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Ryder D, Stone D, Minardi D, Riley A, Avant J, Cross L, Soeffker M, Davidson D, Newman A, Thomson P, Darby C, van Aerle R. De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 2024; 25:233. [PMID: 38438840 PMCID: PMC10910785 DOI: 10.1186/s12864-024-10141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. RESULTS A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. CONCLUSIONS We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
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Affiliation(s)
- David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK.
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ainsley Riley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Justin Avant
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Lisa Cross
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Marta Soeffker
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Collaborative Centre for Sustainable Use of the Seas, University of East Anglia, Norwich, UK
| | | | | | | | - Chris Darby
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Centre for Sustainable Aquaculture Futures , University of Exeter, Exeter, UK
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Cano I, Blaker E, Hartnell D, Farbos A, Moore KA, Cobb A, Santos EM, van Aerle R. Transcriptomic Responses to Koi Herpesvirus in Isolated Blood Leukocytes from Infected Common Carp. Viruses 2024; 16:380. [PMID: 38543746 PMCID: PMC10974277 DOI: 10.3390/v16030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 04/01/2024] Open
Abstract
Koi herpesvirus (KHV, CyHV-3) causes severe economic losses in carp farms. Its eradication is challenging due to the establishment of latency in blood leukocytes and other tissues. To understand the molecular mechanisms leading to KHV infection in leukocytes, common carp were bath-exposed to KHV at 17 °C. After confirming the presence of viral transcripts in blood leukocytes at ten days post infection, RNA-Seq was performed on peripheral blood leukocytes on the Illumina NovaSeq. KHV infection triggered a robust immune response mediated by pattern recognition receptors, mainly toll-like receptors (tlr2, tlr5, tlr7, and tlr13), urokinase plasminogen activator surface receptor-like, galectin proteins, and lipid mediators such as leukotriene B4 receptor 1. Enriched pathways showed increased mitochondria oxidative phosphorylation and the activation of signalling pathways such as mitogen-activated protein kinases (MAPKs) and vascular endothelial growth factor (VEGF). KHV-infected leukocytes showed low production of reactive oxygen species (ROS) and glutathione metabolism, high iron export and phagocytosis activity, and low autophagy. Macrophage polarization was deduced from the up-regulation of genes such as arginase non-hepatic 1-like, macrophage mannose receptor-1, crem, il-10, and il-13 receptors, while markers for cytotoxic T cells were observed to be down-regulated. Further work is required to characterise these leukocyte subsets and the molecular events leading to KHV latency in blood leukocytes.
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Affiliation(s)
- Irene Cano
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX2 4TH, UK;
| | - Ellen Blaker
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
| | - David Hartnell
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
| | - Audrey Farbos
- Biosciences, Faculty of Life and Health Sciences, University of Exeter, Exeter EX2 4TH, UK; (A.F.); (K.A.M.)
| | - Karen A. Moore
- Biosciences, Faculty of Life and Health Sciences, University of Exeter, Exeter EX2 4TH, UK; (A.F.); (K.A.M.)
| | - Adele Cobb
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
| | - Eduarda M. Santos
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX2 4TH, UK;
- Biosciences, Faculty of Life and Health Sciences, University of Exeter, Exeter EX2 4TH, UK; (A.F.); (K.A.M.)
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Dorset DT4 8UB, UK; (E.B.); (D.H.); (A.C.); (R.v.A.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX2 4TH, UK;
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Brunner FS, Payne A, Cairns E, Airey G, Gregory R, Pickwell ND, Wilson M, Carlile M, Holmes N, Hill V, Child H, Tomlinson J, Ahmed S, Denise H, Rowe W, Frazer J, Aerle RV, Evens N, Porter J, Templeton K, Jeffries AR, Loose M, Paterson S. Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England. Water Res 2023; 247:120804. [PMID: 37925861 DOI: 10.1016/j.watres.2023.120804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
The world has moved into a new stage of managing the SARS-CoV-2 pandemic with minimal restrictions and reduced testing in the population, leading to reduced genomic surveillance of virus variants in individuals. Wastewater-based epidemiology (WBE) can provide an alternative means of tracking virus variants in the population but decision-makers require confidence that it can be applied to a national scale and is comparable to individual testing data. We analysed 19,911 samples from 524 wastewater sites across England at least twice a week between November 2021 and February 2022, capturing sewage from >70% of the English population. We used amplicon-based sequencing and the phylogeny based de-mixing tool Freyja to estimate SARS-CoV-2 variant frequencies and compared these to the variant dynamics observed in individual testing data from clinical and community settings. We show that wastewater data can reconstruct the spread of the Omicron variant across England since November 2021 in close detail and aligns closely with epidemiological estimates from individual testing data. We also show the temporal and spatial spread of Omicron within London. Our wastewater data further reliably track the transition between Omicron subvariants BA1 and BA2 in February 2022 at regional and national levels. Our demonstration that WBE can track the fast-paced dynamics of SARS-CoV-2 variant frequencies at a national scale and closely match individual testing data in time shows that WBE can reliably fill the monitoring gap left by reduced individual testing in a more affordable way.
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Affiliation(s)
- Franziska S Brunner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Alexander Payne
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Edward Cairns
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Richard Gregory
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Natalie D Pickwell
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Myles Wilson
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Matthew Carlile
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Nadine Holmes
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Harry Child
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jasmine Tomlinson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Suhel Ahmed
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Hubert Denise
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - William Rowe
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - Jacob Frazer
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Barrack Road, Weymouth, DT 8UB, UK
| | - Nicholas Evens
- Monitoring Laboratories, National Monitoring, Environment Agency EX6 8FD, UK
| | - Jonathan Porter
- Monitoring Laboratories, National Monitoring, Environment Agency EX6 8FD, UK
| | - Kate Templeton
- NHS Lothian, Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Aaron R Jeffries
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matt Loose
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK.
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Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, van Aerle R, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. mBio 2023; 14:e0146823. [PMID: 37877702 PMCID: PMC10746264 DOI: 10.1128/mbio.01468-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Wastewater-based epidemiology is a powerful tool for monitoring the emergence and spread of viral pathogens at the population scale. Typical polymerase chain reaction (PCR)-based methods of quantitative and genomic monitoring of viruses in wastewater provide high sensitivity and specificity. However, these methods are limited to the surveillance of target viruses in a single assay and require prior knowledge of the target genome(s). Metagenomic sequencing methods may represent a target-agnostic approach to viral wastewater monitoring, allowing for the detection of a broad range of target viruses, including potentially novel and emerging pathogens. In this study, targeted and untargeted metagenomic sequencing methods were compared with tiled-PCR sequencing for the detection and genotyping of viral pathogens in wastewater samples. Deep shotgun metagenomic sequencing was unable to generate sufficient genome coverage of human pathogenic viruses for robust genomic epidemiology, with samples dominated by bacteria. Hybrid-capture enrichment of shotgun libraries for respiratory viruses led to significant increases in genome coverage for a range of targets. Tiled-PCR sequencing led to further improvements in genome coverage compared to hybrid capture for severe acute respiratory syndrome coronavirus 2, enterovirus D68, norovirus GII, and human adenovirus F41 in wastewater samples. In conclusion, untargeted shotgun sequencing was unsuitable for genomic monitoring of the low virus concentrations in wastewater samples analyzed in this study. Hybrid-capture enrichment represented a viable method for simultaneous genomic epidemiology of a range of viral pathogens, while tiled-PCR sequencing provided the optimal genome coverage for individual viruses with the minimum sequencing depth. IMPORTANCE Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel M. Maloney
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Suzie McGinley
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Kate Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Weymouth, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Matthew J. Wade
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
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5
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Child HT, O’Neill PA, Moore K, Rowe W, Denise H, Bass D, Wade MJ, Loose M, Paterson S, van Aerle R, Jeffries AR. Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing. PLoS One 2023; 18:e0284211. [PMID: 37058515 PMCID: PMC10104291 DOI: 10.1371/journal.pone.0284211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/24/2023] [Indexed: 04/15/2023] Open
Abstract
Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Paul A. O’Neill
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - William Rowe
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - Hubert Denise
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Weymouth, United Kingdom
| | - Matthew J. Wade
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - Matt Loose
- Deep Seq, Centre for Genetics and Genomics, Queen’s Medical Centre, The University of Nottingham, Nottingham, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Weymouth, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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6
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Campbell AM, Hauton C, Baker-Austin C, van Aerle R, Martinez-Urtaza J. An integrated eco-evolutionary framework to predict population-level responses of climate-sensitive pathogens. Curr Opin Biotechnol 2023; 80:102898. [PMID: 36739640 DOI: 10.1016/j.copbio.2023.102898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023]
Abstract
It is critical to gain insight into how climate change impacts evolutionary responses within climate-sensitive pathogen populations, such as increased resilience, opportunistic responses and the emergence of dominant variants from highly variable genomic backgrounds and subsequent global dispersal. This review proposes a framework to support such analysis, by combining genomic evolutionary analysis with climate time-series data in a novel spatiotemporal dataframe for use within machine learning applications, to understand past and future evolutionary pathogen responses to climate change. Recommendations are presented to increase the feasibility of interdisciplinary applications, including the importance of robust spatiotemporal metadata accompanying genome submission to databases. Such workflows will inform accessible public health tools and early-warning systems, to aid decision-making and mitigate future human health threats.
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Affiliation(s)
- Amy M Campbell
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, UK; Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, UK
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK; Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain.
