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Nicolaï BM, Xiao H, Han Q, Tran DT, Crouch E, Hertog MLATM, Verboven P. Spatio-temporal dynamics of the metabolome of climacteric fruit during ripening and post-harvest storage. J Exp Bot 2023; 74:6321-6330. [PMID: 37317945 DOI: 10.1093/jxb/erad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/13/2023] [Indexed: 06/16/2023]
Abstract
Fruit quality traits are determined to a large extent by their metabolome. The metabolite content of climacteric fruit changes drastically during ripening and post-harvest storage, and has been investigated extensively. However, the spatial distribution of metabolites and how it changes in time has received much less attention as fruit are usually considered as homogenous plant organs. Yet, spatio-temporal changes of starch, which is hydrolyzed during ripening, has been used for a long time as a ripening index. As vascular transport of water, and hence convective transport of metabolites, slows down in mature fruit and even stalls after detachment, spatio-temporal changes in their concentration are probably affected by diffusive transport of gaseous molecules that act as substrate (O2), inhibitor (CO2), or regulator (ethylene and NO) of the metabolic pathways that are active during climacteric ripening. In this review, we discuss such spatio-temporal changes of the metabolome and how they are affected by transport of metabolic gases and gaseous hormones. As there are currently no techniques available to measure the metabolite distribution repeatedly by non-destructive means, we introduce reaction-diffusion models as an in silico tool to compute it. We show how the different components of such a model can be integrated and used to better understand the role of spatio-temporal changes of the metabolome in ripening and post-harvest storage of climacteric fruit that is detached from the plant, and discuss future research needs.
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Affiliation(s)
- Bart M Nicolaï
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- Flanders Centre of Postharvest Technology, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Hui Xiao
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Qianyun Han
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Dinh Thi Tran
- Department of Food Processing Technology, Faculty of Food Science and Technology, Vietnam National University of Agriculture, Vietnam
| | - Elke Crouch
- Department of Horticultural Sciences, Faculty of AgriSciences, Lombardi Building, c/o Victoria and Neethling Street, Stellenbosch, South Africa
| | | | - Pieter Verboven
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
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2
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Nguyen TMV, Hertog MLATM, Van de Poel B, Tran DT, Nicolaï B. Targeted system approach to ethylene biosynthesis and signaling of a heat tolerant tomato cultivar; the impact of growing season on fruit ripening. Front Plant Sci 2023; 14:1195020. [PMID: 37457344 PMCID: PMC10348052 DOI: 10.3389/fpls.2023.1195020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
Growing tomato in hot weather conditions is challenging for fruit production and yield. Tomato cv. Savior is a heat-tolerant cultivar which can be grown during both the Vietnamese winter (mild condition) and summer (hot condition) season. Understanding the mechanisms of ethylene biosynthesis and signaling are important for agriculture, as manipulation of these pathways can lead to improvements in crop yield, stress tolerance, and fruit ripening. The objective of this study was to investigate an overview of ethylene biosynthesis and signaling from target genes to proteins and metabolites and the impact of growing season on a heat tolerant tomato cultivar throughout fruit ripening and postharvest storage. This work also showed the feasibility of absolute protein quantification of ethylene biosynthesis enzymes. Summer fruit showed the delayed peak of ethylene production until the red ripe stage. The difference in postharvest ethylene production between winter and summer fruit appears to be regulated by the difference in accumulation of 1-aminocyclopropane-1-carboxylic acid (ACC) which depends on the putative up-regulation of SAM levels. The lack of differences in protein concentrations between winter and summer fruit indicate that heat stress did not alter the ethylene biosynthesis-related protein abundance in heat tolerant cultivar. The analysis results of enzymatic activity and proteomics showed that in both winter and summer fruit, the majority of ACO activity could be mainly contributed to the abundance of ACO5 and ACO6 isoforms, rather than ACO1. Likewise, ethylene signal transduction was largely controlled by the abundance of ethylene receptors ETR1, ETR3, ETR6, and ETR7 together with the constitute triple response regulator CTR1 for both winter and summer grown tomatoes. Altogether our results indicate that in the heat tolerant tomato cv. Savior, growing season mainly affects the ethylene biosynthesis pathway and leaves the signaling pathway relatively unaffected.
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Affiliation(s)
- Thao Minh Viet Nguyen
- KU Leuven, BIOSYST-MeBioS Postharvest Lab, Leuven, Belgium
- Vietnam National University of Agriculture, Faculty of Food Science and Technology, Hanoi, Vietnam
- KU Leuven Plant Institute (LPI), Leuven, Belgium
| | - Maarten L. A. T. M. Hertog
- KU Leuven, BIOSYST-MeBioS Postharvest Lab, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Leuven, Belgium
| | - Bram Van de Poel
- KU Leuven Plant Institute (LPI), Leuven, Belgium
- KU Leuven, BIOSYST- Crop Biotechnics, Molecular Plant Hormone Physiology Lab, Leuven, Belgium
| | - Dinh Thi Tran
- Vietnam National University of Agriculture, Faculty of Food Science and Technology, Hanoi, Vietnam
| | - Bart Nicolaï
- KU Leuven, BIOSYST-MeBioS Postharvest Lab, Leuven, Belgium
- KU Leuven Plant Institute (LPI), Leuven, Belgium
- Flanders Centre of Postharvest Technology, Leuven, Belgium
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3
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Janssens M, Verlinden BE, Hertog MLATM, Nicolaï BM. Quality Evolution and Aroma Profile of Pointed Cabbage in Different Storage Regimes. Front Plant Sci 2022; 13:852817. [PMID: 35498690 PMCID: PMC9051525 DOI: 10.3389/fpls.2022.852817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
With its increasing popularity, the need for optimal storage conditions of pointed cabbages becomes more important to meet the year-round demand. Storage of the pointed varieties, however, is more difficult compared to the traditional, round varieties and is limited to a few weeks in normal air. Pointed cabbages are more susceptible to quality loss (shriveling, yellowing of leaves, weight loss, fungal, and bacterial infections) and tend to spoil much faster. In order to provide a year-round availability of the fresh product, storage under controlled atmosphere (CA) could offer a solution. In this study, pointed, white cabbage heads (Brassica oleracea var. capitata for. alba L. subv. Conica cv. 'Caraflex') were stored at 1°C from November 2018 to May 2019 under four different CA conditions (1 kPa O2 + 1.5 kPa CO2, 1 kPa O2 + 5 kPa CO2, 3 kPa O2 + 1.5 kPa CO2, and 3 kPa O2 + 5 kPa CO2), and compared to storage under normal air. Results showed that CA storage resulted in a prolonged storage life with a good quality retention for both texture and aroma. CA-stored cabbages showed less weight loss, shriveling, and yellowing. Internal quality parameters [color, soluble solids content (SSC)] were stable over the whole storage period for all objects. The aroma profiles of both the storage atmosphere and cabbage samples were impacted by storage duration. The aroma of cabbage juice was also affected by the storage regime. A clear separation was found for cabbage stored under CA compared to the reference group. From the CA-treatments studied, a combination of low oxygen (1 kPa O2) and elevated carbon dioxide levels (5 kPa CO2) showed the best results maintaining quality. Storage under CA resulted in a better resemblance to the aroma of freshly, harvested produce compared to cabbages stored in normal air.
