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Li J, Ulloa GM, Mayor P, Santolalla Robles ML, Greenwood AD. Nucleic acid degradation after long-term dried blood spot storage. Mol Ecol Resour 2024; 24:e13979. [PMID: 38780145 DOI: 10.1111/1755-0998.13979] [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: 10/25/2023] [Revised: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid-based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose-based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long-term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold-chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free-ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses.
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Affiliation(s)
- Juan Li
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Gabriela M Ulloa
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- Grupo de Enfermedades Infecciosas Re-emergentes, Universidad Científica del Sur (UCSUR), Lima, Peru
| | - Pedro Mayor
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- ComFauna, Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica, Iquitos, Peru
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Meddly L Santolalla Robles
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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2
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Schulte J, Hotz G, Szinnai G, Christ E, Foderà G, Krüsi K, Nussberger P, Kron S, Schulz I. Exploring the potential of genetic analysis in historical blood spots for patients with iodine-deficient goiter and thyroid carcinomas in Switzerland and Germany (1929-1989). BMC Med Genomics 2024; 17:171. [PMID: 38943113 PMCID: PMC11212273 DOI: 10.1186/s12920-024-01947-y] [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: 09/14/2023] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Iodine deficiency-induced goiter continues to be a global public health concern, with varying manifestations based on geography, patient's age, and sex. To gain insights into clinical occurrences, a retrospective study analyzed medical records from patients with iodine deficiency-induced goiter or thyroid cancer who underwent surgery at the Community Hospital in Riehen, Switzerland, between 1929 and 1989. Despite today's adequate iodine supplementation, a significant risk for iodine-independent goiter remains in Switzerland, suggesting that genetic factors, among others, might be involved. Thus, a pilot study exploring the feasibility of genetic analysis of blood spots from these medical records was conducted to investigate and enhance the understanding of goiter development, potentially identify genetic variations, and explore the influence of dietary habits and other environmental stimuli on the disease.Blood prints from goiter patients' enlarged organs were collected per decade from medical records. These prints had been made by pressing, drawing, or tracing (i.e., pressed and drawn) the removed organs onto paper sheets. DNA analysis revealed that its yields varied more between the prints than between years. A considerable proportion of the samples exhibited substantial DNA degradation unrelated to sample collection time and DNA mixtures of different contributors. Thus, each goiter imprint must be individually evaluated and cannot be used to predict the success rate of genetic analysis in general. Collecting a large sample or the entire blood ablation for genetic analysis is recommended to mitigate potential insufficient DNA quantities. Researchers should also consider degradation and external biological compounds' impact on the genetic analysis of interest, with the dominant contributor anticipated to originate from the patient's blood.
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Affiliation(s)
- Janine Schulte
- Health Department Basel-Stadt, Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, Basel, 4056, Switzerland
| | - Gerhard Hotz
- Natural History Museum Basel, Augustinergasse 2, Basel, 4001, Switzerland
| | - Gabor Szinnai
- Pediatric Endocrinology/Diabetology, University Children's Hospital Basel UKBB, University of Basel, Basel, 4056, Switzerland
| | - Emanuel Christ
- Division of Endocrinology, Diabetology, Metabolism and Center of Endocrine and Neuroendocrine Tumors, University Hospital Basel, Basel, 4056, Switzerland
| | - Gaspare Foderà
- Documentation Center, Municipal Administration, Riehen, 4125, Switzerland
| | - Karl Krüsi
- Documentation Center, Municipal Administration, Riehen, 4125, Switzerland
| | | | - Sarah Kron
- Health Department Basel-Stadt, Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, Basel, 4056, Switzerland
| | - Iris Schulz
- Health Department Basel-Stadt, Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, Basel, 4056, Switzerland.
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Taesuji M, Rattanamas K, Yim PB, Ruenphet S. Stability and Detection Limit of Avian Influenza, Newcastle Disease Virus, and African Horse Sickness Virus on Flinders Technology Associates Card by Conventional Polymerase Chain Reaction. Animals (Basel) 2024; 14:1242. [PMID: 38672390 PMCID: PMC11047397 DOI: 10.3390/ani14081242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
The Flinders Technology Associates (FTA) card, a cotton-based cellulose membrane impregnated with a chaotropic agent, effectively inactivates infectious microorganisms, lyses cellular material, and fixes nucleic acid. The aim of this study is to assess the stability and detection limit of various RNA viruses, especially the avian influenza virus (AIV), Newcastle disease virus (NDV), and African horse sickness virus (AHSV), on the FTA card, which could significantly impact virus storage and transport practices. To achieve this, each virus dilution was inoculated onto an FTA card and stored at room temperature in plastic bags for durations ranging from 1 week to 6 months. Following storage, the target genome was detected using conventional reverse transcription polymerase chain reaction. The present study demonstrated that the detection limit of AIV ranged from 1.17 to 6.17 EID50 values over durations ranging from 1 week to 5 months, while for NDV, it ranged from 2.83 to 5.83 ELD50 over the same duration. Additionally, the detection limit of AHSV was determined as 4.01 PFU for both 1 and 2 weeks, respectively. Based on the demonstrated effectiveness, stability, and safety implications observed in the study, FTA cards are recommended for virus storage and transport, thus facilitating the molecular detection and identification of RNA viral pathogens.
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Affiliation(s)
- Machimaporn Taesuji
- Clinic for Horse, Faculty of Veterinary Medicine, Mahanakorn University of Technology, Bangkok 10530, Thailand;
| | - Khate Rattanamas
- Master of Science Program in Animal Biotechnology, Mahanakorn University of Technology, Bangkok 10530, Thailand; (K.R.); (P.B.Y.)
| | - Peter B. Yim
- Master of Science Program in Animal Biotechnology, Mahanakorn University of Technology, Bangkok 10530, Thailand; (K.R.); (P.B.Y.)
| | - Sakchai Ruenphet
- Master of Science Program in Animal Biotechnology, Mahanakorn University of Technology, Bangkok 10530, Thailand; (K.R.); (P.B.Y.)
- Immunology and Virology Department, Mahanakorn University of Technology, Bangkok 10530, Thailand
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Si H, Tucciarone CM, Cecchinato M, Legnardi M, Mazzariol S, Centelleghe C. Comparison between Sampling Techniques for Virological Molecular Analyses: Dolphin Morbillivirus and Herpesvirus Detection from FTA ® Card and Frozen Tissue. Viruses 2023; 15:2422. [PMID: 38140663 PMCID: PMC10747605 DOI: 10.3390/v15122422] [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: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Stranded animals offer valuable information on marine mammal physiology and pathology; however, the decomposition state of the carcasses and lack of a rigorous cold chain for sample preservation can sometimes discourage diagnostic analyses based on nucleic acid detection. The present paper aims at evaluating the reliability of FTA® card tissue imprints as an alternative matrix to frozen tissues for virological analyses based on biomolecular methods. Given the contribution of Cetacean morbillivirus (CeMV) to strandings and the increase of herpesvirus detection in cetaceans, these two pathogens were selected as representative of RNA and DNA viruses. Dolphin morbillivirus (DMV) and herpesvirus presence was investigated in parallel on tissue imprints on FTA® cards and frozen tissues collected during necropsy of dolphins stranded in Italy. Samples were analysed by nested RT-PCR for DMV and nested-PCR for herpesvirus. Only one animal was positive for herpesvirus, hampering further considerations on this virus. DMV was detected in all animals, both in FTA® card imprints and tissue samples, with differences possibly related to the decomposition condition category of the carcasses. Tissue sampling on FTA® cards seems a promising alternative to frozen tissues for biomolecular analyses, especially when ensuring adequate storage and shipment conditions for frozen tissues is difficult.
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Affiliation(s)
- Haiyang Si
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Matteo Legnardi
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food Science (BCA), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (S.M.); (C.C.)
| | - Cinzia Centelleghe
- Department of Comparative Biomedicine and Food Science (BCA), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (S.M.); (C.C.)
