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He Y, Ye G, Chi S, Tan B, Dong X, Yang Q, Liu H, Zhang S. Integrative Transcriptomic and Small RNA Sequencing Reveals Immune-Related miRNA-mRNA Regulation Network for Soybean Meal-Induced Enteritis in Hybrid Grouper, Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂. Front Immunol 2020; 11:1502. [PMID: 32903657 PMCID: PMC7438716 DOI: 10.3389/fimmu.2020.01502] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
A 10-week feeding experiment was conducted to reveal the immune mechanism for soybean meal-induced enteritis (SBMIE) in hybrid grouper, Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂. Four isonitrogenous and isolipidic diets were formulated by replacing 0, 10, 30, and 50% fish meal protein with soybean meal (namely FM, SBM10, SBM30, and SBM50, respectively). The weight gain rate of the SBM50 group was significantly lower than those of the other groups. Plica height, muscular layer thickness, and goblet cells of the distal intestine in the SBM50 group were much lower than those in the FM group. The intestinal transcriptomic data, including the transcriptome and miRNAome, showed that a total of 6,390 differentially expressed genes (DEGs) and 92 DEmiRNAs were identified in the SBM50 and FM groups. DEmiRNAs (10 known and 1 novel miRNAs) and their DE target genes were involved in immune-related phagosome, natural killer cell-mediated cytotoxicity, Fc gamma R-mediated phagocytosis, and the intestinal immune network for IgA production pathways. Our study is the first to offer transcriptomic and small RNA profiling for SBMIE in hybrid grouper. Our findings offer important insights for the understanding of the RNA profile and further elucidation of the underlying molecular immune mechanism for SBMIE in carnivorous fish.
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Affiliation(s)
- Yuanfa He
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Guanlin Ye
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Shuyan Chi
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangdong Ocean University, Zhanjiang, China
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Xiaohui Dong
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Qihui Yang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Hongyu Liu
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
| | - Shuang Zhang
- Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Aquatic Animals Precision Nutrition and High-Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, China
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Estruch G, Martínez-Llorens S, Tomás-Vidal A, Monge-Ortiz R, Jover-Cerdá M, Brown PB, Peñaranda DS. Impact of high dietary plant protein with or without marine ingredients in gut mucosa proteome of gilthead seabream (Sparus aurata, L.). J Proteomics 2020; 216:103672. [PMID: 32004726 DOI: 10.1016/j.jprot.2020.103672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/23/2019] [Accepted: 01/26/2020] [Indexed: 02/08/2023]
Abstract
The digestive tract, particularly the intestine, represents one of the main sites of interactions with the environment, playing the gut mucosa a crucial role in the digestion and absorption of nutrients, and in the immune defence. Previous researches have proven that the fishmeal replacement by plant sources could have an impact on the intestinal status at both digestive and immune level, compromising relevant productive parameters, such as feed efficiency, growth or survival. In order to evaluate the long-term impact of total fishmeal replacement on intestinal mucosa, the gut mucosa proteome was analysed in fish fed with a fishmeal-based diet, against plant protein-based diets with or without alternative marine sources inclusion. Total fishmeal replacement without marine ingredients inclusion, reported a negative impact in growth and biometric parameters, further an altered gut mucosa proteome. However, the inclusion of a low percentage of marine ingredients in plant protein-based diets was able to maintain the growth, biometrics parameters and gut mucosa proteome with similar values to FM group. A total fishmeal replacement induced a big set of underrepresented proteins in relation to several biological processes such as intracellular transport, assembly of cellular macrocomplex, protein localization and protein catabolism, as well as several molecular functions, mainly related with binding to different molecules and the maintenance of the cytoskeleton structure. The set of downregulated proteins also included molecules which have a crucial role in the maintenance of the normal function of the enterocytes, and therefore, of the epithelium, including permeability, immune and inflammatory response regulation and nutritional absorption. Possibly, the amino acid imbalance presented in VM diet, in a long-term feeding, may be the main reason of these alterations, which can be prevented by the inclusion of 15% of alternative marine sources. SIGNIFICANCE: Long-term feeding with plant protein based diets may be considered as a stress factor and lead to a negative impact on digestive and immune system mechanisms at the gut, that can become apparent in a reduced fish performance. The need for fishmeal replacement by alternative ingredients such as plant sources to ensure the sustainability of the aquaculture sector has led the research assessing the intestinal status of fish to be of increasing importance. This scientific work provides further knowledge about the proteins and biologic processes altered in the gut in response to plant protein based diets, suggesting the loss of part of gut mucosa functionality. Nevertheless, the inclusion of alternative marine ingredients was able to reverse these negative effects, showing as a feasible option to develop sustainable aquafeeds.