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Affiliation(s)
| | | | | | - Bart M. Nicolaï
- Flanders Centre of Postharvest Technology, Leuven, Belgium
- BIOSYST-MeBioS Postharvest Research Group, KU Leuven, Leuven, Belgium
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4
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Boeckx J, Pols S, Hertog MLATM, Nicolaï BM. Regulation of the Central Carbon Metabolism in Apple Fruit Exposed to Postharvest Low-Oxygen Stress. Front Plant Sci 2019; 10:1384. [PMID: 31737012 PMCID: PMC6831743 DOI: 10.3389/fpls.2019.01384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/07/2019] [Indexed: 05/07/2023]
Abstract
After harvest, fruit remain metabolically active and continue to ripen. The main goal of postharvest storage is to slow down the metabolic activity of the detached fruit. In many cases, this is accomplished by storing fruit at low temperature in combination with low oxygen (O2) and high carbon dioxide (CO2) partial pressures. However, altering the normal atmospheric conditions is not without any risk and can induce low-O2 stress. This review focuses on the central carbon metabolism of apple fruit during postharvest storage, both under normal O2 conditions and under low-O2 stress conditions. While the current review is focused on apple fruit, most research on the central carbon metabolism, low-O2 stress, and O2 sensing has been done on a range of different model plants (e.g., Arabidopsis, potato, rice, and maize) using various plant organs (e.g., seedlings, tubers, roots, and leaves). This review pulls together this information from the various sources into a coherent overview to facilitate the research on the central carbon metabolism in apple fruit exposed to postharvest low-O2 stress.
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Affiliation(s)
| | | | | | - Bart M. Nicolaï
- KU Leuven, BIOSYST-MeBioS, Leuven, Belgium
- Flanders Centre of Postharvest Technology, Leuven, Belgium
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Beshir WF, Tohge T, Watanabe M, Hertog MLATM, Hoefgen R, Fernie AR, Nicolaï BM. Non-aqueous fractionation revealed changing subcellular metabolite distribution during apple fruit development. Hortic Res 2019; 6:98. [PMID: 31666959 PMCID: PMC6804870 DOI: 10.1038/s41438-019-0178-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 05/07/2023]
Abstract
In developing apple fruit, metabolic compartmentation is poorly understood due to the lack of experimental data. Distinguishing subcellular compartments in fruit using non-aqueous fractionation has been technically difficult due to the excess amount of sugars present in the different subcellular compartments limiting the resolution of the technique. The work described in this study represents the first attempt to apply non-aqueous fractionation to developing apple fruit, covering the major events occurring during fruit development (cell division, cell expansion, and maturation). Here we describe the non-aqueous fractionation method to study the subcellular compartmentation of metabolites during apple fruit development considering three main cellular compartments (cytosol, plastids, and vacuole). Evidence is presented that most of the sugars and organic acids were predominantly located in the vacuole, whereas some of the amino acids were distributed between the cytosol and the vacuole. The results showed a shift in the plastid marker from the lightest fractions in the early growth stage to the dense fractions in the later fruit growth stages. This implies that the accumulation of starch content with progressing fruit development substantially influenced the distribution of plastidial fragments within the non-aqueous density gradient applied. Results from this study provide substantial baseline information on assessing the subcellular compartmentation of metabolites in apple fruit in general and during fruit growth in particular.
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Affiliation(s)
- Wasiye F. Beshir
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Maarten L. A. T. M. Hertog
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology (MPI-MP), Potsdam-Golm, Germany
| | - Bart M. Nicolaï
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Leuven, Belgium
- Flanders Centre of Postharvest Technology (VCBT), Leuven, Belgium
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6
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Mata CI, Fabre B, Parsons HT, Hertog MLATM, Van Raemdonck G, Baggerman G, Van de Poel B, Lilley KS, Nicolaï BM. Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. Front Plant Sci 2018; 9:1626. [PMID: 30467512 PMCID: PMC6235968 DOI: 10.3389/fpls.2018.01626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
Ethylene, the plant ripening hormone of climacteric fruit, is perceived by ethylene receptors which is the first step in the complex ethylene signal transduction pathway. Much progress has been made in elucidating the mechanism of this pathway, but there is still a lot to be done in the proteomic quantification of the main proteins involved, particularly during fruit ripening. This work focuses on the mass spectrometry based identification and quantification of the ethylene receptors (ETRs) and the downstream components of the pathway, CTR-like proteins (CTRs) and ETHYLENE INSENSITIVE 2 (EIN2). We used tomato as a model fruit to study changes in protein abundance involved in the ethylene signal transduction during fruit ripening. In order to detect and quantify these low abundant proteins located in the membrane of the endoplasmic reticulum, we developed a workflow comprising sample fractionation and MS analysis using parallel reaction monitoring. This work shows the feasibility of the identification and absolute quantification of all seven ethylene receptors, three out of four CTRs and EIN2 in four ripening stages of tomato. In parallel, gene expression was analyzed through real-time qPCR. Correlation between transcriptomic and proteomic profiles during ripening was only observed for three of the studied proteins, suggesting that the other signaling proteins are likely post-transcriptionally regulated. Based on our quantification results we were able to show that the protein levels of SlETR3 and SlETR4 increased during ripening, probably to control ethylene sensitivity. The other receptors and CTRs showed either stable levels that could sustain, or decreasing levels that could promote fruit ripening.
