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De Vos S, Rombauts S, Coussement L, Dermauw W, Vuylsteke M, Sorgeloos P, Clegg JS, Nambu Z, Van Nieuwerburgh F, Norouzitallab P, Van Leeuwen T, De Meyer T, Van Stappen G, Van de Peer Y, Bossier P. The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments. BMC Genomics 2021; 22:635. [PMID: 34465293 PMCID: PMC8406910 DOI: 10.1186/s12864-021-07937-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors. RESULTS AND DISCUSSION Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions. CONCLUSIONS A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.
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Affiliation(s)
- Stephanie De Vos
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wannes Dermauw
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Patrick Sorgeloos
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - James S Clegg
- Coastal and Marine Sciences Institute, University of California, Bodega Bay, Davis, CA, USA
| | - Ziro Nambu
- Department of Medical Technology, School of Health Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Fukuoka, Japan
| | - Filip Van Nieuwerburgh
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Parisa Norouzitallab
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Department of Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
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Asem A, Eimanifar A, Rastegar-Pouyani N, Hontoria F, Vos SD, Stappen GV, Sun SC. An overview on the nomenclatural and phylogenetic problems of native Asian brine shrimps of the genus Artemia Leach, 1819 (Crustacea, Anostraca). Zookeys 2020; 902:1-15. [PMID: 33061769 PMCID: PMC6971158 DOI: 10.3897/zookeys.902.34593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/12/2019] [Indexed: 11/12/2022] Open
Abstract
The genus Artemia Leach, 1819 is a cosmopolitan halophilic crustacean, consisting of bisexual species and obligate parthenogenetic populations. Asia is rich in Artemia biodiversity. More than 530 Artemia sites have been recorded from this area and more than 20 species/subspecies/variety names have been used for them. There exist various problems in the nomenclature, identification, and phylogenetic status of Artemia native to Asia, which are discussed in this paper.
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Affiliation(s)
- Alireza Asem
- Institute of Evolution and Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China Ocean University of China Qingdao China.,College of Life Sciences and Ecology, Hainan Tropical Ocean University, Yucai Rd, Sanya 572000, China Hainan Tropical Ocean University Sanya China
| | - Amin Eimanifar
- Independent Senior Research Scientist, Industrial District, 21601 Easton, Maryland, USA Unaffiliated Maryland United States of America
| | - Nasrullah Rastegar-Pouyani
- Department of Biology, Faculty of Science, Razi University, 6714967346 Kermanshah, Iran Razi University Kermanshah Iran
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC). 12595 Ribera de Cabanes, Castellón, Spain Instituto de Acuicultura de Torre de la Sal Castellón Spain
| | - Stephanie De Vos
- Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience Engineering - Blok F, Ghent University, Coupure Links 653, B-9000 Gent, Belgium Ghent University Gent Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience Engineering - Blok F, Ghent University, Coupure Links 653, B-9000 Gent, Belgium Ghent University Gent Belgium
| | - Shi-Chun Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China Ocean University of China Qingdao China
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Li AQ, Sun ZP, Liu X, Yang JS, Jin F, Zhu L, Jia WH, De Vos S, Van Stappen G, Bossier P, Yang WJ. The chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) controls cellular quiescence by hyperpolarizing the cell membrane during diapause in the crustacean Artemia. J Biol Chem 2019; 294:6598-6611. [PMID: 30765604 DOI: 10.1074/jbc.ra118.005900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/10/2019] [Indexed: 01/10/2023] Open
Abstract
Cellular quiescence, a reversible state in which growth, proliferation, and other cellular activities are arrested, is important for self-renewal, differentiation, development, regeneration, and stress resistance. However, the physiological mechanisms underlying cellular quiescence remain largely unknown. In the present study, we used embryos of the crustacean Artemia in the diapause stage, in which these embryos remain quiescent for prolonged periods, as a model to explore the relationship between cell-membrane potential (V mem) and quiescence. We found that V mem is hyperpolarized and that the intracellular chloride concentration is high in diapause embryos, whereas V mem is depolarized and intracellular chloride concentration is reduced in postdiapause embryos and during further embryonic development. We identified and characterized the chloride ion channel