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Casali F, Ciavaglia SA, Gannicliffe C, Lidstone N, Webster LMI. Validation of presumptive tests for non-human blood using Kastle Meyer and Hemastix reagents. Sci Justice 2020; 60:30-35. [PMID: 31924286 DOI: 10.1016/j.scijus.2019.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 10/01/2019] [Accepted: 10/06/2019] [Indexed: 11/29/2022]
Abstract
Kastle Meyer and Hemastix reagents are presumptive tests commonly used in forensic casework for the detection of blood, and their suitability has been reviewed in numerous publications. However, studies to date have focused on the validation of these tests on human blood alone, and no published work has looked at the sensitivity, specificity and effect on DNA analysis when using these reagents to presumptively test for animal blood. The aim of this study was to validate the two reagents for use with animal blood, and compare their performance in order to choose the best test based on the circumstances in wildlife crime investigation. The sensitivity, specificity, stability and robustness of the methods were assessed by experiments with dilutions of animal blood (from 1:4 to 1:65536) using direct and indirect (rub) tests, potential interfering substances, blood sources from different species and aged blood. The effects of the two reagents on subsequent DNA analysis were also investigated. During the direct tests, Kastle Meyer showed a higher sensitivity, detecting blood down to a dilution of 1:16,384, one order of magnitude lower than Hemastix. However during the rub test, Hemastix showed a higher sensitivity, detecting blood down to a dilution of 1:64 on porous materials while Kastle Meyer was positive only down to a dilution of 1:16. Moreover, when using the same swab for presumptive testing and DNA extraction, Hemastix testing allowed amplification of a sufficient amount of DNA for species identification at its limit of sensitivity on porous materials (1:64) while Kastle Meyer inhibited most amplification of DNA at its less sensitive limit of 1:16 dilution. On the other hand, Hemastix showed a much lower specificity, producing false positive results when exposed to tomato, potato, rust, avian uric acid, bleach and sink rot, while Kastle Meyer only produced a faint positive reaction from potato. Both tests performed equally well detecting fresh blood of different animal species. The stability test gave comparable results among the tests except for aged fish blood stains, where the Kastle Meyer test performed poorly. Owing to its ease of use, higher sensitivity, and lack of interference with downstream DNA analysis, and despite its reduced specificity compared to Kastle Meyer, the Hemastix method is more appropriate for use in wildlife crime investigations. Positive results would always be confirmed with DNA analysis and the low interference of the reagent will allow the use of a single swab for presumptive testing and DNA sampling.
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Affiliation(s)
- F Casali
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom; Wildlife DNA Forensics Unit, SASA, Edinburgh EH12 9FJ, United Kingdom
| | - S A Ciavaglia
- Wildlife DNA Forensics Unit, SASA, Edinburgh EH12 9FJ, United Kingdom
| | - C Gannicliffe
- Forensic Services, Scottish Police Authority, United Kingdom
| | - N Lidstone
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom; University of Staffordshire, United Kingdom
| | - L M I Webster
- Wildlife DNA Forensics Unit, SASA, Edinburgh EH12 9FJ, United Kingdom.
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Mcleish K, Ferguson S, Gannicliffe C, Campbell S, Thomson PIT, Webster LMI. Profiling in wildlife crime: Recovery of human DNA deposited outside. Forensic Sci Int Genet 2018; 35:65-69. [PMID: 29673693 DOI: 10.1016/j.fsigen.2018.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 12/20/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
Incidents of bird of prey persecution receive a lot of media coverage in the UK, with investigations rarely recovering sufficient evidence to proceed to prosecution. One of the main challenges is to identify a suspect, as these offences are carried out in remote locations without witnesses, and crime scenes may not be found for days. However, traps, poisoned baits and bird of prey carcasses can be recovered from these crime scenes. This study aimed to determine whether reportable human DNA profiles could be recovered from any of these substrates after periods of time outside. Experiments depositing human touch DNA on duplicate substrates (traps, rabbit baits and corvid carcasses) set for 0, 1, 2, 4, 7 and 10 days outside were carried out, with DNA recovery and profiling following standard operating procedures for Scottish Police Authority Forensic Services. Weather conditions varied among experiments, including some heavy rainfall. Results demonstrated that it was possible to obtain reportable DNA profiles from all substrates after at least 1 day outside. Most promisingly, the traps showed no drop-off in DNA persistence over the experiments as complete DNA profiles were obtained after the full 10 days outside. A further experiment using 4 bird of prey carcasses confirmed that it is possible to obtain reportable human DNA profiles from them after 1 day outside (n = 2 reportable profiles). These results show that touch DNA can persist in an outdoor environment, and provide a tantalising avenue for inquiry in bird of prey persecution investigations.
