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Brandi J, Robotti E, Manfredi M, Barberis E, Marengo E, Novelli E, Cecconi D. Kohonen Artificial Neural Network and Multivariate Analysis in the Identification of Proteome Changes during Early and Long Aging of Bovine Longissimus dorsi Muscle Using SWATH Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11512-11522. [PMID: 34523341 PMCID: PMC8485349 DOI: 10.1021/acs.jafc.1c03578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 06/13/2023]
Abstract
To study proteomic changes involved in tenderization of Longissimus dorsi, Charolais heifers and bulls muscles were sampled after early and long aging (12 or 26 days). Sensory evaluation and instrumental tenderness measurement were performed. Proteins were analyzed by gel-free proteomics. By pattern recognition (principal component analysis and Kohonen's self-organizing maps) and classification (partial least squares-discriminant analysis) tools, 58 and 86 dysregulated proteins were detected after 12 and 26 days of aging, respectively. Tenderness was positively correlated mainly with metabolic enzymes (PYGM, PGAM2, TPI1, PGK1, and PFKM) and negatively with keratins. Downregulation in hemoglobin subunits and carbonic anhydrase 3 levels was relevant after 12 days of aging, while mimecan and collagen chains levels were reduced after 26 days of aging. Bioinformatics indicated that aging involves a prevalence of metabolic pathways after late and long periods. These findings provide a deeper understanding of changes involved in aging of beef and indicate a powerful method for future proteomics studies.
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Affiliation(s)
- Jessica Brandi
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, Verona 37134, Italy
| | - Elisa Robotti
- Department
of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria 15121, Italy
| | - Marcello Manfredi
- Department
of Translational Medicine and Center for Translational Research on
Autoimmune Diseases, University of Piemonte
Orientale, Novara 28100, Italy
- Department
of Translational Medicine, University of
Piemonte Orientale, Novara 28100, Italy
| | - Elettra Barberis
- Department
of Translational Medicine and Center for Translational Research on
Autoimmune Diseases, University of Piemonte
Orientale, Novara 28100, Italy
- Department
of Translational Medicine, University of
Piemonte Orientale, Novara 28100, Italy
| | - Emilio Marengo
- Department
of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria 15121, Italy
| | - Enrico Novelli
- Department
of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua 35122, Italy
| | - Daniela Cecconi
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, Verona 37134, Italy
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2
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Two-Dimensional Gel Electrophoresis Image Analysis. Methods Mol Biol 2021; 2361:3-13. [PMID: 34236652 DOI: 10.1007/978-1-0716-1641-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Gel-based proteomics is still quite widespread due to its high-resolution power; the experimental approach is based on differential analysis, where groups of samples (e.g., control vs diseased) are compared to identify panels of potential biomarkers. However, the reliability of the result of the differential analysis is deeply influenced by 2D-PAGE maps image analysis procedures. The analysis of 2D-PAGE images consists of several steps, such as image preprocessing, spot detection and quantitation, image warping and alignment, spot matching. Several approaches are present in literature, and classical or last-generation commercial software packages exploit different algorithms for each step of the analysis. Here, the most widespread approaches and a comparison of the different strategies are presented.
