1
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Zilberstein G, Zilberstein S, Righetti PG. Holy Grail possibly made from clay. Electrophoresis 2024. [PMID: 38234009 DOI: 10.1002/elps.202300249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
The main goal of the work was to find biochemical protein markers specific for grapes and wine in ancient amphorae shards and fermentation pools. Grape-specific proteins are more reliable markers than tartaric acid and other small organic acids (tartaric acid natural source are not only grape but also apple, mango, and other plants). The Yavne winery (located in the Central District of Israel) is stated to be the largest known wine production complex from the Byzantine period (ca. 1500 years ago). The site has been excavated recently, and a number of wine jar have been recovered. We have applied our ethylene vinyl acetate (EVA) (EVA studded with strong cation and anion exchangers) diskettes to the inner surface of a number of jars, thus capturing residual grape proteins therein. Via mass spectrometry analyses, we have been able to identify four grape and three yeast proteins. This has been possible because the EVA films, applied to such surfaces, are able to harvest and concentrate any trace species, rendering them amenable to instrumental analysis. Our analysis makes it possible to propose an explanation for the Holy Grail phenomenon as a dish in which wine or water begins to smell pleasant. We attribute this to the slow release of terpenes, aldehydes, and ketones from the clay walls of pottery. After digital modeling, we identified that "scallop-shaped" niches in winery were used for the condensation of high percentage alcohol by passive evaporation from fermentation tanks.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta, ", Milan, Italy
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2
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Albuquerque W, Ghezellou P, Seidel L, Burkert J, Will F, Schweiggert R, Spengler B, Zorn H, Gand M. Mass Spectrometry-Based Proteomic Profiling of a Silvaner White Wine. Biomolecules 2023; 13:biom13040650. [PMID: 37189397 DOI: 10.3390/biom13040650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/16/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
The comprehensive identification of the proteome content from a white wine (cv. Silvaner) is described here for the first time. The wine protein composition isolated from a representative wine sample (250 L) was identified via mass spectrometry (MS)-based proteomics following in-solution and in-gel digestion methods after being submitted to size exclusion chromatographic (SEC) fractionation to gain a comprehensive insight into proteins that survive the vinification processes. In total, we identified 154 characterized (with described functional information) or so far uncharacterized proteins, mainly from Vitis vinifera L. and Saccharomyces cerevisiae. With the complementarity of the two-step purification, the digestion techniques and the high-resolution (HR)-MS analyses provided a high-score identification of proteins from low to high abundance. These proteins can be valuable for future authentication of wines by tracing proteins derived from a specific cultivar or winemaking process. The proteomics approach presented herein may also be generally helpful to understand which proteins are important for the organoleptic properties and stability of wines.
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Affiliation(s)
- Wendell Albuquerque
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Leif Seidel
- Department of Beverage Research, Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Johannes Burkert
- Institute for Viticulture and Oenology, Bavarian State Institute for Viticulture and Horticulture (LWG), An der Steige 15, 97209 Veitshöchheim, Germany
| | - Frank Will
- Department of Beverage Research, Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Ralf Schweiggert
- Department of Beverage Research, Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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3
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Gut Microbiome Proteomics in Food Allergies. Int J Mol Sci 2023; 24:ijms24032234. [PMID: 36768555 PMCID: PMC9917015 DOI: 10.3390/ijms24032234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.
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4
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Afzaal M, Saeed F, Hussain M, Shahid F, Siddeeg A, Al‐Farga A. Proteomics as a promising biomarker in food authentication, quality and safety: A review. Food Sci Nutr 2022; 10:2333-2346. [PMID: 35844910 PMCID: PMC9281926 DOI: 10.1002/fsn3.2842] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/07/2022] [Accepted: 03/12/2022] [Indexed: 12/18/2022] Open
Abstract
Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced ingredients may cause a food allergy or toxicity to vulnerable consumers. Moreover, foodborne pathogens also pose a major threat to food safety. There is a dire need to develop strong analytical tools to deal with related issues. In this context, proteomics stands out as a promising tool used to report the aforementioned issues. The development in the field of omics has inimitable advantages in enabling the understanding of various biological fields especially in the discipline of food science. In this review, current applications and the role of proteomics in food authenticity, safety, and quality and food traceability are highlighted comprehensively. Additionally, the other components of proteomics have also been comprehensively described. Furthermore, this review will be helpful in the provision of new intuition into the use of proteomics in food analysis. Moreover, the pathogens in food can also be identified based on differences in their protein profiling. Conclusively, proteomics, an indicator of food properties, its origin, the processes applied to food, and its composition are also the limelight of this article.