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Cundy ME, Santana-Garcon J, McLennan AG, Ayad ME, Bayer PE, Cooper M, Corrigan S, Harrison E, Wilcox C. Seafood label quality and mislabelling rates hamper consumer choices for sustainability in Australia. Sci Rep 2023; 13:10146. [PMID: 37537170 PMCID: PMC10400555 DOI: 10.1038/s41598-023-37066-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/15/2023] [Indexed: 08/05/2023] Open
Abstract
Seafood mislabelling and species substitution, compounded by a convoluted seafood supply chain with significant traceability challenges, hinder efforts towards more sustainable, responsible, and ethical fishing and business practices. We conducted the largest evaluation of the quality and accuracy of labels for 672 seafood products sold in Australia, assessing six seafood groups (i.e., hoki, prawns, sharks and rays, snapper, squid and cuttlefish, and tuna) from fishmongers, restaurants, and supermarkets, including domestically caught and imported products. DNA barcoding revealed 11.8% of seafood tested did not match their label with sharks and rays, and snappers, having the highest mislabelling rate. Moreover, only 25.5% of products were labelled at a species-level, while most labels used vague common names or umbrella terms such as 'flake' and 'snapper'. These poor-quality labels had higher rates of mislabelling than species-specific labels and concealed the sale of threatened or overfished taxa, as well as products with lower nutritional quality, reduced economic value, or potential health risks. Our results highlight Australia's weak seafood labelling regulations and ambiguous non-mandatory naming conventions, which impede consumer choice for accurately represented, sustainable, and responsibly sourced seafood. We recommend strengthening labelling regulations to mitigate seafood mislabelling and substitution, ultimately improving consumer confidence when purchasing seafood.
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Affiliation(s)
- Megan E Cundy
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
| | - Julia Santana-Garcon
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia.
- Centre for Marine Socioecology, University of Tasmania, Hobart, TAS, Australia.
| | | | - Marcelle E Ayad
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
| | - Philipp E Bayer
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
| | - Madalyn Cooper
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
| | - Shannon Corrigan
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
| | - Emily Harrison
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
| | - Chris Wilcox
- Flourishing Oceans Initiative, Minderoo Foundation, Perth, WA, Australia
- Centre for Marine Socioecology, University of Tasmania, Hobart, TAS, Australia
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Chen Y, Hu Y, Lu X. An Integrated Paper Microfluidic Device Based on Isothermal Amplification for Simple Sample-to-Answer Detection of Campylobacter jejuni. Appl Environ Microbiol 2023; 89:e0069523. [PMID: 37382522 PMCID: PMC10370333 DOI: 10.1128/aem.00695-23] [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: 04/27/2023] [Accepted: 06/03/2023] [Indexed: 06/30/2023] Open
Abstract
Campylobacter jejuni is recognized as the most common species in the genus Campylobacter that causes foodborne diseases. The main reservoirs harboring C. jejuni are poultry products, which are associated with most illnesses, creating a demand for effective detection methods to achieve point-of-need diagnostics. We developed an easy-to-use, hybrid paper/polymer-based microfluidic device that integrates paper-based DNA extraction, isothermal nucleic acid amplification, and lateral flow detection. Overall, the recombinase polymerase amplification (RPA) reaction was completed in 20 min and demonstrated 100% specificity to C. jejuni, including 2 reference strains and 6 wild strains isolated from the agroecosystem, 9 other Campylobacter subspecies strains, and 11 non-Campylobacter strains. The limit of detection (LOD) was 46 CFU/mL with DNA extracted on the cellulose paper. The sensitivity was reduced to 460 CFU/mL on the integrated hybrid paper/polymer-based microfluidic device. This device could detect C. jejuni spiked at concentrations ranging from 101 to 102 CFU/g in chicken meat after an enrichment of 5 to 10 h. For C. jejuni levels of >102 CFU/g, it managed to confirm positive results immediately, without bacterial enrichment. RPA reagents and primers remained stable on the paper platform at 22°C for 12 h. After lyophilization and storage on paper, the RPA reaction showed consistent sensitivity for 3 days, and the LOD was reduced to 103 CFU/mL when storage was extended to 25 days. The use of this hybrid paper/polymer-based microfluidic device enabled detection of Campylobacter in foods with high specificity and sensitivity, demonstrating its potential as a reliable point-of-need diagnostic platform for on-site conditions due to its low cost, portability, and simplicity. IMPORTANCE The global health and economic burden of Campylobacter prompts the development of novel detection techniques that can be implemented in resource-limited and on-site settings. This study described point-of-need identification of C. jejuni using a hybrid paper/polymer-based microfluidic device that is easy to operate. This device had high specificity and sensitivity toward C. jejuni and significantly reduced the total analysis time compared to conventional culture-based methods. Nucleic acid extraction was simplified from intensive pipetting to a paper dipstick, making it more convenient for use in the field as a promising tool for future routine surveillance and outbreak investigation.
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Affiliation(s)
- Yunxuan Chen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yaxi Hu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Food Science Program, Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, McGill University Macdonald Campus, Quebec, Canada
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Meireles ACA, Rios FGF, Feitoza LHM, da Silva LR, Julião GR. Nondestructive Methods of Pathogen Detection: Importance of Mosquito Integrity in Studies of Disease Transmission and Control. Pathogens 2023; 12:816. [PMID: 37375506 DOI: 10.3390/pathogens12060816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Mosquitoes are vectors of many pathogens, including viruses, protozoans, and helminths, spreading these pathogens to humans as well as to wild and domestic animals. As the identification of species and the biological characterization of mosquito vectors are cornerstones for understanding patterns of disease transmission, and the design of control strategies, we conducted a literature review on the current use of noninvasive and nondestructive techniques for pathogen detection in mosquitoes, highlighting the importance of their taxonomic status and systematics, and some gaps in the knowledge of their vectorial capacity. Here, we summarized the alternative techniques for pathogen detection in mosquitoes based on both laboratory and field studies. Parasite infection and dissemination by mosquitoes can also be obtained via analyses of saliva- and excreta-based techniques or of the whole mosquito body, using a near-infrared spectrometry (NIRS) approach. Further research should be encouraged to seek strategies for detecting target pathogens while preserving mosquito morphology, especially in biodiversity hotspot regions, thus enabling the discovery of cryptic or new species, and the determination of more accurate taxonomic, parasitological, and epidemiological patterns.
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Affiliation(s)
- Anne Caroline Alves Meireles
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Biodiversity and Health, PhD in Sciences-Fiocruz Rondônia/Oswaldo Cruz Institute, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
| | - Flávia Geovana Fontineles Rios
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Luiz Henrique Maciel Feitoza
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Lucas Rosendo da Silva
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Genimar Rebouças Julião
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
- National Institute of Epidemiology of Western Amazônia-INCT-EpiAmO, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
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de Oliveira MM, Ferrando CPR, Gómez-Hernández C, de Oliveira KR, Araújo IAC, Ribeiro PVA, Mineo TWP, Leiner NO, Mineo JR, da Silva SM. Prevalence of Trypanosoma lainsoni and its effects of parasitism on the health of non-volant small mammals from the Brazilian Cerrado. Parasitol Res 2023:10.1007/s00436-023-07851-1. [PMID: 37129625 DOI: 10.1007/s00436-023-07851-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Small mammals are important hosts and/or reservoirs of Trypanosoma spp. This study aimed to verify the prevalence of Trypanosoma spp. in non-volant small mammals from the Brazilian Cerrado and to test the effects of T. lainsoni on the neutrophil/lymphocyte ratio (N/L) and body condition in rodent and marsupial populations. For this, we collected blood samples of 293 individuals captured in five forest fragments between 2019 and 2020. Blood was used to prepare the blood smears and packed on filter paper for DNA extraction. Generalized linear models were performed to test the effects of T. lainsoni on host health. The DNA was submitted to nested PCR targeting the Trypanosoma spp. 18S rRNA gene. From blood smears analyzed by microscopy, we obtained a positivity rate of 7.2% for Trypanosoma spp. About 31.1% of Gracilinanus agilis, Didelphis albiventris, and Rhipidomys macrurus samples were positive in nested PCR. From the obtained sequences, 83.3% were genetically identical to T. lainsoni and about 11% to T. cruzi TcI. In addition, we reported the infection of T. lainsoni in Hylaeamys megacephalus. We suggest that T. lainsoni does not influence the body condition and N/L ratio for either G. agilis or R. macrurus. Overall, our results expand the host list of T. lainsoni and demonstrate the infection of small mammals by T. cruzi TcI in peri-urban areas.
