1
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Corcionivoschi N, Balta I, McCleery D, Pet I, Iancu T, Julean C, Marcu A, Stef L, Morariu S. Blends of Organic Acids Are Weaponizing the Host iNOS and Nitric Oxide to Reduce Infection of Piscirickettsia salmonis in vitro. Antioxidants (Basel) 2024; 13:542. [PMID: 38790647 PMCID: PMC11118739 DOI: 10.3390/antiox13050542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
For the last 30 years, Piscirickettsia salmonis has caused major economic losses to the aquaculture industry as the aetiological agent for the piscirickettsiosis disease. Replacing the current interventions, based on antibiotics, with natural alternatives (e.g., organic acids) represents a priority. With this study, we aimed to better understand their biological mechanism of action in an in vitro model of infection with salmon epithelial cells (CHSE-214). Our first observation revealed that at the sub-inhibitory concentration of 0.5%, the organic acid blend (Aq) protected epithelial cell integrity and significantly reduced P. salmonis invasion. The MIC was established at 1% Aq and the MBC at 2% against P. salmonis. The sub-inhibitory concentration significantly increased the expression of the antimicrobial peptides Cath2 and Hepcidin1, and stimulated the activity of the innate immune effector iNOS. The increase in iNOS activity also led to higher levels of nitric oxide (NO) being released in the extracellular space. The exposure of P. salmonis to the endogenous NO caused an increase in bacterial lipid peroxidation levels, a damaging effect which can ultimately reduce the pathogen's ability to attach or multiply intracellularly. We also demonstrate that the increased NO release by the host CHSE-214 cells is a consequence of direct exposure to Aq and is not dependent on P. salmonis infection. Additionally, the presence of Aq during P. salmonis infection of CHSE-214 cells significantly mitigated the expression of the pro-inflammatory cytokines IL-1β, IL-8, IL-12, and IFNγ. Taken together, these results indicate that, unlike antibiotics, natural antimicrobials can weaponize the iNOS pathway and secreted nitric oxide to reduce infection and inflammation in a Piscirickettsia salmonis in vitro model of infection.
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Affiliation(s)
- Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, Northern Ireland, UK;
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania; (I.P.); (C.J.); (A.M.); (L.S.)
- Academy of Romanian Scientists, Ilfov Street, No. 3, 050044 Bucharest, Romania
| | - Igori Balta
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania; (I.P.); (C.J.); (A.M.); (L.S.)
| | - David McCleery
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, Northern Ireland, UK;
| | - Ioan Pet
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania; (I.P.); (C.J.); (A.M.); (L.S.)
| | - Tiberiu Iancu
- Faculty of Management and Rural Development, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Calin Julean
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania; (I.P.); (C.J.); (A.M.); (L.S.)
| | - Adela Marcu
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania; (I.P.); (C.J.); (A.M.); (L.S.)
| | - Lavinia Stef
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania; (I.P.); (C.J.); (A.M.); (L.S.)
| | - Sorin Morariu
- Faculty of Veterinary Medicine, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania;
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Sánchez-Roncancio C, García B, Gallardo-Hidalgo J, Yáñez JM. GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout ( Oncorhynchus mykiss). Genes (Basel) 2022; 14:114. [PMID: 36672855 PMCID: PMC9859203 DOI: 10.3390/genes14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium Piscirickettsia salmonis, which affects farmed rainbow trout, Oncorhynchus mykiss, in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with P. salmonis under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with P. salmonis resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout.