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Affiliation(s)
- K Mcleish
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom
| | - S Ferguson
- Forensic Services, Scottish Police Authority, United Kingdom.
| | - C Gannicliffe
- Forensic Services, Scottish Police Authority, United Kingdom
| | - S Campbell
- Wildlife DNA Forensics Unit, Science and Advice for Scottish Agriculture, Edinburgh, United Kingdom
| | - P I T Thomson
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom
| | - L M I Webster
- Wildlife DNA Forensics Unit, Science and Advice for Scottish Agriculture, Edinburgh, United Kingdom
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Maroso F, Hillen JEJ, Pardo BG, Gkagkavouzis K, Coscia I, Hermida M, Franch R, Hellemans B, Van Houdt J, Simionati B, Taggart JB, Nielsen EE, Maes G, Ciavaglia SA, Webster LMI, Volckaert FAM, Martinez P, Bargelloni L, Ogden R. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species. Mar Genomics 2018; 39:64-72. [PMID: 29496460 DOI: 10.1016/j.margen.2018.02.002] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/29/2023]
Abstract
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies.
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Affiliation(s)
- F Maroso
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy.
| | - J E J Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - B G Pardo
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - K Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - I Coscia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; School of Environmental and Life Science, Rm 332, Peel Building, University of Salford, Salford M5 4WT, UK
| | - M Hermida
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - R Franch
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - B Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - J Van Houdt
- Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium
| | - B Simionati
- BMR Genomics, Via Redipuglia 21a, Padova, Italy
| | - J B Taggart
- Division of Environmental and Evolutionary Biology, School of Biology and Biochemistry, The Queen's University of Belfast, Belfast BT7 INN, UK
| | - E E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - G Maes
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium; Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Marine and Environmental Sciences, Faculty of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia
| | - S A Ciavaglia
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - L M I Webster
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - F A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - P Martinez
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - L Bargelloni
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - R Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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Wenzel MA, Webster LMI, Segelbacher G, Reid JM, Piertney SB. Isolation and characterisation of 17 microsatellite loci for the red-billed chough (Pyrrhocorax pyrrhocorax). CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-011-9446-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Webster LMI, Paterson S, Mougeot F, Martinez-Padilla J, Piertney SB. Transcriptomic response of red grouse to gastro-intestinal nematode parasites and testosterone: implications for population dynamics. Mol Ecol 2010; 20:920-31. [PMID: 21073676 DOI: 10.1111/j.1365-294x.2010.04906.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A central issue in ecology is in understanding the relative influences of intrinsic and extrinsic effects on population regulation. Previous studies on the cyclic population dynamics of red grouse (Lagopus lagopus scoticus) have emphasized the destabilizing effects of either nematode parasites or territorial behaviour and aggression. The potential interacting effects of these processes, mediated through density-dependent, environmentally induced alterations of host immunocompetence influencing susceptibility to parasites have not been considered. Male red grouse at high density are more aggressive, associated with increased testosterone, which potentially could lead to reduced immunocompetence at a stage when parasites are most prevalent. This could depress individual condition, breeding performance and survival and thus drive or contribute to overall reductions in population size. Here, we characterize the transcriptomic response of grouse to nematode parasite infection and investigate how this is subsequently affected by testosterone, using a microarray approach contrasting red grouse with high and low parasite load at both high and low testosterone titre. A suite of 52 transcripts showed a significant level of up-regulation to either chronic parasite load or experimental parasite infection. Of these, 51 (98%) showed a reduced level of expression under conditions of high parasite load and high testosterone. The genes up-regulated by parasites and then down-regulated at high testosterone titre were not necessarily associated with immune response, as might be intuitively expected. The results are discussed in relation to the fitness and condition of individual red grouse and factors influencing the regulation of abundance in natural populations.
