1
|
Franck N, Vera Candioti L, Gerlero GS, Urteaga R, Kler PA. A simple method for the assessment of electrophoretic mobility in porous media. Electrophoresis 2024; 45:589-598. [PMID: 37853649 DOI: 10.1002/elps.202300180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Developing paper-based electrophoretic methods involve dealing with significant uncertainty levels when compared to their capillary counterparts. Critical information for developing these kinds of methods are the electrophoretic mobility of background electrolytes and samples. This work presents the design and characterization of a device for measuring the electrophoretic mobilities of dyes in porous media. The device was developed with the aim of validating a previously presented model and also proposing a protocol for the straightforward determination of electrophoretic mobilities in porous media when open-channel values are already known. Whatman #1 paper was used as a model substrate as far as it is the most common porous medium substrate for paper-based electrophoresis. The device was designed using a numerical simulation-assisted approach, utilizing OpenFOAM® and specific solvers for capillary transport and electromigration, namely porousMicroTransport and electroMicroTransport, respectively. The electrophoretic mobilities of five dyes were analyzed experimentally with the proposed device. To establish appropriate comparative values at different pHs, experiments in fused silica capillaries were also performed. An effective parameter model for describing the electrophoretic behavior of dyes in porous media, that is, the constriction factor, was found consistent with previous reports for the Whatman #1 paper. This consistency was found after considering (via direct measurements) the chromatographic effect of the medium over each dye. Consequently, the recorded values hold significant worth due to their potential for direct application in designing new experiments or devices in Whatman #1 paper. With the validation of the model through the experiments with the proposed device, those researchers interested on developing electrophoretic methods in porous substrates can make use of the open-channel electrophoretic mobilities reported in the literature, or in the well-known software databases, and correct them for the media of interest just by performing two simple characterization steps.
Collapse
Affiliation(s)
- Nicolás Franck
- Centro de Investigación en Métodos Computacionales (CIMEC, UNL-CONICET), Santa Fe, Argentina
- Instituto de Física del Litoral (IFIS Litoral, UNL-CONICET), Santa Fe, Argentina
| | - Luciana Vera Candioti
- Departamento de Ciencias Biológicas, Cátedra de Bromatología y Nutrición-(FBCB,UNL-CONICET), Ciudad Universitaria, Santa Fe, Argentina
| | - Gabriel S Gerlero
- Centro de Investigación en Métodos Computacionales (CIMEC, UNL-CONICET), Santa Fe, Argentina
- Universidad Nacional de Rafaela, Rafaela, Santa Fe, Argentina
| | - Raúl Urteaga
- Instituto de Física del Litoral (IFIS Litoral, UNL-CONICET), Santa Fe, Argentina
| | - Pablo A Kler
- Centro de Investigación en Métodos Computacionales (CIMEC, UNL-CONICET), Santa Fe, Argentina
- Departamento de Ingeniería en Sistemas de Información, FRSF-UTN, Lavaise, Santa Fe, Argentina
| |
Collapse
|
2
|
Analysis of flavonoids in citrus fruits by capillary zone electrophoresis coupled with quadrupole time-of-flight mass spectrometry using chemometrics. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
Aiello D, Siciliano C, Mazzotti F, Di Donna L, Risoluti R, Napoli A. Protein Extraction, Enrichment and MALDI MS and MS/MS Analysis from Bitter Orange Leaves ( Citrus aurantium). Molecules 2020; 25:molecules25071485. [PMID: 32218285 PMCID: PMC7181213 DOI: 10.3390/molecules25071485] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Citrus aurantium is a widespread tree in the Mediterranean area, and it is mainly used as rootstock for other citrus. In the present study, a vacuum infiltration centrifugation procedure, followed by solid phase extraction matrix-assisted laser desorption ionization tandem mass spectrometry (SPE MALDI MS/MS) analysis, was adopted to isolate proteins from leaves. The results of mass spectrometry (MS) profiling, combined with the top-down proteomics approach, allowed the identification of 78 proteins. The bioinformatic databases TargetP, SignalP, ChloroP, WallProtDB, and mGOASVM-Loc were used to predict the subcellular localization of the identified proteins. Among 78 identified proteins, 20 were targeted as secretory pathway proteins and 36 were predicted to be in cellular compartments including cytoplasm, nucleus, and cell membrane. The largest subcellular fraction was the secretory pathway, accounting for 25% of total proteins. Gene Ontology (GO) of Citrus sinensis was used to simplify the functional annotation of the proteins that were identified in the leaves. The Kyoto Encyclopedia of Genes and Genomes (KEGG) showed the enrichment of metabolic pathways including glutathione metabolism and biosynthesis of secondary metabolites, suggesting that the response to a range of environmental factors is the key processes in citrus leaves. Finally, the Lipase GDSL domain-containing protein GDSL esterase/lipase, which is involved in plant development and defense response, was for the first time identified and characterized in Citrus aurantium.