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3
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Todeschini V, AitLahmidi N, Mazzucco E, Marsano F, Gosetti F, Robotti E, Bona E, Massa N, Bonneau L, Marengo E, Wipf D, Berta G, Lingua G. Impact of Beneficial Microorganisms on Strawberry Growth, Fruit Production, Nutritional Quality, and Volatilome. FRONTIERS IN PLANT SCIENCE 2018; 9:1611. [PMID: 30505312 PMCID: PMC6250784 DOI: 10.3389/fpls.2018.01611] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/17/2018] [Indexed: 05/24/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) colonize the roots of most terrestrial plant species, improving plant growth, nutrient uptake and biotic/abiotic stress resistance and tolerance. Similarly, plant growth promoting bacteria (PGPB) enhance plant fitness and production. In this study, three different AMF (Funneliformis mosseae, Septoglomus viscosum, and Rhizophagus irregularis) were used in combination with three different strains of Pseudomonas sp. (19Fv1t, 5Vm1K and Pf4) to inoculate plantlets of Fragaria × ananassa var. Eliana F1. The effects of the different fungus/bacterium combinations were assessed on plant growth parameters, fruit production and quality, including health-promoting compounds. Inoculated and uninoculated plants were maintained in a greenhouse for 4 months and irrigated with a nutrient solution at two different phosphate levels. The number of flowers and fruits were recorded weekly. At harvest, fresh and dry weights of roots and shoots, mycorrhizal colonization and concentration of leaf photosynthetic pigments were measured in each plant. The following fruit parameters were recorded: pH, titratable acids, concentration of organic acids, soluble sugars, ascorbic acids, and anthocyanidins; volatile and elemental composition were also evaluated. Data were statistically analyzed by ANOVA and PCA/PCA-DA. Mycorrhizal colonization was higher in plants inoculated with R. irregularis, followed by F. mosseae and S. viscosum. In general, AMF mostly affected the parameters associated with the vegetative portion of the plant, while PGPB were especially relevant for fruit yield and quality. The plant physiological status was differentially affected by inoculations, resulting in enhanced root and shoot biomass. Inoculation with Pf4 bacterial strain increased flower and fruit production per plant and malic acid content in fruits, while decreased the pH value, regardless of the used fungus. Inoculations affected fruit nutritional quality, increasing sugar and anthocyanin concentrations, and modulated pH, malic acid, volatile compounds and elements. In the present study, we show for the first time that strawberry fruit concentration of some elements and/or volatiles can be affected by the presence of specific beneficial soil microorganisms. In addition, our results indicated that it is possible to select the best plant-microorganism combination for field applications, and improving fruit production and quality, also in terms of health promoting properties.
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Affiliation(s)
- Valeria Todeschini
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Nassima AitLahmidi
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Eleonora Mazzucco
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Francesco Marsano
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Fabio Gosetti
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Elisa Robotti
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Elisa Bona
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Nadia Massa
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Laurent Bonneau
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Emilio Marengo
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Graziella Berta
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
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4
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Al‐Obaidi JR, Jamil NAM, Rahmad N, Rosli NHM. Proteomic and metabolomic study of wax apple (
Syzygium samarangense
) fruit during ripening process. Electrophoresis 2018; 39:2954-2964. [DOI: 10.1002/elps.201800185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/10/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Jameel R. Al‐Obaidi
- Agro‐Biotechnology Institute Malaysia (ABI)c/o MARDI Headquarters Serdang Selangor Malaysia
| | - Nor Azreen Mohd Jamil
- Agro‐Biotechnology Institute Malaysia (ABI)c/o MARDI Headquarters Serdang Selangor Malaysia
| | - Norasfaliza Rahmad
- Agro‐Biotechnology Institute Malaysia (ABI)c/o MARDI Headquarters Serdang Selangor Malaysia
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Abstract
2D-DIGE is still a very widespread technique in proteomics for the identification of panels of biomarkers, allowing to tackle with some important drawback of classical two-dimensional gel-electrophoresis. However, once 2D-gels are obtained, they must undergo a quite articulated multistep image analysis procedure before the final differential analysis via statistical mono- and multivariate methods. Here, the main steps of image analysis software are described and the most recent procedures reported in the literature are briefly presented.
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Affiliation(s)
- Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy.
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy
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6
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Manfredi M, Robotti E, Quasso F, Mazzucco E, Calabrese G, Marengo E. Fast classification of hazelnut cultivars through portable infrared spectroscopy and chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 189:427-435. [PMID: 28843196 DOI: 10.1016/j.saa.2017.08.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/13/2017] [Accepted: 08/16/2017] [Indexed: 06/07/2023]
Abstract
The authentication and traceability of hazelnuts is very important for both the consumer and the food industry, to safeguard the protected varieties and the food quality. This study investigates the use of a portable FTIR spectrometer coupled to multivariate statistical analysis for the classification of raw hazelnuts. The method discriminates hazelnuts from different origins/cultivars based on differences of the signal intensities of their IR spectra. The multivariate classification methods, namely principal component analysis (PCA) followed by linear discriminant analysis (LDA) and partial least square discriminant analysis (PLS-DA), with or without variable selection, allowed a very good discrimination among the groups, with PLS-DA coupled to variable selection providing the best results. Due to the fast analysis, high sensitivity, simplicity and no sample preparation, the proposed analytical methodology could be successfully used to verify the cultivar of hazelnuts, and the analysis can be performed quickly and directly on site.
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Affiliation(s)
- Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, Viale Michel 11, 15121 Alessandria, Italy.
