1
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Chen W, He Y, Fang C, Lu H. A rapid and convenient sample treatment method based on the dissolvable polyacrylamide gel for S-acylation proteomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4590-4598. [PMID: 38920099 DOI: 10.1039/d4ay00937a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Protein S-acylation is an important lipid modification and plays a series of biological functions. As a classic proteomic method for S-acylated proteome analysis, the acyl-biotin exchange and its derivative methods are known to be very labour-intensive and time-consuming all the time, and will result in significant sample loss. Multiple methanol-chloroform precipitations are involved in order to remove the substances that would interfere with enrichment and identification including detergents, the residual reduction and alkylation reagents. Here, we developed a rapid and convenient method for S-acylation proteomics by combining a dissolvable tube gel and the classic ABE method, a Dissolvable Gel based One-Tube sample Treatment method (DGOTT) method. The protein fixation rate, impact of the gel size on analysis performance and feasibility for analyzing complex samples were evaluated. This method enabled the alkylation and chemical substitution reactions to be conducted in a single EP tube, and convenient removal of interferents through gel washing, which could obviously simplify operations and shorten the sample treatment duration. Finally, we identified a total of 1625 potential S-acylated proteins from 800 μg of mouse brain cerebral cortex proteins. We believe that our method could offer potential for high-throughput analysis of protein S-acylation.
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Affiliation(s)
- Weiyu Chen
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Yufei He
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Caiyun Fang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, People's Republic of China
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2
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Ravi Kumar R, Ndiaye MM, Haddad I, Vinh J, Verdier Y. ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia. J Proteome Res 2024; 23:869-880. [PMID: 38353246 PMCID: PMC10913871 DOI: 10.1021/acs.jproteome.3c00288] [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: 05/11/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The metaproteomic approach is an attractive way to describe a microbiome at the functional level, allowing the identification and quantification of proteins across a broad dynamic range as well as the detection of post-translational modifications. However, it remains relatively underutilized, mainly due to technical challenges that should be addressed, including the complexity of extracting proteins from heterogeneous microbial communities. Here, we show that a ChipFilter microfluidic device coupled to a liquid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the identification of microbial proteins. Using cultures of Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow the identification of a higher number of proteins and peptides than that by standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amounts of 16 of these species. These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density. The mass spectrometry data have been deposited on the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD039581.
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Affiliation(s)
- Ranjith
Kumar Ravi Kumar
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Massamba Mbacke Ndiaye
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Iman Haddad
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Joelle Vinh
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Yann Verdier
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
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3
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A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications. J Proteomics 2022; 261:104576. [DOI: 10.1016/j.jprot.2022.104576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/20/2022]
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4
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André MR, Neupane P, Lappin M, Herrin B, Smith V, Williams TI, Collins L, Bai H, Jorge GL, Balbuena TS, Bradley J, Maggi RG, Breitschwerdt EB. Using Proteomic Approaches to Unravel the Response of Ctenocephalides felis felis to Blood Feeding and Infection With Bartonella henselae. Front Cell Infect Microbiol 2022; 12:828082. [PMID: 35155282 PMCID: PMC8831700 DOI: 10.3389/fcimb.2022.828082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/07/2022] [Indexed: 01/19/2023] Open
Abstract
Among the Ctenocephalides felis felis-borne pathogens, Bartonella henselae, the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of B. henselae as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect. Even though recent developments in vector and pathogen -omics have advanced the understanding of the genetic factors and molecular pathways involved at the tick-pathogen interface, leading to discovery of candidate protective antigens, only a few studies have focused on the interaction between fleas and flea-borne pathogens. Taking into account the period of time needed for B. henselae replication in flea digestive tract, the present study investigated flea-differentially abundant proteins (FDAP) in unfed fleas, fleas fed on uninfected cats, and fleas fed on B. henselae-infected cats at 24 hours and 9 days after the beginning of blood feeding. Proteomics approaches were designed and implemented to interrogate differentially expressed proteins, so as to gain a better understanding of proteomic changes associated with the initial B. henselae transmission period (24 hour timepoint) and a subsequent time point 9 days after blood ingestion and flea infection. As a result, serine proteases, ribosomal proteins, proteasome subunit α-type, juvenile hormone epoxide hydrolase 1, vitellogenin C, allantoinase, phosphoenolpyruvate carboxykinase, succinic semialdehyde dehydrogenase, glycinamide ribotide transformylase, secreted salivary acid phosphatase had high abundance in response of C. felis blood feeding and/or infection by B. henselae. In contrast, high abundance of serpin-1, arginine kinase, ribosomal proteins, peritrophin-like protein, and FS-H/FSI antigen family member 3 was strongly associated with unfed cat fleas. Findings from this study provide insights into proteomic response of cat fleas to B. henselae infected and uninfected blood meal, as well as C. felis response to invading B. henselae over an infection time course, thus helping understand the complex interactions between cat fleas and B. henselae at protein levels.