Collapse
Affiliation(s)
- Donatella Aiello
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.A.); (F.M.); (L.D.D.)
| | - Carlo Siciliano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy;
| | - Fabio Mazzotti
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.A.); (F.M.); (L.D.D.)
| | - Leonardo Di Donna
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.A.); (F.M.); (L.D.D.)
| | - Roberta Risoluti
- Department of Chemistry, Università degli Studi di Roma La Sapienza, 00185 Rome, Italy;
| | - Anna Napoli
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.A.); (F.M.); (L.D.D.)
- Correspondence: ; Tel.: +39-0984-492-852
| |
Collapse
|
4
|
Faddetta T, Abbate L, Renzone G, Palumbo Piccionello A, Maggio A, Oddo E, Scaloni A, Puglia AM, Gallo G, Carimi F, Fatta Del Bosco S, Mercati F. An integrated proteomic and metabolomic study to evaluate the effect of nucleus-cytoplasm interaction in a diploid citrus cybrid between sweet orange and lemon. PLANT MOLECULAR BIOLOGY 2018; 98:407-425. [PMID: 30341661 DOI: 10.1007/s11103-018-0787-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Our results provide a comprehensive overview how the alloplasmic condition might lead to a significant improvement in citrus plant breeding, developing varieties more adaptable to a wide range of conditions. Citrus cybrids resulting from somatic hybridization hold great potential in plant improvement. They represent effective products resulting from the transfer of organelle-encoded traits into cultivated varieties. In these cases, the plant coordinated array of physiological, biochemical, and molecular functions remains the result of integration among different signals, which derive from the compartmentalized genomes of nucleus, plastids and mitochondria. To dissect the effects of genome rearrangement into cybrids, a multidisciplinary study was conducted on a diploid cybrid (C2N), resulting from a breeding program aimed to improve interesting agronomical traits for lemon, the parental cultivars 'Valencia' sweet orange (V) and 'femminello' lemon (F), and the corresponding somatic allotetraploid hybrid (V + F). In particular, a differential proteomic analysis, based on 2D-DIGE and MS procedures, was carried out on leaf proteomes of C2N, V, F and V + F, using the C2N proteome as pivotal condition. This investigation revealed differentially represented protein patterns that can be associated with genome rearrangement and cell compartment interplay. Interestingly, most of the up-regulated proteins in the cybrid are involved in crucial biological processes such as photosynthesis, energy production and stress tolerance response. The cybrid differential proteome pattern was concomitant with a general increase of leaf gas exchange and content of volatile organic compounds, highlighting a stimulation of specific pathways that can be related to observed plant performances. Our results contribute to a better understanding how the alloplasmic condition might lead to a substantial improvement in plant breeding, opening new opportunities to develop varieties more adaptable to a wide range of conditions.
Collapse
Affiliation(s)
- Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
- Advanced Technologies Network (ATeN) Center, University of Palermo, Palermo, Italy
| | - Loredana Abbate
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Giovanni Renzone
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Antonella Maggio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Elisabetta Oddo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
- Advanced Technologies Network (ATeN) Center, University of Palermo, Palermo, Italy
| | - Francesco Carimi
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Sergio Fatta Del Bosco
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy.
| |
Collapse
|
5
|
Kumar M, Singh R, Meena A, Patidar BS, Prasad R, Chhabra SK, Bansal SK. An Improved 2-Dimensional Gel Electrophoresis Method for Resolving Human Erythrocyte Membrane Proteins. PROTEOMICS INSIGHTS 2017; 8:1178641817700880. [PMID: 28469466 PMCID: PMC5398320 DOI: 10.1177/1178641817700880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Abstract
The 2-dimensional gel electrophoresis (2-DE) technique is widely used for the analysis of complex protein mixtures extracted from biological samples. It is one of the most commonly used analytical techniques in proteomics to study qualitative and quantitative protein changes between different states of a cell or an organism (eg, healthy and diseased), conditionally expressed proteins, posttranslational modifications, and so on. The 2-DE technique is used for its unparalleled ability to separate thousands of proteins simultaneously. The resolution of the proteins by 2-DE largely depends on the quality of sample prepared during protein extraction which increases results in terms of reproducibility and minimizes protein modifications that may result in artifactual spots on 2-DE gels. The buffer used for the extraction and solubilization of proteins influences the quality and reproducibility of the resolution of proteins on 2-DE gel. The purification by cleanup kit is another powerful process to prevent horizontal streaking which occurs during isoelectric focusing due to the presence of contaminants such as salts, lipids, nucleic acids, and detergents. Erythrocyte membrane proteins serve as prototypes for multifunctional proteins in various erythroid and nonerythroid cells. In this study, we therefore optimized the selected major conditions of 2-DE for resolving various proteins of human erythrocyte membrane. The modification included the optimization of conditions for sample preparation, cleanup of protein sample, isoelectric focusing, equilibration, and storage of immobilized pH gradient strips, which were further carefully examined to achieve optimum conditions for improving the quality of protein spots on 2-DE gels. The present improved 2-DE analysis method enabled better detection of protein spots with higher quality and reproducibility. Therefore, the conditions established in this study may be used for the 2-DE analysis of erythrocyte membrane proteins for different diseases, which may help to identify the proteins that may serve as markers for diagnostics as well as targets for development of new therapeutic potential.