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7
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Bassano I, Ramachandran VK, Khalifa MS, Lilley CJ, Brown MR, van Aerle R, Denise H, Rowe W, George A, Cairns E, Wierzbicki C, Pickwell ND, Carlile M, Holmes N, Payne A, Loose M, Burke TA, Paterson S, Wade MJ, Grimsley JMS. Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples. Microb Genom 2023; 9. [PMID: 37074153 DOI: 10.1099/mgen.0.000933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Wastewater-based epidemiology has been used extensively throughout the COVID-19 (coronavirus disease 19) pandemic to detect and monitor the spread and prevalence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and its variants. It has proven an excellent, complementary tool to clinical sequencing, supporting the insights gained and helping to make informed public-health decisions. Consequently, many groups globally have developed bioinformatics pipelines to analyse sequencing data from wastewater. Accurate calling of mutations is critical in this process and in the assignment of circulating variants; yet, to date, the performance of variant-calling algorithms in wastewater samples has not been investigated. To address this, we compared the performance of six variant callers (VarScan, iVar, GATK, FreeBayes, LoFreq and BCFtools), used widely in bioinformatics pipelines, on 19 synthetic samples with known ratios of three different SARS-CoV-2 variants of concern (VOCs) (Alpha, Beta and Delta), as well as 13 wastewater samples collected in London between the 15th and 18th December 2021. We used the fundamental parameters of recall (sensitivity) and precision (specificity) to confirm the presence of mutational profiles defining specific variants across the six variant callers. Our results show that BCFtools, FreeBayes and VarScan found the expected variants with higher precision and recall than GATK or iVar, although the latter identified more expected defining mutations than other callers. LoFreq gave the least reliable results due to the high number of false-positive mutations detected, resulting in lower precision. Similar results were obtained for both the synthetic and wastewater samples.
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Affiliation(s)
- Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
| | - Vinoy K Ramachandran
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - Mohammad S Khalifa
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London UB8 3PH, UK
| | - Chris J Lilley
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - Mathew R Brown
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Ronny van Aerle
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Clyst Honiton EX5 2FN, UK
| | - Hubert Denise
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - William Rowe
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - Airey George
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Edward Cairns
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Claudia Wierzbicki
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Natalie D Pickwell
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Matthew Carlile
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Nadine Holmes
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Alexander Payne
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Matthew Loose
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Terry A Burke
- NERC Environmental Omics Facility, Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Steve Paterson
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Matthew J Wade
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
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Millard RS, Bickley LK, Bateman KS, Verbruggen B, Farbos A, Lange A, Moore KA, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Resistance to white spot syndrome virus in the European shore crab is associated with suppressed virion trafficking and heightened immune responses. Front Immunol 2022; 13:1057421. [PMID: 36636327 PMCID: PMC9831657 DOI: 10.3389/fimmu.2022.1057421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/01/2022] [Indexed: 12/28/2022] Open
Abstract
Introduction All decapod crustaceans are considered potentially susceptible to White Spot Syndrome Virus (WSSV) infection, but the degree of White Spot Disease (WSD) susceptibility varies widely between species. The European shore crab Carcinus maenas can be infected with the virus for long periods of time without signs of disease. Given the high mortality rate of susceptible species, the differential susceptibility of these resistant hosts offers an opportunity to investigate mechanisms of disease resistance. Methods Here, the temporal transcriptional responses (mRNA and miRNA) of C. maenas following WSSV injection were analysed and compared to a previously published dataset for the highly WSSV susceptible Penaeus vannamei to identify key genes, processes and pathways contributing to increased WSD resistance. Results We show that, in contrast to P. vannamei, the transcriptional response during the first 2 days following WSSV injection in C. maenas is limited. During the later time points (7 days onwards), two groups of crabs were identified, a recalcitrant group where no replication of the virus occurred, and a group where significant viral replication occurred, with the transcriptional profiles of the latter group resembling those of WSSV-susceptible species. We identify key differences in the molecular responses of these groups to WSSV injection. Discussion We propose that increased WSD resistance in C. maenas may result from impaired WSSV endocytosis due to the inhibition of internal vesicle budding by dynamin-1, and a delay in movement to the nucleus caused by the downregulation of cytoskeletal transcripts required for WSSV cytoskeleton docking, during early stages of the infection. This response allows resistant hosts greater time to fine-tune immune responses associated with miRNA expression, apoptosis and the melanisation cascade to defend against, and clear, invading WSSV. These findings suggest that the initial stages of infection are key to resistance to WSSV in the crab and highlight possible pathways that could be targeted in farmed crustacean to enhance resistance to WSD.
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Affiliation(s)
- Rebecca S. Millard
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,*Correspondence: Rebecca S. Millard, ; Eduarda M. Santos,
| | - Lisa K. Bickley
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly S. Bateman
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Bas Verbruggen
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Audrey Farbos
- University of Exeter Sequencing Facility, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Anke Lange
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Karen A. Moore
- University of Exeter Sequencing Facility, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Grant D. Stentiford
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Charles R. Tyler
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Laboratory, Weymouth, United Kingdom,Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Eduarda M. Santos
- Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom,Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom,*Correspondence: Rebecca S. Millard, ; Eduarda M. Santos,
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9
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Urrutia A, Mitsi K, Foster R, Ross S, Carr M, Ward GM, van Aerle R, Marigomez I, Leger MM, Ruiz-Trillo I, Feist SW, Bass D. Txikispora philomaios n. sp., n. g., a Micro-Eukaryotic Pathogen of Amphipods, Reveals Parasitism and Hidden Diversity in Class Filasterea. J Eukaryot Microbiol 2021; 69:e12875. [PMID: 34726818 DOI: 10.1111/jeu.12875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study provides a morphological, ultrastructural, and phylogenetic characterization of a novel micro-eukaryotic parasite (2.3-2.6 µm) infecting amphipod genera Echinogammarus and Orchestia. Longitudinal studies across two years revealed that infection prevalence peaked in late April and May, reaching 64% in Echinogammarus sp. and 15% in Orchestia sp., but was seldom detected during the rest of the year. The parasite infected predominantly haemolymph, connective tissue, tegument, and gonad, although hepatopancreas and nervous tissue were affected in heavier infections, eliciting melanization and granuloma formation. Cell division occurred inside walled parasitic cysts, often within host haemocytes, resulting in haemolymph congestion. Small subunit (18S) rRNA gene phylogenies including related environmental sequences placed the novel parasite as a highly divergent lineage within Class Filasterea, which together with Choanoflagellatea represent the closest protistan relatives of Metazoa. We describe the new parasite as Txikispora philomaios n. sp. n. g., the first confirmed parasitic filasterean lineage, which otherwise comprises four free-living flagellates and a rarely observed endosymbiont of snails. Lineage-specific PCR probing of other hosts and surrounding environments only detected T. philomaios in the platyhelminth Procerodes sp. We expand the known diversity of Filasterea by targeted searches of metagenomic datasets, resulting in 13 previously unknown lineages from environmental samples.
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Affiliation(s)
- Ander Urrutia
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK.,Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology (Faculty of Science and Technology), Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Areatza Pasealekua z/g, Plentzia, 48620, Basque Country, Spain
| | - Konstantina Mitsi
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain
| | - Rachel Foster
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Stuart Ross
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK
| | - Martin Carr
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Georgia M Ward
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK
| | - Ionan Marigomez
- Cell Biology in Environmental Toxicology Research Group, Department of Zoology and Animal Cell Biology (Faculty of Science and Technology), Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Areatza Pasealekua z/g, Plentzia, 48620, Basque Country, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain.,Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, 08028, Catalonia, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Stephen W Feist
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries, and Aquaculture Science (CEFAS), Barrack Road, Weymouth, DT4 8UB, UK.,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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10
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Dimitriadou S, Santos EM, Croft DP, van Aerle R, Ramnarine IW, Filby AL, Darden SK. Social partner cooperativeness influences brain oxytocin transcription in Trinidadian guppies (Poecilia reticulata). Behav Brain Res 2021; 423:113643. [PMID: 34757109 DOI: 10.1016/j.bbr.2021.113643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/08/2021] [Revised: 10/01/2021] [Accepted: 10/25/2021] [Indexed: 11/02/2022]
Abstract
For non-kin cooperation to be maintained, individuals need to respond adaptively to the cooperative behaviour of their social partners. Currently, however, little is known about the biological responses of individuals to experiencing cooperation. Here, we quantify the neuroregulatory response of Trinidadian guppies (Poecilia reticulata) experiencing cooperation or defection by examining the transcriptional response of the oxytocin gene (oxt; also known as isotocin), which has been implicated in cooperative decision-making. We exposed wild-caught females to social environments where partners either cooperated or defected during predator inspection, or to a control (non-predator inspection) context, and quantified the relative transcription of the oxt gene. We tested an experimental group, originating from a site where individuals are under high predation threat and have previous experience of large aquatic predators (HP), and a control group, where individuals are under low predation threat and naïve to large aquatic predators (LP). LP, but not HP, fish showed different behavioural responses to the behaviour of their social environment, cooperating with cooperative partners and defecting when paired with defecting ones. In HP, but not LP, fish brain mid-section oxt relative transcription varied depending on social partner behaviour. HP fish experiencing cooperation during predator inspection had lower oxt transcription than those experiencing defection. This effect was not present in the control population or in the control context, where the behaviour of social partners did not affect oxt transcription. Our findings provide insight into the neuromodulation underpinning behavioural responses to social experiences, and ultimately to the proximate mechanisms underlying social decision-making.
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Affiliation(s)
- Sylvia Dimitriadou
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK.
| | - Eduarda M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Darren P Croft
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Ronny van Aerle
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK; International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Weymouth, UK
| | - Indar W Ramnarine
- Department of Life Sciences, University of West Indies, St. Augustine, Trinidad and Tobago
| | - Amy L Filby
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Safi K Darden
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
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11
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Millard RS, Bickley LK, Bateman KS, Farbos A, Minardi D, Moore K, Ross SH, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp. Viruses 2021; 13:v13061140. [PMID: 34199268 PMCID: PMC8231841 DOI: 10.3390/v13061140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/01/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed—with limited differential expression from 3–12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.