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Affiliation(s)
- Marco Miguel de Oliveira
- Institute of Biomedical Sciences, Department of Parasitology, Leishmania Bioassays Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
| | - Claire Pauline Röpke Ferrando
- Institute of Biology, Department of Zoology, Mammal Ecology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - César Gómez-Hernández
- Immunology Laboratory, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Karine Rezende de Oliveira
- Institute of Exact and Natural Sciences of Pontal, Federal University of Uberlândia, Ituiutaba, Minas Gerais, Brazil
| | - Iasmin Aparecida Cunha Araújo
- Institute of Biomedical Sciences, Department of Parasitology, Leishmania Bioassays Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Paulo Vitor Alves Ribeiro
- Institute of Biomedical Sciences, Department of Parasitology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Tiago Wilson Patriarca Mineo
- Institute of Biomedical Sciences, Department of Immunology, Immunoparasitology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Natália Oliveira Leiner
- Institute of Biology, Department of Zoology, Mammal Ecology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - José Roberto Mineo
- Institute of Biomedical Sciences, Department of Immunology, Immunoparasitology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Sydnei Magno da Silva
- Institute of Biomedical Sciences, Department of Parasitology, Leishmania Bioassays Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
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9
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Effect of storage temperature and duration on direct PCR amplification of various feather types and DBS matrices. Gene 2023; 854:147116. [PMID: 36526120 DOI: 10.1016/j.gene.2022.147116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The use of direct PCR has been pioneered over the last decade for DNA analysis of biological specimens of distinct origins. The information on how longer these specimens can be stored and amplified by direct PCR is however scanty. Such a piece of information could expedite research and diagnostic studies without compromising the reliability of results. The current study was therefore designed to analyze the effect of storage temperature and duration on direct PCR amplification of biological specimens having either low quantity or high quantity of DNA. Whole blood, dried blood spots (DBS), and feathers from chicken were stored for five years at three different temperatures, viz. room temperature (∼25 °C), 4 °C, and -20 °C. These samples were subjected to crude DNA extraction by diluting them in PBS buffer and heating at 98 °C after 1 day, 7 days, 15 days, 1 month, 3 months, 6 months, 1 year, 3 years and 5 years of storage. The crude DNA was PCR-amplified with the use of DNA sexing primers as well as DNA barcoding primers. Incubation at 98 °C for 10 min of any type of sample in PBS buffer was sufficient for crude DNA extraction. There was irrelevant impact of feather type, DBS matrix nature and storage temperature on amplification success over the period of analysis. It was possible to successfully accomplish the amplification of 96 samples with the use of routine PCR reagents within 3.5-6.0 hrs. In short, economical and fast genetic analysis of commonly used avian samples is feasible after their storage for longer time at room temperature.
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Alternate Approach in Storing and Shipment of SARS-CoV-2 RNA Samples with the Use of FTA Cards. Curr Microbiol 2022; 79:396. [PMID: 36352332 PMCID: PMC9646263 DOI: 10.1007/s00284-022-03079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022]
Abstract
Shipment of COVID-19 specimens within the country or overseas at long distances requires cold chain facility using dry ice and triple packing to prevent the risk of COVID-19 infection to the personnel involved in sample transport. The present study aimed to utilize FTA card technology as an alternate means of sample transport and storage across the country. Twenty-one SARS-CoV-2 lab confirmed samples with different Ct value (High, medium & low) were used to detect viral load in samples loaded on FTA card and further compared with VTM samples. The SARS-CoV-2 RNA was detected by rRT-PCR after storing for 14 days at 4 °C and 37 °C. The present study evaluated the utility of FTA cards for preserving the SARS CoV-2 RNA for 14-day period. A significant difference (P < 0.05) was observed in the cycle threshold (ΔCt 4–5) values obtained from FTA and VTM viral samples but it did not affect the positivity. The SARS-CoV-2 RNA could be recovered efficiently from FTA sample stored at 4 °C and 37 °C for 14 days. Thus, FTA cards could be an alternate option for transporting the samples at ambient temperature for a long time.
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Keck H, Eschbaumer M, Beer M, Hoffmann B. Comparison of Biosafety and Diagnostic Utility of Biosample Collection Cards. Viruses 2022; 14:2392. [PMID: 36366491 PMCID: PMC9697902 DOI: 10.3390/v14112392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 01/31/2023] Open
Abstract
Six different biosample collection cards, often collectively referred to as FTA (Flinders Technology Associates) cards, were compared for their ability to inactivate viruses and stabilize viral nucleic acid for molecular testing. The cards were tested with bluetongue virus, foot-and-mouth disease virus (FMDV), small ruminant morbillivirus (peste des petits ruminants virus), and lumpy skin disease virus (LSDV), encompassing non-enveloped and enveloped representatives of viruses with double-stranded and single-stranded RNA genomes, as well as an enveloped DNA virus. The cards were loaded with virus-containing cell culture supernatant and tested after one day, one week, and one month. The inactivation of the RNA viruses was successful for the majority of the cards and filters. Most of them completely inactivated the viruses within one day or one week at the latest, but the inactivation of LSDV presented a greater challenge. Three of the six cards inactivated LSDV within one day, but the others did not achieve this even after an incubation period of 30 days. Differences between the cards were also evident in the stabilization of nucleic acid. The amount of detectable viral genome on the cards remained approximately constant for all viruses and cards over an incubation period of one month. With some cards, however, a bigger loss of detectable nucleic acid compared with a directly extracted sample was observed. Using FMDV, it was confirmed that the material applied to the cards was sufficiently conserved to allow detailed molecular characterization by sequencing. Furthermore, it was possible to successfully recover infectious FMDV by chemical transfection from some cards, confirming the preservation of full-length RNAs.
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Affiliation(s)
| | | | | | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald-Insel Riems, Germany
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Galvin AN, Pandit PS, English SG, Quock RC, Bandivadekar RR, Colwell RR, Robinson BW, Ernest HB, Brown MH, Sehgal RNM, Tell LA. Evaluation of minimally invasive sampling methods for detecting Avipoxvirus: Hummingbirds as a case example. Front Vet Sci 2022; 9:924854. [PMID: 36090172 PMCID: PMC9450938 DOI: 10.3389/fvets.2022.924854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Avian pox is a common avian virus that in its cutaneous form can cause characteristic lesions on a bird's dermal surfaces. Detection of avian pox in free-ranging birds historically relied on observations of visual lesions and/or histopathology, both which can underestimate avian pox prevalence. We compared traditional visual observation methods for avian pox with molecular methods that utilize minimally invasive samples (blood, toenail clipping, feathers, and dermal swabs) in an ecologically important group of birds, hummingbirds. Specifically, avian pox prevalence in several species of hummingbirds were examined across multiple locations using three different methods: (1) visual inspection of hummingbirds for pox-like lesions from a long-term banding data set, (2) qPCR assay of samples from hummingbird carcasses from wildlife rehabilitation centers, and (3) qPCR assay of samples from live-caught hummingbirds. A stark difference in prevalences among these three methods was identified, with an avian pox prevalence of 1.5% from banding data, 20.4% from hummingbird carcasses, and 32.5% from live-caught hummingbirds in California. This difference in detection rates underlines the necessity of a molecular method to survey for avian pox, and this study establishes one such method that could be applied to other wild bird species. Across all three methods, Anna's hummingbirds harbored significantly higher avian pox prevalence than other species examined, as did males compared with females and birds caught in Southern California compared with Northern California. After hatch-year hummingbirds also harbored higher avian pox prevalences than hatch-year hummingbirds in the California banding data set and the carcass data set. This is the first study to estimate the prevalence of avian pox in hummingbirds and address the ecology of this hummingbird-specific strain of avian pox virus, providing vital information to inform future studies on this charismatic and ecologically important group of birds.
