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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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2
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Brunner FS, Brown MR, Bassano I, Denise H, Khalifa MS, Wade MJ, van Aerle R, Kevill JL, Jones DL, Farkas K, Jeffries AR, Cairns E, Wierzbicki C, Paterson S. City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants. Water Res 2022; 226:119306. [PMID: 36369689 PMCID: PMC9614697 DOI: 10.1016/j.watres.2022.119306] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Received: 07/14/2022] [Revised: 10/13/2022] [Accepted: 10/26/2022] [Indexed: 05/08/2023]
Abstract
Genomic surveillance of SARS-CoV-2 has provided a critical evidence base for public health decisions throughout the pandemic. Sequencing data from clinical cases has helped to understand disease transmission and the spread of novel variants. Genomic wastewater surveillance can offer important, complementary information by providing frequency estimates of all variants circulating in a population without sampling biases. Here we show that genomic SARS-CoV-2 wastewater surveillance can detect fine-scale differences within urban centres, specifically within the city of Liverpool, UK, during the emergence of Alpha and Delta variants between November 2020 and June 2021. Furthermore, wastewater and clinical sequencing match well in the estimated timing of new variant rises and the first detection of a new variant in a given area may occur in either clinical or wastewater samples. The study's main limitation was sample quality when infection prevalence was low in spring 2021, resulting in a lower resolution of the rise of the Delta variant compared to the rise of the Alpha variant in the previous winter. The correspondence between wastewater and clinical variant frequencies demonstrates the reliability of wastewater surveillance. However, discrepancies in the first detection of the Alpha variant between the two approaches highlight that wastewater monitoring can also capture missing information, possibly resulting from asymptomatic cases or communities less engaged with testing programmes, as found by a simultaneous surge testing effort across the city.
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Affiliation(s)
- F S Brunner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - M R Brown
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - I Bassano
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK; Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
| | - H Denise
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - M S Khalifa
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK; Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London, UB8 3PH, UK
| | - M J Wade
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - R van Aerle
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries & Aquaculture Science, Dorset, DT4 8UB, UK
| | - J L Kevill
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries & Aquaculture Science, Dorset, DT4 8UB, UK
| | - D L Jones
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries & Aquaculture Science, Dorset, DT4 8UB, UK; Food Futures Institute, Murdoch University, Murdoch WA 6105, Australia
| | - K Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - A R Jeffries
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - E Cairns
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - C Wierzbicki
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - S Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK.
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3
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Bates KA, Sommer U, Hopkins KP, Shelton JMG, Wierzbicki C, Sergeant C, Tapley B, Michaels CJ, Schmeller DS, Loyau A, Bosch J, Viant MR, Harrison XA, Garner TWJ, Fisher MC. Microbiome function predicts amphibian chytridiomycosis disease dynamics. Microbiome 2022; 10:44. [PMID: 35272699 PMCID: PMC8908643 DOI: 10.1186/s40168-021-01215-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood. METHODS Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection. RESULTS Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes. CONCLUSIONS Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.
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Affiliation(s)
- Kieran A Bates
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Ulf Sommer
- NERC Biomolecular Analysis Facility - Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kevin P Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Jennifer M G Shelton
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Claudia Wierzbicki
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Christopher Sergeant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Benjamin Tapley
- ZSL London Zoo, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | | | - Dirk S Schmeller
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France
| | - Adeline Loyau
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Jaime Bosch
- IMIB Biodiversity Research Institute (CSIC-University of Oviedo), 33600, Mieres, Spain
| | - Mark R Viant
- NERC Biomolecular Analysis Facility - Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4DQ, UK
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Matthew C Fisher
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
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Jackson B, Boni MF, Bull MJ, Colleran A, Colquhoun RM, Darby AC, Haldenby S, Hill V, Lucaci A, McCrone JT, Nicholls SM, O'Toole Á, Pacchiarini N, Poplawski R, Scher E, Todd F, Webster HJ, Whitehead M, Wierzbicki C, Loman NJ, Connor TR, Robertson DL, Pybus OG, Rambaut A. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell 2021; 184:5179-5188.e8. [PMID: 34499854 PMCID: PMC8367733 DOI: 10.1016/j.cell.2021.08.014] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [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: 06/16/2021] [Revised: 07/29/2021] [Accepted: 08/11/2021] [Indexed: 12/27/2022]
Abstract
We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances, there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of 2 months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7's set of mutations.