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Affiliation(s)
- Charles Sánchez-Roncancio
- Doctorado en Acuicultura, Programa Cooperativo: Universidad de Chile. Universidad Católica del Norte. Pontificia Universidad Católica de Valparaíso, Chile
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
| | - Baltasar García
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
| | - Jousepth Gallardo-Hidalgo
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
| | - José M. Yáñez
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
- Núcleo Milenio de Salmonidos Invasores Australes (INVASAL), Concepcion 4030000, Chile
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3
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Mukiibi R, Peñaloza C, Gutierrez A, Yáñez JM, Houston RD, Robledo D. The impact of Piscirickettsia salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon. Genomics 2022; 114:110503. [PMID: 36244592 DOI: 10.1016/j.ygeno.2022.110503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022]
Abstract
Salmon rickettsial septicaemia (SRS), caused by the bacteria Piscirickettsia salmonis (P. salmonis), is responsible for significant mortality in farmed Atlantic salmon in Chile. Currently there are no effective treatments or preventive measures for this disease, although genetic selection or genome engineering to increase salmon resistance to SRS are promising strategies. The accuracy and efficiency of these strategies are usually influenced by the available biological background knowledge of the disease. The aim of this study was to investigate DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The head kidney and liver methylomes of 66 juvenile salmon were profiled using reduced representation bisulphite sequencing (RRBS), and compared between P. salmonis infected animals (3 and 9 days post infection) and uninfected controls, and between SRS resistant and susceptible fish. Methylation was correlated with matching RNA-Seq data from the same animals, revealing that methylation in the first exon leads to an important repression of gene expression. Head kidney methylation showed a clear response to the infection, associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases and could inform the incorporation of epigenetic markers into genomic selection for disease resistant and the design of diagnostic epigenetic markers to better manage fish health in salmon aquaculture.
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Affiliation(s)
- Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Alejandro Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK; Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
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4
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Yoshida GM, Yáñez JM. Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data. Evol Appl 2022; 15:537-552. [PMID: 35505881 PMCID: PMC9046923 DOI: 10.1111/eva.13240] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/01/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Through imputation of genotypes, genome-wide association study (GWAS) and genomic prediction (GP) using whole-genome sequencing (WGS) data are cost-efficient and feasible in aquaculture breeding schemes. The objective was to dissect the genetic architecture of growth traits under chronic heat stress in rainbow trout (Oncorhynchus mykiss) and to assess the accuracy of GP based on imputed WGS and different preselected single nucleotide polymorphism (SNP) arrays. A total of 192 and 764 fish challenged to a heat stress experiment for 62 days were genotyped using a customized 1 K and 26 K SNP panels, respectively, and then, genotype imputation was performed from a low-density chip to WGS using 102 parents (36 males and 66 females) as the reference population. Imputed WGS data were used to perform GWAS and test GP accuracy under different preselected SNP scenarios. Heritability was estimated for body weight (BW), body length (BL) and average daily gain (ADG). Estimates using imputed WGS data ranged from 0.33 ± 0.05 to 0.55 ± 0.05 for growth traits under chronic heat stress. GWAS revealed that the top five cumulatively SNPs explained a maximum of 0.94%, 0.86% and 0.51% of genetic variance for BW, BL and ADG, respectively. Some important functional candidate genes associated with growth-related traits were found among the most important SNPs, including signal transducer and activator of transcription 5B and 3 (STAT5B and STAT3, respectively) and cytokine-inducible SH2-containing protein (CISH). WGS data resulted in a slight increase in prediction accuracy compared with pedigree-based method, whereas preselected SNPs based on the top GWAS hits improved prediction accuracies, with values ranging from 1.2 to 13.3%. Our results support the evidence of the polygenic nature of growth traits when measured under heat stress. The accuracies of GP can be improved using preselected variants from GWAS, and the use of WGS marginally increases prediction accuracy.
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Affiliation(s)
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Núcleo Milenio INVASALConcepciónChile
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5
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Cáceres P, Barría A, Christensen KA, Bassini LN, Correa K, Garcia B, Lhorente JP, Yáñez JM. Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout. Sci Rep 2021; 11:13231. [PMID: 34168167 PMCID: PMC8225872 DOI: 10.1038/s41598-021-92425-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/10/2021] [Indexed: 11/08/2022] Open
Abstract
Sea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.
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Affiliation(s)
- Pablo Cáceres
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av. Santa Rosa 11735, La Pintana, 8820808, Santiago, Chile
| | - Agustín Barría
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, UK
| | - Kris A Christensen
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, Canada
| | - Liane N Bassini
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Katharina Correa
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av. Santa Rosa 11735, La Pintana, 8820808, Santiago, Chile
| | - Baltasar Garcia
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av. Santa Rosa 11735, La Pintana, 8820808, Santiago, Chile
- School of Agricultural and Veterinary Sciences, UNESP-Sao Paulo State University, Jaboticabal, 14884900, Brazil
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av. Santa Rosa 11735, La Pintana, 8820808, Santiago, Chile.
