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Leong RZL, Lim LH, Chew YL, Teo SS. de novo transcriptome assembly for discovering gene expressed in Holothuria leucospilota with exposed to copper. Anim Biotechnol 2023; 34:4474-4487. [PMID: 36576030 DOI: 10.1080/10495398.2022.2158094] [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: 12/29/2022]
Abstract
Sea cucumber is a bioremediator as it can composite organic matter and excrete inorganic matter. Sea cucumber has the potential to serve as a bioindicator in marine habitat as they provide an integrated insight into the status of their environment over long periods. Sea cucumbers are sensitive to the organic concentration in the marine environment and can effectively provide an early warning system for any organic contamination that can negatively impact the ecosystem. The availability of a reference transcriptome for sea cucumber would constitute an essential tool for identifying genes involved in crucial steps of the defence pathway. De novo assembly of RNA-seq data enables researchers to study the transcriptomes without needing a genome sequence. In this study, sea cucumbers fed with Kappaphycus alvarezii powder were treated with 0.20 mg/L copper concentration comprehensive transcriptome data containing 75,149 Unigenes, with a total length of 20,460,032 bp. A total of 8820 genes were predicted from the unigenes, annotated, and functionally categorized into 25 functional groups with approximately 20% cluster in signal transduction mechanism. The reference transcriptome presented and validated in this study is meaningful for identifying a wide range of gene(s) related to the bioindication of sea cucumber in a high copper environment.
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Affiliation(s)
| | - Lai Huat Lim
- Faculty of Applied Sciences, UCSI University, W. P. Kuala Lumpur, Malaysia
| | - Yik Ling Chew
- Faculty of Pharmaceutical Sciences, UCSI University, W. P. Kuala Lumpur, Malaysia
| | - Swee Sen Teo
- Faculty of Applied Sciences, UCSI University, W. P. Kuala Lumpur, Malaysia
- Centre of Research for Advanced Aquaculture (CORAA), UCSI University, Kuala Lumpur, Malaysia
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2
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Chien HJ, Zheng YF, Wang WC, Kuo CY, Hsu YM, Lai CC. Determination of adulteration, geographical origins, and species of food by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2273-2323. [PMID: 35652168 DOI: 10.1002/mas.21780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Food adulteration, mislabeling, and fraud, are rising global issues. Therefore, a number of precise and reliable analytical instruments and approaches have been proposed to ensure the authenticity and accurate labeling of food and food products by confirming that the constituents of foodstuffs are of the kind and quality claimed by the seller and manufacturer. Traditional techniques (e.g., genomics-based methods) are still in use; however, emerging approaches like mass spectrometry (MS)-based technologies are being actively developed to supplement or supersede current methods for authentication of a variety of food commodities and products. This review provides a critical assessment of recent advances in food authentication, including MS-based metabolomics, proteomics and other approaches.
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Affiliation(s)
- Han-Ju Chien
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Feng Zheng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ming Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center For Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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3
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Analysis of texture properties and water-soluble fraction proteome of sea cucumber body wall with different boiling heating treatment. Food Chem 2023; 409:135333. [PMID: 36592605 DOI: 10.1016/j.foodchem.2022.135333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Label-free quantitative proteomic analysis was utilized to determine the key proteins that affect texture properties of sea cucumber body wall (SCBW) with different boiling heating treatment. 862, 363, 315, and 258 proteins were confirmed in water-soluble fractions from fresh group, 0.5 h-, 2 h- and 4 h-heat treatment group, respectively. During boiling heating treatment, proteins with an increased abundance in water-soluble fraction primarily belong to structural proteins, such as collagens, microfibril-associated proteins, glycoproteins, and muscle proteins. It was speculated that the degradation of these structural proteins caused the progressive disintegration of network skeleton of collagen fibres and FMs as well as the gelatinization, thus resulted in the decrease of hardness and shear force. Besides, the degradation of FMs was occurred layer by layer during boiling heating treatment, and the fibrilin-1 outer layer degraded first, followed by the fibrilin-2 core component.