protein cystic fibrosis transmembrane conductance regulator (CFTR) of Artemia (Ar-CFTR) and found that its expression is silenced in quiescent cells of Artemia diapause embryos but remains constant in all other embryonic stages. Ar-CFTR knockdown and GlyH-101-mediated chemical inhibition of Ar-CFTR produced diapause embryos having a high V mem and intracellular chloride concentration, whereas control Artemia embryos released free-swimming nauplius larvae. Transcriptome analysis of embryos at different developmental stages revealed that proliferation, differentiation, and metabolism are suppressed in diapause embryos and restored in postdiapause embryos. Combined with RNA sequencing (RNA-Seq) of GlyH-101-treated MCF-7 breast cancer cells, these analyses revealed that CFTR inhibition down-regulates the Wnt and Aurora Kinase A (AURKA) signaling pathways and up-regulates the p53 signaling pathway. Our findings provide insight into CFTR-mediated regulation of cellular quiescence and V mem in the Artemia model.
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Affiliation(s)
- An-Qi Li
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhan-Peng Sun
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xu Liu
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jin-Shu Yang
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Feng Jin
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lin Zhu
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wen-Huan Jia
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Stephanie De Vos
- the Laboratory of Aquaculture and Artemia Reference Center, Department of Animal Production, Ghent University, B-9000 Ghent, Belgium, and
| | - Gilbert Van Stappen
- the Laboratory of Aquaculture and Artemia Reference Center, Department of Animal Production, Ghent University, B-9000 Ghent, Belgium, and
| | - Peter Bossier
- the Laboratory of Aquaculture and Artemia Reference Center, Department of Animal Production, Ghent University, B-9000 Ghent, Belgium, and
| | - Wei-Jun Yang
- From the College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China, .,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
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Asem A, Li W, Wang PZ, Eimanifar A, Shen CY, De Vos S, Van Stappen G. The complete mitochondrial genome of Artemia sinica Cai, 1989 (Crustacea: Anostraca) using next-generation sequencing. Mitochondrial DNA Part B 2019. [DOI: 10.1080/23802359.2019.1565933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Alireza Asem
- College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China
| | - Weidong Li
- College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China
| | - Pei-Zheng Wang
- College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China
| | - Amin Eimanifar
- Independent Research Scientist, Industrial District, Easton, Maryland, USA
| | - Chun-Yang Shen
- Medical College, Chengde Medical University, Chengde, China
| | - Stephanie De Vos
- Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience Engineering - Blok F, Ghent University, Gent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience Engineering - Blok F, Ghent University, Gent, Belgium
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Ye HL, Li DR, Yang JS, Chen DF, De Vos S, Vuylsteke M, Sorgeloos P, Van Stappen G, Bossier P, Nagasawa H, Yang WJ. Molecular characterization and functional analyses of a diapause hormone receptor-like gene in parthenogenetic Artemia. Peptides 2017; 90:100-110. [PMID: 28174072 DOI: 10.1016/j.peptides.2017.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 01/03/2023]
Abstract
In arthropods, mature females under certain conditions produce and release encysted gastrula embryos that enter diapause, a state of obligate dormancy. The process is presumably regulated by diapause hormone (DH) and diapause hormone receptor (DHR) that were identified in the silkworm, Bombyx mori and other insects. However, the molecular structure and function of DHR in crustaceans remains unknown. Here, a DHR-like gene from parthenogenetic Artemia (Ar-DHR) was isolated and sequenced. The cDNA sequence consists of 1410bp with a 1260-bp open reading frame encoding a protein consisting of 420 amino acid residues. The results of real-time PCR (qRT-PCR) and Western blot analysis showed that the mRNA and protein of Ar-DHR were mainly expressed at the diapause stage. Furthermore, we found that Ar-DHR was located on the cell membrane of the pre-diapause cyst but in the cytoplasm of the diapause cyst by analysis of immunofluorescence. In vivo knockdown of Ar-DHR by RNA interference (RNAi) and antiserum neutralization consistently inhibited diapause cysts formation. The results indicated that Ar-DHR plays an important role in the induction and maintenance of embryonic diapause in Artemia. Thus, our findings provide an insight into the regulation of diapause formation in Artemia and the function of Ar-DHR.