- Núcleo Milenio INVASAL, Concepción, Chile.
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Santiago, Chile.
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6
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Moraleda CP, Robledo D, Gutiérrez AP, Del-Pozo J, Yáñez JM, Houston RD. Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing. BMC Genomics 2021; 22:156. [PMID: 33676414 PMCID: PMC7936450 DOI: 10.1186/s12864-021-07443-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 12/29/2022] Open
Abstract
Background Salmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection. Results A significant and moderate heritability (h2 = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38 K imputed SNP genotypes across 2265 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome. Conclusions While resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07443-2.
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Affiliation(s)
- Carolina P Moraleda
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Alejandro P Gutiérrez
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Jorge Del-Pozo
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - José M Yáñez
- Faculty of Veterinary and Livestock Sciences, University of Chile, Santiago, Chile.
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
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7
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Cañon-Jones H, Cortes H, Castillo-Ruiz M, Schlotterbeck T, San Martín R. Quillaja saponaria (Molina) Extracts Inhibits In Vitro Piscirickettsia salmonis Infections. Animals (Basel) 2020; 10:E2286. [PMID: 33287333 PMCID: PMC7761688 DOI: 10.3390/ani10122286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/26/2022] Open
Abstract
P. salmonis infections are the cause of major bacterial disease in salmonids in Chile, and the reason for using more antibiotics compared to other salmon-producing countries. Vaccination and antibiotics have not been efficient and new approaches are needed. The safety of Quillaja saponaria extracts was measured by cytotoxicity using flow cytometry of cytopathic and death of fish cell cultures and efficacy was assessed using in vitro infection models with pathogenic P. salmonis. Cytotoxicity was low and control of in vitro infections was achieved with all products, with protection of over 90%. Minimum inhibitory concentrations were much higher than those in the infection using cell cultures. These results suggest a dual mechanism of action where less purified extracts with a combination of saponin and non-saponin components simultaneously decrease P. salmonis infection while protecting cell lines, rather than exerting a direct antimicrobial effect. Quillaja saponins controlled in vitro infections with P. salmonis and could be considered good candidates for a new, safe and sustainable method of controlling fish bacterial infectious diseases.
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Affiliation(s)
- Hernán Cañon-Jones
- Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago 7500975, Chile
| | | | - Mario Castillo-Ruiz
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago 8370146, Chile;
- Departamento de Ciencias Químicas y Biológicas, Facultad de Ciencias de la Salud, Universidad Bernardo O Higgins, Santiago 8370993, Chile
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8
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Caruffo M, Mandakovic D, Mejías M, Chávez-Báez I, Salgado P, Ortiz D, Montt L, Pérez-Valenzuela J, Vera-Tamargo F, Yánez JM, Wacyk J, Pulgar R. Pharmacological iron-chelation as an assisted nutritional immunity strategy against Piscirickettsia salmonis infection. Vet Res 2020; 51:134. [PMID: 33115510 PMCID: PMC7592559 DOI: 10.1186/s13567-020-00845-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
Salmonid Rickettsial Septicaemia (SRS), caused by Piscirickettsia salmonis, is a severe bacterial disease in the Chilean salmon farming industry. Vaccines and antibiotics are the current strategies to fight SRS; however, the high frequency of new epizootic events confirms the need to develop new strategies to combat this disease. An innovative opportunity is perturbing the host pathways used by the microorganisms to replicate inside host cells through host-directed antimicrobial drugs (HDAD). Iron is a critical nutrient for P. salmonis infection; hence, the use of iron-chelators becomes an excellent alternative to be used as HDAD. The aim of this work was to use the iron chelator Deferiprone (DFP) as HDAD to treat SRS. Here, we describe the protective effect of the iron chelator DFP over P. salmonis infections at non-antibiotic concentrations, in bacterial challenges both in vitro and in vivo. At the cellular level, our results indicate that DFP reduced the intracellular iron content by 33.1% and P. salmonis relative load during bacterial infections by 78%. These findings were recapitulated in fish, where DFP reduced the mortality of rainbow trout challenged with P. salmonis in 34.9% compared to the non-treated group. This is the first report of the protective capacity of an iron chelator against infection in fish, becoming a potential effective host-directed therapy for SRS and other animals against ferrophilic pathogens.