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Affiliation(s)
- Clara I. Mata
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Harriet T. Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Maarten L. A. T. M. Hertog
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Geert Van Raemdonck
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics and Mass Spectrometry, University of Antwerp, Antwerp, Belgium
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Bram Van de Poel
- Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Bart M. Nicolaï
- Postharvest Group, Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
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7
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Fabre B, Korona D, Mata CI, Parsons HT, Deery MJ, Hertog MLATM, Nicolaï BM, Russell S, Lilley KS. Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum. Proteomics 2018; 17. [PMID: 28922568 DOI: 10.1002/pmic.201700216] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/02/2017] [Indexed: 12/21/2022]
Abstract
Quantitative proteomics methods have emerged as powerful tools for measuring protein expression changes at the proteome level. Using MS-based approaches, it is now possible to routinely quantify thousands of proteins. However, prefractionation of the samples at the protein or peptide level is usually necessary to go deep into the proteome, increasing both MS analysis time and technical variability. Recently, a new MS acquisition method named SWATH is introduced with the potential to provide good coverage of the proteome as well as a good measurement precision without prior sample fractionation. In contrast to shotgun-based MS however, a library containing experimental acquired spectra is necessary for the bioinformatics analysis of SWATH data. In this study, spectral libraries for two widely used models are built to study crop ripening or animal embryogenesis, Solanum lycopersicum (tomato) and Drosophila melanogaster, respectively. The spectral libraries comprise fragments for 5197 and 6040 proteins for S. lycopersicum and D. melanogaster, respectively, and allow reproducible quantification for thousands of peptides per MS analysis. The spectral libraries and all MS data are available in the MassIVE repository with the dataset identifiers MSV000081074 and MSV000081075 and the PRIDE repository with the dataset identifiers PXD006493 and PXD006495.
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Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Bertrand Fabre, Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Dagmara Korona
- Department of Genetics University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Harriet T Parsons
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Department of Plant and Environmental Sciences, Copenhagen University, Copenhagen, Denmark
| | - Michael J Deery
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | | | - Steven Russell
- Department of Genetics University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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8
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Ho QT, Hertog MLATM, Verboven P, Ambaw A, Rogge S, Verlinden BE, Nicolaï BM. Down-regulation of respiration in pear fruit depends on temperature. J Exp Bot 2018; 69:2049-2060. [PMID: 29394374 PMCID: PMC6018969 DOI: 10.1093/jxb/ery031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/24/2018] [Indexed: 05/23/2023]
Abstract
The respiration rate of plant tissues decreases when the amount of available O2 is reduced. There is, however, a debate on whether the respiration rate is controlled either by diffusion limitation of oxygen or through regulatory processes at the level of the transcriptome. We used experimental and modelling approaches to demonstrate that both diffusion limitation and metabolic regulation affect the response of respiration of bulky plant organs such as fruit to reduced O2 levels in the surrounding atmosphere. Diffusion limitation greatly affects fruit respiration at high temperature, but at low temperature respiration is reduced through a regulatory process, presumably a response to a signal generated by a plant oxygen sensor. The response of respiration to O2 is time dependent and is highly sensitive, particularly at low O2 levels in the surrounding atmosphere. Down-regulation of the respiration at low temperatures may save internal O2 and relieve hypoxic conditions in the fruit.
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Affiliation(s)
- Quang Tri Ho
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan, Leuven, Belgium
| | | | - Pieter Verboven
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan, Leuven, Belgium
| | - Alemayehu Ambaw
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan, Leuven, Belgium
| | - Seppe Rogge
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan, Leuven, Belgium
| | - Bert E Verlinden
- Flanders Centre of Postharvest Technology, Willem de Croylaan, Leuven, Belgium
| | - Bart M Nicolaï
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan, Leuven, Belgium
- Flanders Centre of Postharvest Technology, Willem de Croylaan, Leuven, Belgium
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9
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Mata CI, Fabre B, Hertog MLATM, Parsons HT, Deery MJ, Lilley KS, Nicolaï BM. In-depth characterization of the tomato fruit pericarp proteome. Proteomics 2017; 17. [PMID: 27957804 DOI: 10.1002/pmic.201600406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 12/19/2022]
Abstract
Since the genome of Solanum lycopersicum L. was published in 2012, some studies have explored its proteome although with a limited depth. In this work, we present an extended characterization of the proteome of the tomato pericarp at its ripe red stage. Fractionation of tryptic peptides generated from pericarp proteins by off-line high-pH reverse-phase phase chromatography in combination with LC-MS/MS analysis on a Fisher Scientific Q Exactive and a Sciex Triple-TOF 6600 resulted in the identification of 8588 proteins with a 1% FDR both at the peptide and protein levels. Proteins were mapped through GO and KEGG databases and a large number of the identified proteins were associated with cytoplasmic organelles and metabolic pathways categories. These results constitute one of the most extensive proteome datasets of tomato so far and provide an experimental confirmation of the existence of a high number of theoretically predicted proteins. All MS data are available in the ProteomeXchange repository with the dataset identifiers PXD004947 and PXD004932.
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Affiliation(s)
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Harriet T Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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Gapper NE, Hertog MLATM, Lee J, Buchanan DA, Leisso RS, Fei Z, Qu G, Giovannoni JJ, Johnston JW, Schaffer RJ, Nicolaï BM, Mattheis JP, Watkins CB, Rudell DR. Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis. BMC Plant Biol 2017; 17:77. [PMID: 28431510 PMCID: PMC5399402 DOI: 10.1186/s12870-017-1030-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/12/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Superficial scald is a physiological disorder of apple fruit characterized by sunken, necrotic lesions appearing after prolonged cold storage, although initial injury occurs much earlier in the storage period. To determine the degree to which the transition to cell death is an active process and specific metabolism involved, untargeted metabolic and transcriptomic profiling was used to follow metabolism of peel tissue over 180 d of cold storage. RESULTS The metabolome and transcriptome of peel destined to develop scald began to diverge from peel where scald was controlled using antioxidant (diphenylamine; DPA) or rendered insensitive to ethylene using 1-methylcyclopropene (1-MCP) beginning between 30 and 60 days of storage. Overall metabolic and transcriptomic shifts, representing multiple pathways and processes, occurred alongside α-farnesene oxidation and, later, methanol production alongside symptom development. CONCLUSIONS Results indicate this form of peel necrosis is a product of an active metabolic transition involving multiple pathways triggered by chilling temperatures at cold storage inception rather than physical injury. Among multiple other pathways, enhanced methanol and methyl ester levels alongside upregulated pectin methylesterases are unique to peel that is developing scald symptoms similar to injury resulting from mechanical stress and herbivory in other plants.