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Affiliation(s)
- Muhammad Afzaal
- Department of Food Science Government College University Faisalabad Faisalabad Pakistan
| | - Farhan Saeed
- Department of Food Science Government College University Faisalabad Faisalabad Pakistan
| | - Muzzamal Hussain
- Department of Food Science Government College University Faisalabad Faisalabad Pakistan
| | - Farheen Shahid
- Department of Food Science Government College University Faisalabad Faisalabad Pakistan
| | - Azhari Siddeeg
- Department of Food Engineering and Technology Faculty of Engineering and Technology University of Gezira Wad Medani Sudan
| | - Ammar Al‐Farga
- Department of Biochemistry College of Sciences University of Jeddah Jeddah Saudi Arabia
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5
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Valletta M, Ragucci S, Landi N, Di Maro A, Pedone PV, Russo R, Chambery A. Mass spectrometry-based protein and peptide profiling for food frauds, traceability and authenticity assessment. Food Chem 2021; 365:130456. [PMID: 34243122 DOI: 10.1016/j.foodchem.2021.130456] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 01/03/2023]
Abstract
The ever-growing use of mass spectrometry (MS) methodologies in food authentication and traceability originates from their unrivalled specificity, accuracy and sensitivity. Such features are crucial for setting up analytical strategies for detecting food frauds and adulterations by monitoring selected components within food matrices. Among MS approaches, protein and peptide profiling has become increasingly consolidated. This review explores the current knowledge on recent MS techniques using protein and peptide biomarkers for assessing food traceability and authenticity, with a specific focus on their use for unmasking potential frauds and adulterations. We provide a survey of the current state-of-the-art instrumentation including the most reliable and sensitive acquisition modes highlighting advantages and limitations. Finally, we summarize the recent applications of MS to protein/peptide analyses in food matrices and examine their potential in ensuring the quality of agro-food products.
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Affiliation(s)
- Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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6
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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7
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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8
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Carrera M, Cañas B, Gallardo JM. Advanced proteomics and systems biology applied to study food allergy. Curr Opin Food Sci 2018. [DOI: 10.1016/j.cofs.2017.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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9
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Development of a mass spectrometry immunoassay for unambiguous detection of egg allergen traces in wines. Anal Bioanal Chem 2016; 409:1581-1589. [DOI: 10.1007/s00216-016-0099-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/04/2016] [Accepted: 11/14/2016] [Indexed: 02/05/2023]
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10
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Review on proteomics for food authentication. J Proteomics 2016; 147:212-225. [PMID: 27389853 DOI: 10.1016/j.jprot.2016.06.033] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/21/2016] [Accepted: 06/28/2016] [Indexed: 12/24/2022]
Abstract
UNLABELLED Consumers have the right to know what is in the food they are eating. Accordingly, European and global food regulations require that the provenance of the food can be guaranteed from farm to fork. Many different instrumental techniques have been proposed for food authentication. Although traditional methods are still being used, new approaches such as genomics, proteomics, and metabolomics are helping to complement existing methodologies for verifying the claims made about certain food products. During the last decade, proteomics (the large-scale analysis of proteins in a particular biological system at a particular time) has been applied to different research areas within food technology. Since proteins can be used as markers for many properties of a food, even indicating processes to which the food has been subjected, they can provide further evidence of the foods labeling claim. This review is a comprehensive and updated overview of the applications, drawbacks, advantages, and challenges of proteomics for food authentication in the assessment of the foods compliance with labeling regulations and policies. SIGNIFICANCE This review paper provides a comprehensive and critical overview of the application of proteomics approaches to determine the authenticity of several food products updating the performances and current limitations of the applied techniques in both laboratory and industrial environments.