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Affiliation(s)
- Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew J Bull
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff CF14 4AY, UK
| | - Amy Colleran
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rachel M Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sam Haldenby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Anita Lucaci
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Samuel M Nicholls
- The COVID-19 Genomics UK (COG-UK) Consortium, https://www.cogconsortium.uk/
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Nicole Pacchiarini
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff CF14 4AY, UK
| | - Radoslaw Poplawski
- The COVID-19 Genomics UK (COG-UK) Consortium, https://www.cogconsortium.uk/
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Flora Todd
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Hermione J Webster
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark Whitehead
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claudia Wierzbicki
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff CF14 4AY, UK; School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK; Department of Pathobiology and Population Sciences, The Royal Veterinary College, London AL9 7TA, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
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5
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Jervis P, Pintanel P, Hopkins K, Wierzbicki C, Shelton JMG, Skelly E, Rosa GM, Almeida-Reinoso D, Eugenia-Ordoñez M, Ron S, Harrison X, Merino-Viteri A, Fisher MC. Post-epizootic microbiome associations across communities of neotropical amphibians. Mol Ecol 2021; 30:1322-1335. [PMID: 33411382 DOI: 10.1111/mec.15789] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022]
Abstract
Microbiome-pathogen interactions are increasingly recognized as an important element of host immunity. While these host-level interactions will have consequences for community disease dynamics, the factors which influence host microbiomes at larger scales are poorly understood. We here describe landscape-scale pathogen-microbiome associations within the context of post-epizootic amphibian chytridiomycosis, a disease caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. We undertook a survey of Neotropical amphibians across altitudinal gradients in Ecuador ~30 years following the observed amphibian declines and collected skin swab-samples which were metabarcoded using both fungal (ITS-2) and bacterial (r16S) amplicons. The data revealed marked variation in patterns of both B. dendrobatidis infection and microbiome structure that are associated with host life history. Stream breeding amphibians were most likely to be infected with B. dendrobatidis. This increased probability of infection was further associated with increased abundance and diversity of non-Batrachochytrium chytrid fungi in the skin and environmental microbiome. We also show that increased alpha diversity and the relative abundance of fungi are lower in the skin microbiome of adult stream amphibians compared to adult pond-breeding amphibians, an association not seen for bacteria. Finally, stream tadpoles exhibit lower proportions of predicted protective microbial taxa than pond tadpoles, suggesting reduced biotic resistance. Our analyses show that host breeding ecology strongly shapes pathogen-microbiome associations at a landscape scale, a trait that may influence resilience in the face of emerging infectious diseases.
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Affiliation(s)
- Phillip Jervis
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK.,Institute of Zoology, Zoological Society of London, London, UK.,Department of Chemistry, UCL, London, UK.,Laboratorio de Ecofisiología and Museo de Zoología (QCAZ), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Pol Pintanel
- Laboratorio de Ecofisiología and Museo de Zoología (QCAZ), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.,Department of Evolutionary Ecology, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, London, UK
| | - Claudia Wierzbicki
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK.,Institute of Zoology, Zoological Society of London, London, UK
| | - Jennifer M G Shelton
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK
| | - Emily Skelly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK.,Institute of Zoology, Zoological Society of London, London, UK
| | - Gonçalo M Rosa
- Institute of Zoology, Zoological Society of London, London, UK.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Diego Almeida-Reinoso
- Museo de Zoologίa (QCAZ), Escuela de Ciencias Biológicas, Pontificia Universidad Catόlica del Ecuador, Quito, Ecuador.,SARgrillo: Ex situ Management Program of Endangered Amphibians and Insect Breeding program, Quito, Ecuador
| | - Maria Eugenia-Ordoñez
- Fungario QCAM, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Santiago Ron
- Museo de Zoologίa (QCAZ), Escuela de Ciencias Biológicas, Pontificia Universidad Catόlica del Ecuador, Quito, Ecuador
| | - Xavier Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Andrés Merino-Viteri
- Laboratorio de Ecofisiología and Museo de Zoología (QCAZ), Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, UK
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6