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Affiliation(s)
- Nigel E. Gapper
- School of Plant Science, Horticulture Section, Cornell University, Ithaca, NY 14853 USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
- Present addresses: AgroFresh, Wenatchee, WA 98801 USA
| | | | - Jinwook Lee
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
- Present addresses: Department of Horticultural Sciences, Mokpo National University, Muan, Korea
| | - David A. Buchanan
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | - Rachel S. Leisso
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - Guiqin Qu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853 USA
- United States Department of Agriculture, Agricultural Research Service, Plant, Soil, and Nutrition Laboratory, Ithaca, NY 14853 USA
| | - Jason W. Johnston
- The New Zealand Institute for Plant and Food Research, Ltd, Havelock North, New Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research, Ltd, Auckland, New Zealand
| | | | - James P. Mattheis
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | | | - David R. Rudell
- Tree Fruit Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1104 N. Western Ave, Wenatchee, WA 98801 USA
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Tran DT, Hertog MLATM, Tran TLH, Quyen NT, Van de Poel B, Mata CI, Nicolaï BM. Population Modeling Approach to Optimize Crop Harvest Strategy. The Case of Field Tomato. Front Plant Sci 2017; 8:608. [PMID: 28473843 PMCID: PMC5397500 DOI: 10.3389/fpls.2017.00608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/04/2017] [Indexed: 05/30/2023]
Abstract
In this study, the aim is to develop a population model based approach to optimize fruit harvesting strategies with regard to fruit quality and its derived economic value. This approach was applied to the case of tomato fruit harvesting under Vietnamese conditions. Fruit growth and development of tomato (cv. "Savior") was monitored in terms of fruit size and color during both the Vietnamese winter and summer growing seasons. A kinetic tomato fruit growth model was applied to quantify biological fruit-to-fruit variation in terms of their physiological maturation. This model was successfully calibrated. Finally, the model was extended to translate the fruit-to-fruit variation at harvest into the economic value of the harvested crop. It can be concluded that a model based approach to the optimization of harvest date and harvest frequency with regard to economic value of the crop as such is feasible. This approach allows growers to optimize their harvesting strategy by harvesting the crop at more uniform maturity stages meeting the stringent retail demands for homogeneous high quality product. The total farm profit would still depend on the impact a change in harvesting strategy might have on related expenditures. This model based harvest optimisation approach can be easily transferred to other fruit and vegetable crops improving homogeneity of the postharvest product streams.
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Affiliation(s)
- Dinh T. Tran
- Faculty of Food Science and Technology, Vietnam National University of AgricultureHanoi, Vietnam
| | | | - Thi L. H. Tran
- Faculty of Food Science and Technology, Vietnam National University of AgricultureHanoi, Vietnam
| | - Nguyen T. Quyen
- Faculty of Food Science and Technology, Vietnam National University of AgricultureHanoi, Vietnam
| | | | | | - Bart M. Nicolaï
- KU Leuven, BIOSYST-MeBioSLeuven, Belgium
- Flanders Center of Postharvest TechnologyLeuven, Belgium
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12
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Beshir WF, Mbong VBM, Hertog MLATM, Geeraerd AH, Van den Ende W, Nicolaï BM. Dynamic Labeling Reveals Temporal Changes in Carbon Re-Allocation within the Central Metabolism of Developing Apple Fruit. Front Plant Sci 2017; 8:1785. [PMID: 29093725 PMCID: PMC5651688 DOI: 10.3389/fpls.2017.01785] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/02/2017] [Indexed: 05/05/2023]
Abstract
In recent years, the application of isotopically labeled substrates has received extensive attention in plant physiology. Measuring the propagation of the label through metabolic networks may provide information on carbon allocation in sink fruit during fruit development. In this research, gas chromatography coupled to mass spectrometry based metabolite profiling was used to characterize the changing metabolic pool sizes in developing apple fruit at five growth stages (30, 58, 93, 121, and 149 days after full bloom) using 13C-isotope feeding experiments on hypanthium tissue discs. Following the feeding of [U-13C]glucose, the 13C-label was incorporated into the various metabolites to different degrees depending on incubation time, metabolic pathway activity, and growth stage. Evidence is presented that early in fruit development the utilization of the imported sugars was faster than in later developmental stages, likely to supply the energy and carbon skeletons required for cell division and fruit growth. The declined 13C-incorporation into various metabolites during growth and maturation can be associated with the reduced metabolic activity, as mirrored by the respiratory rate. Moreover, the concentration of fructose and sucrose increased during fruit development, whereas concentrations of most amino and organic acids and polyphenols declined. In general, this study showed that the imported compounds play a central role not only in carbohydrate metabolism, but also in the biosynthesis of amino acid and related protein synthesis and secondary metabolites at the early stage of fruit development.
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Affiliation(s)
- Wasiye F. Beshir
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Victor B. M. Mbong
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Maarten L. A. T. M. Hertog
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Annemie H. Geeraerd
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Bart M. Nicolaï
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Leuven, Belgium
- Flanders Centre of Postharvest Technology, Leuven, Belgium
- *Correspondence: Bart M. Nicolaï
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13
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Leisso RS, Gapper NE, Mattheis JP, Sullivan NL, Watkins CB, Giovannoni JJ, Schaffer RJ, Johnston JW, Hanrahan I, Hertog MLATM, Nicolaï BM, Rudell DR. Gene expression and metabolism preceding soft scald, a chilling injury of 'Honeycrisp' apple fruit. BMC Genomics 2016; 17:798. [PMID: 27733113 PMCID: PMC5062943 DOI: 10.1186/s12864-016-3019-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/13/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND 'Honeycrisp' is an apple cultivar that is susceptible to soft scald, a chilling injury expressed as necrotic patches on the peel. Improved understanding of metabolism associated with the disorder would improve our understanding of soft scald and contribute to developing more effective management strategies for apple storage. It was expected that specific gene expression and specific metabolite levels in the peel would be linked with soft scald risk at harvest and/or specific time points during cold storage. RESULTS Fruit from nine 'Honeycrisp' apple orchards that would eventually develop different incidences of soft scald between 4 and 8 weeks of cold air storage were used to contrast and determine differential transcriptomic and metabolomic changes during storage. Untargeted metabolic profiling revealed changes in a number of distinct pathways preceding and concurrent with soft scald symptom development, including elevated γ-aminobutryic acid (GABA), 1-hexanol, acylated steryl glycosides, and free p-coumaryl acyl esters. At harvest, levels of sesquiterpenoid and triterpenoid acyl esters were relatively higher in peel of fruit that did not later develop the disorder. RNA-seq driven gene expression profiling highlighted possible involvement of genes and associated metabolic processes with soft scald development. These included elevated expression of genes involved in lipid peroxidation and phenolic metabolism in fruit with soft scald, and isoprenoid/brassinosteroid metabolism in fruit that did not develop soft scald. Expression of other stress-related genes in fruit that developed soft scald included chlorophyll catabolism, cell wall loosening, and lipid transport while superoxide dismutases were up-regulated in fruit that did not develop the disorder. CONCLUSIONS This study delineates the sequential transcriptomic and metabolomic changes preceding soft scald symptom development. Changes were differential depending on susceptibility of fruit to the disorder and could be attributed to key stress related and mediating pathways.