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11
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Challenging the Limit of Detection for Egg Allergen Detection in Red Wines by Surface Plasmon Resonance Biosensor. FOOD ANAL METHOD 2016. [DOI: 10.1007/s12161-016-0464-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Candiano G, Santucci L, Petretto A, Lavarello C, Inglese E, Bruschi M, Ghiggeri GM, Boschetti E, Righetti PG. Widening and Diversifying the Proteome Capture by Combinatorial Peptide Ligand Libraries via Alcian Blue Dye Binding. Anal Chem 2015; 87:4814-20. [DOI: 10.1021/acs.analchem.5b00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Giovanni Candiano
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Laura Santucci
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Andrea Petretto
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Chiara Lavarello
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Elvira Inglese
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Maurizio Bruschi
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Gian Marco Ghiggeri
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | | | - Pier Giorgio Righetti
- Department
of Chemistry, Materials and Chemical Engineering, “Giulio
Natta”, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
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13
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Prado M, Ortea I, Vial S, Rivas J, Calo-Mata P, Barros-Velázquez J. Advanced DNA- and Protein-based Methods for the Detection and Investigation of Food Allergens. Crit Rev Food Sci Nutr 2015; 56:2511-2542. [DOI: 10.1080/10408398.2013.873767] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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Rapid and label-free detection of egg allergen traces in wines by surface plasmon resonance biosensor. Anal Bioanal Chem 2015; 407:3787-97. [DOI: 10.1007/s00216-015-8607-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/25/2015] [Accepted: 02/27/2015] [Indexed: 11/25/2022]
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15
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Righetti PG, Boschetti E. Sample treatment methods involving combinatorial peptide ligand libraries for improved proteomes analyses. Methods Mol Biol 2015; 1243:55-82. [PMID: 25384740 DOI: 10.1007/978-1-4939-1872-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians. Orientations for optional routes are also given according to the objective of the experimental investigations. This covers different approaches to capture proteins of very low abundance. Total protein harvestings to prevent partial losses are also described such as single exhaustive desorption and fractionated elutions for more detailed analyses. Documented results are also reported demonstrating the capability of the technology well beyond what is the common assumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
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16
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Abstract
One of the main challenges in proteomics investigation, protein biomarker research, and protein purity and contamination analysis is how to efficiently enrich and detect low-abundance proteins in biological samples. One approach that makes the detection of rare species possible is the treatment of biological samples with solid-phase combinatorial peptide ligand libraries, ProteoMiner. This method utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but remove most of the high-abundance proteins, therefore compresses the protein abundance range in the samples. This work describes optimized protocols and highlights on the successful application of ProteoMiner to protein identification and analysis.
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Affiliation(s)
- Lei Li
- Protein Technologies R&D, Life Science Group, Bio-Rad Laboratories, 1000 Alfred Nobel Drive, Hercules, CA, 94547, USA,
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17
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Red wine proteins: Two dimensional (2-D) electrophoresis and mass spectrometry analysis. Food Chem 2014; 164:413-7. [DOI: 10.1016/j.foodchem.2014.05.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/14/2014] [Accepted: 05/07/2014] [Indexed: 01/16/2023]
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18
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Deckwart M, Carstens C, Webber-Witt M, Schäfer V, Eichhorn L, Kang S, Fischer M, Brockow K, Christmann M, Paschke-Kratzin A. Development of a sensitive ELISA for the detection of casein-containing fining agents in red and white wines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:6803-6812. [PMID: 24960632 DOI: 10.1021/jf5006098] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fining of wine with proteinogenic fining agents such as casein from cow's milk is a traditional and commonly used technique all over the world. Casein and other proteins from cow's milk are well-known food allergens, which pose a risk for allergic consumers. Temporary regulations exempting the labeling of milk and products thereof in wine expired. Since July 1, 2012, these fining agents have to be declared on the wine label under Regulation (EU) No. 579/2012 in conjunction to article 120g of Regulation (EU) No. 1234/2007 if exceeding the threshold of 0.25 mg/L allergenic protein. The aim of the presented study was to develop sensitive ELISA methods for the detection of casein in white and red wines and to investigate the risk of allergenic residues in fined wines. In this context it was shown that the used substance for calibration is highly relevant. Casein wine fining agents of different commercial producers were investigated by LDS-PAGE and immunoblot. In addition to casein, they contain other milk proteins, which are potentially allergic and therefore have to be incorporated in the development of antibodies for an ELISA method to be set up. An indirect ELISA for the investigation of white wine was developed. The LOD is 0.1 mg/L. For red wine the LOD is 0.2 mg/L in an indirect sandwich ELISA setup. The LOD of the indirect sandwich ELISA for white wine depends on the calibration standard. It is 0.1 mg/L for the fining agent casein and 0.01 mg/L for casein from a chemical trader. It is also shown that the use of different technological procedures during winemaking leads to no detectable amounts of casein in various wine samples.