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Affiliation(s)
- Rebecca S. Millard
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
| | - Lisa K. Bickley
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Kelly S. Bateman
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Audrey Farbos
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Diana Minardi
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Stuart H. Ross
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Grant D. Stentiford
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Charles R. Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Eduarda M. Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
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12
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Cano I, Santos EM, Moore K, Farbos A, van Aerle R. Evidence of Transcriptional Shutoff by Pathogenic Viral Haemorrhagic Septicaemia Virus in Rainbow Trout. Viruses 2021; 13:v13061129. [PMID: 34208332 PMCID: PMC8231187 DOI: 10.3390/v13061129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
The basis of pathogenicity of viral haemorrhagic septicaemia virus (VHSV) was analysed in the transcriptome of a rainbow trout cell line inoculated with pathogenic and non-pathogenic VHSV isolates. Although both VHSV isolates showed similar viral replication patterns, the number of differentially expressed genes was 42-fold higher in cells inoculated with the non-pathogenic VHSV at 3 h post inoculation (hpi). Infection with the non-pathogenic isolate resulted in Gene Ontologies (GO) enrichment of terms such as immune response, cytokine-mediated signalling pathway, regulation of translational initiation, unfolded protein binding, and protein folding, and induced an over-representation of the p53, PPAR, and TGF-β signalling pathways. Inoculation with the pathogenic isolate resulted in the GO enrichment of terms related to lipid metabolism and the salmonella infection KEGG pathway involved in the rearrangement of the cytoskeleton. Antiviral response was evident at 12hpi in cells infected with the pathogenic isolate. Overall, the data showed a delay in the response of genes involved in immune responses and viral sensing in cells inoculated with the pathogenic isolate and suggest transcriptional shutoff and immune avoidance as a critical mechanism of pathogenicity in VHSV. These pathways offer opportunities to further understand and manage VHSV pathogenicity in rainbow trout.
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Affiliation(s)
- Irene Cano
- International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, Dorset, UK;
- Correspondence:
| | - Eduarda M. Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, UK;
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, UK
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, Devon, UK; (K.M.); (A.F.)
| | - Audrey Farbos
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, Devon, UK; (K.M.); (A.F.)
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, Dorset, UK;
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, Devon, UK
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13
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Hooper C, Debnath PP, Biswas S, van Aerle R, Bateman KS, Basak SK, Rahman MM, Mohan CV, Islam HMR, Ross S, Stentiford GD, Currie D, Bass D. A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh. Viruses 2020; 12:v12101120. [PMID: 33023199 PMCID: PMC7601004 DOI: 10.3390/v12101120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 09/05/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single‑stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of Macrobrachium rosenbergii golda virus (MrGV) suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.
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Affiliation(s)
- Chantelle Hooper
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Sciences (Cefas), Weymouth, Dorset DT4 8UB, UK; (R.v.A.); (K.S.B.); (S.R.); (G.D.S.); (D.B.)
- Correspondence: (C.H.); (P.P.D.)
| | - Partho P. Debnath
- WorldFish Bangladesh, Dhaka 1213, Bangladesh; (S.K.B.); (M.M.R.)
- Correspondence: (C.H.); (P.P.D.)
| | - Sukumar Biswas
- Winrock Bangladesh, Dhaka 1212, Bangladesh; (S.B.); (D.C.)
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Sciences (Cefas), Weymouth, Dorset DT4 8UB, UK; (R.v.A.); (K.S.B.); (S.R.); (G.D.S.); (D.B.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QY, UK
| | - Kelly S. Bateman
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Sciences (Cefas), Weymouth, Dorset DT4 8UB, UK; (R.v.A.); (K.S.B.); (S.R.); (G.D.S.); (D.B.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QY, UK
| | | | | | | | - H. M. Rakibul Islam
- Bangladesh Fisheries Research Institute, Shrimp Research Station, Bagerhat 9300, Bangladesh;
| | - Stuart Ross
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Sciences (Cefas), Weymouth, Dorset DT4 8UB, UK; (R.v.A.); (K.S.B.); (S.R.); (G.D.S.); (D.B.)
| | - Grant D. Stentiford
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Sciences (Cefas), Weymouth, Dorset DT4 8UB, UK; (R.v.A.); (K.S.B.); (S.R.); (G.D.S.); (D.B.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QY, UK
| | - David Currie
- Winrock Bangladesh, Dhaka 1212, Bangladesh; (S.B.); (D.C.)
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Sciences (Cefas), Weymouth, Dorset DT4 8UB, UK; (R.v.A.); (K.S.B.); (S.R.); (G.D.S.); (D.B.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QY, UK
- Department of Life Sciences, the Natural History Museum, London SW7 5BD, UK
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14
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Batista FM, Stapleton T, Lowther JA, Fonseca VG, Shaw R, Pond C, Walker DI, van Aerle R, Martinez-Urtaza J. Whole Genome Sequencing of Hepatitis A Virus Using a PCR-Free Single-Molecule Nanopore Sequencing Approach. Front Microbiol 2020; 11:874. [PMID: 32523561 PMCID: PMC7261825 DOI: 10.3389/fmicb.2020.00874] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatitis A virus (HAV) is one of the most common causes of acute viral hepatitis in humans. Although HAV has a relatively small genome, there are several factors limiting whole genome sequencing such as PCR amplification artefacts and ambiguities in de novo assembly. The recently developed Oxford Nanopore technologies (ONT) allows single-molecule sequencing of long-size fragments of DNA or RNA using PCR-free strategies. We have sequenced the whole genome of HAV using a PCR-free approach by direct reverse-transcribed sequencing. We were able to sequence HAV cDNA and obtain reads over 7 kilobases in length containing almost the whole genome of the virus. The comparison of these raw long nanopore reads with the HAV reference wild type revealed a nucleotide sequence identity between 81.1 and 96.6%. By de novo assembly of all HAV reads we obtained a consensus sequence of 7362 bases, with a nucleotide sequence identity of 99.0% with the genome of the HAV strain pHM175/18f. When the assembly was performed using as reference the HAV strain pHM175/18f a consensus with a sequence similarity of 99.8 % was obtained. We have also used an ONT amplicon-based assay to sequence two fragments of the VP3 and VP1 regions which showed a sequence similarity of 100% with matching regions of the consensus sequence obtained using the direct cDNA sequencing approach. This study showed the applicability of ONT sequencing technologies to obtain the whole genome of HAV by direct cDNA nanopore sequencing, highlighting the utility of this PCR-free approach for HAV characterization and potentially other viruses of the Picornaviridae family.
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Affiliation(s)
- Frederico M Batista
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Tina Stapleton
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - James A Lowther
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Vera G Fonseca
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Rebecca Shaw
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Christopher Pond
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - David I Walker
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Jaime Martinez-Urtaza
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom.,Department of Genetics and Microbiology, Facultat de Biociències - Edifici C, Campus Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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15
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Millard RS, Ellis RP, Bateman KS, Bickley LK, Tyler CR, van Aerle R, Santos EM. How do abiotic environmental conditions influence shrimp susceptibility to disease? A critical analysis focussed on White Spot Disease. J Invertebr Pathol 2020; 186:107369. [PMID: 32272137 DOI: 10.1016/j.jip.2020.107369] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 09/23/2019] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/14/2023]
Abstract
White Spot Syndrome Virus (WSSV) causes White Spot Disease (WSD) and is historically the most devastating disease in the shrimp industry. Global losses from this disease have previously exceeded $3 bn annually, having a major impact on a global industry worth US$19 bn per annum. Shrimp are cultured predominantly in enclosed ponds that are subject to considerable fluctuations in abiotic conditions and WSD outbreaks are increasingly linked to periods of extreme weather, which may cause major fluctuations in pond culture conditions. Combined with the intensity of production in these systems, the resulting suboptimal physicochemical conditions have a major bearing on the susceptibility of shrimp to infection and disease. Current knowledge indicates that pond temperature and salinity are major factors determining outbreak severity. WSSV appears to be most virulent in water temperatures between 25 and 28 °C and salinities far removed from the isoosmotic point of shrimp. Elevated temperatures (>30 °C) may protect against WSD, depending on the stage of infection, however the mechanisms mediating this effect have not been well established. Other factors relating to water quality that may play key roles in determining outbreak severity include dissolved oxygen concentration, nitrogenous compound concentration, partial pressure of carbon dioxide and pH, but data on their impacts on WSSV susceptibility in cultured shrimps is scarce. This illustrates a major research gap in our understanding of the influence of environmental conditions on disease. For example, it is not clear whether temperature manipulations can be used effectively to prevent or mitigate WSD in cultured shrimp. Therefore, developing our understanding of the impact of environmental conditions on shrimp susceptibility to WSSV may provide insight for WSD mitigation when, even after decades of research, there is no effective practical prophylaxis or treatment.
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Affiliation(s)
- Rebecca S Millard
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, United Kingdom.
| | - Robert P Ellis
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Kelly S Bateman
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, United Kingdom; OIE Collaborating Centre - Emerging Aquatic Animal Diseases, Barrack Road, The Nothe, Weymouth DT4 8UB, United Kingdom
| | - Lisa K Bickley
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth DT4 8UB, United Kingdom; OIE Collaborating Centre - Emerging Aquatic Animal Diseases, Barrack Road, The Nothe, Weymouth DT4 8UB, United Kingdom
| | - Eduarda M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom.
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16
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Chaput DL, Bass D, Alam MM, Al Hasan N, Stentiford GD, van Aerle R, Moore K, Bignell JP, Haque MM, Tyler CR. The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh. Viruses 2020; 12:v12030258. [PMID: 32120863 PMCID: PMC7150994 DOI: 10.3390/v12030258] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/26/2022] Open
Abstract
Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.
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Affiliation(s)
- Dominique L. Chaput
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK
- Correspondence: (D.L.C.); (C.R.T.); Tel.: +44-(0)-1392-724450 (C.R.T.)
| | - David Bass
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Md. Mehedi Alam
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh; (M.M.A.); (N.A.H.); (M.M.H.)
| | - Neaz Al Hasan
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh; (M.M.A.); (N.A.H.); (M.M.H.)
| | - Grant D. Stentiford
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK;
| | - John P. Bignell
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK;
| | - Mohammad Mahfujul Haque
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh; (M.M.A.); (N.A.H.); (M.M.H.)
| | - Charles R. Tyler
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4QD, UK
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, Devon EX4 4QD, UK; (D.B.); (G.D.S.); (R.v.A.)