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Affiliation(s)
- L M I Webster
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
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Webster LMI, Mello LV, Mougeot F, Martinez-Padilla J, Paterson S, Piertney SB. Identification of genes responding to nematode infection in red grouse. Mol Ecol Resour 2010; 11:305-13. [PMID: 21429137 DOI: 10.1111/j.1755-0998.2010.02912.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The identification of genes involved in a host's response to parasite infection provides both a means for understanding the pathways involved in immune defence and a target for examining host-parasite co-evolution. Most studies rely on a candidate gene approach derived from model systems to identify gene targets of interest, and there have been a dearth of studies geared towards providing a holistic overview of immune response from natural populations. We carried out an experiment in a natural population of red grouse (Lagopus lagopus scoticus) to manipulate levels of Trichostrongylus tenuis parasite infection. The transcriptomic response of individuals was examined from standard cDNA and suppressive subtractive hybridization (SSH) libraries produced from gut, liver and spleen, enriching for genes expressed in response to T. tenuis infection. A total of 2209 and 3716 unique transcript sequences were identified from the cDNA and SSH libraries, respectively. Forty-five of these had Gene Ontology annotation associated with immune response. Some of these genes have previously been reported from laboratory-based studies of model species as important in immune response to gastrointestinal parasite infection; however, multiple novel genes were also identified. These may reveal novel pathways involved in the host response of grouse to T. tenuis and provide a resource that can be utilized as candidate genes in other species. All sequences described have been deposited in GenBank (accession numbers GW698221-GW706922)
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Affiliation(s)
- L M I Webster
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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Mougeot F, Martínez-Padilla J, Blount JD, Pérez-Rodríguez L, Webster LMI, Piertney SB. Oxidative stress and the effect of parasites on a carotenoid-based ornament. J Exp Biol 2010. [DOI: 10.1242/jeb.044933] [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: 11/20/2022]
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Mougeot F, Martínez-Padilla J, Blount JD, Pérez-Rodríguez L, Webster LMI, Piertney SB. Oxidative stress and the effect of parasites on a carotenoid-based ornament. ACTA ACUST UNITED AC 2010; 213:400-7. [PMID: 20086124 DOI: 10.1242/jeb.037101] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Oxidative stress, the physiological condition whereby the production of reactive oxygen and nitrogen species overwhelms the capacity of antioxidant defences, causes damage to key bio-molecules. It has been implicated in many diseases, and is proposed as a reliable currency in the trade-off between individual health and ornamentation. Whether oxidative stress mediates the expression of carotenoid-based signals, which are among the commonest signals of many birds, fish and reptiles, remains controversial. In the present study, we explored interactions between parasites, oxidative stress and the carotenoid-based ornamentation of red grouse Lagopus lagopus scoticus. We tested whether removing nematode parasites influenced both oxidative balance (levels of oxidative damage and circulating antioxidant defences) and carotenoid-based ornamentation. At the treatment group level, parasite purging enhanced the size and colouration of ornaments but did not significantly affect circulating carotenoids, antioxidant defences or oxidative damage. However, relative changes in these traits among individuals indicated that males with a greater number of parasites prior to treatment (parasite purging) showed a greater increase in the levels of circulating carotenoids and antioxidants, and a greater decrease in oxidative damage, than those with initially fewer parasites. At the individual level, a greater increase in carotenoid pigmentation was associated with a greater reduction in oxidative damage. Therefore, an individual's ability to express a carotenoid-based ornament appeared to be linked to its current oxidative balance and susceptibility to oxidative stress. Our experimental results suggest that oxidative stress can mediate the impact of parasites on carotenoid-based signals, and we discuss possible mechanisms linking carotenoid-based ornaments to oxidative stress.
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Affiliation(s)
- F Mougeot
- Estación Experimental de Zonas Aridas, CSIC, General Segura 1, 04001 Almeria, Spain.
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