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Linsky JMJ, Dunlop RA, McMichael LA. A novel RT-qPCR health assay reveals differential expression of stress and immunoregulatory genes between the seasonal migrations of humpback whales (Megaptera novaeangliae). Mol Ecol 2024; 33:e17209. [PMID: 38018561 DOI: 10.1111/mec.17209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
Health information is essential for the conservation management of whale species. However, assessing the health of free-ranging whales is challenging as samples are primarily limited to skin and blubber tissue. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers a method to measure health from blubber RNA, providing insights into energetic status, stress and immune activity. To identify changes in health, natural differences in baseline gene expression linked to an individual's sex, reproductive status and life-history stage must first be quantified. This study aimed to establish baseline gene expression indices of health in migrating humpback whales (Megaptera novaeangliae). To do this, we developed an assay to quantify seven health-related gene transcripts (Leptin, Leptin Receptor, Adiponectin, Aryl Hydrocarbon Receptor, Tumour Necrosis Factor-α, Interleukin-6, Heat Shock Protein-70) and used Bayesian mixed effect models to assess differential baseline expression based on sex, lactation status and migration stage (northbound to and southbound from the annual breeding grounds). Results showed no significant contribution of sex to differential baseline expression. However, lactating individuals exhibited downregulated AhR and HSP-70 compared to non-lactating conspecifics. Additionally, southbound individuals demonstrated significantly upregulated HSP-70 and downregulated TNF-alpha, suggesting a relationship between these inflammation-linked transcripts and migratory fasting. Our results suggest that baseline differences due to migratory stage and lactation status should be considered in health applications of this assay. Future monitoring efforts can use our baseline measurements to better understand how gene expression is tied to population-level impacts, such as reduced prey availability or migratory stressors.
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Affiliation(s)
- Jacob M J Linsky
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Rebecca A Dunlop
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee A McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
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2
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Everest DJ, Green C, Dastjerdi A, Davies H, Cripps R, McKinney C, Podgornik G, Stinson M, O'Hare S, Sapsford B, Mill A, Van der Waal Z, Robinson N, Trotter S, Shuttleworth CM. Opportunistic viral surveillance confirms the ongoing disease threat grey squirrels pose to sympatric red squirrel populations in the UK. Vet Rec 2023; 192:e2834. [PMID: 37024300 DOI: 10.1002/vetr.2834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/29/2022] [Accepted: 03/01/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND Red Squirrels United was a UK landscape-scale grey squirrel management programme undertaken between 2016 and 2020. METHODS A total of 11034 grey squirrels were removed by culling, with 1506 necropsied and 1405 suitable for adenovirus (AdV) or squirrelpox virus (SQPV) quantitative PCR (qPCR) analysis. Spleen, lip or hair were extracted, and DNA was isolated, with samples tested in duplicate by qPCR. RESULTS Of 1378 tissue samples, 43% were positive for AdV and 10% for SQPV. Of 1031 hair samples, 11% were positive for AdV and 10% for SQPV. Overall, 762 of 1405 (54%) animals were positive for one or both viruses. LIMITATIONS Ad hoc sampling was undertaken from limited geographical areas but provided the only dataset from that period, instead of extrapolating from historical data. CONCLUSIONS The grey squirrel is an asymptomatic reservoir host for AdV and SQPV. Interspecific infection transmission potential is demonstrated. Grey squirrel management by culling is essential for mainland red squirrel viability until other suitable management tools are available.
