living plant cells. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:351-75. [PMID: 23506334 DOI: 10.1146/annurev-arplant-042110-103843] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The advent of fluorescent proteins and access to modern imaging technologies have dramatically accelerated the pace of discovery in plant cell biology. Remarkable new insights into such diverse areas as plant pathogenesis, cytoskeletal dynamics, sugar transport, cell wall synthesis, secretory control, and hormone signaling have come from careful examination of living cells using advanced optical probes. New technologies, both commercially available and on the horizon, promise a continued march toward more quantitative methods for imaging and for extending the optical exploration of biological structure and activity to molecular scales. In this review, we lay out fundamental issues in imaging plant specimens and look ahead to several technological innovations in molecular tools, instrumentation, imaging methods, and specimen handling that show promise for shaping the coming era of plant cell biology.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Sweetlove LJ, Fernie AR. The spatial organization of metabolism within the plant cell. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:723-46. [PMID: 23330793 DOI: 10.1146/annurev-arplant-050312-120233] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Identifying the correct subcellular locations for all enzymes and metabolites in plant metabolic networks is a major challenge, but is critically important for the success of the new generation of large-scale metabolic models that are driving a network-level appreciation of metabolic behavior. Even though the subcellular compartmentation of many central metabolic processes is thought to be well understood, recent gene-by-gene studies have revealed several unexpected enzyme localizations. Metabolite transport between subcellular compartments is crucial because it fundamentally affects the metabolic network structure. Although new metabolite transporters are being steadily identified, modeling work suggests that we have barely scratched the surface of the catalog of intracellular metabolite transporter proteins. In addition to compartmentation among organelles, it is increasingly apparent that microcompartment formation via the interactions of enzyme groups with intracellular membranes, the cytoskeleton, or other proteins is an important regulatory mechanism. In particular, this mechanism can promote metabolite channeling within the metabolic microcompartment, which can help control reaction specificity as well as dictate flux routes through the network. This has clear relevance for both synthetic biology in general and the engineering of plant metabolic networks in particular.
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Affiliation(s)
- Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom.
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Gjetting SK, Schulz A, Fuglsang AT. Perspectives for using genetically encoded fluorescent biosensors in plants. FRONTIERS IN PLANT SCIENCE 2013; 4:234. [PMID: 23874345 PMCID: PMC3709170 DOI: 10.3389/fpls.2013.00234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/13/2013] [Indexed: 05/08/2023]
Abstract
Genetically encoded fluorescent biosensors have long proven to be excellent tools for quantitative live imaging, but sensor applications in plants have been lacking behind those in mammalian systems with respect to the variety of sensors and tissue types used. How can this be improved, and what can be expected for the use of genetically encoded fluorescent biosensors in plants in the future? In this review, we present a table of successful physiological experiments in plant tissue using fluorescent biosensors, and draw some conclusions about the specific challenges plant cell biologists are faced with and some of the ways they have been overcome so far.
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Affiliation(s)
- Sisse K. Gjetting
- Transport Biology Section, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagen, Denmark
| | - Alexander Schulz
- Transport Biology Section, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagen, Denmark
| | - Anja T. Fuglsang
- Transport Biology Section, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagen, Denmark
- Center of Excellence for Membrane Pumps and Disease, PUMPKINAarhus, Denmark
- *Correspondence: Anja T. Fuglsang, Transport Biology Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Copenhagen, DK-1871, Denmark e-mail:
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Schachtman DP. Recent advances in nutrient sensing and signaling. MOLECULAR PLANT 2012; 5:1170-1172. [PMID: 23041939 DOI: 10.1093/mp/sss109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Bunsupa S, Yamazaki M, Saito K. Quinolizidine alkaloid biosynthesis: recent advances and future prospects. FRONTIERS IN PLANT SCIENCE 2012; 3:239. [PMID: 23112802 PMCID: PMC3481059 DOI: 10.3389/fpls.2012.00239] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/09/2012] [Indexed: 05/03/2023]
Abstract
Lys-derived alkaloids, including piperidine, quinolizidine, indolizidine, and lycopodium alkaloids, are widely distributed throughout the plant kingdom. Several of these alkaloids have beneficial properties for humans and have been used in medicine. However, the molecular mechanisms underlying the biosynthesis of these alkaloids are not well understood. In the present article, we discuss recent advances in our understanding of Lys-derived alkaloids, especially the biochemistry, molecular biology, and biotechnology of quinolizidine alkaloid (QA) biosynthesis. We have also highlighted Lys decarboxylase (LDC), the enzyme that catalyzes the first committed step of QA biosynthesis and answers a longstanding question about the molecular entity of LDC activity in plants. Further prospects using current advanced technologies, such as next-generation sequencing, in medicinal plants have also been discussed.
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Affiliation(s)
- Somnuk Bunsupa
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan
- RIKEN Plant Science CenterYokohama, Japan
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Middleton AM, Farcot E, Owen MR, Vernoux T. Modeling regulatory networks to understand plant development: small is beautiful. THE PLANT CELL 2012; 24:3876-91. [PMID: 23110896 PMCID: PMC3517225 DOI: 10.1105/tpc.112.101840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We now have unprecedented capability to generate large data sets on the myriad genes and molecular players that regulate plant development. Networks of interactions between systems components can be derived from that data in various ways and can be used to develop mathematical models of various degrees of sophistication. Here, we discuss why, in many cases, it is productive to focus on small networks. We provide a brief and accessible introduction to relevant mathematical and computational approaches to model regulatory networks and discuss examples of small network models that have helped generate new insights into plant biology (where small is beautiful), such as in circadian rhythms, hormone signaling, and tissue patterning. We conclude by outlining some of the key technical and modeling challenges for the future.
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Affiliation(s)
- Alistair M. Middleton
- Center for Modeling and Simulation in the Biosciences and Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Etienne Farcot
- Virtual Plants Inria Team, Université Montpellier 2, 34095 Montpellier cedex 5, France
| | - Markus R. Owen
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, Université Lyon I, Université de Lyon, 69364 Lyon cedex 07, France
- Address correspondence to
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Okumoto S, Jones A, Frommer WB. Quantitative imaging with fluorescent biosensors. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:663-706. [PMID: 22404462 DOI: 10.1146/annurev-arplant-042110-103745] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Molecular activities are highly dynamic and can occur locally in subcellular domains or compartments. Neighboring cells in the same tissue can exist in different states. Therefore, quantitative information on the cellular and subcellular dynamics of ions, signaling molecules, and metabolites is critical for functional understanding of organisms. Mass spectrometry is generally used for monitoring ions and metabolites; however, its temporal and spatial resolution are limited. Fluorescent proteins have revolutionized many areas of biology-e.g., fluorescent proteins can report on gene expression or protein localization in real time-yet promoter-based reporters are often slow to report physiologically relevant changes such as calcium oscillations. Therefore, novel tools are required that can be deployed in specific cells and targeted to subcellular compartments in order to quantify target molecule dynamics directly. We require tools that can measure enzyme activities, protein dynamics, and biophysical processes (e.g., membrane potential or molecular tension) with subcellular resolution. Today, we have an extensive suite of tools at our disposal to address these challenges, including translocation sensors, fluorescence-intensity sensors, and Förster resonance energy transfer sensors. This review summarizes sensor design principles, provides a database of sensors for more than 70 different analytes/processes, and gives examples of applications in quantitative live cell imaging.
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Affiliation(s)
- Sakiko Okumoto
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
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