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Affiliation(s)
- Mario Caruffo
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Santo Tomás, Santiago, Chile.,Laboratorio Inmunología en Peces, Facultad de Ciencia de la Vida, Universidad Andrés Bello, República 239, Santiago, Chile.,Scimetrica Lab, Santiago, Chile
| | - Dinka Mandakovic
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile.,GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile.,Scimetrica Lab, Santiago, Chile
| | - Madelaine Mejías
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Ignacio Chávez-Báez
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Pablo Salgado
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile.,Laboratorio de Nutrición Animal (LABNA). Facultad de Ciencias Agronómicas, Producción Animal, Universidad de Chile, Santa Rosa, 11315, La Pintana, Chile
| | - Daniela Ortiz
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile.,Laboratorio de Nutrición Animal (LABNA). Facultad de Ciencias Agronómicas, Producción Animal, Universidad de Chile, Santa Rosa, 11315, La Pintana, Chile
| | - Liliana Montt
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Javiera Pérez-Valenzuela
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Francisca Vera-Tamargo
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile.,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - José Manuel Yánez
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile.,Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santa Rosa, 11735, La Pintana, Chile
| | - Jurij Wacyk
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile.,Laboratorio de Nutrición Animal (LABNA). Facultad de Ciencias Agronómicas, Producción Animal, Universidad de Chile, Santa Rosa, 11315, La Pintana, Chile
| | - Rodrigo Pulgar
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimento, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile. .,Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile. .,Laboratory for Research in Functional Nutrition, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Av. El Líbano 5524, Macul, 7830490, Santiago, Chile. .,Scimetrica Lab, Santiago, Chile.
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Mastrochirico-Filho VA, Borges CHS, Freitas MV, Ariede RB, Pilarski F, Utsunomia R, Carvalheiro R, Gutierrez AP, Peñaloza C, Yáñez JM, Houston RD, Hashimoto DT. Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus). BMC Genomics 2020; 21:672. [PMID: 32993504 PMCID: PMC7526211 DOI: 10.1186/s12864-020-07090-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contributors to the declining levels of pacu production. The current implementation of genomic selection for disease resistance has been adopted as a powerful strategy for improvement in fish species. This study aimed to investigate the genetic architecture of resistance to A. hydrophila in pacu via Genome-Wide Association Study (GWAS), the identification of suggestive Quantitative Trait Loci (QTLs) and putative genes associated with this trait. The genetic data were obtained from 381 juvenile individuals belonging to 14 full-sibling families. An experimental challenge was performed to gain access to the levels of genetic variation for resistance against the bacteria using the following trait definitions: binary test survival (TS) and time of death (TD). RESULTS The analyses of genetic parameters estimated moderate heritability (h2) for both resistance traits: 0.20 (± 0.09) for TS and 0.35 (± 0.15) for TD. A linkage map for pacu was developed to enable the GWAS, resulting in 27 linkage groups (LGs) with 17,453 mapped Single Nucleotide Polymorphisms (SNPs). The length of the LGs varied from 79.95 (LG14) to 137.01 (LG1) cM, with a total map length of 2755.60 cM. GWAS identified 22 putative QTLs associated to A. hydrophila resistance. They were distributed into 17 LGs, and were considered suggestive genomic regions explaining > 1% of the additive genetic variance (AGV) for the trait. Several candidate genes related to immune response were located close to the suggestive QTLs, such as tbk1, trim16, Il12rb2 and lyz2. CONCLUSION This study describes the development of the first medium density linkage map for pacu, which will be used as a framework to study relevant traits to the production of this species. In addition, the resistance to A. hydrophila was found to be moderately heritable but with a polygenic architecture suggesting that genomic selection, instead of marker assisted selection, might be useful for efficiently improving resistance to one of the most problematic diseases that affects the South American aquaculture.