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Affiliation(s)
- Marina Deckwart
- Institute for Food Chemistry, Hamburg School of Food Science, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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19
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Slade WO, Werth EG, Chao A, Hicks LM. Phosphoproteomics in photosynthetic organisms. Electrophoresis 2014; 35:3441-51. [PMID: 24825726 DOI: 10.1002/elps.201400154] [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] [Received: 03/21/2014] [Revised: 04/18/2014] [Accepted: 04/29/2014] [Indexed: 02/04/2023]
Abstract
As primarily sessile organisms, photosynthetic species survive in dynamic environments by using elegant signaling pathways to manifest molecular responses to extracellular cues. These pathways exploit phosphorylation of specific amino acids (e.g. serine, threonine, tyrosine), which impact protein structure, function, and localization. Despite substantial progress in implementation of phosphoproteomics to understand photosynthetic organisms, researchers still struggle to translate a biological question into an experimental strategy and vice versa. This review evaluates the current status of phosphoproteomics in photosynthetic organisms and concludes with recommendations based on current knowledge.
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Affiliation(s)
- William O Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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20
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Righetti PG, Fasoli E, D'Amato A, Boschetti E. The "Dark Side" of Food Stuff Proteomics: The CPLL-Marshals Investigate. Foods 2014; 3:217-237. [PMID: 28234315 PMCID: PMC5302364 DOI: 10.3390/foods3020217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 11/17/2022] Open
Abstract
The present review deals with analysis of the proteome of animal and plant-derived food stuff, as well as of non-alcoholic and alcoholic beverages. The survey is limited to those systems investigated with the help of combinatorial peptide ligand libraries, a most powerful technique allowing access to low- to very-low-abundance proteins, i.e., to those proteins that might characterize univocally a given biological system and, in the case of commercial food preparations, attest their genuineness or adulteration. Among animal foods the analysis of cow's and donkey's milk is reported, together with the proteomic composition of egg white and yolk, as well as of honey, considered as a hybrid between floral and animal origin. In terms of plant and fruits, a survey is offered of spinach, artichoke, banana, avocado, mango and lemon proteomics, considered as recalcitrant tissues in that small amounts of proteins are dispersed into a large body of plant polymers and metabolites. As examples of non-alcoholic beverages, ginger ale, coconut milk, a cola drink, almond milk and orgeat syrup are analyzed. Finally, the trace proteome of white and red wines, beer and aperitifs is reported, with the aim of tracing the industrial manipulations and herbal usage prior to their commercialization.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy.
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy.
| | - Alfonsina D'Amato
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy.
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Cilindre C, Fasoli E, D'Amato A, Liger-Belair G, Righetti PG. It's time to pop a cork on champagne's proteome! J Proteomics 2014; 105:351-62. [PMID: 24594285 DOI: 10.1016/j.jprot.2014.02.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/18/2014] [Accepted: 02/20/2014] [Indexed: 11/16/2022]
Abstract
UNLABELLED Champagne is a world-renowned French sparkling wine, which undergoes many steps (fermentation, aging …) for its elaboration. Various compounds might evolve during this winemaking process and thus modify its final quality. Here, we report the first proteome analysis of two standard commercial Champagne wines, using the powerful Combinatorial Peptide Ligand Library (CPLL) technique. Indeed, wine proteins are present in small amounts but they are key compounds, likely to impact on both foam quality and aroma behavior. Forty-three unique gene products were retrieved in a single-varietal champagne and a blended champagne. Several proteins from Vitis vinifera together with seven yeast proteins were undoubtedly identified in these Champagne wines. BIOLOGICAL SIGNIFICANCE The main advantage of CPLLs was the detection of low abundance proteins despite the absence of purification or pre-concentration step. It is an important fact to take into account, since Champagne wines generally contain a low amount of proteins (5-10mg/L) that implies to usually concentrate wine proteins before 1D or 2D electrophoresis. Most Champagne proteins are grape and yeast glycoproteins which are considered as good foam "promoters". Some of these proteins might also interact with wine aromas, and thus contribute to the overall quality of Champagne wines. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Clara Cilindre
- Equipe Effervescence, Champagne et Applications, GSMA UMR CNRS 7331, Université de Reims Champagne Ardenne, Moulin de la Housse, BP 1039, 51687 Reims Cedex 2, France; Laboratoire d'oenologie et chimie appliquée, URVVC EA 4707, Université de Reims Champagne Ardenne, Moulin de la Housse, BP 1039, 51687 Reims Cedex 2, France.