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Affiliation(s)
- Guillem Estruch
- Aquaculture and Biodiversity Research Group, Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Silvia Martínez-Llorens
- Aquaculture and Biodiversity Research Group, Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ana Tomás-Vidal
- Aquaculture and Biodiversity Research Group, Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Raquel Monge-Ortiz
- Aquaculture and Biodiversity Research Group, Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Miguel Jover-Cerdá
- Aquaculture and Biodiversity Research Group, Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Paul B Brown
- Department of Forestry and Natural Resources, Purdue University, 715 West State Street, 47907 West Lafayette, IN, USA
| | - David S Peñaranda
- Aquaculture and Biodiversity Research Group, Institute of Science and Animal Technology, (ICTA), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain.
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Kumar G, Hummel K, Razzazi-Fazeli E, El-Matbouli M. Modulation of posterior intestinal mucosal proteome in rainbow trout (Oncorhynchus mykiss) after Yersinia ruckeri infection. Vet Res 2019; 50:54. [PMID: 31315687 PMCID: PMC6637484 DOI: 10.1186/s13567-019-0673-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/05/2019] [Indexed: 11/13/2022] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease in salmonids. In fish, the intestine represents an important site of nutrient uptake, host–pathogen interactions, and defense. The posterior intestine can be inflamed, reddened, and filled with an opaque, yellowish fluid during Y. ruckeri infection. Herein, we report an investigation on the proteome alteration in the posterior intestinal mucosa of rainbow trout (Oncorhynchus mykiss) after exposure to Y. ruckeri. The intestinal mucosal proteins were identified and quantified by a shotgun proteomic approach by applying data-independent quantification with sequential windowed acquisition of all theoretical mass spectra (SWATH). A total of 437 proteins were found to be differentially up- or downregulated in the posterior intestine. Gene ontology of upregulated proteins pointed to their involvement into exopeptidase, endopeptidase, and hydrolase activities, while the downregulated proteins were involved in lipid metabolism, actin binding, and translation processes. Additionally, upregulated proteins were predicted to be involved in lysosome, oxidative phosphorylation, and metabolic pathways, while downregulated proteins were implicated in focal adhesion, regulation of actin cytoskeleton, protein digestion and absorption pathways. This study showed that Y. ruckeri infection can alter protein abundance involved in serine-type carboxypeptidase, cysteine and aspartic-type endopeptidases, metallopeptidases, antioxidant defense, calcium ion binding, glycolytic and carbohydrate metabolic processes in the proteome of the intestinal mucosa of rainbow trout.
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Affiliation(s)
- Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria.
| | - Karin Hummel
- VetCore Facility for Research/Proteomics Unit, University of Veterinary Medicine, Vienna, Austria
| | - Ebrahim Razzazi-Fazeli
- VetCore Facility for Research/Proteomics Unit, University of Veterinary Medicine, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
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Effects of Graded Dietary Inclusion Level of Full-Fat Hermetia illucens Prepupae Meal in Practical Diets for Rainbow Trout ( Oncorhynchus mykiss). Animals (Basel) 2019; 9:ani9050251. [PMID: 31108939 PMCID: PMC6562532 DOI: 10.3390/ani9050251] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/09/2019] [Accepted: 05/12/2019] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The sustainability of fish production is mainly driven by the protein source used in aquafeeds. In conventional fish feed, protein sources are mostly vegetable ingredients and fishmeal. The present study explored the potential use of full-fat Hermetia illucens prepupae meal (H) replacing 0% (H0), 25% (H25), and 50% (H50) conventional ingredients in practical diets for rainbow trout. No significant differences in growth were observed in all experimental groups, while in fish fed the H50 diet both hepatic and intestinal alterations were detected. In addition, in the same fish group, genes related to stress and immune-response were significantly up-regulated. The results obtained so far highlighted an overall physiological adaptation of fish to the dietary manipulation, suggesting an adverse effect of full-fat H at the highest inclusion level. Abstract This study investigated the effects of dietary inclusion levels of full-fat Hermetia illucens prepupae meal (H) on growth and gastrointestinal integrity in rainbow trout (Oncorhynchus mykiss). A 98-day study was conducted using triplicate groups of trout (initial body weight, 137 ± 10.5 g) kept in 1-m3 tanks in a flow-through well water system. Three dietary treatments were prepared: one based on fishmeal and purified protein-rich vegetable ingredients (H0), and two experimental diets including graded levels of H meal (25% and 50%, referred to as H25 and H50, respectively). At the end of the feeding trial, no differences were observed in growth performance and plasma metabolite levels, with the biometric data confirmed by the liver expression of the genes involved in somatic growth regulation (igf1 and mstn1a). In the H50 group, a three-fold up regulation of liver hsp70 was observed. An activation of the stress/immune response (il-10, tnf-α, and tlr-5) was observed in medium intestine in the H25 and H50 groups (p < 0.05) together with a villi length reduction detected through histological analyses. Liver histology and Fourier Transform Infrared Imaging (FTIRI) spectroscopy highlighted an increase in lipid deposition. These findings suggest that caution should be taken into account when 50% replacement of conventional ingredients with H is selected.