- Correspondence: (D.L.C.); (C.R.T.); Tel.: +44-(0)-1392-724450 (C.R.T.)
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17
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Santos A, van Aerle R, Barrientos L, Martinez-Urtaza J. Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Comput Struct Biotechnol J 2020; 18:296-305. [PMID: 32071706 PMCID: PMC7013242 DOI: 10.1016/j.csbj.2020.01.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 12/23/2022] Open
Abstract
Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throughput sequencing technologies. An additional innovation introduced by these technologies was the need of developing new strategies to manage and investigate the massive amount of sequencing data generated. This situation stimulated the rapid expansion of the field of bioinformatics with the release of new tools to be applied to the downstream analysis and interpretation of sequencing data mainly generated using Illumina technology. In recent years, a third generation of sequencing technologies has been developed and have been applied in parallel and complementarily to the former sequencing strategies. In particular, Oxford Nanopore Technologies (ONT) introduced nanopore sequencing which has become very popular among molecular ecologists. Nanopore technology offers a low price, portability and fast sequencing throughput. This powerful technology has been recently tested for 16S rRNA analyses showing promising results. However, compared with previous technologies, there is a scarcity of bioinformatic tools and protocols designed specifically for the analysis of Nanopore 16S sequences. Due its notable characteristics, researchers have recently started performing assessments regarding the suitability MinION on 16S rRNA sequencing studies, and have obtained remarkable results. Here we present a review of the state-of-the-art of MinION technology applied to microbiome studies, the current possible application and main challenges for its use on 16S rRNA metabarcoding.
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Affiliation(s)
- Andres Santos
- Applied and Molecular Biology Laboratory, Centre of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, 4810296 Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Avenida Francisco Salazar 01145, 481123 Temuco, Chile
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Leticia Barrientos
- Applied and Molecular Biology Laboratory, Centre of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, 4810296 Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Avenida Francisco Salazar 01145, 481123 Temuco, Chile
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, UK
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18
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Stockdale WT, Lemieux ME, Killen AC, Zhao J, Hu Z, Riepsaame J, Hamilton N, Kudoh T, Riley PR, van Aerle R, Yamamoto Y, Mommersteeg MTM. Heart Regeneration in the Mexican Cavefish. Cell Rep 2019; 25:1997-2007.e7. [PMID: 30462998 PMCID: PMC6280125 DOI: 10.1016/j.celrep.2018.10.072] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/18/2018] [Accepted: 10/19/2018] [Indexed: 01/30/2023] Open
Abstract
Although Astyanax mexicanus surface fish regenerate their hearts after injury, their Pachón cave-dwelling counterparts cannot and, instead, form a permanent fibrotic scar, similar to the human heart. Myocardial proliferation peaks at similar levels in both surface fish and Pachón 1 week after injury. However, in Pachón, this peak coincides with a strong scarring and immune response, and ultimately, cavefish cardiomyocytes fail to replace the scar. We identified lrrc10 to be upregulated in surface fish compared with Pachón after injury. Similar to cavefish, knockout of lrrc10 in zebrafish impairs heart regeneration without affecting wound cardiomyocyte proliferation. Furthermore, using quantitative trait locus (QTL) analysis, we have linked the degree of heart regeneration to three loci in the genome, identifying candidate genes fundamental to the difference between scarring and regeneration. Our study provides evidence that successful heart regeneration entails a delicate interplay between cardiomyocyte proliferation and scarring. Astyanax mexicanus surface fish regenerate their hearts, but Pachón cavefish cannot Successful regeneration is a delicate interplay between proliferation and scarring lrrc10 is required for heart regeneration Using QTL analysis, we have identified three genomic loci linked to heart regeneration
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Affiliation(s)
- William T Stockdale
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK
| | | | - Abigail C Killen
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK
| | - Juanjuan Zhao
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK
| | - Zhilian Hu
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK
| | - Joey Riepsaame
- Genome Engineering Oxford, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Noémie Hamilton
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Tetsuhiro Kudoh
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, UK
| | - Yoshiyuki Yamamoto
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - Mathilda T M Mommersteeg
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, UK; Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
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19
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Bean TP, Khatir Z, Lyons BP, van Aerle R, Minardi D, Bignell JP, Smyth D, Giraldes BW, Leitão A. De novo transcriptome assembly of the Qatari pearl oyster Pinctada imbricata radiata. Mar Genomics 2019; 51:100734. [PMID: 31818705 DOI: 10.1016/j.margen.2019.100734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/18/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 11/28/2022]
Abstract
The pearl oyster Pinctada imbricata radiata is an iconic species in Qatar, representing an integral part of the nation's cultural heritage and one of the main economic foundations upon which the nation developed. During the early part of the 20th century, nearly half the Qatar population was involved in the pearl oyster industry. However, the fishery has undergone steady decline since the 1930s, and the species is now under threat due to multiple confounding pressures. This manuscript presents the first de novo transcriptome of the Qatari pearl oyster assembled into 30,739 non-redundant coding sequences and with a BUSCO completeness score of 98.4%. Analysis of the transcriptome reveals the close evolutionary distance to the conspecific animal Pinctada imbricata fucata but also highlights differences in immune genes and the presence of distinctive transposon families, suggesting recent adaptive divergence. This data is made available for all to utilise in future studies on the species.
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Affiliation(s)
- Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
| | - Zenaba Khatir
- Environmental Science Center (ESC), Qatar University, P. O. Box: 2713, Doha, Qatar
| | | | | | | | | | - David Smyth
- Environmental Science Center (ESC), Qatar University, P. O. Box: 2713, Doha, Qatar; School of Ocean Science, Bangor University, Wales LL59 5AB, UK
| | | | - Alexandra Leitão
- Environmental Science Center (ESC), Qatar University, P. O. Box: 2713, Doha, Qatar
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20
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McMurtrie J, Verner-Jeffreys DW, Cochrane-Dyet T, White P, van Aerle R, Ryder D, Stone D, Green M, Feist SW, Cano I. Health assessment of the cleaner fish ballan wrasse Labrus bergylta from the British south-west coast. Dis Aquat Organ 2019; 136:133-146. [PMID: 31621646 DOI: 10.3354/dao03394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wild-caught ballan wrasse Labrus bergylta are translocated en masse from the British south-west coast to Scotland for use as cleaner fish to tackle Atlantic salmon Salmo salar sea lice infestations; however, very little is known about the background health status of this species. This is the first health assessment of wild ballan wrasse from the British south-west. Wild-caught ballan wrasse (n = 75) from coastal populations off Dorset and Cornwall were subjected to a full health screen for viral, bacterial and parasitic infections and associated pathology. A range of metazoan and protozoan parasites were observed in histological sections, including copepods (sea lice Caligus centrodonti), nematodes, cestodes, digenean metacercariae, Cryptocaryon-like ciliates and an intestinal coccidian (Eimeria sp.) observed in 26.6% of the samples. The mycoplasma Acholeplasma laidlawii was associated with cytopathic effect in cell culture inoculated with tissue homogenates. The opportunistic pathogen Photobacterium damselae damselae was isolated from a single fish with a systemic infection. The isolate was confirmed to possess the virulence factors hlyAch and plpV, previously associated with cell toxicity and pathogenicity to fish. There are no immediate concerns for the continued mass translation of ballan wrasse, however careful monitoring of the population is recommended.
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Affiliation(s)
- Jamie McMurtrie
- Cefas Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science, Weymouth DT4 8UB, UK
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21
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Christie L, van Aerle R, Paley RK, Verner-Jeffreys DW, Tidbury H, Green M, Feist SW, Cano I. The skin immune response of rainbow trout, Oncorhynchus mykiss (Walbaum), associated with puffy skin disease (PSD). Fish Shellfish Immunol 2018; 78:355-363. [PMID: 29709592 DOI: 10.1016/j.fsi.2018.04.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Puffy skin disease (PSD) is an emerging skin condition which affects rainbow trout, Oncorhynchus mykiss (Walbaum). The transmission pattern of PSD suggests an infectious aetiology, however, the actual causative infectious agent(s) remain(s) unknown. In the present study, the rainbow trout epidermal immune response to PSD was characterised. Skin samples from infected fish were analysed and classified as mild, moderate or severe PSD by gross pathology and histological assessment. The level of expression of 26 immune-associated genes including cytokines, immunoglobulins and cell markers were examined by TaqMan qPCR assays. A significant up-regulation of the gene expression of C3, lysozyme, IL-1β and T-bet and down-regulation of TGFβ and TLR3 was observed in PSD fish compared to control fish. MHCI gene expression was up-regulated only in severe PSD lesions. Histological examinations of the epidermis showed a significant increase in the number of eosinophil cells and dendritic melanocytes in PSD fish. In severe lesions, mild diffuse lymphocyte infiltration was observed. IgT and CD8 positive cells were detected locally in the skin of PSD fish by in situ hybridisation (ISH), however, the gene expression of those genes was not different from control fish. Total IgM in serum of diseased animals was not different from control fish, measured by a sandwich ELISA, nor was significant up regulation of IgM gene expression in PSD lesions observed. Taken together, these results show activation of the complement pathway, up-regulation of a Th17 type response and eosinophilia during PSD. This is typical of a response to extracellular pathogens (i.e. bacteria and parasites) and allergens, commonly associated with acute dermatitis.