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Affiliation(s)
- Vito A Mastrochirico-Filho
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Carolina H S Borges
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Milena V Freitas
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Raquel B Ariede
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Fabiana Pilarski
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil
| | - Ricardo Utsunomia
- Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Roberto Carvalheiro
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, Brazil
- National Council for Scientific and Technological Development (CNPq), Brasília, DF, 71605-001, Brazil
| | - Alejandro P Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, UK
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Diogo T Hashimoto
- São Paulo State University (Unesp), Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, SP, 14884-900, Brazil.
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Fraslin C, Quillet E, Rochat T, Dechamp N, Bernardet JF, Collet B, Lallias D, Boudinot P. Combining Multiple Approaches and Models to Dissect the Genetic Architecture of Resistance to Infections in Fish. Front Genet 2020; 11:677. [PMID: 32754193 PMCID: PMC7365936 DOI: 10.3389/fgene.2020.00677] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/02/2020] [Indexed: 12/25/2022] Open
Abstract
Infectious diseases represent a major threat for the sustainable development of fish farming. Efficient vaccines are not available against all diseases, and growing antibiotics resistance limits the use of antimicrobial drugs in aquaculture. It is therefore important to understand the basis of fish natural resistance to infections to help genetic selection and to develop new approaches against infectious diseases. However, the identification of the main mechanisms determining the resistance or susceptibility of a host to a pathogenic microbe is challenging, integrating the complexity of the variation of host genetics, the variability of pathogens, and their capacity of fast evolution and adaptation. Multiple approaches have been used for this purpose: (i) genetic approaches, QTL (quantitative trait loci) mapping or GWAS (genome-wide association study) analysis, to dissect the genetic architecture of disease resistance, and (ii) transcriptomics and functional assays to link the genetic constitution of a fish to the molecular mechanisms involved in its interactions with pathogens. To date, many studies in a wide range of fish species have investigated the genetic determinism of resistance to many diseases using QTL mapping or GWAS analyses. A few of these studies pointed mainly toward adaptive mechanisms of resistance/susceptibility to infections; others pointed toward innate or intrinsic mechanisms. However, in the majority of studies, underlying mechanisms remain unknown. By comparing gene expression profiles between resistant and susceptible genetic backgrounds, transcriptomics studies have contributed to build a framework of gene pathways determining fish responsiveness to a number of pathogens. Adding functional assays to expression and genetic approaches has led to a better understanding of resistance mechanisms in some cases. The development of knock-out approaches will complement these analyses and help to validate putative candidate genes critical for resistance to infections. In this review, we highlight fish isogenic lines as a unique biological material to unravel the complexity of host response to different pathogens. In the future, combining multiple approaches will lead to a better understanding of the dynamics of interaction between the pathogen and the host immune response, and contribute to the identification of potential targets of selection for improved resistance.
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Affiliation(s)
- Clémence Fraslin
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Edwige Quillet
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Tatiana Rochat
- INRAE, UVSQ, VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nicolas Dechamp
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Bertrand Collet
- INRAE, UVSQ, VIM, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphine Lallias
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pierre Boudinot
- INRAE, UVSQ, VIM, Université Paris-Saclay, Jouy-en-Josas, France
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11
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Yáñez JM, Yoshida G, Barria A, Palma-Véjares R, Travisany D, Díaz D, Cáceres G, Cádiz MI, López ME, Lhorente JP, Jedlicki A, Soto J, Salas D, Maass A. High-Throughput Single Nucleotide Polymorphism (SNP) Discovery and Validation Through Whole-Genome Resequencing in Nile Tilapia (Oreochromis niloticus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:109-117. [PMID: 31938972 DOI: 10.1007/s10126-019-09935-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Nile tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world. Currently, the estimation of genetic merit of breeders is typically based on genealogical and phenotypic information. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure into the breeding goal. Thus, single nucleotide polymorphisms (SNPs) are required to investigate phenotype-genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed Nile tilapia. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps, including removing SNP based on genotype and site quality, presence of Mendelian errors, and non-unique position in the genome, a total of 50,000 high-quality SNPs were selected for the development of a custom Illumina BeadChip SNP panel. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNPs in Hardy-Weinberg Equilibrium; 37,843 (76%) and 45,171(90%) SNPs with a minor allele frequency (MAF) higher than 0.05; and 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The 50K SNP panel developed in the current work will be useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection, as well as supporting genetic studies in farmed populations of Nile tilapia using dense genome-wide information.