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Salinas I, Magadán S. Omics in fish mucosal immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:99-108. [PMID: 28235585 DOI: 10.1016/j.dci.2017.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 05/22/2023]
Abstract
The mucosal immune system of fish is a complex network of immune cells and molecules that are constantly surveilling the environment and protecting the host from infection. A number of "omics" tools are now available and utilized to understand the complexity of mucosal immune systems in non-traditional animal models. This review summarizes recent advances in the implementation of "omics" tools pertaining to the four mucosa-associated lymphoid tissues in teleosts. Genomics, transcriptomics, proteomics, and "omics" in microbiome research require interdisciplinary collaboration and careful experimental design. The data-rich datasets generated are proving really useful at discovering new innate immune players in fish mucosal secretions, identifying novel markers of specific mucosal immune responses, unraveling the diversity of the B and T cell repertoires and characterizing the diversity of the microbial communities present in teleost mucosal surfaces. Bioinformatics, data analysis and storage platforms should be developed to facilitate rapid processing of large datasets, especially when mammalian tools such as bioinformatics analysis software are not available in fishes.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Susana Magadán
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA; Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Campus Lagoas Marcosende, Vigo, Pontevedra 36310, Spain.
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Wu N, Song YL, Wang B, Zhang XY, Zhang XJ, Wang YL, Cheng YY, Chen DD, Xia XQ, Lu YS, Zhang YA. Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies. Sci Rep 2016; 6:36048. [PMID: 27808112 PMCID: PMC5093735 DOI: 10.1038/srep36048] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/10/2016] [Indexed: 12/11/2022] Open
Abstract
The gut-associated lymphoid tissue, connected with liver via bile and blood, constructs a local immune environment of both defense and tolerance. The gut-liver immunity has been well-studied in mammals, yet in fish remains largely unknown, even though enteritis as well as liver and gallbladder syndrome emerged as a limitation in aquaculture. In this study, we performed integrative bioinformatic analysis for both transcriptomic (gut and liver) and proteomic (intestinal mucus and bile) data, in both healthy and infected tilapias. We found more categories of immune transcripts in gut than liver, as well as more adaptive immune in gut meanwhile more innate in liver. Interestingly reduced differential immune transcripts between gut and liver upon inflammation were also revealed. In addition, more immune proteins in bile than intestinal mucus were identified. And bile probably providing immune effectors to intestinal mucus upon inflammation was deduced. Specifically, many key immune transcripts in gut or liver as well as key immune proteins in mucus or bile were demonstrated. Accordingly, we proposed a hypothesized profile of fish gut-liver immunity, during either homeostasis or inflammation. Current data suggested that fish gut and liver may collaborate immunologically while keep homeostasis using own strategies, including potential unique mechanisms.
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Affiliation(s)
- Nan Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yu-Long Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,Demorgen Bioinformation Technology Co. Ltd, Wuhan 430072, China
| | - Bei Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiang-Yang Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu-Jie Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Ya-Li Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ying-Yin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dan-Dan Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yi-Shan Lu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yong-An Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Wuhan 430072, China
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Puangpila C, Mayadunne E, El Rassi Z. 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 2011-2014. Electrophoresis 2015; 36:238-52. [PMID: 25287967 PMCID: PMC4485988 DOI: 10.1002/elps.201400434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 11/07/2022]
Abstract
This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As 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, however, is distinguished from its earlier version by expanding on capturing/enriching subphosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid-2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.
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Affiliation(s)
- Chanida Puangpila
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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Wulff T, Silva T, Nielsen ME. Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics. Proteomics 2013; 13:2180-90. [PMID: 23596053 DOI: 10.1002/pmic.201200488] [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: 10/29/2012] [Revised: 02/13/2013] [Accepted: 03/26/2013] [Indexed: 11/08/2022]
Abstract
The response to tissue damage is a complex process, which involves the coordinated regulation of multiple proteins to ensure tissue repair. In order to investigate the effect of tissue damage in a lower vertebrate, samples were taken from rainbow trout (Oncorhynchus mykiss) at day 7 after damage and proteins were separated using 2DE. The experimental design included two groups of rainbow trout, which were fed organic feed either with or without astaxanthin. In total, 96 proteins were found to be affected by tissue damage, clearly demonstrating in this lower vertebrate the complexity and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes such as apoptosis, iron homeostasis, and regulation of muscular structure. Interestingly, it was established that exclusively within the astaxanthin feed group, three members of the annexin protein family (annexin IV, V, and VI) were regulated in response to tissue damage.
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Affiliation(s)
- Tune Wulff
- DTU Food, National Food Institute, Technical University of Denmark, Søltofts Plads, Lyngby, Denmark.
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