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Jaiswal S, Nandi S, Iquebal MA, Jasrotia RS, Patra S, Mishra G, Udit UK, Sahu DK, Angadi UB, Meher PK, Routray P, Sundaray JK, Verma DK, Das P, Jayasankar P, Rai A, Kumar D. Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing. BMC Genomics 2021; 22:685. [PMID: 34548034 PMCID: PMC8456608 DOI: 10.1186/s12864-021-08001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/26/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samiran Nandi
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunita Patra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Gayatri Mishra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Uday Kumar Udit
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Dinesh Kumar Sahu
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prem Kumar Meher
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Padmanav Routray
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | | | - Paramananda Das
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Shang-Guan XY, Cai YJ, Xu HZ, Cheng X, Zhang RF, Liu HX. A C-type lectin with a single CRD from Onychostoma macrolepis mediates immune recognition against bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2021; 115:160-170. [PMID: 34147614 DOI: 10.1016/j.fsi.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
C-type lectins (CTL) are a large group of pattern-recognition proteins and to play important roles in glycoprotein metabolism, multicellular integration, and immunity. Based on their overall domain structure, they can be classified as different groups that possess different physiological functions. A typical C-type lectin (named as OmLec1) was identified from the fish, Onychostoma macrolepis, an important cultured fish in China. Open reading frame of OmLec1 contains a 570 bp, encoding a protein of 189 amino acids that includes a signal peptide and a single carbohydrate-recognition domain. The phylogenetic analysis showed that OmLec1 could be grouped with C-type lectin from other fish. OmLec1 was expressed in all the tissues in our study, and the expression level was highest in liver. And its relative expression levels were significantly upregulated following infection with Aeromonas hydrophila. The recombinant OmLec1 protein (rOmLec1) could agglutinate some Gram-negative bacteria and Gram-positive bacteria in vitro in the presence of Ca2+, showing a typical Ca2+-dependent carbohydrate-binding protein. Furthermore, rOmLec1 purified from E. coli BL21 (DE3), strongly bound to LPS and PGN, as well as all tested bacteria in a Ca2+-dependent manner. These results indicate that OmLec1 plays a central role in the innate immune response and as a pattern recognition receptor that recognizes diverse pathogens among O. macrolepis.
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Affiliation(s)
- Xin-Yan Shang-Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shan'xi, 712100, China
| | - Ying-Jie Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shan'xi, 712100, China
| | - Hong-Zhou Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shan'xi, 712100, China
| | - Xu Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shan'xi, 712100, China
| | - Rui-Fang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shan'xi, 712100, China
| | - Hai-Xia Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shan'xi, 712100, China.
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Shang-Guan XY, Xu HZ, Cheng X, Zhang RF, Lu YT, Liu HX. A C-type lectin (OmCTL) in Onychostoma macrolepis: Binding ability to LPS, PGN and agglutinating activity against bacteria. Mol Immunol 2021; 132:21-29. [PMID: 33524771 DOI: 10.1016/j.molimm.2021.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/19/2022]
Abstract
C-type lectins (CTLs) are calcium-dependent carbohydrate-binding proteins that mainly bind to carbohydrate-based or other ligands to mediate cell adhesion, recognize pathogens, and play important roles in the immune system. In the present study, a novel C-type lectin (OmCTL) isolated from Onychostoma macrolepis was investigated. The open reading frame of OmCTL comprises 468 bp, encoding a 155 amino acid polypeptide with an 18 amino acid putative signaling peptide. The predicted primary OmCTL structure contains a signal peptide, a single carbohydrate recognition domain (CRD) and an EPN/WND motif required for carbohydrate-binding specificity. Using tissue expression pattern analysis, OmCTL has been shownto be highly expressed in the liver, and is also detected in other tissues. OmCTL was significantly upregulated in the liver and spleen following infection with Aeromonas hydrophila, suggesting its involvement in immune response. The recombinant OmCTL protein (rOmCTL) agglutinated two gram-negative bacteria, Escherichia coli and A. hydrophila, in vitro in the presence of Ca2+, showing that it is a typical Ca2+-dependent carbohydrate-binding protein.Furthermore, rOmCTL purified from E. coli BL21 (DE3) strongly bound to LPS and PGN, as well as all tested bacteria in a Ca2+-independent manner. These results indicate that OmCTL plays a central role in the innate immune response and as a pattern recognition receptor that recognizes diverse pathogens among O. macrolepis.
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Affiliation(s)
- Xin-Yan Shang-Guan
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shan'xi, 712100, China
| | - Hong-Zhou Xu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shan'xi, 712100, China
| | - Xu Cheng
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shan'xi, 712100, China
| | - Rui-Fang Zhang
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shan'xi, 712100, China
| | - Yi-Tong Lu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shan'xi, 712100, China
| | - Hai-Xia Liu
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shan'xi, 712100, China.