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Affiliation(s)
- Marcos Rogério André
- Laboratory of Immunoparasitology, Department of Pathology, Reproduction and One Health, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV/UNESP), Jaboticabal, Brazil
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Pradeep Neupane
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Michael Lappin
- Department of Clinical Sciences, Center for Companion Animal Studies, Colorado State University, Fort Collins, CO, United States
| | - Brian Herrin
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Vicki Smith
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Taufika Islam Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, United States
| | - Leonard Collins
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, United States
| | - Hongxia Bai
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, United States
| | - Gabriel Lemes Jorge
- Departmento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV/UNESP), Jaboticabal, Brazil
| | - Tiago Santana Balbuena
- Departmento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV/UNESP), Jaboticabal, Brazil
| | - Julie Bradley
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Ricardo G. Maggi
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Edward B. Breitschwerdt
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Edward B. Breitschwerdt,
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5
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Do T, Guran R, Adam V, Zitka O. Use of MALDI-TOF mass spectrometry for virus identification: a review. Analyst 2022; 147:3131-3154. [DOI: 10.1039/d2an00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.
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Affiliation(s)
- Tomas Do
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Roman Guran
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
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6
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Nunes MDGP, Pizzutti IR, Brackmann A, Reichert B, Zorzella Fontana ME, Duarte Dos Santos I, Cuti LK, Jänisch BD, Panciera MP, Ludwig V, Cardoso CD. Multimycotoxin Determination in Grains: A Comprehensive Study on Method Validation and Assessment of Effectiveness of Controlled Atmosphere Storage in Preventing Mycotoxin Contamination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11440-11450. [PMID: 34520209 DOI: 10.1021/acs.jafc.1c03208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two simple and low-cost QuEChERS approaches were optimized and validated for multimycotoxin determination in grains by UPLC-MS/MS and applied to assess effectiveness of controlled atmosphere (CA) storage in preventing mycotoxin contamination. Common bean, soybean, and maize samples were stored for 6 months. CA treatments were conducted varying O2 and CO2 partial pressures, temperatures, and moisture contents of the chambers. In the validation study for common bean and maize, 8 out of 11 mycotoxins were successfully validated. For soybean, 10 out of 11 mycotoxins were validated. Aflatoxin B1 was detected in all commodities. Statistical tests suggest that storage temperature played a key role in aflatoxin B1 concentrations in common bean and soybean, but had no influence on maize. Maize was also positive for fumonisins B1 and B2. Differences in fumonisin concentrations were not significant among different treatments. Concentrations of aflatoxin B1 in some samples exceeded legislation's maximum levels. Thus, some of the CA treatments applied were effective in preventing mycotoxin contamination in common bean and soybean but were not effective for maize.