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, Viale Michel 11, 15121 Alessandria, Italy.
| | - Fabio Quasso
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, Viale Michel 11, 15121 Alessandria, Italy.
| | - Eleonora Mazzucco
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, Viale Michel 11, 15121 Alessandria, Italy.
| | - Giorgio Calabrese
- Department of Pharmaceutical and Toxicological Chemistry, University of Napoli Federico II, Via Montesano 49, 80131 Naples, Italy.
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, Viale Michel 11, 15121 Alessandria, Italy.
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7
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Salzano AM, Sobolev A, Carbone V, Petriccione M, Renzone G, Capitani D, Vitale M, Minasi P, Pasquariello MS, Novi G, Zambrano N, Scortichini M, Mannina L, Scaloni A. A proteometabolomic study of Actinidia deliciosa fruit development. J Proteomics 2017; 172:11-24. [PMID: 29133123 DOI: 10.1016/j.jprot.2017.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Anatoly Sobolev
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Milena Petriccione
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Donatella Capitani
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy
| | - Monica Vitale
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy
| | - Paola Minasi
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Maria Silvia Pasquariello
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Gianfranco Novi
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
| | - Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Naples, Italy; CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Marco Scortichini
- Centro di Ricerca per Olivicoltura, Frutticoltura e Agrumicoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, 81100 Caserta, Italy
| | - Luisa Mannina
- Magnetic Resonance Laboratory "Annalaura Segre", Institute of Chemical Methodologies, National Research Council, 00015, Monterotondo, Rome, Italy; Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy.
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8
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Comparative analysis of constitutive proteome between resistant and susceptible tomato genotypes regarding to late blight. Funct Integr Genomics 2017; 18:11-21. [DOI: 10.1007/s10142-017-0570-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/18/2017] [Accepted: 08/23/2017] [Indexed: 01/07/2023]
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10
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Shiratake K, Suzuki M. Omics studies of citrus, grape and rosaceae fruit trees. BREEDING SCIENCE 2016; 66:122-38. [PMID: 27069397 PMCID: PMC4780796 DOI: 10.1270/jsbbs.66.122] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/06/2023]
Abstract
Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.
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Affiliation(s)
- Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
- Corresponding author (e-mail: )
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
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11
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Robotti E, Marengo E, Quasso F. Image Pretreatment Tools II: Normalization Techniques for 2-DE and 2-D DIGE. Methods Mol Biol 2016; 1384:91-107. [PMID: 26611411 DOI: 10.1007/978-1-4939-3255-9_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gel electrophoresis is usually applied to identify different protein expression profiles in biological samples (e.g., control vs. pathological, control vs. treated). Information about the effect to be investigated (a pathology, a drug, a ripening effect, etc.) is however generally confounded with experimental variability that is quite large in 2-DE and may arise from small variations in the sample preparation, reagents, sample loading, electrophoretic conditions, staining and image acquisition. Obtaining valid quantitative estimates of protein abundances in each map, before the differential analysis, is therefore fundamental to provide robust candidate biomarkers. Normalization procedures are applied to reduce experimental noise and make the images comparable, improving the accuracy of differential analysis. Certainly, they may deeply influence the final results, and to this respect they have to be applied with care. Here, the most widespread normalization procedures are described both for what regards the applications to 2-DE and 2D Difference Gel-electrophoresis (2-D DIGE) maps.
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Affiliation(s)
- Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy.
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy
| | - Fabio Quasso
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy
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12
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A single gene all3940 (Dps) overexpression in Anabaena sp. PCC 7120 confers multiple abiotic stress tolerance via proteomic alterations. Funct Integr Genomics 2015; 16:67-78. [DOI: 10.1007/s10142-015-0467-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022]
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13
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Negri AS, Prinsi B, Failla O, Scienza A, Espen L. Proteomic and metabolic traits of grape exocarp to explain different anthocyanin concentrations of the cultivars. FRONTIERS IN PLANT SCIENCE 2015; 6:603. [PMID: 26300900 PMCID: PMC4523781 DOI: 10.3389/fpls.2015.00603] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/21/2015] [Indexed: 05/28/2023]
Abstract
The role of grape berry skin as a protective barrier against damage by physical injuries and pathogen attacks requires a metabolism able to sustain biosynthetic activities such as those relating to secondary compounds (i.e., flavonoids). In order to draw the attention on these biochemical processes, a proteomic and metabolomic comparative analysis was performed among Riesling Italico, Pinot Gris, Pinot Noir, and Croatina cultivars, which are known to accumulate anthocyanins to a different extent. The application of multivariate statistics on the dataset pointed out that the cultivars were distinguishable from each other and the order in which they were grouped mainly reflected their relative anthocyanin contents. Sorting the spots according to their significance 100 proteins were characterized by LC-ESI-MS/MS. Through GC-MS, performed in Selected Ion Monitoring (SIM) mode, 57 primary metabolites were analyzed and the differences in abundance of 16 of them resulted statistically significant to ANOVA test. Considering the functional distribution, the identified proteins were involved in many physiological processes such as stress, defense, carbon metabolism, energy conversion and secondary metabolism. The trends of some metabolites were related to those of the protein data. Taken together, the results permitted to highlight the relationships between the secondary compound pathways and the main metabolism (e.g., glycolysis and TCA cycle). Moreover, the trend of accumulation of many proteins involved in stress responses, reinforced the idea that they could play a role in the cultivar specific developmental plan.