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Affiliation(s)
- Aoife N. Galvin
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Pranav S. Pandit
- EpiCenter for Disease Dynamics, One Health Insititute, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Simon G. English
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rachel C. Quock
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Ruta R. Bandivadekar
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rita R. Colwell
- Hummingbird Monitoring Network, Patagonia, AZ, United States
| | | | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, United States
| | - Mollie H. Brown
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ravinder N. M. Sehgal
- Department of Biology, San Francisco State University, San Francisco, CA, United States
- *Correspondence: Ravinder N. M. Sehgal
| | - Lisa A. Tell
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Lisa A. Tell
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Samsonova JV, Saushkin NY, Osipov AP. Dried Blood Spots technology for veterinary applications and biological investigations: technical aspects, retrospective analysis, ongoing status and future perspectives. Vet Res Commun 2022; 46:655-698. [PMID: 35771305 PMCID: PMC9244892 DOI: 10.1007/s11259-022-09957-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Abstract
Dried Blood Spots (DBS) technology has become a valuable tool in medical studies, however, in veterinary and biological research DBS technology applications are still limited. Up-to-date no review has comprehensively integrated all the evidence existing across the fields, technologies and animal species. In this paper we summarize the current applications of DBS technology in the mentioned areas, and provide a scope of different types of dried sample carriers (cellulose and non-cellulose), sampling devices, applicable methods for analyte extraction and detection. Mammals, birds, insects and other species are represented as the study objects. Besides the blood, the review considers a variety of specimens, such as milk, saliva, tissue samples and others. The main applications of dried samples highlighted in the review include epidemiological surveys and monitoring for infections agents or specific antibodies for disease/vaccination control in households and wildlife. Besides the genetic investigations, the paper describes detection of environmental contaminants, pregnancy diagnosis and many other useful applications of animal dried samples. The paper also analyses dried sample stability and storage conditions for antibodies, viruses and other substances. Finally, recent developments and future research for DBS technology in veterinary medicine and biological sciences are discussed.
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Affiliation(s)
- Jeanne V Samsonova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
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14
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Samsonova JV, Saushkin NY, Osipov AP. Dried Samples of Biological Fluids on Porous Membranes as a Promising Sample Preparation Method for Biomedical and Veterinary Diagnostics. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822040104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Ding X, Li Z, Avery L, Ballesteros E, Makol R, Liu C. pH-EVD: A pH-Paper-Based Extraction and Visual Detection System for Instrument-Free SARS-CoV-2 Diagnostics. ADVANCED NANOBIOMED RESEARCH 2022; 2:2100101. [PMID: 35441159 PMCID: PMC9011642 DOI: 10.1002/anbr.202100101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/29/2021] [Indexed: 11/28/2022] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide. However, most SARS-CoV-2 detection methods depend on time-consuming sample preparation and large detection instruments. Herein, a method employing nonbleeding pH paper to achieve both RNA extraction and visual isothermal amplification is proposed, enabling rapid, instrument-free SARS-CoV-2 detection. By taking advantage of capillary forces, pH-paper-based RNA extraction can be accomplished within 1 min without need for any equipment. Further, the pH paper can mediate dye-free visual isothermal amplification detection. In less than a 46-min sample-to-answer time, pH-paper-based extraction and visual detection (termed pH-EVD) can consistently detect 1200 genome equivalents per microliter of SARS-CoV-2 in saliva, which is comparable to TaqMan probe-based quantitative reverse transcription PCR (RT-qPCR). Through coupling with a chemically heated incubator called a smart cup, the instrument-free, pH-EVD-based SARS-CoV-2 detection method on 30 nasopharyngeal swab samples and 33 contrived saliva samples is clinically validated. Thus, the pH-EVD method provides simple, rapid, reliable, low-cost, and instrument-free SARS-CoV-2 detection and has the potential to streamline onsite COVID-19 diagnostics.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
| | - Ziyue Li
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
| | - Lori Avery
- Department of Pathology and Laboratory MedicineUniversity of Connecticut Health CenterFarmingtonCT06030USA
| | - Enrique Ballesteros
- Department of Pathology and Laboratory MedicineUniversity of Connecticut Health CenterFarmingtonCT06030USA
| | - Rohit Makol
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
| | - Changchun Liu
- Department of Biomedical EngineeringUniversity of Connecticut Health Center263 Farmington AveFarmingtonCT06030USA
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16
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Chong MD, Wallin J. A single direct amplification method for forensic casework references on a variety of substrates. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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17
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Rogers MJ, McManus DP, Muhi S, Gordon CA. Membrane Technology for Rapid Point-of-Care Diagnostics for Parasitic Neglected Tropical Diseases. Clin Microbiol Rev 2021; 34:e0032920. [PMID: 34378956 PMCID: PMC8404699 DOI: 10.1128/cmr.00329-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Parasitic neglected tropical diseases (NTDs) affect over one billion people worldwide, with individuals from communities in low-socioeconomic areas being most at risk and suffering the most. Disease management programs are hindered by the lack of infrastructure and resources for clinical sample collection, storage, and transport and a dearth of sensitive diagnostic methods that are inexpensive as well as accurate. Many diagnostic tests and tools have been developed for the parasitic NTDs, but the collection and storage of clinical samples for molecular and immunological diagnosis can be expensive due to storage, transport, and reagent costs, making these procedures untenable in most areas of endemicity. The application of membrane technology, which involves the use of specific membranes for either sample collection and storage or diagnostic procedures, can streamline this process, allowing for long-term sample storage at room temperature. Membrane technology can be used in serology-based diagnostic assays and for nucleic acid purification prior to molecular analysis. This facilitates the development of relatively simple and rapid procedures, although some of these methods, mainly due to costs, lack accessibility in low-socioeconomic regions of endemicity. New immunological procedures and nucleic acid storage, purification, and diagnostics protocols that are simple, rapid, accurate, and cost-effective must be developed as countries progress control efforts toward the elimination of the parasitic NTDs.
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Affiliation(s)
- Madeleine J. Rogers
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen Muhi
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Catherine A. Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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18
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Coudy D, Colotte M, Luis A, Tuffet S, Bonnet J. Long term conservation of DNA at ambient temperature. Implications for DNA data storage. PLoS One 2021; 16:e0259868. [PMID: 34763344 PMCID: PMC8585539 DOI: 10.1371/journal.pone.0259868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022] Open
Abstract
DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.
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Affiliation(s)
- Delphine Coudy
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
| | - Marthe Colotte
- Imagene, plateforme de production, Genopole, Evry, France
| | - Aurélie Luis
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
| | - Sophie Tuffet
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
- Imagene, plateforme de production, Genopole, Evry, France
| | - Jacques Bonnet
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
- Université de Bordeaux, Institut Bergonié, INSERM, Bordeaux, France
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19
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Veiga IB, Mühldorfer K, Hafez HM, Lüschow D. Whatman® FTA® Cards Performance for Ornithobacterium rhinotracheale DNA Amplification. Avian Dis 2021; 64:496-498. [PMID: 33570099 DOI: 10.1637/aviandiseases-d20-00030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/25/2020] [Indexed: 11/05/2022]
Abstract
The avian pathogen Ornithobacterium rhinotracheale (ORT) has been implied in the etiology of poultry respiratory disease in recent years. To evaluate whether Whatman® Flinders Technology Associates (FTA®) cards can be used for hazard-free transport and storage of ORT samples for posterior DNA amplification, a controlled assay was performed. Three 10-fold dilutions of an ORT culture suspension were spotted on FTA cards and stored at room temperature (RT) for 6 mo. Sterile swabs were immersed in the same three 10-fold culture dilutions and stored at RT and 4 and -20 C without storage medium for the same time. DNA was extracted from both the FTA cards and swabs 1 day, 1 and 6 wk, and 6 mo following sample preparation and stored at -20 C. At the end of the experiment, real-time PCR amplification of the 16S ribosomal RNA gene was performed from DNA extracted throughout a 6-mo period from all ORT samples stored on both FTA cards and swabs. The obtained threshold cycle values for each ORT DNA extraction date were within the same range for all samples in a dilution-dependent fashion, regardless of storage temperature or used material. Pure ORT colonies could be reisolated 1 day after sample preparation from the swab dilutions stored at all temperatures but not from the FTA cards. We conclude that the efficiency of ORT DNA amplification from samples stored on FTA cards or in swabs is similar. However, FTA cards have the advantage of preventing microorganism growth, thus allowing safe transport and storage, for at least 6 mo, for bacterial dilutions down to at least 104-105 colony-forming units/ml.