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Young RM, Hawkins TA, Cavodeassi F, Stickney HL, Schwarz Q, Lawrence LM, Wierzbicki C, Cheng BY, Luo J, Ambrosio EM, Klosner A, Sealy IM, Rowell J, Trivedi CA, Bianco IH, Allende ML, Busch-Nentwich EM, Gestri G, Wilson SW. Compensatory growth renders Tcf7l1a dispensable for eye formation despite its requirement in eye field specification. eLife 2019; 8:40093. [PMID: 30777146 PMCID: PMC6380838 DOI: 10.7554/elife.40093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 07/13/2018] [Accepted: 01/26/2019] [Indexed: 12/18/2022] Open
Abstract
The vertebrate eye originates from the eye field, a domain of cells specified by a small number of transcription factors. In this study, we show that Tcf7l1a is one such transcription factor that acts cell-autonomously to specify the eye field in zebrafish. Despite the much-reduced eye field in tcf7l1a mutants, these fish develop normal eyes revealing a striking ability of the eye to recover from a severe early phenotype. This robustness is not mediated through genetic compensation at neural plate stage; instead, the smaller optic vesicle of tcf7l1a mutants shows delayed neurogenesis and continues to grow until it achieves approximately normal size. Although the developing eye is robust to the lack of Tcf7l1a function, it is sensitised to the effects of additional mutations. In support of this, a forward genetic screen identified mutations in hesx1, cct5 and gdf6a, which give synthetically enhanced eye specification or growth phenotypes when in combination with the tcf7l1a mutation. Left and right eyes develop independently, yet they consistently grow to roughly the same size in humans and other creatures. How they do this remains a mystery, though scientists have learned that both eyes originate from a single group of cells in the developing nervous system called the eye field. As development progresses, the eye field splits in two, and buds into the two separate compartments from which each eye forms. As the eyes grow, the cells in each compartment specialize, or ‘differentiate’, to make working left and right eyes. Scientists often study eye development in zebrafish embryos because it is easy to see each step in the process. Now, Young at al. show that zebrafish with a mutation that causes the eye field to be half its normal size go on to form normal-sized eyes. Somehow these developing embryos overcome this deleterious mutation. It turns out that the eyes of zebrafish with this mutation grow for a longer period of time than typical zebrafish eyes. This change allows the mutant fish’s eyes to catch up and reach normal size. When Young et al. removed some cells from one of the forming eyes of normal zebrafish embryos they found that same thing happened. The smaller eye developed for a longer time and delayed its differentiation until both eyes were the same size. Conversely, when eyes developed from a larger than normal eye field, growth stopped prematurely and differentiation began early preventing the eyes from ending up oversized. Though the fish were able to overcome the effects of one mutation to develop normal-sized eyes, adding a second mutation that affected eye development led to unusual sized eyes or absence of eyes. Together the experiments identify genes and mechanisms essential for the formation and size of the eyes. Given that the processes underlying eye formation are very similar in many animals, this new information should help scientists to better understand eye abnormalities in humans.
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Affiliation(s)
- Rodrigo M Young
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Thomas A Hawkins
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Florencia Cavodeassi
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Heather L Stickney
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Quenten Schwarz
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Lisa M Lawrence
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Claudia Wierzbicki
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Bowie Yl Cheng
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Jingyuan Luo
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | | | - Allison Klosner
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Ian M Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jasmine Rowell
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chintan A Trivedi
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Isaac H Bianco
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Miguel L Allende
- Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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7
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Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, Bataille A, Berger L, Böll S, Bosch J, Clare FC, A Courtois E, Crottini A, Cunningham AA, Doherty-Bone TM, Gebresenbet F, Gower DJ, Höglund J, James TY, Jenkinson TS, Kosch TA, Lambertini C, Laurila A, Lin CF, Loyau A, Martel A, Meurling S, Miaud C, Minting P, Ndriantsoa S, O'Hanlon SJ, Pasmans F, Rakotonanahary T, Rabemananjara FCE, Ribeiro LP, Schmeller DS, Schmidt BR, Skerratt L, Smith F, Soto-Azat C, Tessa G, Toledo LF, Valenzuela-Sánchez A, Verster R, Vörös J, Waldman B, Webb RJ, Weldon C, Wombwell E, Zamudio KR, Longcore JE, Garner TWJ. Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi. Sci Rep 2018; 8:7772. [PMID: 29773857 PMCID: PMC5958081 DOI: 10.1038/s41598-018-24472-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 01/23/2018] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.