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Affiliation(s)
| | | | | | | | - Luca Espen
- *Correspondence: Luca Espen, Dipartimento di Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, Università degli Studi di Milano, via Celoria n.2, Milano 20133, Italy
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14
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Fraige K, González-Fernández R, Carrilho E, Jorrín-Novo JV. Metabolite and proteome changes during the ripening of Syrah and Cabernet Sauvignon grape varieties cultured in a nontraditional wine region in Brazil. J Proteomics 2015; 113:206-25. [DOI: 10.1016/j.jprot.2014.09.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/22/2014] [Accepted: 09/26/2014] [Indexed: 01/19/2023]
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15
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Marengo E, Robotti E. Biomarkers for pancreatic cancer: Recent achievements in proteomics and genomics through classical and multivariate statistical methods. World J Gastroenterol 2014; 20:13325-13342. [PMID: 25309068 PMCID: PMC4188889 DOI: 10.3748/wjg.v20.i37.13325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 06/04/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is one of the most aggressive and lethal neoplastic diseases. A valid alternative to the usual invasive diagnostic tools would certainly be the determination of biomarkers in peripheral fluids to provide less invasive tools for early diagnosis. Nowadays, biomarkers are generally investigated mainly in peripheral blood and tissues through high-throughput omics techniques comparing control vs pathological samples. The results can be evaluated by two main strategies: (1) classical methods in which the identification of significant biomarkers is accomplished by monovariate statistical tests where each biomarker is considered as independent from the others; and (2) multivariate methods, taking into consideration the correlations existing among the biomarkers themselves. This last approach is very powerful since it allows the identification of pools of biomarkers with diagnostic and prognostic performances which are superior to single markers in terms of sensitivity, specificity and robustness. Multivariate techniques are usually applied with variable selection procedures to provide a restricted set of biomarkers with the best predictive ability; however, standard selection methods are usually aimed at the identification of the smallest set of variables with the best predictive ability and exhaustivity is usually neglected. The exhaustive search for biomarkers is instead an important alternative to standard variable selection since it can provide information about the etiology of the pathology by producing a comprehensive set of markers. In this review, the most recent applications of the omics techniques (proteomics, genomics and metabolomics) to the identification of exploratory biomarkers for PC will be presented with particular regard to the statistical methods adopted for their identification. The basic theory related to classical and multivariate methods for identification of biomarkers is presented and then, the most recent applications in this field are discussed.
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16
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Wu HX, Jia HM, Ma XW, Wang SB, Yao QS, Xu WT, Zhou YG, Gao ZS, Zhan RL. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits. J Proteomics 2014; 105:19-30. [PMID: 24704857 DOI: 10.1016/j.jprot.2014.03.030] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. BIOLOGICAL SIGNIFICANCE Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Hong-xia Wu
- Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Hui-min Jia
- Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Xiao-wei Ma
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Song-biao Wang
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Quan-sheng Yao
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Wen-tian Xu
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Yi-gang Zhou
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
| | - Zhong-shan Gao
- Department of Horticulture, State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Zhejiang University, Hangzhou 310058, China.