| | - Elisa Fasoli
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, 20131 Milano, Italy
| | - Alfonsina D'Amato
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, 20131 Milano, Italy
| | - Gérard Liger-Belair
- Equipe Effervescence, Champagne et Applications, GSMA UMR CNRS 7331, Université de Reims Champagne Ardenne, Moulin de la Housse, BP 1039, 51687 Reims Cedex 2, France; Laboratoire d'oenologie et chimie appliquée, URVVC EA 4707, Université de Reims Champagne Ardenne, Moulin de la Housse, BP 1039, 51687 Reims Cedex 2, France
| | - Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, 20131 Milano, Italy.
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Abstract
The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience. Detailed methods are described and their pertinence highlighted according to various situations of plant sample origin, size of the sample, and analytical methods intended to be used for protein identifications.
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Losito I, Introna B, Monaci L, Minella S, Palmisano F. Development of a method for the quantification of caseinate traces in Italian commercial white wines based on liquid chromatography-electrospray ionization-ion trap-mass spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:12436-12444. [PMID: 24279401 DOI: 10.1021/jf4034909] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A method using the combination of size exclusion-solid phase extraction and ultrafiltration, followed by tryptic digestion and analysis of the protein digest by liquid chromatography-electrospray ionization-3D ion trap-mass spectrometry (LC-ESI-3D IT-MS), was developed for the detection and quantification of caseinate traces potentially resulting from fining processes in white wines. In particular, several tryptic peptides generated from the main proteins constituting caseinate (β-, αS1-, and αS2-caseins) were used as markers of its presence in the wine matrices; among them, the β-casein peptide GPFPIIV was found to be the best marker for quantification purposes. Method linearity and sensitivity were assessed on a series of Italian commercial white wines, first checked for the absence of any peptide signal attributable to caseins introduced during their production and subsequently spiked with increasing concentrations of caseinate, to provide samples for matrix-matched calibrations. Limits of detection ranging between 0.09 and 0.29 mg/L (S/N = 3), according to the wine, were achieved using a 10 mL sample volume and the MS signal of GPFPIIV as the response related to the caseinate concentration. Such levels are comparable or even lower than the one (0.25 mg/L) recently adopted as a threshold by European Union legislation concerning the indication of milk- and egg-derived fining agents on wine labels, that is, the most restrictive one among those currently proposed in the world.
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Affiliation(s)
- Ilario Losito
- Department of Chemistry, University of Bari "Aldo Moro" , Via Orabona 4, 70126 Bari, Italy
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Monaci L, Losito I, De Angelis E, Pilolli R, Visconti A. Multi-allergen quantification of fining-related egg and milk proteins in white wines by high-resolution mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2009-2018. [PMID: 23939969 DOI: 10.1002/rcm.6662] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/15/2013] [Accepted: 06/20/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE A method based on High-Resolution Mass Spectrometry was developed for the simultaneous determination of fining agents containing potentially allergenic milk (casein) and egg-white (lysozyme and ovalbumin) proteins, added to commercial white wines at sub-ppm levels. Selected tryptic peptides were used as quantitative markers. An evaluation of protein digestion yields was also performed by implementing the (15)N-valine-labelled analogues of the best peptide markers identified for αS1 -casein and ovalbumin. METHODS The method was based on the combination of ultrafiltration (UF) of protein-containing wines, tryptic digestion of the dialyzed wine extracts and liquid chromatography/high resolution mass spectrometry (LC/HRMS) analysis of tryptic digests. Peptides providing the most intense electrospray ionization (ESI)-MS response were chosen as quantitative markers of the proteins under investigation. RESULTS Six-point calibrations were performed by adding caseinate and egg-white powder in the concentration range between 0.25 and 10 µg/mL, to an allergen-free white wine. The following three peptide markers, LTEWTSSNVMEER, GGLEPINFQTAADQAR and ELINSWVESQTNGIIR, were highlighted as best markers for ovalbumin, while GTDVQAWIR and NTDGSTDYGILQINSR for lysozyme and YLGYLEQLLR, GPFPIIV and FFVAPFPEVFGK for caseinate. Limits of detection (LODs) ranged from 0.4 to 1.1 µg/mL. CONCLUSIONS The developed method is suited for assessing the contemporary presence of allergenic milk and egg proteins characterizing egg white and caseinate, fining agents typically employed for wine clarification. The LODs of the method enable the detection of sub-ppm concentrations of residual fining agents, that could represent a potential risk for allergic consumers.