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Affiliation(s)
| | - Chalin Green
- Animal and Plant Health Agency-Weybridge, Addlestone, UK
| | | | - Hannah Davies
- Animal and Plant Health Agency-Weybridge, Addlestone, UK
| | - Rachel Cripps
- Lancashire Wildlife Trust, Seaforth Nature Reserve, Liverpool, UK
| | | | | | | | - Simon O'Hare
- Northumberland Wildlife Trust, Newcastle Upon Tyne, UK
| | | | - Aileen Mill
- Centre for Wildlife Management, School of Biology, Newcastle University, Newcastle Upon Tyne, UK
| | - Zelda Van der Waal
- Centre for Wildlife Management, School of Biology, Newcastle University, Newcastle Upon Tyne, UK
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Wauters LA, Lurz PWW, Santicchia F, Romeo C, Ferrari N, Martinoli A, Gurnell J. Interactions between native and invasive species: A systematic review of the red squirrel-gray squirrel paradigm. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1083008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
The eastern gray squirrel (Sciurus carolinensis) has been labeled as one of the 100 worst invasive alien species by the IUCN. In Europe, the species has been introduced to Britain, Ireland and Italy, and its subsequent spread has resulted in wide-scale extinction of native Eurasian red squirrels (Sciurus vulgaris) from the areas colonized by the gray squirrel. This replacement of a native by an alien competitor is one of the best documented cases of the devastating effects of biological invasions on native fauna. To understand how this replacement occurs, we present a systematic review of the literature on competition and interactions between red and gray squirrels. We describe the patterns of red and gray squirrel distribution in those parts of Europe where gray squirrels occur and summarize the evidence on the different processes and mechanisms determining the outcome of competition between the native and alien species including the influence of predators and pathogens. Some of the drivers behind the demise of the red squirrel have been intensively studied and documented in the past 30 years, but recent field studies and mathematical models revealed that the mechanisms underlying the red-gray paradigm are more complex than previously thought and affected by landscape-level processes. Therefore, we consider habitat type and multi-species interactions, including host-parasite and predator-prey relationships, to determine the outcome of the interaction between the two species and to better address gray squirrel control efforts.
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Linsky JMJ, Dunlop RA, Noad MJ, McMichael LA. A mammalian messenger RNA sex determination method from humpback whale ( Megaptera novaeangliae) blubber biopsies. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220556. [PMID: 36016912 PMCID: PMC9399696 DOI: 10.1098/rsos.220556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The large size of free-ranging mysticetes, such as humpback whales (Megaptera novaeangliae), make capture and release health assessments unfeasible for conservation research. However, individual energetic condition or reproductive health may be assessed from the gene expression of remotely biopsied tissue. To do this, researchers must reliably extract RNA and interpret gene expression measurements within the context of an individual's sex. Here, we outline an RNA extraction protocol from blubber tissue and describe a novel mammalian RNA sex determination method. Our method consists of a duplex reverse transcription-quantitative (real-time) polymerase chain reaction (RT-qPCR) with primer sets for a control gene (ACTB) and the X-chromosome inactivation gene (XIST). Products of each RT-qPCR had distinct melting temperature profiles based on the presence (female) or absence (male) of the XIST transcript. Using high-resolution melt analysis, reactions were sorted into one of two clusters (male/female) based on their melting profiles. We validated the XIST method by comparing results with a standard DNA-based method. With adequate quantities of RNA (minimum of approx. 9 ng µl-1), the XIST sex determination method shows 100% agreement with traditional DNA sex determination. Using the XIST method, future cetacean health studies can interpret gene expression within the context of an individual's sex, all from a single extraction.
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Affiliation(s)
- Jacob M. J. Linsky
- School of Biological Sciences The University of Queensland, St Lucia, Queensland 4072, Australia
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Rebecca A. Dunlop
- School of Biological Sciences The University of Queensland, St Lucia, Queensland 4072, Australia
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Michael J. Noad
- Centre for Marine Science, The University of Queensland, St Lucia, Queensland 4072, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Lee A. McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
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5
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Disease monitoring and surveillance: case studies in the applied conservation of fragmented red squirrel (Sciurus vulgaris) populations in England and Wales. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Edson J, Brown J, Miller WL, Walter WD. Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses. Sci Rep 2021; 11:10003. [PMID: 33976279 PMCID: PMC8113455 DOI: 10.1038/s41598-021-89390-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer (Odocoileus virginianus). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.
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Affiliation(s)
- Jessie Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
| | - Justin Brown
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - William L Miller
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546, USA
| | - W David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 403 Forest Resources Building, University Park, PA, 16802, USA.