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Recent advance in the investigation of aquatic “blue foods” at a molecular level: A proteomics strategy. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Gajahin Gamage NT, Miyashita R, Takahashi K, Asakawa S, Senevirathna JDM. Proteomic Applications in Aquatic Environment Studies. Proteomes 2022; 10:proteomes10030032. [PMID: 36136310 PMCID: PMC9505238 DOI: 10.3390/proteomes10030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
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Affiliation(s)
- Nadeeka Thushari Gajahin Gamage
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Rina Miyashita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jayan Duminda Mahesh Senevirathna
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
- Correspondence:
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Investigation of oyster Crassostrea gigas lipid profile from three sea areas of China based on non-targeted lipidomics for their geographic region traceability. Food Chem 2022; 386:132748. [PMID: 35344724 DOI: 10.1016/j.foodchem.2022.132748] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/20/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022]
Abstract
The present study sought to analyze the lipid profiles of oyster Crassostrea gigas from Yellow Sea (YS), East China Sea, and South China Sea (SCS) through the untargeted lipidomics strategy based on UPLC-Q-Exactive Orbitrap mass spectrometry and multivariate statistics. The results elucidated that geographical differences had profound effects on the lipid content, composition, and lipid molecular profiles. Notably, oysters from the YS group contained the highest lipid content, including triacylglycerol, diacylglycerols, and the majority of phospholipid molecule species, while oysters from the ECS group contained most of the phosphatidylcholine species and the SCS group contained most of the sphingolipid species. Totally, 1155 lipid molecular species belonging to 21 subclasses were identified; of them, 45 lipid molecular species could serve as differential marker for lipid of oysters from different sea areas. Overall, lipidomics could be a potential approach for discrimination of lipid characters between marine shellfishes for geographical origin traceability.
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Luan Y, Dong Y, Duan X, Wang X, Pang Y, Li Q, Gou M. TMT-based quantitative proteomics reveals protein biomarkers from cultured Pacific abalone (Haliotis discus hannai) in different regions. Food Chem X 2022; 14:100355. [PMID: 35693453 PMCID: PMC9184861 DOI: 10.1016/j.fochx.2022.100355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/22/2022] [Accepted: 06/01/2022] [Indexed: 11/07/2022] Open
Abstract
TMT-based proteomics was used to study and compare the muscle protein profiles of Pacific abalones between northern and southern China. 729 differential abundance proteins were identified in different regions. Fatty acid synthase and other 3 proteins were identified as candidate biomarkers for identification of northern and southern abalone.
Due to latitude, the growth cycle of abalone in southern China is significantly lower than that in the northern regions. Therefore, it often occurs merchants use southern abalone to disguise as northern abalone. This study aims to explore the differences in the muscle proteome of Pacific abalone (Haliotis discus hannai) in different regions. A total of 1,569 proteins were detected and 729 proteins were identified as differential abundance proteins (DAPs) in Haliotis discus hannai cultured in Northern (Liaoning Province) and Southern (Fujian Province) China. Bioinformatics analysis revealed and Western blot verified that fatty acid synthase, troponin I, calpain small subunit 1, and myosin light chain 6 are candidate biomarkers for abalone cultured in different regions. This study provides a deeper understanding of how to distinguish which region abalone is harvested from to improve abalone quality controls, and prevent food fraud.
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Comprehensive proteomic analysis of sea cucumbers (Stichopus japonicus) in thermal processing by HPLC-MS/MS. Food Chem 2022; 373:131368. [PMID: 34717088 DOI: 10.1016/j.foodchem.2021.131368] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/11/2021] [Accepted: 10/06/2021] [Indexed: 01/22/2023]
Abstract
Thermal processing is the most frequently adopted processing technology for sea cucumbers, which can significantly affect their protein composition. In this paper, three thermal processing methods high pressure steaming (HPS), atmospheric pressure boiling (APB), and atmospheric pressure steaming (APS) were adopted and protein compositions of both body walls and cooking liquors by thermal processing stichopus japonicus were systematically analysis by proteomic strategy. The total proteins loss rates of body walls were 11.6%, 13.0%, and 14.8% for HPS, APS, and APB methods, respectively. However, the main types of protein composition were retained. Similar mechanisms of protein loss may exist even if different thermal processing were applied. The most frequent hydrolysis sites in thermal processing were phenylalanine, leucine, asparagine, and tyrosine at both C and N terminals. This study provides theoretical guidance for optimizing the industry thermal processing of sea cucumbers.