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Affiliation(s)
- Lyndsay Christie
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Richard K Paley
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - David W Verner-Jeffreys
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Hannah Tidbury
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Matthew Green
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Stephen W Feist
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
| | - Irene Cano
- Centre for Environment, Fisheries and Aquaculture Science Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
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22
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Bojko J, Dunn AM, Stebbing PD, van Aerle R, Bacela-Spychalska K, Bean TP, Urrutia A, Stentiford GD. ‘Candidatus Aquirickettsiella gammari’ (Gammaproteobacteria: Legionellales: Coxiellaceae): A bacterial pathogen of the freshwater crustacean Gammarus fossarum (Malacostraca: Amphipoda). J Invertebr Pathol 2018; 156:41-53. [DOI: 10.1016/j.jip.2018.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 01/24/2023]
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23
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Herman E, Siegesmund MA, Bottery MJ, van Aerle R, Shather MM, Caler E, Dacks JB, van der Giezen M. Membrane Trafficking Modulation during Entamoeba Encystation. Sci Rep 2017; 7:12854. [PMID: 28993644 PMCID: PMC5634486 DOI: 10.1038/s41598-017-12875-6] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
Entamoeba histolytica is an intestinal parasite that infects 50-100 million people and causes up to 55,000 deaths annually. The transmissive form of E. histolytica is the cyst, with a single infected individual passing up to 45 million cysts per day, making cyst production an attractive target for infection control. Lectins and chitin are secreted to form the cyst wall, although little is known about the underlying membrane trafficking processes supporting encystation. As E. histolytica does not readily form cysts in vitro, we assessed membrane trafficking gene expression during encystation in the closely related model Entamoeba invadens. Genes involved in secretion are up-regulated during cyst formation, as are some trans-Golgi network-to-endosome trafficking genes. Furthermore, endocytic and general trafficking genes are up-regulated in the mature cyst, potentially preserved as mRNA in preparation for excystation. Two divergent dynamin-related proteins found in Entamoeba are predominantly expressed during cyst formation. Phylogenetic analyses indicate that they are paralogous to, but quite distinct from, classical dynamins found in human, suggesting that they may be potential drug targets to block encystation. The membrane-trafficking machinery is clearly regulated during encystation, providing an additional facet to understanding this crucial parasitic process.
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Affiliation(s)
- Emily Herman
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, Alberta, Canada
| | | | - Michael J Bottery
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ronny van Aerle
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, UK
| | | | - Elisabet Caler
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD, 20892-7950, USA
| | - Joel B Dacks
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, Alberta, Canada.
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24
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Bickley LK, van Aerle R, Brown AR, Hargreaves A, Huby R, Cammack V, Jackson R, Santos EM, Tyler CR. Bioavailability and Kidney Responses to Diclofenac in the Fathead Minnow (Pimephales promelas). Environ Sci Technol 2017; 51:1764-1774. [PMID: 28068076 DOI: 10.1021/acs.est.6b05079] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Diclofenac is one of the most widely prescribed nonsteroidal anti-inflammatory drugs worldwide. It is frequently detected in surface waters; however, whether this pharmaceutical poses a risk to aquatic organisms is debated. Here we quantified the uptake of diclofenac by the fathead minnow (Pimephales promelas) following aqueous exposure (0.2-25.0 μg L-1) for 21 days, and evaluated the tissue and biomolecular responses in the kidney. Diclofenac accumulated in a concentration- and time-dependent manner in the plasma of exposed fish. The highest plasma concentration observed (for fish exposed to 25 μg L-1 diclofenac) was within the therapeutic range for humans. There was a strong positive correlation between exposure concentration and the number of developing nephrons observed in the posterior kidney. Diclofenac was not found to modulate the expression of genes in the kidney associated with its primary mode of action in mammals (prostaglandin-endoperoxide synthases) but modulated genes associated with kidney repair and regeneration. There were no significant adverse effects following 21 days exposure to concentrations typical of surface waters. The combination of diclofenac's uptake potential, effects on kidney nephrons and relatively small safety margin for some surface waters may warrant a longer term chronic health effects analysis for diclofenac in fish.
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Affiliation(s)
- Lisa K Bickley
- Biosciences, College of Life and Environmental Sciences, University of Exeter , Exeter, EX4 4QD, U.K
| | - Ronny van Aerle
- Biosciences, College of Life and Environmental Sciences, University of Exeter , Exeter, EX4 4QD, U.K
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, U.K
| | - A Ross Brown
- Biosciences, College of Life and Environmental Sciences, University of Exeter , Exeter, EX4 4QD, U.K
| | - Adam Hargreaves
- AstraZeneca Drug Safety and Metabolism, Alderley Park, Macclesfield, Cheshire SK10 4TF, U.K
- PathCelerate Ltd. The BioHub at Alderley Park, Alderley Edge, Cheshire SK10 4TG, U.K
| | - Russell Huby
- Bioscript, St Peter's Institute , Macclesfield, Cheshire SK11 7HS, U.K
| | - Victoria Cammack
- AstraZeneca Global Environment, Alderley Park, Macclesfield, Cheshire SK10 4TF, U.K
| | - Richard Jackson
- AstraZeneca Drug Safety and Metabolism, Alderley Park, Macclesfield, Cheshire SK10 4TF, U.K
- Institute of Psychiatry, Psychology and Neuroscience, King's College London , De Crespigny Park, Box 63, SE5 8AF, London, U.K
| | - Eduarda M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter , Exeter, EX4 4QD, U.K
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter , Exeter, EX4 4QD, U.K
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Cano I, Collet B, Pereira C, Paley R, van Aerle R, Stone D, Taylor NG. Corrigendum to “In vivo virulence of viral haemorrhagic septicaemia virus (VHSV) in rainbow trout Oncorhynchus mykiss correlates inversely with in vitro Mx gene expression” [Vet. Microbiol. 187 (2016) 31–40]. Vet Microbiol 2016; 195:58-59. [DOI: 10.1016/j.vetmic.2016.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cano I, Verner-Jeffreys DW, van Aerle R, Paley RK, Peeler EJ, Green M, Rimmer GSE, Savage J, Joiner CL, Bayley AE, Mewett J, Hulland J, Feist SW. Puffy Skin Disease Is an Emerging Transmissible Condition in Rainbow Trout Oncorhynchus mykiss Walbaum. PLoS One 2016; 11:e0158151. [PMID: 27391648 PMCID: PMC4938586 DOI: 10.1371/journal.pone.0158151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022] Open
Abstract
The transmission of puffy skin disease (PSD) to rainbow trout Oncorhynchus mykiss Walbaum was tested in the laboratory by conducting co-habitation challenges with puffy skin (PS)-affected fish (Trojans) collected from the field. Two separate challenges were conducted using Trojans sourced from two different sites and diploid (first trial) or triploid (second trial) naïve fish. PSD-specific clinical signs were observed in both groups of naïve fish, with 66% of the fish sampled during the challenges showing signs of varying severity. The first clinical features of PSD were presented as white oval skin patches on one or both flanks 15–21 days post-challenge (dpc). The extent of the lesions ranged from 10 to 90% of the body surface, depending on the severity of the lesion. Both the severity and number of affected fish increased during the challenge. Macroscopically, oedema of the skin and multifocal petechial haemorrhaging were observed towards the end of the trials. Abnormal fish behaviour consisting of “flashing” and excessive mucous production was noted from 15 dpc onwards. Fish with severe PSD lesions also displayed inappetence and associated emaciation. Rodlet cells were observed in 41% of the fresh skin scrapes analysed from the second trial. Histologically epidermal oedema was observed in 31% of the naive fish showing gross pathology, with additional 12% displaying epidermal hyperplasia, mostly observed at the end of the challenge. Other concomitant features of the PSD lesions in challenged fish were epithelial erosion and sloughing, and occasionally mild or focal inflammation. No consistent pathology of internal organs was observed. The parasites Ichthyophthirius multifiliis and Ichthyobodo necator were observed in skin samples of a proportion of naïve challenged fish and in Trojans but not in control fish. The presence of these and other known fish pathogens in the skin of PSD-fish was confirmed by high-throughput sequencing analysis. In summary, we have demonstrated that PSD is a transmissible condition. However, even though a number of known fish pathogens were identified in the skin tissues of PSD-fish, the actual causative infectious agent(s) remain(s) unknown.
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Affiliation(s)
- Irene Cano
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - David W. Verner-Jeffreys
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
- * E-mail:
| | - Ronny van Aerle
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Richard K. Paley
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Edmund J. Peeler
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Matthew Green
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Georgina S. E. Rimmer
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Jacqueline Savage
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Claire L. Joiner
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Amanda E. Bayley
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Jason Mewett
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Jonathan Hulland
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
| | - Stephen W. Feist
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, United Kingdom
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Cano I, Collet B, Pereira C, Paley R, Aerle RV, Stone D, Taylor NGH. In vivo virulence of viral haemorrhagic septicaemia virus (VHSV) in rainbow trout Oncorhynchus mykiss correlates inversely with in vitro Mx gene expression. Vet Microbiol 2016; 187:31-40. [PMID: 27066706 DOI: 10.1016/j.vetmic.2016.02.012] [Citation(s) in RCA: 16] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/14/2022]
Abstract
The in vitro replication of viral haemorrhagic septicaemia virus (VHSV) isolates from each VHSV genotype and the associated cellular host Mx gene expression were analysed. All the isolates were able to infect RTG-2 cells and induce increased Mx gene expression (generic assay detecting isoforms 1 and 3 [Mx1/3]). A trout pathogenic, genotype Ia isolate (J167), showing high replication in RTG-2 cells (by infective titre and N gene expression) induced lower Mx1/3 gene expression than observed in VHSV isolates known to be non-pathogenic to rainbow trout: 96-43/8, 96-43/10 (Ib); 1p49, 1p53 (II); and MI03 (IVb). Paired co-inoculation assays were analysed using equal number of plaque forming units per ml (PFU) of J167 (Ia genotype) with other less pathogenic VHSV genotypes. In these co-inoculations, the Mx1/3 gene expression was significantly lower than for the non-pathogenic isolate alone. Of the three rainbow trout Mx isoforms, J167 did not induce Mx1 up-regulation in RTG-2 or RTgill-W1 cells. Co-inoculating isolates resulted in greater inhibition of Mx in both rainbow trout cell lines studied. Up-regulation of sea bream Mx in SAF-1 cells induced by 96-43/8 was also lower in co-inoculation assays with J167. The RTG-P1 cell line, expressing luciferase under the control of the interferon-induced Mx rainbow trout gene promoter, showed low luciferase activity when inoculated with pathogenic strains: J167, DK-5131 (Ic), NO-A-163/68 (Id), TR-206239-1, TR-22207111 (Ie), 99-292 (IVa), and CA-NB00-01 (IVc). Co-inoculation assays showed a J167-dose dependent inhibition of the luciferase activity. The data suggest that virulent VHSV isolates may interfere in the interferon pathways, potentially determining higher pathogenicity.