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Affiliation(s)
- Inês Berenguer Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Kristin Mühldorfer
- Leibniz Institute for Zoo and Wildlife Research, Department of Wildlife Diseases, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Hafez Mohamed Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Freie Universität Berlin, Königsweg 63, 14163 Berlin, Germany
| | - Dörte Lüschow
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Freie Universität Berlin, Königsweg 63, 14163 Berlin, Germany
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20
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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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21
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Colombelli‐Négrel D, Kleindorfer S. Behavioural response to songs between genetically diverged allopatric populations of Darwin's small tree finch in the Galápagos. J Evol Biol 2021; 34:816-829. [PMID: 33714212 PMCID: PMC8251970 DOI: 10.1111/jeb.13783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
Empirical data that identify contemporary mechanisms of divergence shed light on how species could multiply. In this study, we measured population genetic structure, song syllable diversity and response to simulated intruder song in Darwin's small tree finch (Camarhynchus parvulus) on Santa Cruz and Floreana Islands, Galápagos archipelago. Our aim was to test whether the magnitude of contemporary behavioural response in resident birds was consistent with patterns of genetic or cultural differences between populations. We analysed genetic structure and the occurrence of song syllable types, and experimentally measured the response of resident birds to intruder bird song from different geographical origin (i.e., island) or syllable type. We discovered a weak signal of population genetic structure between Santa Cruz and Floreana Islands. Although some song syllables occurred on both islands, others were unique to each island; Santa Cruz Island males used more unique syllables than Floreana Island males. Both Santa Cruz and Floreana resident males discriminated their response towards a simulated intruder song based on the geographical origin of the intruder song, but not on the syllable type sung by the intruder. We conclude that the populations are diverging in genetic and cultural traits and identified a signal of contemporary behavioural response that could maintain divergence upon secondary contact.
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Affiliation(s)
| | - Sonia Kleindorfer
- College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
- Konrad Lorenz Research Centre for Behaviour and CognitionDepartment of Behavioural and Cognitive BiologyUniversity of ViennaViennaAustria
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22
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Srisomwat C, Yakoh A, Chuaypen N, Tangkijvanich P, Vilaivan T, Chailapakul O. Amplification-free DNA Sensor for the One-Step Detection of the Hepatitis B Virus Using an Automated Paper-Based Lateral Flow Electrochemical Device. Anal Chem 2020; 93:2879-2887. [DOI: 10.1021/acs.analchem.0c04283] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Chawin Srisomwat
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Abdulhadee Yakoh
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Center of Excellence (EOSCE), Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
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23
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Olah G, Stojanovic D, Webb MH, Waples RS, Heinsohn R. Comparison of three techniques for genetic estimation of effective population size in a critically endangered parrot. Anim Conserv 2020. [DOI: 10.1111/acv.12655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Olah
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
- Wildlife Messengers Richmond VA USA
| | - D. Stojanovic
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
| | - M. H. Webb
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
| | - R. S. Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA
| | - R. Heinsohn
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
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Baek HE, Bandivadekar RR, Pandit P, Mah M, Sehgal RNM, Tell LA. TaqMan quantitative real-time PCR for detecting Avipoxvirus DNA in various sample types from hummingbirds. PLoS One 2020; 15:e0230701. [PMID: 32526768 PMCID: PMC7289624 DOI: 10.1371/journal.pone.0230701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/25/2020] [Indexed: 11/19/2022] Open
Abstract
Background Avian pox is a viral disease documented in a wide range of bird species. Disease-related detrimental effects can cause dyspnea and dysphagia, and birds with high metabolic requirements, such as hummingbirds, are thus especially vulnerable to the pathogen. Hummingbirds have a strong presence in California, especially in urban environments. However, little is understood regarding the impact of pox virus on hummingbird populations. Currently, diagnosing a pox infection relies on obtaining a tissue biopsy, which poses significant risks to birds and challenges in the field. Understanding the ecology of hummingbird pox viral infections could be advanced by a minimally invasive ante-mortem diagnostic method. Our aim was to address whether pox infections can be diagnosed using integumentary system samples besides tissue biopsies. To meet this goal, we tested multiple integumentary sample types using a quantitative real-time PCR assay. A secondary study goal was to determine which sample types (ranging from minimally to highly invasive sampling) were optimal for identifying infected birds. Methodology and principal findings Pox-like lesion tissue, pectoral muscle, feathers, toenail clippings, blood, and swabs (both pox-like lesion tissue and non pox-like lesion tissue) were taken from live birds and carcasses of two species of hummingbirds found in California. To maximize successful diagnosis, especially for samples with low viral load, a real-time quantitative PCR assay was developed for detecting the hummingbird-specific Avipoxvirus 4b core protein gene. Avipoxvirus DNA was successfully amplified from all sample types obtained from 27 individuals. These results were compared to those of conventional PCR and comparisons were also made among sample types, utilizing lesion tissue samples as the gold standard. Conclusions and significance Hummingbird avian pox can be diagnosed without relying on tissue biopsies. We identify that feather samples, of which contour feathers yielded the best results, can be used for diagnosing infected birds, thus reducing sampling risk. In sum, the real-time PCR assay detected viral DNA in various integumentary system sample types and will be useful in future studies of hummingbird disease ecology.
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Affiliation(s)
- Hanna E Baek
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Ruta R Bandivadekar
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Michelle Mah
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Ravinder N M Sehgal
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Lisa A Tell
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
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25
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Subtle genetic clustering among South Australian colonies of little penguins (Eudyptula minor). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01284-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Jia B, Colling A, Stallknecht DE, Blehert D, Bingham J, Crossley B, Eagles D, Gardner IA. Validation of laboratory tests for infectious diseases in wild mammals: review and recommendations. J Vet Diagn Invest 2020; 32:776-792. [PMID: 32468923 DOI: 10.1177/1040638720920346] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Evaluation of the diagnostic sensitivity (DSe) and specificity (DSp) of tests for infectious diseases in wild animals is challenging, and some of the limitations may affect compliance with the OIE-recommended test validation pathway. We conducted a methodologic review of test validation studies for OIE-listed diseases in wild mammals published between 2008 and 2017 and focused on study design, statistical analysis, and reporting of results. Most published papers addressed Mycobacterium bovis infection in one or more wildlife species. Our review revealed limitations or missing information about sampled animals, identification criteria for positive and negative samples (case definition), representativeness of source and target populations, and species in the study, as well as information identifying animals sampled for calculations of DSe and DSp as naturally infected captive, free-ranging, or experimentally challenged animals. The deficiencies may have reflected omissions in reporting rather than design flaws, although lack of random sampling might have induced bias in estimates of DSe and DSp. We used case studies of validation of tests for hemorrhagic diseases in deer and white-nose syndrome in hibernating bats to demonstrate approaches for validation when new pathogen serotypes or genotypes are detected and diagnostic algorithms are changed, and how purposes of tests evolve together with the evolution of the pathogen after identification. We describe potential benefits of experimental challenge studies for obtaining DSe and DSp estimates, methods to maintain sample integrity, and Bayesian latent class models for statistical analysis. We make recommendations for improvements in future studies of detection test accuracy in wild mammals.
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Affiliation(s)
- Beibei Jia
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Axel Colling
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - David E Stallknecht
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - David Blehert
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - John Bingham
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Beate Crossley
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Debbie Eagles
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Ian A Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
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Habimana R, Okeno TO, Ngeno K, Mboumba S, Assami P, Gbotto AA, Keambou CT, Nishimwe K, Mahoro J, Yao N. Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS One 2020; 15:e0225084. [PMID: 32240167 PMCID: PMC7117670 DOI: 10.1371/journal.pone.0225084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/08/2020] [Indexed: 11/19/2022] Open
Abstract
Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.