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Affiliation(s)
- Matthew C Fisher
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.
| | - Pria Ghosh
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.,Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
| | - Jennifer M G Shelton
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Kieran Bates
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Lola Brookes
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Gonçalo M Rosa
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK.,Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Rhys A Farrer
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - David M Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.,Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridgeshire, UK
| | - Mario Alvarado-Rybak
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.,CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Lee Berger
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Susanne Böll
- Agency for Population Ecology and Nature Conservancy, Gerbrunn, Germany
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC c/Jose Gutierrez Abascal 2, 28006, Madrid, Spain
| | - Frances C Clare
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK
| | - Elodie A Courtois
- Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, 97300, Cayenne, French Guiana
| | - Angelica Crottini
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, 4485-661, Vairão, Portugal
| | | | | | - Fikirte Gebresenbet
- Department of Integrative Biology, Oklahoma State University, 113 Life Sciences West, Stillwater, OK, 74078, USA
| | - David J Gower
- Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Jacob Höglund
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Thomas S Jenkinson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tiffany A Kosch
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.,One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Carolina Lambertini
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Anssi Laurila
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, 1 Ming-shen East Road, Jiji, Nantou, 552, Taiwan
| | - Adeline Loyau
- Helmholtz Centre for Environmental Research - UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318, Leipzig, Germany.,ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Sara Meurling
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Claude Miaud
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Biogéographie et Ecologie des vertébrés, Montpellier, France
| | - Pete Minting
- Amphibian and Reptile Conservation (ARC) Trust, 655A Christchurch Road, Boscombe, Bournemouth, Dorset, BH1 4AP, UK
| | - Serge Ndriantsoa
- Durrell Wildlife Conservation Trust, Madagascar Programme, Antananarivo, Madagascar
| | - Simon J O'Hanlon
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine (St Mary's campus), Imperial College London, London, W2 1PG, UK.,Institute of Zoology, Regent's Park, London, NW1 4RY, UK
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | | | - Falitiana C E Rabemananjara
- Durrell Wildlife Conservation Trust, Madagascar Programme, Antananarivo, Madagascar.,IUCN SSC Amphibian Specialist Group-Madagascar, 101, Antananarivo, Madagascar
| | - Luisa P Ribeiro
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Dirk S Schmeller
- Helmholtz Centre for Environmental Research - UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318, Leipzig, Germany.,ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Info Fauna Karch, Université de Neuchâtel, Bellevaux 51, UniMail Bâtiment 6, 2000, Neuchâtel, Switzerland
| | - Lee Skerratt
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Freya Smith
- National Wildlife Management Centre, APHA, Woodchester Park, Gloucestershire, GL10 3UJ, UK
| | - Claudio Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Giulia Tessa
- Non-profit Association Zirichiltaggi - Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100, Sassari, Italy
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Andrés Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile.,ONG Ranita de Darwin, Nataniel Cox 152, Santiago, Chile
| | - Ruhan Verster
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
| | - Judit Vörös
- Collection of Amphibians and Reptiles, Department of Zoology, Hungarian Natural History Museum, Budapest, Baross u, 13., 1088, Hungary
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Rebecca J Webb
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4811, Australia
| | - Che Weldon
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
| | - Emma Wombwell
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, Maine, 04469, USA
| | - Trenton W J Garner
- Institute of Zoology, Regent's Park, London, NW1 4RY, UK.,Non-profit Association Zirichiltaggi - Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100, Sassari, Italy.,Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom, 2520, South Africa
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8
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O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA, Brankovics B, Fumagalli M, Martin MD, Wales N, Alvarado-Rybak M, Bates KA, Berger L, Böll S, Brookes L, Clare F, Courtois EA, Cunningham AA, Doherty-Bone TM, Ghosh P, Gower DJ, Hintz WE, Höglund J, Jenkinson TS, Lin CF, Laurila A, Loyau A, Martel A, Meurling S, Miaud C, Minting P, Pasmans F, Schmeller DS, Schmidt BR, Shelton JMG, Skerratt LF, Smith F, Soto-Azat C, Spagnoletti M, Tessa G, Toledo LF, Valenzuela-Sánchez A, Verster R, Vörös J, Webb RJ, Wierzbicki C, Wombwell E, Zamudio KR, Aanensen DM, James TY, Gilbert MTP, Weldon C, Bosch J, Balloux F, Garner TWJ, Fisher MC. Recent Asian origin of chytrid fungi causing global amphibian declines. Science 2018; 360:621-627. [PMID: 29748278 PMCID: PMC6311102 DOI: 10.1126/science.aar1965] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [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: 10/14/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.