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Affiliation(s)
- Irene Cano
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe Weymouth, Dorset DT4 8UB, United Kingdom.
| | - Bertrand Collet
- Marine Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, United Kingdom
| | - Clarissa Pereira
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe Weymouth, Dorset DT4 8UB, United Kingdom
| | - Richard Paley
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe Weymouth, Dorset DT4 8UB, United Kingdom
| | - Ronny van Aerle
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe Weymouth, Dorset DT4 8UB, United Kingdom
| | - David Stone
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe Weymouth, Dorset DT4 8UB, United Kingdom
| | - Nick G H Taylor
- Aquatic Animal Disease, Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe Weymouth, Dorset DT4 8UB, United Kingdom
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Verbruggen B, Bickley LK, van Aerle R, Bateman KS, Stentiford GD, Santos EM, Tyler CR. Molecular Mechanisms of White Spot Syndrome Virus Infection and Perspectives on Treatments. Viruses 2016; 8:E23. [PMID: 26797629 PMCID: PMC4728583 DOI: 10.3390/v8010023] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [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: 11/07/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 02/07/2023] Open
Abstract
Since its emergence in the 1990s, White Spot Disease (WSD) has had major economic and societal impact in the crustacean aquaculture sector. Over the years shrimp farming alone has experienced billion dollar losses through WSD. The disease is caused by the White Spot Syndrome Virus (WSSV), a large dsDNA virus and the only member of the Nimaviridae family. Susceptibility to WSSV in a wide range of crustacean hosts makes it a major risk factor in the translocation of live animals and in commodity products. Currently there are no effective treatments for this disease. Understanding the molecular basis of disease processes has contributed significantly to the treatment of many human and animal pathogens, and with a similar aim considerable efforts have been directed towards understanding host-pathogen molecular interactions for WSD. Work on the molecular mechanisms of pathogenesis in aquatic crustaceans has been restricted by a lack of sequenced and annotated genomes for host species. Nevertheless, some of the key host-pathogen interactions have been established: between viral envelope proteins and host cell receptors at initiation of infection, involvement of various immune system pathways in response to WSSV, and the roles of various host and virus miRNAs in mitigation or progression of disease. Despite these advances, many fundamental knowledge gaps remain; for example, the roles of the majority of WSSV proteins are still unknown. In this review we assess current knowledge of how WSSV infects and replicates in its host, and critique strategies for WSD treatment.
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Affiliation(s)
- Bas Verbruggen
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
| | - Lisa K Bickley
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
| | - Ronny van Aerle
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK.
| | - Kelly S Bateman
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK.
| | - Grant D Stentiford
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK.
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4, UK.
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Verbruggen B, Bickley LK, Santos EM, Tyler CR, Stentiford GD, Bateman KS, van Aerle R. De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways. BMC Genomics 2015; 16:458. [PMID: 26076827 PMCID: PMC4469326 DOI: 10.1186/s12864-015-1667-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/29/2015] [Indexed: 11/25/2022] Open
Abstract
Background The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. However, the genomic resources for this organism are still sparse, limiting research progress in these fields. To address this resource shortfall we produced a C. maenas transcriptome, enabled by the progress in next-generation sequencing technologies, and applied this to assemble information on the innate immune system in this species. Results We isolated and pooled RNA for twelve different tissues and organs from C. maenas individuals and sequenced the RNA using next generation sequencing on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome was generated encompassing 212,427 transcripts (153,699 loci). The transcripts were filtered, annotated and characterised using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including NCBI, Gene Ontology and KEGG). There were differential patterns of expression for between 1,223 and 2,741 transcripts across tissues and organs with over-represented Gene Ontology terms relating to their specific function. Based on sequence homology to immune system components in other organisms, we show both the presence of transcripts for a series of known pathogen recognition receptors and response proteins that form part of the innate immune system, and transcripts representing the RNAi, Toll-like receptor signalling, IMD and JAK/STAT pathways. Conclusions We have produced an assembled transcriptome for C. maenas that provides a significant molecular resource for wide ranging studies in this species. Analysis of the transcriptome has revealed the presence of a series of known targets and functional pathways that form part of their innate immune system and illustrate tissue specific differences in their expression patterns. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1667-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bas Verbruggen
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Lisa K Bickley
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Grant D Stentiford
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK.
| | - Kelly S Bateman
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK.
| | - Ronny van Aerle
- Aquatic Health and Hygiene Division, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK.
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Mourabit S, Moles MW, Smith E, van Aerle R, Kudoh T. Bmp suppression in mangrove killifish embryos causes a split in the body axis. PLoS One 2014; 9:e84786. [PMID: 24497921 PMCID: PMC3907431 DOI: 10.1371/journal.pone.0084786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 05/24/2013] [Accepted: 11/19/2013] [Indexed: 11/25/2022] Open
Abstract
Bone morphogenetic proteins (Bmp) are major players in the formation of the vertebrate body plan due to their crucial role in patterning of the dorsal-ventral (DV) axis. Despite the highly conserved nature of Bmp signalling in vertebrates, the consequences of changing this pathway can be species-specific. Here, we report that Bmp plays an important role in epiboly, yolk syncytial layer (YSL) movements, and anterior-posterior (AP) axis formation in embryos of the self-fertilizing mangrove killifish, Kryptolebias marmoratus. Stage and dose specific exposures of embryos to the Bmp inhibitor dorsomorphin (DM) produced three distinctive morphologies, with the most extreme condition creating the splitbody phenotype, characterised by an extremely short AP axis where the neural tube, somites, and notochord were bilaterally split. In addition, parts of caudal neural tissues were separated from the main body and formed cell islands in the posterior region of the embryo. This splitbody phenotype, which has not been reported in other animals, shows that modification of Bmp may lead to significantly different consequences during development in other vertebrate species.
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Affiliation(s)
- Sulayman Mourabit
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Michael W. Moles
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Emma Smith
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ronny van Aerle
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Tetsuhiro Kudoh
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, United Kingdom
- * E-mail:
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van Aerle R, Lange A, Moorhouse A, Paszkiewicz K, Ball K, Johnston BD, de-Bastos E, Booth T, Tyler CR, Santos EM. Molecular mechanisms of toxicity of silver nanoparticles in zebrafish embryos. Environ Sci Technol 2013; 47:8005-14. [PMID: 23758687 PMCID: PMC3854648 DOI: 10.1021/es401758d] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/10/2013] [Accepted: 06/12/2013] [Indexed: 05/17/2023]
Abstract
Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity, however, remain unclear. We examined the effects of exposure to silver in nano-, bulk-, and ionic forms on zebrafish embryos (Danio rerio) using a Next Generation Sequencing approach in an Illumina platform (High-Throughput SuperSAGE). Significant alterations in gene expression were found for all treatments and many of the gene pathways affected, most notably those associated with oxidative phosphorylation and protein synthesis, overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down-regulation of this pathway at 24 h of exposure, but with a recovery at 48 h. This finding was consistent with a dose-dependent decrease in oxygen consumption at 24 h, but not at 48 h, following exposure to silver ions. Overall, our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.
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Affiliation(s)
- Ronny van Aerle
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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Scown TM, Santos EM, Johnston BD, Gaiser B, Baalousha M, Mitov S, Lead JR, Stone V, Fernandes TF, Jepson M, van Aerle R, Tyler CR. Effects of Aqueous Exposure to Silver Nanoparticles of Different Sizes in Rainbow Trout. Toxicol Sci 2010; 115:521-34. [DOI: 10.1093/toxsci/kfq076] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Johnston BD, Scown TM, Moger J, Cumberland SA, Baalousha M, Linge K, van Aerle R, Jarvis K, Lead JR, Tyler CR. Bioavailability of nanoscale metal oxides TiO(2), CeO(2), and ZnO to fish. Environ Sci Technol 2010; 44:1144-51. [PMID: 20050652 DOI: 10.1021/es901971a] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanoparticles (NPs) are reported to be a potential environmental health hazard. For organisms living in the aquatic environment, there is uncertainty on exposure because of a lack of understanding and data regarding the fate, behavior, and bioavailability of the nanomaterials in the water column. This paper reports on a series of integrative biological and physicochemical studies on the uptake of unmodified commercial nanoscale metal oxides, zinc oxide (ZnO), cerium dioxide (CeO(2)), and titanium dioxide (TiO(2)), from the water and diet to determine their potential ecotoxicological impacts on fish as a function of concentration. Particle characterizations were performed and tissue concentrations were measured by a wide range of analytical methods. Definitive uptake from the water column and localization of TiO(2) NPs in gills was demonstrated for the first time by use of coherent anti-Stokes Raman scattering (CARS) microscopy. Significant uptake of nanomaterials was found only for cerium in the liver of zebrafish exposed via the water and ionic titanium in the gut of trout exposed via the diet. For the aqueous exposures undertaken, formation of large NP aggregates (up to 3 mum) occurred and it is likely that this resulted in limited bioavailability of the unmodified metal oxide NPs in fish.