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Affiliation(s)
- Richard Habimana
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Tobias Otieno Okeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Kiplangat Ngeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Sylvere Mboumba
- Faculty of Agronomy and Biotechnologies, Masuku University of Science and Techniques, Franceville, Gabon
| | - Pauline Assami
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
| | - Anique Ahou Gbotto
- Laboratoire de genomique Fonctionnelle et Amélioration Génétique Université Nangui Abrogoua, Abidjan, Cote d'Ivoire
| | - Christian Tiambo Keambou
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
- Faculty of Agriculture and Veterinary medicine, University of Buea, Buea, Cameroon
| | - Kizito Nishimwe
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Janvier Mahoro
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Nasser Yao
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
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Karthikeyan K, Saranya R, Bharath R, Vidya R, Itami T, Sudhakaran R. A simple filter paper-based method for transporting and storing Enterocytozoon hepatopenaei DNA from infected Litopenaeus vannamei tissues. J Invertebr Pathol 2020; 169:107305. [DOI: 10.1016/j.jip.2019.107305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
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Wipf NC, Guidi V, Tonolla M, Ruinelli M, Müller P, Engler O. Evaluation of honey-baited FTA cards in combination with different mosquito traps in an area of low arbovirus prevalence. Parasit Vectors 2019; 12:554. [PMID: 31753035 PMCID: PMC6873520 DOI: 10.1186/s13071-019-3798-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
Background The threat of mosquito-borne diseases is increasing in continental Europe as demonstrated by several autochthonous chikungunya, dengue and West Nile virus outbreaks. In Switzerland, despite the presence of competent vectors, routine surveillance of arboviruses in mosquitoes is not being carried out, mainly due to the high costs associated with the need of a constant cold chain and laborious processing of thousands of mosquitoes. An alternative approach is using honey-baited nucleic acid preserving cards (FTA cards) to collect mosquito saliva that may be analysed for arboviruses. Here, we evaluate whether FTA cards could be used to detect potentially emerging viruses in an area of low virus prevalence in combination with an effective mosquito trap. Methods In a field trial in southern Switzerland we measured side-by-side the efficacy of the BG-Sentinel 2, the BG-GAT and the Box gravid trap to catch Aedes and Culex mosquitoes in combination with honey-baited FTA cards during 80 trapping sessions of 48 hours. We then screened both the mosquitoes and the FTA cards for the presence of arboviruses using reverse-transcription PCR. The efficacy of the compared trap types was evaluated using generalized linear mixed models. Results The Box gravid trap collected over 11 times more mosquitoes than the BG-GAT and BG-Sentinel 2 trap. On average 75.9% of the specimens fed on the honey-bait with no significant difference in feeding rates between the three trap types. From the total of 1401 collected mosquitoes, we screened 507 Aedes and 500 Culex females for the presence of arboviruses. A pool of six Cx. pipiens/Cx. torrentium mosquitoes and also the FTA card from the same Box gravid trap were positive for Usutu virus. Remarkably, only two of the six Culex mosquitoes fed on the honey-bait, emphasising the high sensitivity of the method. In addition, two Ae. albopictus collections but no FTA cards were positive for mosquito-only flaviviruses. Conclusions Based on our results we conclude that honey-baited FTA cards, in combination with the Box gravid trap, are an effective method for arbovirus surveillance in areas of low prevalence, particularly where resources are limited for preservation and screening of individual mosquitoes.![]()
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Affiliation(s)
- Nadja C Wipf
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland.,University of Basel, Petersplatz 1, P.O. Box, 4001, Basel, Switzerland.,Laboratory of Applied Microbiology, University of Applied, Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6501, Bellinzona, Switzerland
| | - Valeria Guidi
- Laboratory of Applied Microbiology, University of Applied, Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6501, Bellinzona, Switzerland
| | - Mauro Tonolla
- Laboratory of Applied Microbiology, University of Applied, Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6501, Bellinzona, Switzerland
| | - Michela Ruinelli
- Laboratory of Applied Microbiology, University of Applied, Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6501, Bellinzona, Switzerland
| | - Pie Müller
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland. .,University of Basel, Petersplatz 1, P.O. Box, 4001, Basel, Switzerland.
| | - Olivier Engler
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700, Spiez, Switzerland
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30
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Taylor AS, Knaus BJ, Grünwald NJ, Burgess T. Population Genetic Structure and Cryptic Species of Plasmopara viticola in Australia. PHYTOPATHOLOGY 2019; 109:1975-1983. [PMID: 31215840 DOI: 10.1094/phyto-04-19-0146-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildew of grape caused by Plasmopara viticola is a global pathogen of economic importance to commercial viticulture. In contrast to populations in the northern hemisphere, few studies have investigated the population biology, genetic diversity, and origin of the pathogen in Australian production systems. DNA was extracted from 381 P. viticola samples from Vitis vinifera and alternate hosts collected via fresh and herbarium leaves from populations within Australia and Whatman FTA cards from North America, Brazil, and Uruguay. A total of 32 DNA samples were provided from a French population. The populations were genotyped using 16 polymorphic microsatellite markers. Representative samples from within Australia, Brazil, and Uruguay were also genotyped to determine which of the cryptic species (clades) within the P. viticola species complex were present. Our findings suggest the Australian and South American populations of P. viticola are more closely related to the European population than the North American population, the reported source of origin of the pathogen. The Western Australian population had similarities to the South Australian population, and the tight clustering of samples suggests a single introduction into Western Australia. P. viticola clade aestivalis was the only clade detected in Australian and South American populations. Analysis of the Western Australian population suggests that it is reproducing clonally, but additional research is required to determine the mechanism as to how this is occurring.
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Affiliation(s)
- Andrew S Taylor
- Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
- Department of Primary Industries and Regional Development, Bunbury, Western Australia 6230, Australia
| | - Brian J Knaus
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330, U.S.A
| | - Treena Burgess
- Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
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Almathen F, Elbir H, Bahbahani H, Mwacharo J, Hanotte O. Polymorphisms in MC1R and ASIP Genes are Associated with Coat Color Variation in the Arabian Camel. J Hered 2019; 109:700-706. [PMID: 29893870 PMCID: PMC6108395 DOI: 10.1093/jhered/esy024] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Pigmentation in mammals is primarily determined by the distribution of eumelanin and pheomelanin, the ratio of which is mostly controlled by the activity of melanocortin 1 receptor (MC1R) and agouti signaling protein (ASIP) genes. Using 91 animals from 10 Arabian camel populations, that included the 4 predominant coat color phenotypes observed in the dromedary (light brown, dark brown, black, and white), we investigated the effects of the MC1R and ASIP sequence variants and identified candidate polymorphisms associated with coat color variation. In particular, we identified a single nucleotide polymorphism (SNP), found in the coding region of MC1R (901C/T), linked to the white coat color, whereas a 1-bp deletion (23delT/T) and a SNP (25G/A) in exon 2 of ASIP are associated with both black and dark-brown coat colors. Our results also indicate support that the light-brown coat color is likely the ancestral coat color for the dromedary. These sequence variations at the MC1R and ASIP genes represent the first documented evidence of candidate polymorphisms associated with Mendelian traits in the dromedary.
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Affiliation(s)
- Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Saudi Arabia.,The Camel Research Center, King Faisal University, Saudi Arabia
| | - Haitham Elbir
- The Camel Research Center, King Faisal University, Saudi Arabia
| | - Hussain Bahbahani
- The Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Joram Mwacharo
- The International Centre for Agricultural Research in the Dry Areas (ICARDA) c/o ILRI-Ethiopia Campus, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- The School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.,LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
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Cardona-Ospina JA, Villalba-Miranda MF, Palechor-Ocampo LA, Mancilla LI, Sepúlveda-Arias JC. A systematic review of FTA cards® as a tool for viral RNA preservation in fieldwork: Are they safe and effective? Prev Vet Med 2019; 172:104772. [PMID: 31607414 PMCID: PMC7126379 DOI: 10.1016/j.prevetmed.2019.104772] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/08/2019] [Accepted: 09/08/2019] [Indexed: 01/06/2023]
Abstract
BackgroundDetection and characterization of viral RNA pathogens from fieldwork are challenging due to the instability of the RNA molecule. FTA cards® have proved useful for sample storage and latter identification of pathogens with importance for agricultural, animal and human health: however, for optimal handling, processing, and biosafety measures are not well-established. ObjectiveThis systematic review aims to summarize the reported effectiveness of FTA cards® for storage and transport of viral RNA, as well as the conditions for their handling and use in downstream processes. Finally, the biosafety measures required to protect researchers and clinical lab workers are considered. MethodsWe performed a systematic review following the PRISMA statement. We searched MEDLINE (PubMed), Scopus and Web of Science using the keywords “FTA cards” AND “RNA”. Articles were screened by title and abstract, and after examination of inclusion and exclusion criteria, relevant information was extracted. The quality of the studies was assessed, and the evidence was qualitatively summarized. ResultsA total of 175 records were retrieved, and 11 additional documents were found by checking references of the eligible articles. A total of 47 articles were included. Samples from animals accounted for 38.3% of the publications, which identified viruses that cause disease in poultry, wild birds, suids, or bovids. Three different methods for RNA extraction were reported. Other factors that vary across reports include the size of RNA amplicon, storage temperature, and duration of storage. Only fourteen articles tested the inactivation of the virus on the FTA card®, and in one case, the virus remained infective. ConclusionFTA cards® could be a suitable option for RNA virus storage and transport for fieldwork in areas where proper conditions for RNA preservation are difficult to achieve. Three different protocols have been used for RNA detection from this matrix. Biospecimens in the form of dried blood spots should be considered potentially infectious unless specifically treated to inactivate viral pathogens.