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Affiliation(s)
- Simon J O'Hanlon
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Adrien Rieux
- CIRAD, UMR PVBMT, 97410 St. Pierre, Reunion, France
| | - Rhys A Farrer
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Gonçalo M Rosa
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
| | - Tiffany A Kosch
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Kris A Murray
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT Utrecht, Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 49, NO-7012 Trondheim, Norway
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mario Alvarado-Rybak
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | - Kieran A Bates
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Lee Berger
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Susanne Böll
- Agency for Population Ecology and Nature Conservancy, Gerbrunn, Germany
| | - Lola Brookes
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Frances Clare
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Elodie A Courtois
- Laboratoire Ecologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, 97300 Cayenne, French Guiana
| | | | | | - Pria Ghosh
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - David J Gower
- Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - William E Hintz
- Biology Department, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Jacob Höglund
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Thomas S Jenkinson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, 1 Ming-shen East Road, Jiji, Nantou 552, Taiwan
| | - Anssi Laurila
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Adeline Loyau
- Department of Conservation Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Sara Meurling
- Department of Ecology and Genetics, EBC, Uppsala University, Norbyv. 18D, SE-75236, Uppsala, Sweden
| | - Claude Miaud
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Pete Minting
- Amphibian and Reptile Conservation (ARC) Trust, Boscombe, Bournemouth, Dorset BH1 4AP, UK
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Dirk S Schmeller
- Department of Conservation Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Benedikt R Schmidt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland, and Info Fauna Karch, UniMail-Bâtiment G, Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Jennifer M G Shelton
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Lee F Skerratt
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Freya Smith
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- National Wildlife Management Centre, APHA, Woodchester Park, Gloucestershire GL10 3UJ, UK
| | - Claudio Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
| | | | - Giulia Tessa
- Non-profit Association Zirichiltaggi-Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100 Sassari, Italy
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Unicamp, Campinas, Brazil
| | - Andrés Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Republica 440, Santiago, Chile
- ONG Ranita de Darwin, Nataniel Cox 152, Santiago, Chile
| | - Ruhan Verster
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - Judit Vörös
- Collection of Amphibians and Reptiles, Department of Zoology, Hungarian Natural History Museum, Budapest, Baross u. 13., 1088, Hungary
| | - Rebecca J Webb
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Claudia Wierzbicki
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Emma Wombwell
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - David M Aanensen
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridgeshire, UK
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 49, NO-7012 Trondheim, Norway
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ché Weldon
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC c/ Jose Gutierrez Abascal 2, 28006 Madrid, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Trenton W J Garner
- Institute of Zoology, Regent's Park, London NW1 4RY, UK
- Unit for Environmental Sciences and Management, Private Bag x6001, North-West University, Potchefstroom 2520, South Africa
- Non-profit Association Zirichiltaggi-Sardinia Wildlife Conservation, Strada Vicinale Filigheddu 62/C, I-07100 Sassari, Italy
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology and MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, UK.