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Chantrey J, Dale T, Jones D, Begon M, Fenton A. The drivers of squirrelpox virus dynamics in its grey squirrel reservoir host. Epidemics 2019; 28:100352. [PMID: 31327730 DOI: 10.1016/j.epidem.2019.100352] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022] Open
Abstract
Many pathogens of conservation concern circulate endemically within natural wildlife reservoir hosts and it is imperative to understand the individual and ecological drivers of natural transmission dynamics, if any threat to a related endangered species is to be assessed. Our study highlights the key drivers of infection and shedding dynamics of squirrelpox virus (SQPV) in its reservoir grey squirrel (Sciurus carolinensis) population. To clarify SQPV dynamics in this population, longitudinal data from a 16-month mark-recapture study were analysed, combining serology with real-time quantitative PCR to identify periods of acute viraemia and chronic viral shedding. At the population level, we found SQPV infection prevalence, viral load and shedding varied seasonally, peaking in autumn and early spring. Individually, SQPV was shown to be a chronic infection in >80% of grey squirrels, with viral loads persisting over time and bouts of potential recrudescence or reinfection occurring. A key recurring factor significantly associated with SQPV infection risk was the presence of co-infecting squirrel adenovirus (ADV). In dual infected squirrels, longitudinal analysis showed that prior ADV viraemia increased the subsequent SQPV load in the blood. However, there was a strong, negative association between prior ADV viraemia and subsequent SQPV shedding from the forearm, probably caused by ADV prolonging the SQPV acute viraemic phase, so delaying onset of the chronic shedding phase, and thereby altering viral shedding patterns over the time scales examined here. Hence, co-circulating ADV infection may be involved in mediating both the quantitative levels of SQPV infection and the timing and degree of subsequent infectiousness of grey squirrels.
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Affiliation(s)
- Julian Chantrey
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK; Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK.
| | - Timothy Dale
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - David Jones
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Michael Begon
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
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Romeo C, McInnes CJ, Dale TD, Shuttleworth C, Bertolino S, Wauters LA, Ferrari N. Disease, invasions and conservation: no evidence of squirrelpox virus in grey squirrels introduced to Italy. Anim Conserv 2018. [DOI: 10.1111/acv.12433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Romeo
- Department of Veterinary Medicine Università degli Studi di Milano Milan Italy
| | | | - T. D. Dale
- Institute of Integrative Biology University of Liverpool Liverpool UK
| | - C. Shuttleworth
- School of Environment, Natural Resources and Geography Bangor University Bangor Gwynedd UK
| | - S. Bertolino
- Department of Life Sciences and Systems Biology Università degli Studi di Torino Torino Italy
| | - L. A. Wauters
- Department of Theoretical and Applied Sciences Università degli Studi dell'Insubria Varese Italy
| | - N. Ferrari
- Department of Veterinary Medicine Università degli Studi di Milano Milan Italy
- Centro di Ricerca Coordinata Epidemiologia e Sorveglianza Molecolare delle Infezioni Università degli Studi di Milano Milan Italy
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Leung WTM, Thomas-Walters L, Garner TWJ, Balloux F, Durrant C, Price SJ. A quantitative-PCR based method to estimate ranavirus viral load following normalisation by reference to an ultraconserved vertebrate target. J Virol Methods 2017; 249:147-155. [PMID: 28844932 DOI: 10.1016/j.jviromet.2017.08.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/18/2017] [Accepted: 08/20/2017] [Indexed: 02/02/2023]
Abstract
Ranaviruses are important pathogens of amphibians, reptiles and fish. To meet the need for an analytical method for generating normalised and comparable infection data for these diverse host species, two standard-curve based quantitative-PCR (qPCR) assays were developed enabling viral load estimation across these host groups. A viral qPCR targeting the major capsid protein (MCP) gene was developed which was specific to amphibian-associated ranaviruses with high analytical sensitivity (lower limit of detection: 4.23 plasmid standard copies per reaction) and high reproducibility across a wide dynamic range (coefficient of variation below 3.82% from 3 to 3×108 standard copies per reaction). The comparative sensitivity of the viral qPCR was 100% (n=78) based on agreement with an established end-point PCR. Comparative specificity with the end-point PCR was also 100% (n=94) using samples from sites with no history of ranavirus infection. To normalise viral quantities, a host qPCR was developed which targeted a single-copy, ultra-conserved non-coding element (UCNE) of vertebrates. Viral and host qPCRs were applied to track ranavirus growth in culture. The two assays offer a robust approach to viral load estimation and the host qPCR can be paired with assays targeting other pathogens to study infection burdens.
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Affiliation(s)
- William T M Leung
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.
| | - Laura Thomas-Walters
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom; Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, CT2 7NZ, United Kingdom
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Francois Balloux
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, United Kingdom
| | - Chris Durrant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom; NatureMetrics Ltd., Ashford, Surrey, TW15 1UU, United Kingdom
| | - Stephen J Price
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom; UCL Genetics Institute, Gower Street, London, WC1E 6BT, United Kingdom
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