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Affiliation(s)
- Jaime A Cardona-Ospina
- Grupo de Investigación Infección e Inmunidad, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Building 14, Carrera 27 #10-02, Barrio Álamos, Pereira, Risaralda, 660003, Colombia; Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Building 14, Carrera 27 #10-02, Barrio Álamos, Pereira, Risaralda, 660003, Colombia; Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Av. Las Américas #98-56, Pereira, Risaralda, 660001, Colombia; Emerging Infectious Diseases and Tropical Medicine Research Group, Instituto para la Investigación en Ciencias Biomédicas - Sci-Help, Cra 37B #36-05, Pereira, Risaralda, 660009, Colombia.
| | - Manuel F Villalba-Miranda
- Grupo de Investigación Infección e Inmunidad, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Building 14, Carrera 27 #10-02, Barrio Álamos, Pereira, Risaralda, 660003, Colombia
| | - Leidy A Palechor-Ocampo
- Grupo de Investigación Infección e Inmunidad, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Building 14, Carrera 27 #10-02, Barrio Álamos, Pereira, Risaralda, 660003, Colombia
| | - Lida I Mancilla
- Grupo de Investigación Infección e Inmunidad, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Building 14, Carrera 27 #10-02, Barrio Álamos, Pereira, Risaralda, 660003, Colombia
| | - Juan C Sepúlveda-Arias
- Grupo de Investigación Infección e Inmunidad, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Building 14, Carrera 27 #10-02, Barrio Álamos, Pereira, Risaralda, 660003, Colombia
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Ward A, Hide G, Jehle R. Skin swabs with FTA® cards as a dry storage source for amphibian DNA. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-018-1018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Groenenboom AE, Smid EJ, Schoustra SE. Robust sampling and preservation of DNA for microbial community profiling in field experiments. BMC Res Notes 2019; 12:159. [PMID: 30902062 PMCID: PMC6429817 DOI: 10.1186/s13104-019-4187-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
Objective Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product. Results Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas. Electronic supplementary material The online version of this article (10.1186/s13104-019-4187-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anneloes E Groenenboom
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands. .,Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sijmen E Schoustra
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands.,Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia
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35
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Heinsohn R, Olah G, Webb M, Peakall R, Stojanovic D. Sex ratio bias and shared paternity reduce individual fitness and population viability in a critically endangered parrot. J Anim Ecol 2018; 88:502-510. [DOI: 10.1111/1365-2656.12922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/25/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Heinsohn
- Fenner School of Environment and Society Australian National University Canberra Australian Capital Territory Australia
| | - George Olah
- Fenner School of Environment and Society Australian National University Canberra Australian Capital Territory Australia
- Research School of Biology The Australian National University Canberra Australian Capital Territory Australia
| | - Matthew Webb
- Fenner School of Environment and Society Australian National University Canberra Australian Capital Territory Australia
| | - Rod Peakall
- Research School of Biology The Australian National University Canberra Australian Capital Territory Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society Australian National University Canberra Australian Capital Territory Australia
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36
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Love Stowell SM, Bentley EG, Gagne RB, Gustafson KD, Rutledge LY, Ernest HB. Optimal DNA extractions from blood on preservation paper limits conservation genomic but not conservation genetic applications. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Hacking J, Bradford T, Pierce K, Gardner M. De novo genotyping of the major histocompatibility complex in an Australian dragon lizard, Ctenophorus decresii. T ROY SOC SOUTH AUST 2018. [DOI: 10.1080/03721426.2018.1542259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jessica Hacking
- College of Science and Engineering, Flinders University, Bedford Park, Australia
| | - Tessa Bradford
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Kelly Pierce
- College of Science and Engineering, Flinders University, Bedford Park, Australia
| | - Michael Gardner
- College of Science and Engineering, Flinders University, Bedford Park, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
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Dawnay N, Flamson R, Hall MJ, Steadman DW. Impact of sample degradation and inhibition on field-based DNA identification of human remains. Forensic Sci Int Genet 2018; 37:46-53. [DOI: 10.1016/j.fsigen.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022]
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Bettridge JM, Psifidi A, Terfa ZG, Desta TT, Lozano-Jaramillo M, Dessie T, Kaiser P, Wigley P, Hanotte O, Christley RM. The role of local adaptation in sustainable village chicken production. NATURE SUSTAINABILITY 2018; 1:574-582. [PMID: 30411000 PMCID: PMC6217978 DOI: 10.1038/s41893-018-0150-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Village chickens are ubiquitous in smallholder farming systems, contributing to household, local and national economies under diverse environmental, economic and cultural settings. However, they are raised in challenging environments where productivity is low while mortality is high. There is much interest in utilizing indigenous genetic resources to produce a chicken resilient to its environment, whilst providing the basis of an economically sustainable enterprise. Globally, however, a wide variety of interventions have so far proved unable to deliver sustainable improvements. Here, we show that regional differences in trait preferences and parasite burden are associated with distinct chicken genepools, likely in response to interacting natural and human-driven (economic and social) selection pressures. Drivers of regional differences include marketing opportunities, cultural preferences, agro-ecologies and parasite populations, and are evident in system adaptations, such as management practices, population dynamics and bird genotypes. Our results provide sound multidisciplinary evidence to support previous observations that sustainable poultry development interventions for smallholder farmers, including breeding programs, should be locally tailored and designed for flexible implementation.
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Affiliation(s)
- Judy M. Bettridge
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- International Livestock Research Institute, P.O. Box 30709-00100, Nairobi, Kenya
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, Hatfield, UK
| | - Zelalem G. Terfa
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Takele T. Desta
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Maria Lozano-Jaramillo
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, NL-6700 AH Wageningen, the Netherlands
| | - Tadelle Dessie
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
| | - Olivier Hanotte
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert M. Christley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
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40
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Establishment of a Gene Detection System for Hotspot Mutations of Hearing Loss. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6828306. [PMID: 29707576 PMCID: PMC5863321 DOI: 10.1155/2018/6828306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/24/2018] [Indexed: 12/02/2022]
Abstract
Hearing loss is an etiologically heterogeneous trait with a high incidence in China. Though conventional newborn hearing screening program has been widely adopted, gene detection can significantly improve the means of early discovering genetic risk factors. Thus, simple and efficient methods with higher sensitivity and lower cost for detecting hotspot mutations of hearing loss are urgently requested. Here we established a mutation detection system based on multiple fluorescent probe technique, which can detect and genotype nine hotspot mutations of four prominent hearing loss-related genes in two reactions on a four-channel real-time PCR instrument, including GJB2 (rs750188782, rs80338943, rs1110333204, and rs80338939), GJB3 (rs74315319), SLC26A4 (rs111033313 and rs121908362), and mtDNA 12S rRNA (rs267606617 and rs267606619). This system is with high sensitivity that enables detecting as low as 10 DNA copies samples per reaction. A comparison study in 268 clinical samples showed that the detection system had 100% concordance to Sanger sequencing. Besides, blood and saliva samples can be directly detected without DNA extraction process, which greatly simplifies the manipulation. The new system with high sensitivity, accuracy, and specimen type compatibility can be expectedly a reliable tool in clinical application.