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Affiliation(s)
- José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile.
- Núcleo Milenio INVASAL, Concepción, Chile.
| | - Grazyella Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Benchmark Genetics Chile, Puerto Montt, Chile
| | - Agustín Barria
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Ricardo Palma-Véjares
- Centro para la Regulación del Genoma, Universidad de Chile, Santiago, Chile
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- Centro para la Regulación del Genoma, Universidad de Chile, Santiago, Chile
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Diego Díaz
- Centro para la Regulación del Genoma, Universidad de Chile, Santiago, Chile
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Giovanna Cáceres
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María E López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Ana Jedlicki
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - José Soto
- Grupo Acuacorporacion, Internacional (GACI), Cañas, Costa Rica
| | - Diego Salas
- Grupo Acuacorporacion, Internacional (GACI), Cañas, Costa Rica
| | - Alejandro Maass
- Centro para la Regulación del Genoma, Universidad de Chile, Santiago, Chile
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
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Rodríguez FH, Flores-Mara R, Yoshida GM, Barría A, Jedlicki AM, Lhorente JP, Reyes-López F, Yáñez JM. Genome-Wide Association Analysis for Resistance to Infectious Pancreatic Necrosis Virus Identifies Candidate Genes Involved in Viral Replication and Immune Response in Rainbow Trout ( Oncorhynchus mykiss). G3 (BETHESDA, MD.) 2019; 9:2897-2904. [PMID: 31324747 PMCID: PMC6723134 DOI: 10.1534/g3.119.400463] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022]
Abstract
Infectious pancreatic necrosis (IPN) is a viral disease with considerable negative impact on the rainbow trout (Oncorhynchus mykiss) aquaculture industry. The aim of the present work was to detect genomic regions that explain resistance to infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2,278 fish from 58 full-sib families were challenged with IPNV and 768 individuals were genotyped (488 resistant and 280 susceptible), using a 57K SNP panel Axiom, Affymetrix. A genome-wide association study (GWAS) was performed using the phenotypes time to death (TD) and binary survival (BS), along with the genotypes of the challenged fish using a Bayesian model (Bayes C). Heritabilities for resistance to IPNV estimated using genomic information, were 0.53 and 0.82 for TD and BS, respectively. The Bayesian GWAS detected a SNP located on chromosome 5 explaining 19% of the genetic variance for TD. The proximity of Sentrin-specific protease 5 (SENP5) to this SNP makes it a candidate gene for resistance against IPNV. In case of BS, a SNP located on chromosome 23 was detected explaining 9% of the genetic variance. However, the moderate-low proportion of variance explained by the detected marker leads to the conclusion that the incorporation of all genomic information, through genomic selection, would be the most appropriate approach to accelerate genetic progress for the improvement of resistance against IPNV in rainbow trout.
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Affiliation(s)
- Francisco H Rodríguez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, La Pintana, Santiago, Chile
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno, Perú
| | - Raúl Flores-Mara
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, La Pintana, Santiago, Chile
- Escuela Profesional de Medicina Veterinaria y Zootecnia, Facultad de Ciencias de la Salud, Universidad Andina Néstor Cáceres Velásquez, Juliaca, Puno, Perú
| | - Grazyella M Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, La Pintana, Santiago, Chile
- Benchmark Genetics Chile, Puerto Montt, Chile
| | - Agustín Barría
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, La Pintana, Santiago, Chile
| | - Ana M Jedlicki
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, La Pintana, Santiago, Chile
| | | | - Felipe Reyes-López
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain, and
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808, La Pintana, Santiago, Chile
- Núcleo Milenio INVASAL, Concepción 4070386, Chile
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