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Wang L, Zhang J, Kong X, Zhao X, Pei C, Li L. A C-type lectin, Nattectin-like protein (CaNTC) in Qihe crucian carp Carassius auratus: Binding ability with LPS, PGN and various bacteria, and agglutinating activity against bacteria. FISH & SHELLFISH IMMUNOLOGY 2017; 67:382-392. [PMID: 28602683 DOI: 10.1016/j.fsi.2017.06.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/25/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
C-type lectins (CTLs), as the members of pattern-recognition receptors (PRRs), play the significant roles in innate immunity through binding with pathogen-associated molecular patterns (PAMPs) on the surface of microbe. In the present study, a novel CTL, Nattectin-like protein (named as CaNTC), was investigated in Qihe crucian carp Carassius auratus. The full-length cDNA of CaNTC was composed of 776 bp, with a 152 bp 5'-untranslated region (UTR), a 492 bp ORF encoding a 163-aa protein, and a 132 bp 3'-UTR with a polyadenylation signal sequence AATAAA and a poly(A) tail. The deduced amino acid sequence of CaNTC contained a signal peptide, a single carbohydrate recognition domain (CRD) which had four conserved disulfide-bonded cysteine residues (Cys57-Cys150, Cys126-Cys142), and an EPN/WND motif required for carbohydrate-binding specificity. With regard to the mRNA transcript of CaNTC, it was predominately expressed in liver. The temporal expressions of CaNTC were obviously up-regulated in liver, spleen and head-kidney after challenged by Aeromonas hydrophila and poly I: C, respectively, and the change pattern was in the time-depended manner. The recombinant CaNTC (rCaNTC) purified from Escherichia coli BL21 (DE3), exhibited strong binding ability with LPS and PGN, as well as all tested bacteria in a Ca2+-independent manner. With regard to the agglutinating activity of rCaNTC, rCaNTC was able to agglutinate rabbit erythrocytes and three kinds of bacteria (Gram-negative bacteria, Escherichia coli and A. hydrophila, and Gram-positive bacteria Staphylococcus aureus) in a Ca2+-dependent manner. These findings collectively demonstrated that CaNTC, as a PRR, could be involved in the innate immunity and play an important role in immune defense of C. auratus.
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Affiliation(s)
- Li Wang
- College of Life Science, Henan Normal University, Henan province, PR China
| | - Jie Zhang
- College of Fisheries, Henan Normal University, Henan province, PR China
| | - Xianghui Kong
- College of Life Science, Henan Normal University, Henan province, PR China; College of Fisheries, Henan Normal University, Henan province, PR China.
| | - Xianliang Zhao
- College of Fisheries, Henan Normal University, Henan province, PR China
| | - Chao Pei
- College of Fisheries, Henan Normal University, Henan province, PR China
| | - Li Li
- College of Fisheries, Henan Normal University, Henan province, PR China
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Kienzler A, Bony S, Devaux A. DNA repair activity in fish and interest in ecotoxicology: a review. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 134-135:47-56. [PMID: 23571068 DOI: 10.1016/j.aquatox.2013.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 03/06/2013] [Accepted: 03/06/2013] [Indexed: 05/20/2023]
Abstract
The knowledge of DNA repair in a target species is of first importance as it is the primary line of defense against genotoxicants, and a better knowledge of DNA repair capacity in fish could help to interpret genotoxicity data and/or assist in the choice of target species, developmental stage and tissues to focus on, both for environmental biomonitoring studies and DNA repair testing. This review focuses in a first part on what is presently known on a mechanistic basis, about the various DNA repair systems in fish, in vivo and in established cell lines. Data on base excision repair (BER), direct reversal with O⁶-alkylguanine transferase and double strand breaks repair, although rather scarce, are being reviewed, as well as nucleotide excision repair (NER) and photoreactivation repair (PER), which are by far the most studied repair mechanisms in fish. Most of these repair mechanisms seem to be strongly species and tissue dependent; they also depend on the developmental stage of the organisms. BER is efficient in vivo, although no data has been found on in vitro models. NER activity is quite low or even inexistent depending on the studies; however this lack is partly compensated by a strong PER activity, especially in early developmental stage. In a second part, a survey of the ecotoxicological studies integrating DNA repair as a parameter responding to single or mixture of contaminant is realized. Three main approaches are being used: the measurement of DNA repair gene expression after exposure, although it has not yet been clearly established whether gene expression is indicative of repair capacity; the monitoring of DNA damage removal by following DNA repair kinetics; and the modulation of DNA repair activity following exposure in situ, in order to assess the impact of exposure history on DNA repair capacity. Since all DNA repair processes are possible targets for environmental pollutants, we can also wonder at which extent such a modulation of repair capacities in fish could be the base for the development of new biomarkers of genotoxicity. Knowing the importance of the germ cell DNA integrity in the reproductive success of aquatic organisms, the DNA repair capacity of such cells deserve to be more studied, as well as DNA repair capacities of established fish cell lines. The limited amount of available data, which shows low/slow DNA repair capacities of fish cell lines compared with mammalian cell lines, concerned mainly the NER system; thus this point merits to be explored more deeply. Additionally, since some of the DNA repair systems appear more efficient in embryo larval stages, it would be of interest to consider embryonic cell lineages more closely.