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Affiliation(s)
- Rachel S Leisso
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA
| | - Nigel E Gapper
- School of Plant Science, Horticulture Section, Cornell University, Ithaca, NY14853, USA
- AgroFresh Solutions Inc. 130 Technology Center Way Wenatchee, Wenatchee, WA 98801, WA, USA
| | - James P Mattheis
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA
| | - Nathanael L Sullivan
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA
| | - Christopher B Watkins
- School of Plant Science, Horticulture Section, Cornell University, Ithaca, NY14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY14853, USA
- United States Department of Agriculture, Agricultural Research Service, Plant, Soil, and Nutrition Laboratory, Ithaca, NY14853, USA
| | - Robert J Schaffer
- The New Zealand Institute for Plant and Food Research, Ltd, Auckland, New Zealand
| | - Jason W Johnston
- The New Zealand Institute for Plant and Food Research, Ltd, Havelock North, New Zealand
| | - Ines Hanrahan
- Washington Tree Fruit Research Commission, Wenatchee, WA, USA
| | | | | | - David R Rudell
- United States Department of Agriculture, Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA.
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14
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Bekele EA, Beshir WF, Hertog MLATM, Nicolai BM, Geeraerd AH. Metabolic profiling reveals ethylene mediated metabolic changes and a coordinated adaptive mechanism of 'Jonagold' apple to low oxygen stress. Physiol Plant 2015; 155:232-47. [PMID: 26031836 DOI: 10.1111/ppl.12351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 03/30/2015] [Accepted: 05/06/2015] [Indexed: 05/14/2023]
Abstract
Apples are predominantly stored in controlled atmosphere (CA) storage to delay ripening and prolong their storage life. Profiling the dynamics of metabolic changes during ripening and CA storage is vital for understanding the governing molecular mechanism. In this study, the dynamics of the primary metabolism of 'Jonagold' apples during ripening in regular air (RA) storage and initiation of CA storage was profiled. 1-Methylcyclopropene (1-MCP) was exploited to block ethylene receptors and to get insight into ethylene mediated metabolic changes during ripening of the fruit and in response to hypoxic stress. Metabolic changes were quantified in glycolysis, the tricarboxylic acid (TCA) cycle, the Yang cycle and synthesis of the main amino acids branching from these metabolic pathways. Partial least square discriminant analysis of the metabolic profiles of 1-MCP treated and control apples revealed a metabolic divergence in ethylene, organic acid, sugar and amino acid metabolism. During RA storage at 18°C, most amino acids were higher in 1-MCP treated apples, whereas 1-aminocyclopropane-1-carboxylic acid (ACC) was higher in the control apples. The initial response of the fruit to CA initiation was accompanied by an increase of alanine, succinate and glutamate, but a decline in aspartate. Furthermore, alanine and succinate accumulated to higher levels in control apples than 1-MCP treated apples. The observed metabolic changes in these interlinked metabolites may indicate a coordinated adaptive strategy to maximize energy production.
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Affiliation(s)
- Elias A Bekele
- Department of Biosystems (BIOSYST), Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Wasiye F Beshir
- Department of Biosystems (BIOSYST), Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Maarten L A T M Hertog
- Department of Biosystems (BIOSYST), Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Bart M Nicolai
- Department of Biosystems (BIOSYST), Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Annemie H Geeraerd
- Department of Biosystems (BIOSYST), Division of Mechatronics, Biostatistics and Sensors (MeBioS), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
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15
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Leisso RS, Buchanan DA, Lee J, Mattheis JP, Sater C, Hanrahan I, Watkins CB, Gapper N, Johnston JW, Schaffer RJ, Hertog MLATM, Nicolaï BM, Rudell DR. Chilling-related cell damage of apple (Malus × domestica Borkh.) fruit cortical tissue impacts antioxidant, lipid and phenolic metabolism. Physiol Plant 2015; 153:204-20. [PMID: 24944043 DOI: 10.1111/ppl.12244] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 04/07/2014] [Accepted: 05/14/2014] [Indexed: 05/09/2023]
Abstract
'Soggy breakdown' (SB) is an internal flesh disorder of 'Honeycrisp' apple (Malus × domestica Borkh.) fruit that occurs during low temperature storage. The disorder is a chilling injury (CI) in which visible symptoms typically appear after several weeks of storage, but information about the underlying metabolism associated with its induction and development is lacking. The metabolic profile of flesh tissue from wholly healthy fruit and brown and healthy tissues from fruit with SB was characterized using gas chromatography-mass spectrometry (GC-MS) and liquid chromatograph-mass spectrometry (LC-MS). Partial least squares discriminant analysis (PLS-DA) and correlation networks revealed correlation among ester volatile compounds by composition and differences in phytosterol, phenolic and putative triacylglycerides (TAGs) metabolism among the tissues. anova-simultaneous component analysis (ASCA) was used to test the significance of metabolic changes linked with tissue health status. ASCA-significant components included antioxidant compounds, TAGs, and phytosterol conjugates. Relative to entirely healthy tissues, elevated metabolite levels in symptomatic tissue included γ-amino butyric acid, glycerol, sitosteryl (6'-O-palmitoyl) β-d-glucoside and sitosteryl (6'-O-stearate) β-d-glucoside, and TAGs containing combinations of 16:0, 18:3, 18:2 and 18:1 fatty acids. Reduced metabolite levels in SB tissue included 5-caffeoyl quinate, β-carotene, catechin, epicatechin, α-tocopherol, violaxanthin and sitosteryl β-d glucoside. Pathway analysis indicated aspects of primary metabolism differed according to tissue condition, although differences in metabolites involved were more subtle than those of some secondary metabolites. The results implicate oxidative stress and membrane disruption processes in SB development and constitute a diagnostic metabolic profile for the disorder.
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Affiliation(s)
- Rachel S Leisso
- United States Department of Agriculture - Agricultural Research Service, Tree Fruit Research Laboratory, Wenatchee, WA, USA; Department of Horticulture, Washington State University, Pullman, WA, USA
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16
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Herremans E, Verboven P, Hertog MLATM, Cantre D, van Dael M, De Schryver T, Van Hoorebeke L, Nicolaï BM. Spatial development of transport structures in apple (Malus × domestica Borkh.) fruit. Front Plant Sci 2015; 6:679. [PMID: 26388883 PMCID: PMC4554951 DOI: 10.3389/fpls.2015.00679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/17/2015] [Indexed: 05/07/2023]
Abstract
The void network and vascular system are important pathways for the transport of gases, water and solutes in apple fruit (Malus × domestica Borkh). Here we used X-ray micro-tomography at various spatial resolutions to investigate the growth of these transport structures in 3D during fruit development of "Jonagold" apple. The size of the void space and porosity in the cortex tissue increased considerably. In the core tissue, the porosity was consistently lower, and seemed to decrease toward the end of the maturation period. The voids in the core were more narrow and fragmented than the voids in the cortex. Both the void network in the core and in the cortex changed significantly in terms of void morphology. An automated segmentation protocol underestimated the total vasculature length by 9-12% in comparison to manually processed images. Vascular networks increased in length from a total of 5 m at 9 weeks after full bloom, to more than 20 m corresponding to 5 cm of vascular tissue per cubic centimeter of apple tissue. A high degree of branching in both the void network and vascular system and a complex three-dimensional pattern was observed across the whole fruit. The 3D visualizations of the transport structures may be useful for numerical modeling of organ growth and transport processes in fruit.