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Affiliation(s)
- Hui-Li Ye
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Dong-Rui Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Dian-Fu Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Stephanie De Vos
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Marnik Vuylsteke
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University, Belgium
| | - Hiromichi Nagasawa
- Department of Applied Biological Chemistry, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China.
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Li DR, Ye HL, Yang JS, Yang F, Wang MR, De Vos S, Vuylsteke M, Sorgeloos P, Van Stappen G, Bossier P, Yang WJ. Identification and characterization of a Masculinizer (Masc) gene involved in sex differentiation in Artemia. Gene 2017; 614:56-64. [PMID: 28300613 DOI: 10.1016/j.gene.2017.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/17/2017] [Accepted: 03/10/2017] [Indexed: 11/15/2022]
Abstract
The sex of relatively primitive animals such as invertebrates is mostly determined by environmental factors and chromosome ploidy. Heteromorphic chromosomes may also play an important role, as in the ZW system in lepidopterans. However, the mechanisms of these various sex determination systems are still largely undefined. In the present study, a Masculinizer gene (Ar-Masc) was identified in the crustacean Artemia franciscana Kellogg 1906. Sequence analysis revealed that the 1140-bp full-length open reading frame of Ar-Masc encodes a 380-aa protein containing two CCCH-type zinc finger domains having a high degree of shared identities with the MASC protein characterized in the silkworm Bombyx mori, which has been determined to participate in the production of male-specific splice variants. Furthermore, although Ar-Masc could be detected in almost all stages in both sexual and parthenogenetic Artemia, there were significant variations in expression between these two reproductive modes. Firstly, qRT-PCR and Western blot analysis showed that levels of both Ar-Masc mRNA and protein in sexual nauplii were much higher than in parthenogenetic nauplii throughout the hatching process. Secondly, both sexual and parthenogenetic Artemia had decreased levels of Ar-Masc along with the embryonic developmental stages, while the sexual ones had a relatively higher and more stable expression than those of parthenogenetic ones. Thirdly, immunofluorescence analysis determined that sexual individuals had higher levels of Ar-MASC protein than parthenogenetic individuals during embryonic development. Lastly, RNA interference with dsRNA showed that gene silencing of Ar-Masc in sexual A. franciscana caused the female-male ratio of progeny to be 2.19:1. These data suggest that Ar-Masc participates in the process of sex determination in A. franciscana, and provide insight into the evolution of sex determination in sexual organisms.
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Affiliation(s)
- Dong-Rui Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Hui-Li Ye
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Jin-Shu Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Fan Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Mo-Ran Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Department of Fisheries Science, Tianjin Agricultural University, People's Republic of China
| | - Stephanie De Vos
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Marnik Vuylsteke
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture &Artemia Reference center, Ghent University, Belgium
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China.
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De Vos S, Bossier P, Van Stappen G, Vercauteren I, Sorgeloos P, Vuylsteke M. A first AFLP-based genetic linkage map for brine shrimp Artemia franciscana and its application in mapping the sex locus. PLoS One 2013; 8:e57585. [PMID: 23469207 PMCID: PMC3587612 DOI: 10.1371/journal.pone.0057585] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/22/2013] [Indexed: 12/26/2022] Open
Abstract
We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ-ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species.
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Affiliation(s)
- Stephanie De Vos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- * E-mail:
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