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Affiliation(s)
- Aude Kienzler
- UMR LEHNA 5023, Université de Lyon, F-69518 Vaulx-en-Velin, France.
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Ribas L, Pardo BG, Fernández C, Alvarez-Diós JA, Gómez-Tato A, Quiroga MI, Planas JV, Sitjà-Bobadilla A, Martínez P, Piferrer F. A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus). BMC Genomics 2013; 14:180. [PMID: 23497389 PMCID: PMC3700835 DOI: 10.1186/1471-2164-14-180] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/27/2013] [Indexed: 02/02/2023] Open
Abstract
Background Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. Conclusions The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.
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Affiliation(s)
- Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Yu S, Yang H, Chai Y, Liu Y, Zhang Q, Ding X, Zhu Q. Molecular cloning and characterization of a C-type lectin in roughskin sculpin (Trachidermus fasciatus). FISH & SHELLFISH IMMUNOLOGY 2013; 34:582-592. [PMID: 23246922 DOI: 10.1016/j.fsi.2012.11.033] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 11/30/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
C-type lectins, as the members of pattern-recognition receptors (PRRs), play significant roles in innate immunity responses through binding to the pathogen-associated molecular patterns (PAMPs) presented on surfaces of microorganisms. In our study, a C-type lectin gene (TfCTL1) was cloned from the roughskin sculpin using expression sequence tag (EST) and rapid amplification of cDNA ends (RACE) techniques. The full-length of TfCTL1 was 696 bp, consisting of a 95 bp 5' untranslated region (UTR), a 498 bp open reading frame (ORF) encoding a 165 amino acid protein, and a 103 bp 3' UTR with a polyadenylation signal sequence AATAAA and a poly(A) tail. The deduced amino acid sequence of TfCTL1 contained a signal peptide and a single carbohydrate recognition domain (CRD) which had four conserved disulfide-bonded cysteine residues (Cys(61)-Cys(158), Cys(134)-Cys(150)) and a Ca(2+)/carbohydrate-binding site (QPD motif). Results from the qRT-PCR indicated that TfCTL1 mRNA was predominately expressed in the liver. The temporal expression of TfCTL1 was obviously up-regulated in the skin, blood, spleen and heart in time dependent manners by lipopolysaccharide (LPS) challenge, whereas in the liver, TfCTL1 was initially down-regulated from 2 h to 48 h followed by an abrupt up-regulation at 72 h. Recombinant TfCTL1 CRD purified from Escherichia coli BL21 was able to agglutinate some Gram-positive bacteria, Gram-negative bacteria and a yeast in a Ca(2+)-dependent manner. Further analysis showed that TfCTL1 can bind to several kinds of microorganisms selectively in a Ca(2+)-independent manner. These results suggested that TfCTL1 might be involved in the innate response as a PRR.
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Affiliation(s)
- Shanshan Yu
- Ocean College, Shandong University (Weihai), Weihai 264209, PR China
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Mehinto AC, Martyniuk CJ, Spade DJ, Denslow ND. Applications for next-generation sequencing in fish ecotoxicogenomics. Front Genet 2012; 3:62. [PMID: 22539934 PMCID: PMC3336092 DOI: 10.3389/fgene.2012.00062] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 01/23/2023] Open
Abstract
The new technologies for next-generation sequencing (NGS) and global gene expression analyses that are widely used in molecular medicine are increasingly applied to the field of fish biology. This has facilitated new directions to address research areas that could not be previously considered due to the lack of molecular information for ecologically relevant species. Over the past decade, the cost of NGS has decreased significantly, making it possible to use non-model fish species to investigate emerging environmental issues. NGS technologies have permitted researchers to obtain large amounts of raw data in short periods of time. There have also been significant improvements in bioinformatics to assemble the sequences and annotate the genes, thus facilitating the management of these large datasets.The combination of DNA sequencing and bioinformatics has improved our abilities to design custom microarrays and study the genome and transcriptome of a wide variety of organisms. Despite the promising results obtained using these techniques in fish studies, NGS technologies are currently underused in ecotoxicogenomics and few studies have employed these methods. These issues should be addressed in order to exploit the full potential of NGS in ecotoxicological studies and expand our understanding of the biology of non-model organisms.
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Affiliation(s)
- Alvine C Mehinto
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
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