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Affiliation(s)
- Els Herremans
- Division of MeBioS, Department of Biosystems, KU Leuven, University of LeuvenLeuven, Belgium
| | - Pieter Verboven
- Division of MeBioS, Department of Biosystems, KU Leuven, University of LeuvenLeuven, Belgium
| | | | - Dennis Cantre
- Division of MeBioS, Department of Biosystems, KU Leuven, University of LeuvenLeuven, Belgium
| | - Mattias van Dael
- Division of MeBioS, Department of Biosystems, KU Leuven, University of LeuvenLeuven, Belgium
| | - Thomas De Schryver
- Department of Physics and Astronomy, UGCT-Radiation Physics, Ghent UniversityGhent, Belgium
| | - Luc Van Hoorebeke
- Department of Physics and Astronomy, UGCT-Radiation Physics, Ghent UniversityGhent, Belgium
| | - Bart M. Nicolaï
- Division of MeBioS, Department of Biosystems, KU Leuven, University of LeuvenLeuven, Belgium
- Flanders Centre of Postharvest TechnologyLeuven, Belgium
- *Correspondence: Bart M. Nicolaï, Flanders Centre of Postharvest Technology/BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
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17
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Abera MK, Verboven P, Defraeye T, Fanta SW, Hertog MLATM, Carmeliet J, Nicolai BM. A plant cell division algorithm based on cell biomechanics and ellipse-fitting. Ann Bot 2014; 114:605-17. [PMID: 24863687 PMCID: PMC4156124 DOI: 10.1093/aob/mcu078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The importance of cell division models in cellular pattern studies has been acknowledged since the 19th century. Most of the available models developed to date are limited to symmetric cell division with isotropic growth. Often, the actual growth of the cell wall is either not considered or is updated intermittently on a separate time scale to the mechanics. This study presents a generic algorithm that accounts for both symmetrically and asymmetrically dividing cells with isotropic and anisotropic growth. Actual growth of the cell wall is simulated simultaneously with the mechanics. METHODS The cell is considered as a closed, thin-walled structure, maintained in tension by turgor pressure. The cell walls are represented as linear elastic elements that obey Hooke's law. Cell expansion is induced by turgor pressure acting on the yielding cell-wall material. A system of differential equations for the positions and velocities of the cell vertices as well as for the actual growth of the cell wall is established. Readiness to divide is determined based on cell size. An ellipse-fitting algorithm is used to determine the position and orientation of the dividing wall. The cell vertices, walls and cell connectivity are then updated and cell expansion resumes. Comparisons are made with experimental data from the literature. KEY RESULTS The generic plant cell division algorithm has been implemented successfully. It can handle both symmetrically and asymmetrically dividing cells coupled with isotropic and anisotropic growth modes. Development of the algorithm highlighted the importance of ellipse-fitting to produce randomness (biological variability) even in symmetrically dividing cells. Unlike previous models, a differential equation is formulated for the resting length of the cell wall to simulate actual biological growth and is solved simultaneously with the position and velocity of the vertices. CONCLUSIONS The algorithm presented can produce different tissues varying in topological and geometrical properties. This flexibility to produce different tissue types gives the model great potential for use in investigations of plant cell division and growth in silico.
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Affiliation(s)
- Metadel K. Abera
- Flanders Centre of Postharvest Technology/BIOSYST-MeBios, University of Leuven, Willem de Croylaan 42, B-3001, Leuven, Belgium
| | - Pieter Verboven
- Flanders Centre of Postharvest Technology/BIOSYST-MeBios, University of Leuven, Willem de Croylaan 42, B-3001, Leuven, Belgium
| | - Thijs Defraeye
- Flanders Centre of Postharvest Technology/BIOSYST-MeBios, University of Leuven, Willem de Croylaan 42, B-3001, Leuven, Belgium
| | - Solomon Workneh Fanta
- Flanders Centre of Postharvest Technology/BIOSYST-MeBios, University of Leuven, Willem de Croylaan 42, B-3001, Leuven, Belgium
| | - Maarten L. A. T. M. Hertog
- Flanders Centre of Postharvest Technology/BIOSYST-MeBios, University of Leuven, Willem de Croylaan 42, B-3001, Leuven, Belgium
| | - Jan Carmeliet
- Building Physics, Swiss Federal Institute of Technology Zurich (ETHZ), Wolfgang-Pauli-Strasse 15, 8093 Zürich, Switzerland
- Laboratory for Building Science and Technology, Swiss Federal Laboratories for Materials Testing and Research (Empa), Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Bart M. Nicolai
- Flanders Centre of Postharvest Technology/BIOSYST-MeBios, University of Leuven, Willem de Croylaan 42, B-3001, Leuven, Belgium
- For correspondence. E-mail
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18
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Hertog MLATM, Uysal I, McCarthy U, Verlinden BM, Nicolaï BM. Shelf life modelling for first-expired-first-out warehouse management. Philos Trans A Math Phys Eng Sci 2014; 372:20130306. [PMID: 24797134 PMCID: PMC4006170 DOI: 10.1098/rsta.2013.0306] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the supply chain of perishable food products, large losses are incurred between farm and fork. Given the limited land resources and an ever-growing population, the food supply chain is faced with the challenge of increasing its handling efficiency and minimizing post-harvest food losses. Huge value can be added by optimizing warehouse management systems, taking into account the estimated remaining shelf life of the product, and matching it to the requirements of the subsequent part of the handling chain. This contribution focuses on how model approaches estimating quality changes and remaining shelf life can be combined in optimizing first-expired-first-out cold chain management strategies for perishable products. To this end, shelf-life-related performance indicators are used to introduce remaining shelf life and product quality in the cost function when optimizing the supply chain. A combinatorial exhaustive-search algorithm is shown to be feasible as the complexity of the optimization problem is sufficiently low for the size and properties of a typical commercial cold chain. The estimated shelf life distances for a particular batch can thus be taken as a guide to optimize logistics.