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Li M, Gao Y, Qi YX, Song ZY, Li ZB, Lin YT, Zhao QC. Assessment of the Nutritional Value of Cultured Sea Cucumber Apostichopus japonicus. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2021. [DOI: 10.1080/10498850.2021.1949769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Meng Li
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
- Liaoning Provincial Aquatic Products Analyzing, Testing and Processing Technology Scientific Service Centre, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yue Gao
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
| | - Yan-xia Qi
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
- Liaoning Provincial Aquatic Products Analyzing, Testing and Processing Technology Scientific Service Centre, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Zhi-yuan Song
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
- Liaoning Provincial Aquatic Products Analyzing, Testing and Processing Technology Scientific Service Centre, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Zhi-bo Li
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
- Liaoning Provincial Aquatic Products Analyzing, Testing and Processing Technology Scientific Service Centre, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yan-tong Lin
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
| | - Qian-cheng Zhao
- College of Food Science and Engineering, Dalian Ocean University, Dalian, China
- Liaoning Provincial Aquatic Products Analyzing, Testing and Processing Technology Scientific Service Centre, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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Martín-Hernández R, Rodríguez-Canul R, Kantún-Moreno N, Olvera-Novoa MA, Medina-Contreras O, Garikoitz-Legarda C, Triviño JC, Zamora-Briseño JA, May-Solis V, Poot-Salazar A, Pérez-Vega JA, Gil-Zamorano J, Grant G, Dávalos A, Olivera-Castillo L. Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus. Int J Mol Sci 2021; 22:ijms22083882. [PMID: 33918680 PMCID: PMC8070510 DOI: 10.3390/ijms22083882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.
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Affiliation(s)
- Roberto Martín-Hernández
- Bioinformatics and Biostatistics Unit, IMDEA Food Institute, CEI UAM+CSIC, Carretera de Cantoblanco 8, 28049 Madrid, Spain;
| | - Rossanna Rodríguez-Canul
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Nuvia Kantún-Moreno
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Miguel A. Olvera-Novoa
- Laboratorio de Nutrición Acuícola, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (M.A.O.-N.); (V.M.-S.)
| | - Oscar Medina-Contreras
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México “Federico Gómez”, Mexico City 06720, Mexico;
| | - Cristobal Garikoitz-Legarda
- Bioinformatics Department, Sistemas Genómicos S.L., Ronda de Guglielmo Marconi 6, 46980 Paterna, Spain; (C.G.-L.); (J.C.T.)
| | - Juan Carlos Triviño
- Bioinformatics Department, Sistemas Genómicos S.L., Ronda de Guglielmo Marconi 6, 46980 Paterna, Spain; (C.G.-L.); (J.C.T.)
| | - Jesús Alejandro Zamora-Briseño
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Víctor May-Solis
- Laboratorio de Nutrición Acuícola, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (M.A.O.-N.); (V.M.-S.)
| | - Alicia Poot-Salazar
- Centro Regional de Investigaciones Acuícola y Pesqueras en Yucalpetén, Instituto Nacional de Pesca y Acuacultura, Boulevard del Pescador S/N, Puerto de Abrigo, Progreso 97320, Yucatán, Mexico;
| | - Juan Antonio Pérez-Vega
- Laboratorio de Inmunología y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (R.R.-C.); (N.K.-M.); (J.A.Z.-B.); (J.A.P.-V.)
| | - Judit Gil-Zamorano
- Laboratory of Epigenetics of Lipid Metabolism, IMDEA Food Institute, CEI UAM+CSIC, Carretera de Cantoblanco 8, 28049 Madrid, Spain;
| | - George Grant
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Correspondence: (G.G.); (A.D.); (L.O.-C.)
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, IMDEA Food Institute, CEI UAM+CSIC, Carretera de Cantoblanco 8, 28049 Madrid, Spain;
- Correspondence: (G.G.); (A.D.); (L.O.-C.)
| | - Leticia Olivera-Castillo
- Laboratorio de Nutrición Acuícola, Centro de Investigación y de Estudios Avanzados del IPN-Unidad Mérida, Antigua Carretera a Progreso Km. 6, Mérida 97310, Yucatán, Mexico; (M.A.O.-N.); (V.M.-S.)
- Correspondence: (G.G.); (A.D.); (L.O.-C.)
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