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Affiliation(s)
- Linda Monaci
- Institute of Sciences of Food Production, National Research Council of Italy, Via Amendola 122/O, 70126 Bari, Italy.
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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Fasoli E, Colzani M, Aldini G, Citterio A, Righetti PG. Lemon peel and Limoncello liqueur: A proteomic duet. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1484-91. [DOI: 10.1016/j.bbapap.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/23/2022]
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Artichoke and Cynar liqueur: Two (not quite) entangled proteomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:119-26. [DOI: 10.1016/j.bbapap.2012.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 01/13/2023]
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Esteve C, D'Amato A, Marina ML, García MC, Righetti PG. In-depth proteomic analysis of banana (Musaspp.) fruit with combinatorial peptide ligand libraries. Electrophoresis 2012; 34:207-14. [DOI: 10.1002/elps.201200389] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/27/2012] [Accepted: 09/12/2012] [Indexed: 12/21/2022]
Affiliation(s)
- Clara Esteve
- Department of Analytical Chemistry, Faculty of Chemistry; University of Alcalá; Alcalá de Henares; Madrid; Spain
| | - Alfonsina D'Amato
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; Milan; Italy
| | - María Luisa Marina
- Department of Analytical Chemistry, Faculty of Chemistry; University of Alcalá; Alcalá de Henares; Madrid; Spain
| | - María Concepción García
- Department of Analytical Chemistry, Faculty of Chemistry; University of Alcalá; Alcalá de Henares; Madrid; Spain
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30
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Analysis of commercial wines by LC-MS/MS reveals the presence of residual milk and egg white allergens. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.05.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Esteve C, D'Amato A, Marina ML, García MC, Righetti PG. Identification of avocado (Persea americana) pulp proteins by nano-LC-MS/MS via combinatorial peptide ligand libraries. Electrophoresis 2012; 33:2799-805. [DOI: 10.1002/elps.201200254] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Clara Esteve
- Department of Analytical Chemistry; Faculty of Chemistry; University of Alcalá; Madrid; Spain
| | - Alfonsina D'Amato
- Department of Chemistry; Materials and Chemical Engineering “Giulio Natta”; Milan; Italy
| | - María Luisa Marina
- Department of Analytical Chemistry; Faculty of Chemistry; University of Alcalá; Madrid; Spain
| | - María Concepción García
- Department of Analytical Chemistry; Faculty of Chemistry; University of Alcalá; Madrid; Spain
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Boschetti E, Righetti PG. Breakfast at Tiffany's? Only with a low-abundance proteomic signature! Electrophoresis 2012; 33:2228-39. [DOI: 10.1002/elps.201200003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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33
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Assessment of the floral origin of honey via proteomic tools. J Proteomics 2012; 75:3688-93. [DOI: 10.1016/j.jprot.2012.04.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/20/2012] [Accepted: 04/21/2012] [Indexed: 11/19/2022]
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Fasoli E, D'Amato A, Citterio A, Righetti PG. Anyone for an aperitif? Yes, but only a Braulio DOC with its certified proteome. J Proteomics 2012; 75:3374-9. [DOI: 10.1016/j.jprot.2012.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/12/2012] [Accepted: 04/16/2012] [Indexed: 12/25/2022]
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Fasoli E, D'Amato A, Righetti PG, Barbieri R, Bellavia D. Exploration of the sea urchin coelomic fluid via combinatorial peptide ligand libraries. THE BIOLOGICAL BULLETIN 2012; 222:93-104. [PMID: 22589400 DOI: 10.1086/bblv222n2p93] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The urchin Paracentrotus lividus has been characterized via previous capture and enhancement of low-abundance proteins with combinatorial peptide ligand libraries (CPLL, ProteoMiner). Whereas in the control only 26 unique gene products could be identified, 82 species could be detected after CPLL treatment. Due to the overwhelming presence of two major proteins-the toposome (a highly glycosylated, modified calcium-binding, iron-less transferrin) and the major yolk proteins, belonging to the class of cell adhesion proteins-which constituted about 70% of the proteome of this biological fluid and strongly interfered with the capture of the minority proteome, no additional proteins could be detected. Yet, at present, this constitutes the most thorough investigation of the proteome of this biological fluid.