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Affiliation(s)
| | - Ismail Uysal
- RFID Lab for Applied Research, Department of Electrical Engineering, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620-5399, USA
| | - Ultan McCarthy
- RFID Lab for Applied Research, Department of Electrical Engineering, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620-5399, USA
| | - Bert M. Verlinden
- Flanders Centre of Postharvest Technology, Willem de Croylaan 42, 3001 Leuven (Heverlee), Belgium
| | - Bart M. Nicolaï
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, 3001 Leuven (Heverlee), Belgium
- Flanders Centre of Postharvest Technology, Willem de Croylaan 42, 3001 Leuven (Heverlee), Belgium
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19
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Van de Poel B, Bulens I, Hertog MLATM, Nicolai BM, Geeraerd AH. A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms. New Phytol 2014; 202:952-963. [PMID: 24443955 DOI: 10.1111/nph.12685] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/17/2013] [Indexed: 06/03/2023]
Abstract
The gaseous plant hormone ethylene is involved in many physiological processes including climacteric fruit ripening, in which it is a key determinant of fruit quality. A detailed model that describes ethylene biochemistry dynamics is missing. Often, kinetic modeling is used to describe metabolic networks or signaling cascades, mostly ignoring the link with transcriptomic data. We have constructed an elegant kinetic model that describes the transfer of genetic information into abundance and metabolic activity of proteins for the entire ethylene biosynthesis pathway during fruit development and ripening of tomato (Solanum lycopersicum). Our model was calibrated against a vast amount of transcriptomic, proteomic and metabolic data and showed good descriptive qualities. Subsequently it was validated successfully against several ripening mutants previously described in the literature. The model was used as a predictive tool to evaluate novel and existing hypotheses regarding the regulation of ethylene biosynthesis. This bottom-up kinetic network model was used to indicate that a side-branch of the ethylene pathway, the formation of the dead-end product 1-(malonylamino)-1-aminocyclopropane-1-carboxylic acid (MACC), might have a strong effect on eventual ethylene production. Furthermore, our in silico analyses indicated potential (post-) translational regulation of the ethylene-forming enzyme ACC oxidase.
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Affiliation(s)
- Bram Van de Poel
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Inge Bulens
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Maarten L A T M Hertog
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
| | - Bart M Nicolai
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
- Flanders Centre of Postharvest Technology (VCBT), Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Annemie H Geeraerd
- Division of MeBioS, Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, bus 2428, 3001, Leuven, Belgium
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20
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Ampofo-Asiama J, Baiye VMM, Hertog MLATM, Waelkens E, Geeraerd AH, Nicolai BM. The metabolic response of cultured tomato cells to low oxygen stress. Plant Biol (Stuttg) 2014; 16:594-606. [PMID: 24119171 DOI: 10.1111/plb.12094] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/17/2013] [Indexed: 05/10/2023]
Abstract
The storage of fruits and vegetables under a controlled atmosphere can induce low oxygen stress, which can lead to post-harvest losses through the induction of disorders such as core breakdown and browning. To gain better understanding of the metabolic response of plant organs to low oxygen, cultured tomato cells (Lycopersicum esculentum) were used as a model system to study the metabolic stress response to low oxygen (0 and 1 kPa O2). By adding 13C labelled glucose, changes in the levels of polar metabolites and their 13C label accumulation were quantified. Low oxygen stress altered the metabolite profile of tomato cells, with the accumulation of the intermediates of glycolysis in addition to increases in lactate and sugar alcohols. 13C label data showed reduced label accumulation in almost all metabolites except lactate and some sugar alcohols. The results showed that low oxygen stress in tomato cell culture activated fermentative metabolism and sugar alcohol synthesis while inhibiting the activity of the TCA cycle and the biosynthesis of metabolites whose precursors are derived from central metabolism, including fluxes to most organic acids, amino acids and sugars.
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Affiliation(s)
- J Ampofo-Asiama
- Division of Mechatronics, Department of Biosystems (BIOSYST), Biostatistics and Sensors (MeBioS), KU Leuven, Leuven, Belgium
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21
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Buts K, Michielssens S, Hertog MLATM, Hayakawa E, Cordewener J, America AHP, Nicolai BM, Carpentier SC. Improving the identification rate of data independent label-free quantitative proteomics experiments on non-model crops: a case study on apple fruit. J Proteomics 2014; 105:31-45. [PMID: 24565695 DOI: 10.1016/j.jprot.2014.02.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/23/2014] [Accepted: 02/14/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Complex peptide extracts from non-model crops are troublesome for proper identification and quantification. To increase the identification rate of label free DIA experiments of Braeburn apple a new workflow was developed where a DDA database was constructed and linked to the DIA data. At a first level, parent masses found in DIA were searched in the DDA database based on their mass to charge ratio and retention time; at a second level, masses of fragmentation ions were compared for each of the linked spectrum. Following this workflow, a tenfold increase of peptides was identified from a single DIA run. As proof of principle, the designed workflow was applied to determine the changes during a storage experiment, achieving a two-fold identification increase in the number of significant peptides. The corresponding protein families were divided into nine clusters, representing different time profiles of changes in abundances during storage. Up-regulated protein families already show a glimpse of important pathways affecting aging during long-term storage, such as ethylene synthesis, and responses to abiotic stresses and their influence on the central metabolism. BIOLOGICAL SIGNIFICANCE Proteomics research on non-model crops causes additional difficulties in identifying the peptides present in, often complex, samples. This work proposes a new workflow to retrieve more identifications from a set of quantitative data, based on linking DIA and DDA data at two consecutive levels. As proof of principle, a storage experiment on Braeburn apple resulted in twice as much identified storage related peptides. Important proteins involved in central metabolism and stress are significantly up-regulated after long term storage. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Kim Buts
- BIOSYST-MeBioS, KU Leuven, Belgium.
| | - Servaas Michielssens
- Quantum Chemistry and Physical Chemistry Section, KU Leuven, Belgium; Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Eisuke Hayakawa
- Research Group of Functional Genomics and Proteomics, KU Leuven, Belgium
| | | | | | - Bart M Nicolai
- BIOSYST-MeBioS, KU Leuven, Belgium; Flanders Centre of Postharvest Technology, Leuven, Belgium
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Bulens I, Van de Poel B, Hertog MLATM, Cristescu SM, Harren FJM, De Proft MP, Geeraerd AH, Nicolai BM. Dynamic changes of the ethylene biosynthesis in 'Jonagold' apple. Physiol Plant 2014; 150:161-173. [PMID: 23957643 DOI: 10.1111/ppl.12084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 03/21/2013] [Accepted: 06/10/2013] [Indexed: 06/02/2023]
Abstract
In this study, the short-term and dynamic changes of the ethylene biosynthesis of Jonagold apple during and after application of controlled atmosphere (CA) storage conditions were quantified using a systems biology approach. Rapid responses to imposed temperature and atmospheric conditions were captured by continuous online photoacoustic ethylene measurements. Discrete destructive sampling was done to understand observed changes of ethylene biosynthesis at the transcriptional, translational and metabolic level. Application of the ethylene inhibitor 1-methylcyclopropene (1-MCP) allowed for the discrimination between ethylene-mediated changes and ethylene-independent changes related to the imposed conditions. Online ethylene measurements showed fast and slower responses during and after application of CA conditions. The changes in 1-aminocyclopropane-1-carboxylate synthase (ACS) activity were most correlated with changes in ACS1 expression and regulated the cold-induced increase in ethylene production during the early chilling phase. Transcription of ACS3 was found ethylene independent and was triggered upon warming of CA-stored apples. Increased expression of ACO1 during shelf life led to a strong increase in 1-aminocyclopropane-1-carboxylate oxidase (ACO) activity, required for the exponential production of ethylene during system 2. Expression of ACO2 and ACO3 was upregulated in 1-MCP-treated fruit showing a negative correlation with ethylene production. ACO activity never became rate limiting.