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Affiliation(s)
- Blair D Johnston
- The Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
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Santos EM, Ball JS, Williams TD, Wu H, Ortega F, van Aerle R, Katsiadaki I, Falciani F, Viant MR, Chipman JK, Tyler CR. Identifying health impacts of exposure to copper using transcriptomics and metabolomics in a fish model. Environ Sci Technol 2010; 44:820-826. [PMID: 20020678 DOI: 10.1021/es902558k] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Copper (Cu) is a micronutrient essential for the biochemical functioning of numerous processes in vertebrates but is also often present in the aquatic environment at concentrations able to cause adverse health effects in aquatic organisms. This study investigated the signaling pathways mediating the effects of exposure to Cu using a toxicogenomic approach in a fish model, the stickleback ( Gasterosteus aculeatus ). Freshwater-acclimated male fish were exposed via the water to Cu, including at environmentally relevant concentrations (3.2-128 microg of Cu/L for 4 days), and the biological responses explored through analyses of the hepatic transcriptome and metabolome and phenotypic end points, including assessment of DNA damage in blood cells. The Cu exposures resulted in DNA strand breaks in blood cells at all exposure concentrations and alterations in hepatic gene expression and metabolite concentrations in a concentration-dependent manner (from 10 microg of Cu/L). Genes associated with the cholesterol biosynthesis pathway were significantly over-represented and consistently down-regulated (at 128 microg of Cu/L), similar to that occurring in a mouse model for Wilson's disease. Additionally, inductions in metallothionein and catalase were also observed. The concentrations of NAD(+) and lactate increased significantly with the Cu exposure, consistent with a shift toward anaerobic metabolism, and these aligned closely with changes observed in gene expression. The pathways of Cu toxicity identified in our study support the conserved mechanisms of Cu toxicity from lower vertebrates to mammals, provide novel insights into the deleterious effects of Cu in fish, and further demonstrate the utility of fish as environmental sentinels for chemical impacts on both environmental and human health.
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Affiliation(s)
- Eduarda M Santos
- School of Biosciences, University of Exeter, Exeter, Devon EX4 4PS, United Kingdom.
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Scown TM, van Aerle R, Johnston BD, Cumberland S, Lead JR, Owen R, Tyler CR. High Doses of Intravenously Administered Titanium Dioxide Nanoparticles Accumulate in the Kidneys of Rainbow Trout but with no Observable Impairment of Renal Function. Toxicol Sci 2009; 109:372-80. [DOI: 10.1093/toxsci/kfp064] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Filby AL, van Aerle R, Duitman J, Tyler CR. The kisspeptin/gonadotropin-releasing hormone pathway and molecular signaling of puberty in fish. Biol Reprod 2007; 78:278-89. [PMID: 17978278 DOI: 10.1095/biolreprod.107.063420] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The mechanisms underlying the initiation of puberty in fish are poorly understood, and whether the Kiss1 receptor (Kiss1r; previously designated G protein-coupled receptor 54; GPR54) and its ligands, kisspeptins, play a significant role, as has been established in mammals, is not yet known. We determined (via real-time PCR) temporal patterns of expression in the brain of kiss1r, gnrh2, and gnrh3 and a suite of related genes in the hypothalamo-pituitary-gonadal (HPG) axis and analyzed them against the timing of gonadal germ cell development in male and female fathead minnow (Pimephales promelas). Full- or partial-length cDNAs for kiss1r (736 bp), gnrh2 (698 bp), and gnrh3 (804 bp) cloned from fathead minnow were found to be expressed only in the brain, testis, and ovary of adult fish. Localization of kiss1r, gnrh2, and gnrh3 within the brain provided evidence for their physiological roles and a likely hypophysiotropic role for GnRH3 in this species (which, like other cyprinids, does not appear to express gnrh1). In both sexes, kiss1r expression in the brain increased at the onset of puberty and reached maximal expression in males when spermatagonia type B appeared in the testis and in females when cortical alveolus-stage oocytes first appeared in the ovary, the timings of which differed for the two sexes. However, kiss1r expression was considerably lower during more advanced stages of spermatogenesis and oogenesis. The expression of kiss1r closely aligned with that of the gnrh genes (gnrh3 in particular), suggesting the Kiss1r/kisspeptin system in fish has a similar role in puberty to that occurring in mammals, and this hypothesis was supported by the induction of gnrh3 (2.25-fold) and kiss1r (1.5-fold) in early-mid pubertal fish injected with mammalian kisspeptin-10 (2 nmol/g wet weight). An intriguing finding, and contrasting that in mammals, was an elevated expression of esr1, ar, and cyp19a2 (genes involved in sex steroid signaling) in the brain at the onset of puberty, and in females slightly in advance of the elevation in the expression of kiss1r.
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Affiliation(s)
- Amy L Filby
- Environmental and Molecular Fish Biology Group, School of Biosciences, Hatherly Laboratories, University of Exeter, Exeter, Devon, EX4 4PS, United Kingdom.
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Eidem JK, Kleivdal H, Kroll K, Denslow N, van Aerle R, Tyler C, Panter G, Hutchinson T, Goksøyr A. Development and validation of a direct homologous quantitative sandwich ELISA for fathead minnow (Pimephales promelas) vitellogenin. Aquat Toxicol 2006; 78:202-6. [PMID: 16644026 DOI: 10.1016/j.aquatox.2006.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2006] [Revised: 02/27/2006] [Accepted: 02/28/2006] [Indexed: 05/08/2023]
Abstract
Vitellogenin (Vtg) is an established and sensitive endpoint for analysis of exposure to (anti-)oestrogens and their mimics in fish [Sumpter, J.P., 1995. Feminized responses in fish to environmental estrogens. Toxicol. Lett. 82, 737-742; Arukwe, A., Goksøyr, A., 2003. Eggshell and egg yolk proteins in fish: hepatic proteins for the next generation: oogenetic, population, and evolutionary implications of endocrine disruption. Comp. Hepatol. 2, 4. ]. In some instances, links have been drawn between high level induction of Vtg and adverse health effects in fish [Herman, R.L., Kincaide, H.L., 1988. Pathological effects of orally administered estradiol to rainbow trout. Aquaculture 72, 165-172; Schwaiger, J., Spieser, O.H., Bauer, C., Ferling, H., Mallow, U., Kalbfus, W., Negele, R.D., 2000. Chronic toxicity of nonylphenol and ethinyloestraiol: haematological and histopathological effects in juvenile common carp (Cyprinus carpio). Aquat. Toxicol. 51, 69-78]. The widespread use of Vtg as a biomarker has led to the development of a variety of assays to quantitatively measure Vtg concentrations in tissue samples from fish, and hence a need for a standardization of the performance criteria and validation of such assays [Goksøyr, A., Eidem, J.K., Kristiansen, S.I., Nilsen, B.M., 2003. On the need for a standardized set-up for validation studies of fish vitellogenin assays as an endpoint in endocrine disruptor testing and screening-a proposal. ]. One of the most popular test fish species for assessing chemical effects is the fathead minnow (Pimephales promelas), which is now used widely for studies into endocrine disruption [Panter, G.H., Hutchinson, T.H., Lange, R., Lye, C.M., Sumpter, J.P., Zerulla, M., Tyler, C.R., 2002. Utility of a juvenile fathead minnow screening assay for detecting (anti)estrogenic substances. Environ. Toxicol. Chem. 21, 319-326; Hutchinson, T.H., Yokota, H., Hagino, S., Ozato, K., 2003. Development of fish tests for endocrine disruptors. Pure Appl. Chem. 75, 2343-2353]. This paper describes the development and validation of a new, homologous enzyme-linked immunosorbent assay (ELISA) for quantification of Vtg in this fish species.
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Affiliation(s)
- Janne K Eidem
- Biosense Laboratories AS, Thormøhlensgt. 55, 5008 Bergen, Norway
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Schulte-Oehlmann U, Albanis T, Allera A, Bachmann J, Berntsson P, Beresford N, Carnevali DC, Ciceri F, Dagnac T, Falandysz J, Galassi S, Hala D, Janer G, Jeannot R, Jobling S, King I, Klingmüller D, Kloas W, Kusk KO, Levada R, Lo S, Lutz I, Oehlmann J, Oredsson S, Porte C, Rand-Weaver M, Sakkas V, Sugni M, Tyler C, van Aerle R, van Ballegoy C, Wollenberger L. COMPRENDO: Focus and approach. Environ Health Perspect 2006; 114 Suppl 1:98-100. [PMID: 16818253 PMCID: PMC1874174 DOI: 10.1289/ehp.8060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Tens of thousands of man-made chemicals are in regular use and discharged into the environment. Many of them are known to interfere with the hormonal systems in humans and wildlife. Given the complexity of endocrine systems, there are many ways in which endocrine-disrupting chemicals (EDCs) can affect the body's signaling system, and this makes unraveling the mechanisms of action of these chemicals difficult. A major concern is that some of these EDCs appear to be biologically active at extremely low concentrations. There is growing evidence to indicate that the guiding principle of traditional toxicology that "the dose makes the poison" may not always be the case because some EDCs do not induce the classical dose-response relationships. The European Union project COMPRENDO (Comparative Research on Endocrine Disrupters--Phylogenetic Approach and Common Principles focussing on Androgenic/Antiandrogenic Compounds) therefore aims to develop an understanding of potential health problems posed by androgenic and antiandrogenic compounds (AACs) to wildlife and humans by focusing on the commonalities and differences in responses to AACs across the animal kingdom (from invertebrates to vertebrates) .