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9
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Valdivia LE, Lamb DB, Horner W, Wierzbicki C, Tafessu A, Williams AM, Gestri G, Krasnow AM, Vleeshouwer-Neumann TS, Givens M, Young RM, Lawrence LM, Stickney HL, Hawkins TA, Schwarz QP, Cavodeassi F, Wilson SW, Cerveny KL. Antagonism between Gdf6a and retinoic acid pathways controls timing of retinal neurogenesis and growth of the eye in zebrafish. Development 2016; 143:1087-98. [PMID: 26893342 PMCID: PMC4852494 DOI: 10.1242/dev.130922] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 09/11/2015] [Accepted: 02/08/2016] [Indexed: 12/27/2022]
Abstract
Maintaining neurogenesis in growing tissues requires a tight balance between progenitor cell proliferation and differentiation. In the zebrafish retina, neuronal differentiation proceeds in two stages with embryonic retinal progenitor cells (RPCs) of the central retina accounting for the first rounds of differentiation, and stem cells from the ciliary marginal zone (CMZ) being responsible for late neurogenesis and growth of the eye. In this study, we analyse two mutants with small eyes that display defects during both early and late phases of retinal neurogenesis. These mutants carry lesions in gdf6a, a gene encoding a BMP family member previously implicated in dorsoventral patterning of the eye. We show that gdf6a mutant eyes exhibit expanded retinoic acid (RA) signalling and demonstrate that exogenous activation of this pathway in wild-type eyes inhibits retinal growth, generating small eyes with a reduced CMZ and fewer proliferating progenitors, similar to gdf6a mutants. We provide evidence that RA regulates the timing of RPC differentiation by promoting cell cycle exit. Furthermore, reducing RA signalling in gdf6a mutants re-establishes appropriate timing of embryonic retinal neurogenesis and restores putative stem and progenitor cell populations in the CMZ. Together, our results support a model in which dorsally expressed gdf6a limits RA pathway activity to control the transition from proliferation to differentiation in the growing eye. Summary: In the vertebrate eye, dorsally expressed Gdf6a limits RA pathway activity to control the transition from proliferation to differentiation, thereby regulating eye size.
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Affiliation(s)
- Leonardo E Valdivia
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Dayna B Lamb
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Wilson Horner
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Claudia Wierzbicki
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Amanuel Tafessu
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Audrey M Williams
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Gaia Gestri
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Anna M Krasnow
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | | | - McKenzie Givens
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Rodrigo M Young
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Lisa M Lawrence
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Heather L Stickney
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Thomas A Hawkins
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Quenten P Schwarz
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Florencia Cavodeassi
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Kara L Cerveny
- Department of Cell and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
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Cosnay J, Le Marrec C, Gatignol P, Wierzbicki C. Intérêt d’une plateforme de remédiation cognitive virtuelle à distance : cognibulle. Rev Neurol (Paris) 2013. [DOI: 10.1016/j.neurol.2013.01.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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Moro E, Ozhan-Kizil G, Mongera A, Beis D, Wierzbicki C, Young RM, Bournele D, Domenichini A, Valdivia LE, Lum L, Chen C, Amatruda JF, Tiso N, Weidinger G, Argenton F. In vivo Wnt signaling tracing through a transgenic biosensor fish reveals novel activity domains. Dev Biol 2012; 366:327-40. [PMID: 22546689 DOI: 10.1016/j.ydbio.2012.03.023] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 03/09/2012] [Accepted: 03/21/2012] [Indexed: 11/30/2022]
Abstract
The creation of molecular tools able to unravel in vivo spatiotemporal activation of specific cell signaling events during cell migration, differentiation and morphogenesis is of great relevance to developmental cell biology. Here, we describe the generation, validation and applications of two transgenic reporter lines for Wnt/β-catenin signaling, named TCFsiam, and show that they are reliable and sensitive Wnt biosensors for in vivo studies. We demonstrate that these lines sensitively detect Wnt/β-catenin pathway activity in several cellular contexts, from sensory organs to cardiac valve patterning. We provide evidence that Wnt/β-catenin activity is involved in the formation and maintenance of the zebrafish CNS blood vessel network, on which sox10 neural crest-derived cells migrate and proliferate. We finally show that these transgenic lines allow for screening of Wnt signaling modifying compounds, tissue regeneration assessment as well as evaluation of potential Wnt/β-catenin genetic modulators.
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Affiliation(s)
- Enrico Moro
- Department of Biomedical Sciences, University of Padova, I-35121 Padova, Italy.
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