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Affiliation(s)
- Inge Bulens
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), Katholieke Universiteit Leuven, Willem de Croylaan 42, bus 2428, B-3001, Leuven, Belgium
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Nicolaï BM, Defraeye T, De Ketelaere B, Herremans E, Hertog MLATM, Saeys W, Torricelli A, Vandendriessche T, Verboven P. Nondestructive measurement of fruit and vegetable quality. Annu Rev Food Sci Technol 2014; 5:285-312. [PMID: 24387604 DOI: 10.1146/annurev-food-030713-092410] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We review nondestructive techniques for measuring internal and external quality attributes of fruit and vegetables, such as color, size and shape, flavor, texture, and absence of defects. The different techniques are organized according to their physical measurement principle. We first describe each technique and then list some examples. As many of these techniques rely on mathematical models and particular data processing methods, we discuss these where needed. We pay particular attention to techniques that can be implemented online in grading lines.
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Affiliation(s)
- Bart M Nicolaï
- BIOSYST-MeBioS, KU Leuven, 3001 Leuven, Belgium; , , , , , , ,
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Buts K, Hertog MLATM, Baggerman G, Nicolaï BM. A systems biology approach to browning in apple: proteomics. Commun Agric Appl Biol Sci 2011; 76:245-248. [PMID: 21539241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- K Buts
- BIOSTYST-MeBioS, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001 Heverlee, Belgium
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Bulens I, Van De Poel B, Hertog MLATM, De Proft M, Geeraerd A, Nicolaï B. The ethylene biosynthesis in Jonagold apple during ripening, storage and shelf life--a modelling appraoch. Commun Agric Appl Biol Sci 2011; 76:11-14. [PMID: 21539186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- I Bulens
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIO-SYST), Katholieke Universiteit Leuven, Willem de Croylaan 42, bus 2428, B-3001 Leuven, Belgium
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Van de Poel B, Bulens I, Lagrain P, Pollet J, Hertog MLATM, Lammertyn J, De Proft MP, Nicolaï BM, Geeraerd AH. Determination of S-adenosyl-l-methionine in fruits by capillary electrophoresis. Phytochem Anal 2010; 21:602-8. [PMID: 20690158 DOI: 10.1002/pca.1241] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
INTRODUCTION S-adenosyl-l-methionine (SAM) plays an important role in many biochemical reactions in plants. It is mainly used as a methyl donor for methylation reactions, but it also participates in, for example, the biosynthesis of polyamines and the plant hormone ethylene. OBJECTIVE To develop a fast capillary electrophoresis technique to separate SAM in fruits and fruit juices without any pre-purification steps. METHODOLOGY Four different extraction solutions and two extraction times were tested, of which 5% trichloroacetic acid (TCA) for 10 min was found most suited. A glycine : phosphate buffer (200 : 50 mm, pH 2.5) was found optimal to analyse SAM in TCA extracts. Analyses were preformed on different climacteric and non-climacteric fruits and fruit juices. The calibration curve was created in degraded tomato extract. The CE-method was compared with a more conventional HPLC method described in literature. RESULTS The CE technique made it possible to completely separate the S,S- and R,S-diastereoisomeric forms of SAM. The CE method proved to be very fast (20 min total running time instead of 42 min) and more sensitive (limit of detection of 0.5 µm instead of 1 µm) compared with the conventional HPLC method. CONCLUSION Fast measurements of SAM in fruits and juices are favoured by capillary electrophoresis in a 200 : 50 mm glycine : phosphate (pH 2.5) buffer system.
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Affiliation(s)
- Bram Van de Poel
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, Leuven, Belgium.
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Abstract
Untargeted metabolic profiling was employed to characterize metabolomic changes associated with 'Granny Smith' apple superficial scald development following 1-MCP or DPA treatment. Partial least-squares discriminant analyses were used to link metabolites with scald, postharvest treatments, and storage duration. Models revealed metabolomic differentiation between untreated controls and fruit treated with DPA or 1-MCP within 1 week following storage initiation. Metabolic divergence between controls and DPA-treated fruit after 4 weeks of storage preceded scald symptom development by 2 months. alpha-Farnesene oxidation products with known associations to scald, including conjugated trienols, 6-methyl-5-hepten-2-one, and 6-methyl-5-hepten-2-ol, were associated with presymptomatic as well as scalded control fruit. Likewise, a large group of putative triterpenoids with mass spectral features similar to those of ursolic acid and beta-sitosterol were associated with control fruit and scald. Results demonstrate that extensive metabolomic changes associated with scald precede actual symptom development.
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Affiliation(s)
- David R Rudell
- Tree Fruit Research Laboratory, USDA-ARS, Wenatchee, Washington 98801, USA.
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Pedreschi R, Hertog MLATM, Carpentier SC, Lammertyn J, Robben J, Noben JP, Panis B, Swennen R, Nicolaï BM. Treatment of missing values for multivariate statistical analysis of gel-based proteomics data. Proteomics 2008; 8:1371-83. [PMID: 18383008 DOI: 10.1002/pmic.200700975] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The presence of missing values in gel-based proteomics data represents a real challenge if an objective statistical analysis is pursued. Different methods to handle missing values were evaluated and their influence is discussed on the selection of important proteins through multivariate techniques. The evaluated methods consisted of directly dealing with them during the multivariate analysis with the nonlinear estimation by iterative partial least squares (NIPALS) algorithm or imputing them by using either k-nearest neighbor or Bayesian principal component analysis (BPCA) before carrying out the multivariate analysis. These techniques were applied to data obtained from gels stained with classical postrunning dyes and from DIGE gels. Before applying the multivariate techniques, the normality and homoscedasticity assumptions on which parametric tests are based on were tested in order to perform a sound statistical analysis. From the three tested methods to handle missing values in our datasets, BPCA imputation of missing values showed to be the most consistent method.
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Affiliation(s)
- Romina Pedreschi
- BIOSYST-MeBioS Division, Katholieke Universiteit Leuven, Leuven, Belgium.
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