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Affiliation(s)
- Ulrike Schulte-Oehlmann
- Department of Ecology and Evolution, Johann Wolfgang Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
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Jobling S, Williams R, Johnson A, Taylor A, Gross-Sorokin M, Nolan M, Tyler CR, van Aerle R, Santos E, Brighty G. Predicted exposures to steroid estrogens in U.K. rivers correlate with widespread sexual disruption in wild fish populations. Environ Health Perspect 2006; 114 Suppl 1:32-9. [PMID: 16818244 PMCID: PMC1874167 DOI: 10.1289/ehp.8050] [Citation(s) in RCA: 345] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 08/22/2005] [Indexed: 05/10/2023]
Abstract
Steroidal estrogens, originating principally from human excretion, are likely to play a major role in causing widespread endocrine disruption in wild populations of the roach (Rutilus rutilus), a common cyprinid fish, in rivers contaminated by treated sewage effluents. Given the extent of this problem, risk assessment models are needed to predict the location and severity of endocrine disruption in river catchments and to identify areas where regulation of sewage discharges to remove these contaminants is necessary. In this study we attempted to correlate the extent of endocrine disruption in roach in British rivers, with their predicted exposure to steroid estrogens derived from the human population. The predictions of steroid estrogen exposure at each river site were determined by combining the modeled concentrations of the individual steroid estrogens [17beta-estradiol (E2), estrone (E1), and 17alpha-ethinylestradiol (EE2)] in each sewage effluent with their predicted dilution in the immediate receiving water. This model was applied to 45 sites on 39 rivers throughout the United Kingdom. Each site studied was then categorized as either high, medium, or low "risk" on the basis of the assumed additive potency of the three steroid estrogens calculated from data derived from published studies in various cyprinid fish species. We sampled 1,438 wild roach from the predicted high-, medium-, and low-risk river sites and examined them for evidence and severity of endocrine disruption. Both the incidence and the severity of intersex in wild roach were significantly correlated with the predicted concentrations of the natural estrogens (E1 and E2) and the synthetic contraceptive pill estrogen (EE2) present. Predicted steroid estrogen exposure was, however, less well correlated with the plasma vitellogenin concentration measured in the same fish. Moreover, we found no correlation between any of the end points measured in the roach and the proportion of industrial effluents entering the rivers we studied. Overall, our results provide further and substantive evidence to support the hypothesis that steroidal estrogens play a major role in causing intersex in wild freshwater fish in rivers in the United Kingdom and clearly show that the location and severity of these endocrine-disrupting effects can be predicted.
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Affiliation(s)
- Susan Jobling
- Beyond The Basics Ltd, Burnham, Bucks, United Kingdom.
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Vine E, Shears J, van Aerle R, Tyler CR, Sumpter JP. Endocrine (sexual) disruption is not a prominent feature in the pike (Esox lucius), a top predator, living in English waters. Environ Toxicol Chem 2005; 24:1436-43. [PMID: 16117120 DOI: 10.1897/04-447r.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The high incidence of intersex roach (Rutilus rutilus) in some United Kingdom rivers that has been associated with exposure to sewage treatment works (STWs) effluent led us to hypothesize that top predator fish also may be affected by estrogenic chemicals, because they are likely to bioaccumulate lipophilic compounds through a predator-prey relationship. To investigate this possibility, pike (Esox lucius) were sampled both upstream and downstream of STWs and then examined for total estrogenic activity of their bile, as measured using a yeast-based estrogen assay to determine the degree of recent exposure of the pike to estrogens and vitellogenin induction, and for possible disruption of sexual development, as measured using histological analysis of the gonads. No evidence of severe disruption was found in the sampled fish, which came from 16 sampling sites that were representative of English rivers. However, 14% of pike were intersex, of which 15 of 16 showed patches of male germ cells among predominantly female gonadal tissue. The incidence of masculinization was independent of whether the pike had been sampled upstream or downstream of STWs. Although pike are gonochoristic, it is not known if this masculinization of presumptive female pike is normal or, instead, indicative of endocrine disruption. Vitellogenin concentrations were not elevated in male pike at sites either upstream or downstream of STWs. The results suggest that sexual disruption is not common in pike, a fish at the top of the food chain in the freshwaters of England.
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Affiliation(s)
- Emma Vine
- Institute for the Environment, Brunel University, Uxbridge, Middlesex UB8 3PH, United Kingdom.
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Tyler CR, van Aerle R, Santos EM. ELISAs for detecting vitellogenin in the fathead minnow (Pimephales promelas)-a critical analysis. Response to Mylchreest et al., Comp Biochem Physiol C 134: 251-257, 2003. Comp Biochem Physiol C Toxicol Pharmacol 2004; 138:531-2; author reply 533-6. [PMID: 15536061 DOI: 10.1016/j.cca.2004.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 02/19/2004] [Accepted: 02/19/2004] [Indexed: 10/26/2022]
Affiliation(s)
- Charles R Tyler
- School of Biological and Chemical Sciences, University of Exeter, Exeter EX4 4PS, United Kingdom.
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Spanò L, Tyler CR, van Aerle R, Devos P, Mandiki SNM, Silvestre F, Thomé JP, Kestemont P. Effects of atrazine on sex steroid dynamics, plasma vitellogenin concentration and gonad development in adult goldfish (Carassius auratus). Aquat Toxicol 2004; 66:369-379. [PMID: 15168945 DOI: 10.1016/j.aquatox.2003.10.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sexually mature goldfish (Carassius auratus) of both sexes were exposed to two doses (100 and 1000 microg/l) of the widely used herbicide atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) for a period of 21 days and effects on the concentrations of gonad and plasma sex steroids (testosterone (T), 17beta-estradiol (E2) and 11-ketotestosterone (11-KT)), plasma vitellogenin (VTG) and gonad histo-morphology assessed. Atrazine did not show any obvious estrogenic effect in males, as determined by a lack of vitellogenin induction. There were, however, effects of atrazine on plasma androgen concentrations (androgen dynamics) and tissue (plasma and gonad) estrogen concentrations in male goldfish; exposure to 1000 microg/l atrazine induced suppression in both testosterone and 11-ketotestosterone, and resulted in elevated 17beta-estradiol, after 21 day of exposure. Further, these suppressive effects on plasma androgens and the induction in estrogen were dose- and time-related. The highest atrazine exposure dose induced structural disruption in the testis and both 100 and 1000 microg/l induced elevated levels of atresia in ovaries.
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van Aerle R, Pounds N, Hutchinson TH, Maddix S, Tyler CR. Window of sensitivity for the estrogenic effects of ethinylestradiol in early life-stages of fathead minnow, Pimephales promelas. Ecotoxicology 2002; 11:423-434. [PMID: 12521139 DOI: 10.1023/a:1021053217513] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sexual differentiation in fish occurs after hatching during early life-stages and is believed to be a time when the gonad has a heightened sensitivity to disruption by chemicals that mimic hormones. In this study fathead minnows (Pimephales promelas) were exposed to an environmentally relevant concentration of ethinylestradiol (EE2) for short intervals in fish early life-stages and vitellogenic and gonadal responses were measured at 30 and 100 dph (sexual maturity), respectively. All EE2 exposure regimes induced vitellogenin (VTG) synthesis and disruption in duct development (a feminization) in males, with a window of enhanced sensitivity between 10 and 15 dph (where 60% of the males had feminized ducts). There was an altered pattern in sex cell development in males (inhibition of spermatogenesis) in the solvent controls (ethanol 0.1 ml/l) and all EE2 treatments when compared with the dilution water controls. Furthermore, fewer spermatozoa were observed in the testis of males exposed to EE2 from 15 to 20 dph and fertilized eggs (<24 h post-fertilization)-20 dph, compared with both the solvent and dilution water controls. These data show that short exposures of embryos/very early life-stage fathead minnows to an environmentally relevant concentration of EE2 lead to alterations in gonadal development that potentially have reproductive consequences and thus population level effects.
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Affiliation(s)
- Ronny van Aerle
- Environmental and Molecular Fish Biology Group, Hatherly Laboratories, School of Biological Sciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
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Tyler CR, van Aerle R, Nilsen MV, Blackwell R, Maddix S, Nilsen BM, Berg K, Hutchinson TH, Goksøyr A. Monoclonal antibody enzyme-linked immunosorbent assay to quantify vitellogenin for studies on environmental estrogens in the rainbow trout (Oncorhynchus mykiss). Environ Toxicol Chem 2002; 21:47-54. [PMID: 11804060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Vitellogenin (VTG) induction has proved to be a valuable biomarker for assessing exposure to environmental estrogens in fish. The widespread use of VTG in this regard has lead to the need for standardized assays to quantify VTG, and monoclonal antibodies have the potential to help accomplish this. A VTG enzyme-linked immunosorbent assay (ELISA) was developed using a monoclonal antibody prepared against Atlantic salmon (Salmo salar) VTG (MAb BN-5) and its ability to quantify VTG in the rainbow trout (Oncorhynchus mykiss) compared with a rainbow trout vitellogenin (rt-VTG) ELISA that employed homologous polyclonal antibodies (PAb). In routine protocols, the working range of the homologous rt-PAb VTG ELISA was between 9 ng/ml and 70 ng/ml (80- 20% relative maximum binding [B/Bo]) with a 50% B/Bo of 25+/-0.9 ng/ml and inter- and intraassay variations at 50% B/Bo of 7% (n = 7) and 8% (n = 15), respectively. The working range of the MAb BN-5 VTG ELISA was between 60 ng/ml and 850 ng/ml (80-20% B/Bo) with a 50% B/Bo of 227+/-22 ng/ml and inter- and intraassay variations at 50% B/Bo of 5% (n = 10) and 9% (n = 12), respectively. In the routine protocols, detection limits for measurement of plasma VTG in rainbow trout (at 80% B/Bo; and given the requirement to dilute plasma to a minimum of 1:10 for the assays) were 90 ng/ml for the polyclonal rt-VTG assay and approximately 600 ng/ml in the monoclonal antibody assay. In juvenile female rainbow trout exposed to a series of doses of estradiol-17beta (E2) and 4-tert nonylphenol (4-NP), there were no differences in the vitellogenic responses measured in the PAb and MAb BN-5 VTG ELISAs. The monoclonal MAb BN-5 VTG ELISA is likely to be of considerable value for studies on environmental estrogens in juvenile female rainbow trout in standardized tests.
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Affiliation(s)
- Charles R Tyler
- Hatherly Laboratories, School of Biological Sciences, University of Exeter, United Kingdom.
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