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Affiliation(s)
- Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Politecnico di Milano, Via Mancinelli 7, Milan, Italy
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Fasoli E, D'Amato A, Citterio A, Righetti PG. Ginger Rogers? No, Ginger Ale and its invisible proteome. J Proteomics 2012; 75:1960-5. [PMID: 22230808 DOI: 10.1016/j.jprot.2011.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/28/2022]
Abstract
The trace proteome of a Ginger drink, stated to be produced with a ginger root extract, has been investigated via capture with combinatorial peptide ligand libraries (ProteoMiner). Although in traces, we could confirm the presence of five grape proteins and one apple protein, but not even the faintest trace of any ginger root proteins. The first two findings are correct, as the producer stated that this beverage had been reinforced with 12% grape juice and 6% apple juice, but the absence of even traces of ginger proteins does not permit the classification of this beverage as a ginger extract on a proteomics scale. However, organoleptic tasting has confirmed the presence of a ginger extract, due to its piquant and tongue-biting taste. Nevertheless, any ginger root extract must be considered as a minor component as compared to the presence of grape and apple juice. At the light of these findings, it is hoped that the competent authorities will in the future make compulsory the proper labelling also of beverages so that all amounts of compounds utilized will be clearly stated in the label, including the presumptive main component.
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Affiliation(s)
- Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
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Esteve C, D'Amato A, Marina ML, García MC, Citterio A, Righetti PG. Identification of olive (Olea europaea) seed and pulp proteins by nLC-MS/MS via combinatorial peptide ligand libraries. J Proteomics 2012; 75:2396-403. [PMID: 22387115 DOI: 10.1016/j.jprot.2012.02.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/11/2012] [Accepted: 02/15/2012] [Indexed: 01/28/2023]
Abstract
Different types of extraction protocols are described for identifying proteins in seed and pulp of olive (Olea europea), by employing both conventional extraction methods and capture with ProteoMiner as well as with in house-made combinatorial peptide ligand libraries (HM-CPLLs) at pH 7.4 and at pH 2.2. Thanks to the use of CPLLs, able to dramatically amplify the signal of low-abundance species, a quite large number of compounds has been indeed identified: 61 in the seed (vs. only four reported in current literature) and 231 in the pulp (vs. 56 described so far), the deepest investigation up to the present of the olive proteome. In the seed, it highlights the presence of seed storage proteins, oleosins and histones. In the pulp, the allergenic thaumatin-like protein (Ole e 13) was confirmed, among the other 231, as the most abundant protein in the olive pulp. The present research has also been undertaken with the aim of identifying proteins in olive oil and ascertaining the relative contribution of seed and pulp proteins in their presence, if any, in oils.
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Affiliation(s)
- Clara Esteve
- Department of Analytical Chemistry, Faculty of Chemistry, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, E-28871 Alcalá de Henares, Madrid, Spain
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38
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Boschetti E, Righetti P. Mixed Beds. ADVANCES IN CHROMATOGRAPHY 2012. [DOI: 10.1201/b11636-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Selvaraju S, Rassi ZE. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis--an update covering the period 2008-2011. Electrophoresis 2012; 33:74-88. [PMID: 22125262 PMCID: PMC3516880 DOI: 10.1002/elps.201100431] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 11/08/2022]
Abstract
This review article expands on the previous one (Jmeian, Y. and El Rassi, Z. Electrophoresis 2009, 30, 249-261) by reviewing pertinent literature in the period extending from early 2008 to the present. Similar to the previous review article, the present one is concerned with proteomic sample preparation (e.g. depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article differs from the first version published in Electrophoresis 2009, 30, 249-261 by expanding on capturing/enriching subglycoproteomics by lectin affinity chromatography. Ninety-eight articles published in the period extending from early 2008 to the present have been reviewed. By no means is this review article exhaustive: its aim is to give a concise report on the latest developments in the field.
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Affiliation(s)
| | - Ziad El Rassi
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071
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40
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D'Amato A, Fasoli E, Righetti PG. Harry Belafonte and the secret proteome of coconut milk. J Proteomics 2012; 75:914-20. [PMID: 22037231 DOI: 10.1016/j.jprot.2011.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/10/2011] [Accepted: 10/13/2011] [Indexed: 12/11/2022]
Affiliation(s)
- Alfonsina D'Amato
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
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Rivers J, Hughes C, McKenna T, Woolerton Y, Vissers JPC, Langridge JI, Beynon RJ. Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library. PLoS One 2011; 6:e28902. [PMID: 22205978 PMCID: PMC3242751 DOI: 10.1371/journal.pone.0028902] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 11/16/2011] [Indexed: 12/04/2022] Open
Abstract
Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method.