| | - Ru-lin Zhan
- Ministry of Agriculture Key Laboratory of Tropical Fruit Biology, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, Guangdong, China
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Pilati S, Brazzale D, Guella G, Milli A, Ruberti C, Biasioli F, Zottini M, Moser C. The onset of grapevine berry ripening is characterized by ROS accumulation and lipoxygenase-mediated membrane peroxidation in the skin. BMC PLANT BIOLOGY 2014; 14:87. [PMID: 24693871 PMCID: PMC4021102 DOI: 10.1186/1471-2229-14-87] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 03/20/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The ripening of fleshy fruits is a complex developmental program characterized by extensive transcriptomic and metabolic remodeling in the pericarp tissues (pulp and skin) making unripe green fruits soft, tasteful and colored. The onset of ripening is regulated by a plethora of endogenous signals tuned to external stimuli. In grapevine and tomato, which are classified as non-climacteric and climacteric species respectively, the accumulation of hydrogen peroxide (H2O2) and extensive modulation of reactive oxygen species (ROS) scavenging enzymes at the onset of ripening has been reported, suggesting that ROS could participate to the regulatory network of fruit development. In order to investigate this hypothesis, a comprehensive biochemical study of the oxidative events occurring at the beginning of ripening in Vitis vinifera cv. Pinot Noir has been undertaken. RESULTS ROS-specific staining allowed to visualize not only H2O2 but also singlet oxygen (1O2) in berry skin cells just before color change in distinct subcellular locations, i.e. cytosol and plastids. H2O2 peak in sample skins at véraison was confirmed by in vitro quantification and was supported by the concomitant increase of catalase activity. Membrane peroxidation was also observed by HPLC-MS on galactolipid species at véraison. Mono- and digalactosyl diacylglycerols were found peroxidized on one or both α-linolenic fatty acid chains, with a 13(S) absolute configuration implying the action of a specific enzyme. A lipoxygenase (PnLOXA), expressed at véraison and localizing inside the chloroplasts, was indeed able to catalyze membrane galactolipid peroxidation when overexpressed in tobacco leaves. CONCLUSIONS The present work demonstrates the controlled, harmless accumulation of specific ROS in distinct cellular compartments, i.e. cytosol and chloroplasts, at a definite developmental stage, the onset of grape berry ripening. These features strongly candidate ROS as cellular signals in fruit ripening and encourage further studies to identify downstream elements of this cascade. This paper also reports the transient galactolipid peroxidation carried out by a véraison-specific chloroplastic lipoxygenase. The function of peroxidized membranes, likely distinct from that of free fatty acids due to their structural role and tight interaction with photosynthesis protein complexes, has to be ascertained.
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Affiliation(s)
- Stefania Pilati
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele a/Adige, TN, Italy
| | - Daniele Brazzale
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele a/Adige, TN, Italy
| | - Graziano Guella
- Department of Physics, Bioorganic Chemistry Lab, University of Trento, Via Sommarive 14, 38123 Trento, Povo, Italy
- CNR, Istituto di Biofisica Trento, Via alla Cascata 56/C, 38123 Trento, Povo, Italy
| | - Alberto Milli
- Department of Physics, Bioorganic Chemistry Lab, University of Trento, Via Sommarive 14, 38123 Trento, Povo, Italy
| | - Cristina Ruberti
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele a/Adige, TN, Italy
| | - Michela Zottini
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele a/Adige, TN, Italy
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George IS, Haynes PA. Current perspectives in proteomic analysis of abiotic stress in Grapevines. FRONTIERS IN PLANT SCIENCE 2014; 5:686. [PMID: 25538720 PMCID: PMC4258992 DOI: 10.3389/fpls.2014.00686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/18/2014] [Indexed: 05/21/2023]
Abstract
Grapes are an important crop plant which forms the basis of a globally important industry. Grape and wine production is particularly vulnerable to environmental and climatic fluctuations, which makes it essential for us to develop a greater understanding of the molecular level responses of grape plants to various abiotic stresses. The completion of the initial grape genome sequence in 2007 has led to a significant increase in research on grapes using proteomics approaches. In this article, we discuss some of the current research on abiotic stress in grapevines, in the context of abiotic stress research in other plant species. We also highlight some of the current limitations in grapevine proteomics and identify areas with promising scope for potential future research.