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Affiliation(s)
- Maria da Graça Pereira Nunes
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Ionara Regina Pizzutti
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Auri Brackmann
- Plant Science Department, Postharvest Research Center, Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Bárbara Reichert
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Marlos Eduardo Zorzella Fontana
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Ingrid Duarte Dos Santos
- Department of Technology and Food Science, Federal University of Santa Maria (UFSM), 97015-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Lisandra Kopp Cuti
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Bárbara Daiana Jänisch
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Matheus Pelizzaro Panciera
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Vagner Ludwig
- Plant Science Department, Postharvest Research Center, Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Carmem Dickow Cardoso
- Chemistry Department, Center of Research and Analysis of Residues and Contaminants (CEPARC), Federal University of Santa Maria (UFSM), 97105-900 Santa Maria, Rio Grande do Sul, Brazil
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7
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Pérez-Rodriguez S, Wulff T, Voldborg BG, Altamirano C, Trujillo-Roldán MA, Valdez-Cruz NA. Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. ACS OMEGA 2021; 6:12439-12458. [PMID: 34056395 PMCID: PMC8154153 DOI: 10.1021/acsomega.0c06030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 05/11/2023]
Abstract
Different cellular processes that contribute to protein production in Chinese hamster ovary (CHO) cells have been previously investigated by proteomics. However, although the classical secretory pathway (CSP) has been well documented as a bottleneck during recombinant protein (RP) production, it has not been well represented in previous proteomic studies. Hence, the significance of this pathway for production of RP was assessed by identifying its own proteins that were associated to changes in RP production, through subcellular fractionation coupled to shot-gun proteomics. Two CHO cell lines producing a monoclonal antibody with different specific productivities were used as cellular models, from which 4952 protein groups were identified, which represent a coverage of 59% of the Chinese hamster proteome. Data are available via ProteomeXchange with identifier PXD021014. By using SAM and ROTS algorithms, 493 proteins were classified as differentially expressed, of which about 80% was proposed as novel targets and one-third were assigned to the CSP. Endoplasmic reticulum (ER) stress, unfolded protein response, calcium homeostasis, vesicle traffic, glycosylation, autophagy, proteasomal activity, protein synthesis and translocation into ER lumen, and secretion of extracellular matrix components were some of the affected processes that occurred in the secretory pathway. Processes from other cellular compartments, such as DNA replication, transcription, cytoskeleton organization, signaling, and metabolism, were also modified. This study gives new insights into the molecular traits of higher producer cells and provides novel targets for development of new sub-lines with improved phenotypes for RP production.
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Affiliation(s)
- Saumel Pérez-Rodriguez
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Tune Wulff
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Bjørn G. Voldborg
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Claudia Altamirano
- Laboratorio
de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085 Valparaíso, Chile
| | - Mauricio A. Trujillo-Roldán
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
| | - Norma A. Valdez-Cruz
- Programa
de Investigación de Producción de Biomoléculas,
Departamento de Biología Molecular y Biotecnología,
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán 04510 Ciudad de
México, México
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8
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Alahmad W, Kraiya C, Varanusupakul P, Tabani H, Varanusupakul P. Gel electromembrane microextraction followed by ion chromatography for direct determination of iodine in supplements and fortified food samples: Green chemistry for food analysis. Food Chem 2021; 358:129857. [PMID: 33940293 DOI: 10.1016/j.foodchem.2021.129857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/13/2021] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
In this study, a sensitive, selective, and environmentally friendly analytical method for direct extraction and preconcentration of iodine was developed. Iodine, as an iodate ion or iodide ion, was simultaneously extracted and preconcentrated by gel electromembrane microextraction (G-EME) and analyzed for total iodine by ion chromatography. The total iodine was determined by combining the peak areas of both iodate and iodide ions. Under the optimized conditions, linear calibration for iodine using a mixture of iodate and iodide ions was obtained from 10 to 100 µg L-1 (r2 > 0.996). The detection limit was 7.0 µg L-1. Recoveries of spiked iodine (as iodate) in the samples were greater than 90%. The method was applied for the determination of iodine in dietary supplements and fortified food samples, i.e., iodine-enriched eggs. Our developed method could be directly applied for the determination of iodine in different matrix samples including eggs without a pretreatment step.
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Affiliation(s)
- Waleed Alahmad
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Charoenkwan Kraiya
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; Electrochemistry and Optical Spectroscopy Center of Excellence, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Hadi Tabani
- Department of Environmental Geology, Research Institute of Applied Sciences (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Pakorn Varanusupakul
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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