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Affiliation(s)
- Jenny Rivers
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Chris Hughes
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - Thérèse McKenna
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - Yvonne Woolerton
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Johannes P. C. Vissers
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - James I. Langridge
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - Robert J. Beynon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Affiliation(s)
- Angelo D’Alessandro
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 - Viterbo, Italy
| | - Lello Zolla
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 - Viterbo, Italy
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Monaci L, Losito I, Palmisano F, Godula M, Visconti A. Towards the quantification of residual milk allergens in caseinate-fined white wines using HPLC coupled with single-stage Orbitrap mass spectrometry. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2011; 28:1304-14. [DOI: 10.1080/19440049.2011.593191] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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D’Amato A, Fasoli E, Kravchuk AV, Righetti PG. Mehercules, adhuc Bacchus! The Debate on Wine Proteomics Continues. J Proteome Res 2011; 10:3789-801. [DOI: 10.1021/pr200266w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alfonsina D’Amato
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milan, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milan, Italy
| | - Alexander V. Kravchuk
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milan, Italy
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milan, Italy
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46
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Fasoli E, D'Amato A, Kravchuk AV, Citterio A, Righetti PG. In-depth proteomic analysis of non-alcoholic beverages with peptide ligand libraries. I: Almond milk and orgeat syrup. J Proteomics 2011; 74:1080-90. [DOI: 10.1016/j.jprot.2011.03.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/11/2011] [Accepted: 03/15/2011] [Indexed: 11/16/2022]
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47
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Simonato B, Mainente F, Tolin S, Pasini G. Immunochemical and mass spectrometry detection of residual proteins in gluten fined red wine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:3101-3110. [PMID: 21375303 DOI: 10.1021/jf104490z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Recently, wheat gluten has been proposed as technological adjuvant in order to clarify wines. However, the possibility that residual gluten proteins remain in treated wines cannot be excluded, representing a hazard for wheat allergic or celiac disease patients. In this work, commercial wheat glutens, in both partially hydrolyzed (GBS-P51) and nonhydrolyzed (Gluvital 21000) forms, were used as fining agents in red wine at different concentrations. Beside immunoenzymatic analyses using anti-gliadin, anti-prolamin antibodies and pooled sera of wheat allergic patients, a method based on liquid chromatography coupled to mass spectrometry has been proposed to detect residues of gluten proteins. Residual gluten proteins were detected by anti-prolamin antibodies, anti-gliadin antibodies and sera-IgE only in the wine treated with GBS-P51 at concentration 50, 150, and 300 g/hL, respectively, whereas no residual proteins were detected by these systems in the wine treated with Gluvital 21000. In contrast liquid chromatography-mass spectrometry analyses allowed the detection of proteins in red wines fined down to 1 g/hL of Gluvital 21000 and GBS-P51. Our results indicate that MS methods are superior to immunochemical methods in detecting gluten proteins in wines and that adverse reactions against gluten treated wines cannot be excluded.
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Affiliation(s)
- Barbara Simonato
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
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48
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D’Amato A, Fasoli E, Kravchuk AV, Righetti PG. Going Nuts for Nuts? The Trace Proteome of a Cola Drink, as Detected via Combinatorial Peptide Ligand Libraries. J Proteome Res 2011; 10:2684-6. [DOI: 10.1021/pr2001447] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alfonsina D’Amato
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano,Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano,Italy
| | - Alexander V. Kravchuk
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano,Italy
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano,Italy
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49
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Boschetti E, Righetti PG. Mixed-bed chromatography as a way to resolve peculiar protein fractionation situations. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:827-35. [DOI: 10.1016/j.jchromb.2011.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 02/28/2011] [Accepted: 03/03/2011] [Indexed: 11/26/2022]
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50
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Righetti PG, Fasoli E, Boschetti E. Combinatorial peptide ligand libraries: The conquest of the ‘hidden proteome’ advances at great strides. Electrophoresis 2011; 32:960-6. [DOI: 10.1002/elps.201000589] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 11/21/2010] [Accepted: 11/21/2010] [Indexed: 12/27/2022]
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