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Affiliation(s)
| | - Paul A. Haynes
- *Correspondence: Paul A. Haynes, Department of Chemistry and Biomolecular Sciences, Macquarie University, F7B 331, North Ryde, NSW 2109, Australia e-mail:
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19
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Agudelo-Romero P, Bortolloti C, Pais MS, Tiburcio AF, Fortes AM. Study of polyamines during grape ripening indicate an important role of polyamine catabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 67:105-19. [PMID: 23562795 DOI: 10.1016/j.plaphy.2013.02.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/22/2013] [Indexed: 05/25/2023]
Abstract
Grapevine (Vitis species) is the most economically important fruit crop worldwide. Ripening of non-climacteric fruits such as grapes has been the subject of intense research. Despite this interest, little is known on the role played by polyamines in the onset of ripening of non-climacteric fruits. These growth regulators have been involved in plant development and stress responses. Molecular and biochemical studies were developed in three important Portuguese cultivars (Trincadeira, Touriga Nacional and Aragonês) during the year 2008 and in Trincadeira during 2007 in order to gather insights on the role of polyamines in grape ripening. Microarray and real-time qPCR studies revealed up-regulation of a gene coding for arginine decarboxylase (ADC) during grape ripening in all the varieties. This increase was not accompanied by an increase in free and conjugated polyamines that presented a strong decrease. Putrescine and Spermidine levels were higher at earlier stages of development, while Spermine level remained constant. Berries of Trincadeira cultivar presented the highest content in total free and conjugated polyamines at earlier stages of fruit development in particular in the year 2007. The decrease in polyamines content during grape ripening was accompanied by up-regulation of genes coding for diamine oxidase (CuAO) and polyamine oxidase (PAO), together with a significant increase in their enzymatic activity and in the hydrogen peroxide content. These results provide, for the first time, strong evidence of a role of polyamine catabolism in grape ripening possibly through interaction with other growth regulators.
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Affiliation(s)
- Patricia Agudelo-Romero
- Universidade de Lisboa, Faculdade de Ciências de Lisboa, BioFIG, Campo Grande, 1749-016 Lisboa, Portugal
| | - Cristina Bortolloti
- University of Barcelona, Pharmacy Faculty, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Maria Salomé Pais
- Universidade de Lisboa, Faculdade de Ciências de Lisboa, BioFIG, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Ana Margarida Fortes
- Universidade de Lisboa, Faculdade de Ciências de Lisboa, BioFIG, Campo Grande, 1749-016 Lisboa, Portugal.
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20
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Frenkel C, Hartman TG. Decrease in fruit moisture content heralds and might launch the onset of ripening processes. J Food Sci 2013; 77:S365-76. [PMID: 23061891 DOI: 10.1111/j.1750-3841.2012.02910.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UNLABELLED It is known that fruit ripening is a genetically programmed event but it is not entirely clear what metabolic cue(s) stimulate the onset of ripening, ethylene action notwithstanding. Here, we examined the conjecture that fruit ripening might be evoked by an autonomously induced decrease in tissue water status. We found decline in water content occurring at the onset of ripening in climacteric and nonclimacteric fruit, suggesting that this phenomenon might be universal. This decline in water content persisted throughout the ripening process in some fruit, whereas in others it reversed during the progression of the ripening process. Applied ethylene also induced a decrease in water content in potato (Solanum tuberosum) tubers. In ethylene-mutant tomato (Solanum lycopersicum) fruit (antisense to1-aminocyclopropane carboxylate synthase), cold-induced decline in water content stimulated onset of ripening processes apparently independently of ethylene action, suggesting cause-and-effect relationship between decreasing water content and onset of ripening. The decline in tissue water content, occurring naturally or induced by ethylene, was strongly correlated with a decrease in hydration (swelling) efficacy of cell wall preparations suggesting that hydration dynamics of cell walls might account for changes in tissue moisture content. Extent of cell wall swelling was, in turn, related to the degree of oxidative cross-linking of wall-bound phenolic acids, suggesting that oxidant-induced wall restructuring might mediate cell wall and, thus, fruit tissue hydration status. We propose that oxidant-induced cell wall remodeling and consequent wall dehydration might evoke stress signaling for the onset of ripening processes. PRACTICAL APPLICATION This study suggests that decline in fruit water content is an early event in fruit ripening. This information may be used to gauge fruit maturity for appropriate harvest date and for processing. Control of fruit hydration state might be used to regulate the onset of fruit ripening.
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Affiliation(s)
- Chaim Frenkel
- Department of Plant Biology and Pathology, Rutgers-the State University of New Jersey, New Brunswick, NJ 08901, USA.
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21
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D'Ambrosio C, Arena S, Rocco M, Verrillo F, Novi G, Viscosi V, Marra M, Scaloni A. Proteomic analysis of apricot fruit during ripening. J Proteomics 2013. [DOI: 10.1016/j.jprot.2012.11.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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