Collapse
Affiliation(s)
- Manoj Kumar
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Singh
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Anil Meena
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Bhagwan S Patidar
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Prasad
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.,A28, Sector 3, Aliganj, Lucknow, UP, India
| | - Sunil K Chhabra
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.,Department of Pulmonary, Sleep and Critical Care Medicine, Primus Super Speciality Hospital, Chanakyapuri, New Delhi, India
| | - Surendra K Bansal
- Department of Biochemistry, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| |
Collapse
|
6
|
Enzyme-assisted extraction of proteins from Citrus fruits and prediction of their cultivar using protein profiles obtained by capillary gel electrophoresis. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.07.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
7
|
Kazemipour N, Salehi Inchebron M, Valizadeh J, Sepehrimanesh M. Clotting characteristics of milk by Withania coagulans: Proteomic and biochemical study. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2016. [DOI: 10.1080/10942912.2016.1207664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
8
|
|
9
|
Fukao Y, Ferjani A, Fujiwara M, Nishimori Y, Ohtsu I. Identification of Zinc-Responsive Proteins in the Roots of Arabidopsis thaliana Using a Highly Improved Method of Two-Dimensional Electrophoresis. ACTA ACUST UNITED AC 2009; 50:2234-9. [DOI: 10.1093/pcp/pcp154] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
10
|
Maserti BE, Della Croce CM, Luro F, Morillon R, Cini M, Caltavuturo L. A general method for the extraction of citrus leaf proteins and separation by 2D electrophoresis: A follow up. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:351-6. [PMID: 17035105 DOI: 10.1016/j.jchromb.2006.09.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 09/11/2006] [Accepted: 09/18/2006] [Indexed: 11/24/2022]
Abstract
With the aim of studying differentially expressed proteins as a function of abiotic and biotic stress in citrus plants, we optimized a protocol for the extraction of total leaf proteins and their 2-DE separation using commercially available immobilized pH gradient strips (IPGs) in the first dimension. Critical factors for good reproducibility of citrus leaf protein separation were identified: trichloroacetic acid (TCA)/acetone precipitation after extraction in lysis buffer, sample fractionation on narrow range overlapping IPGs and sample-cup loading at the anodic or cathodic end of the strip. The use of thiourea and a strong detergent (C7BzO) in the solubilization/rehydration buffer, coupled with the increase to 10% of SDS in the equilibration buffer before the second dimension seemed to affect positively the resolution of basic proteins. Using our protocol we resolved about 30 basic proteins on 6.3-8.3 pH range strips. Further, our protocol was successfully applied reproducibly on the analysis of control and salt exposed leaf samples of Citrus reshni Hort. Ex Tan.
Collapse
Affiliation(s)
- B E Maserti
- National Research Council (CNR)-Institute of Biophysics (IBF), CNR Research Area, Via Moruzzi 1, 56124 Pisa, Italy.
| | | | | | | | | | | |
Collapse
|
11
|
Rehan M, Younus H. Effect of organic solvents on the conformation and interaction of catalase and anticatalase antibodies. Int J Biol Macromol 2006; 38:289-95. [PMID: 16677702 DOI: 10.1016/j.ijbiomac.2006.03.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 03/22/2006] [Accepted: 03/22/2006] [Indexed: 11/28/2022]
Abstract
Effect of six organic solvents-methanol, ethanol, propanol, dimethyl sulphoxide (DMSO), N,N-dimethyl formamide (DMF), and glycerol on the conformation and interaction of catalase and anticatalase antibodies were studied with the aim of identifying the solvents in which antigen-antibody interactions are strong. The antigen binding activity of the antibodies in the various organic solvents increased in the following order: ethanol<methanol<no organic solvent<propanol<DMSO<DMF<glycerol. The structure of both the antibody and the antigen molecule was affected significantly in 40% concentration of the organic solvents used in this study. Catalase activity was inhibited in DMSO. However, the enzyme was activated in DMF upto about 50% of its concentration.
Collapse
Affiliation(s)
- Mohd Rehan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | | |
Collapse
|
12
|
Current awareness in phytochemical analysis. PHYTOCHEMICAL ANALYSIS : PCA 2006; 17:134-41. [PMID: 16634291 DOI: 10.1002/pca.881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
|