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Dupuis-Desormeaux M, Davy C, Lathrop A, Followes E, Ramesbottom A, Chreston A, MacDonald SE. Colonization and usage of an artificial urban wetland complex by freshwater turtles. PeerJ 2018; 6:e5423. [PMID: 30123718 PMCID: PMC6087426 DOI: 10.7717/peerj.5423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/17/2018] [Indexed: 11/20/2022] Open
Abstract
Conservation authorities invest heavily in the restoration and/or creation of wetlands to counteract the destruction of habitat caused by urbanization. Monitoring the colonization of these new wetlands is critical to an adaptive management process. We conducted a turtle mark-recapture survey in a 250 ha artificially created wetland complex in a large North American city (Toronto, Ontario). We found that two of Ontario’s eight native turtle species (Snapping turtle (SN), Chelydra serpentina, and Midland Painted (MP) turtle, Chrysemys picta marginata) were abundant and both were confirmed nesting. The Blanding’s turtle (Emydoidea blandingii) was present but not well established. Species richness and turtle density were not equally distributed throughout the wetland complex. We noted SN almost exclusively populated one water body, while other areas of the wetland had a varying representation of both species. The sex ratios of both SN and MP turtles were 1:1. We tracked the movement of Snapping and Blanding’s turtles and found that most turtles explored at least two water bodies in the park, that females explored more water bodies than males, and that 95% of turtles showed fidelity to individual overwintering wetlands. We performed DNA analysis of two Blanding’s turtles found in the created wetlands and could not assign these turtles to any known profiled populations. The genetic data suggest that the turtles probably belong to a remnant local population. We discuss the implications of our results for connectivity of artificial wetlands and the importance of the whole wetland complex to this turtle assemblage.
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Affiliation(s)
| | - Christina Davy
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Amy Lathrop
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Emma Followes
- Toronto and Region Conservation Authority, Toronto, ON, Canada
| | | | - Andrea Chreston
- Toronto and Region Conservation Authority, Toronto, ON, Canada
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Stojanovic D, Olah G, Webb M, Peakall R, Heinsohn R. Genetic evidence confirms severe extinction risk for critically endangered swift parrots: implications for conservation management. Anim Conserv 2018. [DOI: 10.1111/acv.12394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- D. Stojanovic
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
| | - G. Olah
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
- Research School of Biology The Australian National University Canberra ACT Australia
| | - M. Webb
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
| | - R. Peakall
- Research School of Biology The Australian National University Canberra ACT Australia
| | - R. Heinsohn
- Fenner School of Environment and Society Australian National University Canberra ACT Australia
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De Paoli-Iseppi R, Polanowski AM, McMahon C, Deagle BE, Dickinson JL, Hindell MA, Jarman SN. DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird. PLoS One 2017; 12:e0189181. [PMID: 29216256 PMCID: PMC5720723 DOI: 10.1371/journal.pone.0189181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 11/19/2017] [Indexed: 11/18/2022] Open
Abstract
Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris). We quantified DNA methylation in several A. tenuirostris genes that have shown age-related methylation changes in mammals. In birds ranging from chicks to 21 years of age, bisulphite treated blood and feather DNA was sequenced and methylation levels analysed in 67 CpG sites in 13 target gene regions. From blood samples, five of the top relationships with age were identified in KCNC3 loci (CpG66: R2 = 0.325, p = 0.019). In feather samples ELOVL2 (CpG42: R2 = 0.285, p = 0.00048) and EDARADD (CpG46: R2 = 0.168, p = 0.0067) were also weakly correlated with age. However, the majority of markers had no clear association with age (of 131 comparisons only 12 had a p-value < 0.05) and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicate that some age-related signatures identified in orthologous mammalian genes are not conserved in the long-lived short tailed shearwater. Alternative molecular approaches will be required to identify a reliable biomarker of chronological age in these seabirds.
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Affiliation(s)
- Ricardo De Paoli-Iseppi
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
- Australian Antarctic Division, Hobart, Tasmania, Australia
- * E-mail:
| | | | - Clive McMahon
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
- Sydney Institute of Marine Science, Sydney, New South Wales, Australia
| | | | - Joanne L. Dickinson
- Cancer, Genetics and Immunology Group, Menzies Institute for Medical Research Tasmania, Hobart, Tasmania, Australia
| | - Mark A. Hindell
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Simon N. Jarman
- Trace and Environmental DNA (TrEnD) laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
- CSIRO Indian Ocean Marine Research Centre, The University of Western Australia, Perth, WA, Australia
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Peters KJ, Myers SA, Dudaniec RY, O'Connor JA, Kleindorfer S. Females drive asymmetrical introgression from rare to common species in Darwin's tree finches. J Evol Biol 2017; 30:1940-1952. [PMID: 28833876 DOI: 10.1111/jeb.13167] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/15/2017] [Indexed: 01/06/2023]
Abstract
The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger-bodied C. pauper to the common, smaller-bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex-specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species-specific.
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Affiliation(s)
- K J Peters
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - S A Myers
- Southern Seas Ecology Laboratory, School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - R Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - J A O'Connor
- Department of Environment, Water and Natural Resources, Adelaide, SA, Australia
| | - S Kleindorfer
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
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Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J. Practical considerations for large-scale gut microbiome studies. FEMS Microbiol Rev 2017; 41:S154-S167. [PMID: 28830090 PMCID: PMC7207147 DOI: 10.1093/femsre/fux027] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
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Affiliation(s)
- Doris Vandeputte
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Raul Y. Tito
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Rianne Vanleeuwen
- Universiteit Antwerpen, Productontwikkeling, Ambtmanstraat 1, B-2000 Antwerpen, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
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46
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Anderson DG, Kvie KS, Davydov VN, Røed KH. Maintaining genetic integrity of coexisting wild and domestic populations: Genetic differentiation between wild and domestic Rangifer with long traditions of intentional interbreeding. Ecol Evol 2017; 7:6790-6802. [PMID: 28904760 PMCID: PMC5587498 DOI: 10.1002/ece3.3230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/30/2017] [Accepted: 06/09/2017] [Indexed: 12/22/2022] Open
Abstract
This study investigates the genetic effect of an indigenous tradition of deliberate and controlled interbreeding between wild and domestic Rangifer. The results are interpreted in the context of conservation concerns and debates on the origin of domestic animals. The study is located in Northeastern Zabaĭkal'e, Russia at approximately 57 degrees North latitude. Blood and skin samples, collected from wild and domestic Rangifer, are analyzed for their mtDNA and microsatellite signatures. Local husbandry traditions are documented ethnographically. The genetic data are analyzed with special reference to indigenous understandings of the distinctions between local domestic types and wild Rangifer. The genetic results demonstrate a strong differentiation between wild and domestic populations. Notably low levels of mtDNA haplotype sharing between wild and domestic reindeer, suggest mainly male‐mediated gene flow between the two gene pools. The nuclear microsatellite results also point to distinct differences between regional domestic clusters. Our results indicate that the Evenki herders have an effective breeding technique which, while mixing pedigrees in the short term, guards against wholesale introgression between wild and domestic populations over the long term. They support a model of domestication where wild males and domestic females are selectively interbred, without hybridizing the two populations. Our conclusions inform a debate on the origins of domestication by documenting a situation where both wild and domestic types are in constant interaction. The study further informs a debate in conservation biology by demonstrating that certain types of controlled introgression between wild and domestic types need not reduce genetic diversity.
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Affiliation(s)
| | - Kjersti S Kvie
- Department of Environmental Studies University College of Southeast Norway Bø in Telemark Norway.,Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences Oslo Norway
| | - Vladimir N Davydov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) Russian Academy of Sciences St. Petersburg Russia
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences Oslo Norway
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Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9306564. [PMID: 28785592 PMCID: PMC5529626 DOI: 10.1155/2017/9306564] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.
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48
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Magro L, Escadafal C, Garneret P, Jacquelin B, Kwasiborski A, Manuguerra JC, Monti F, Sakuntabhai A, Vanhomwegen J, Lafaye P, Tabeling P. Paper microfluidics for nucleic acid amplification testing (NAAT) of infectious diseases. LAB ON A CHIP 2017. [PMID: 28632278 DOI: 10.1039/c7lc00013h] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The diagnosis of infectious diseases is entering a new and interesting phase. Technologies based on paper microfluidics, coupled to developments in isothermal amplification of Nucleic Acids (NAs) raise opportunities for bringing the methods of molecular biology in the field, in a low setting environment. A lot of work has been performed in the domain over the last few years and the landscape of contributions is rich and diverse. Most often, the level of sample preparation differs, along with the sample nature, the amplification and detection methods, and the design of the device, among other features. In this review, we attempt to offer a structured description of the state of the art. The domain is not mature and there exist bottlenecks that hamper the realization of Nucleic Acid Amplification Tests (NAATs) complying with the constraints of the field in low and middle income countries. In this domain however, the pace of progress is impressively fast. This review is written for a broad Lab on a Chip audience.
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Affiliation(s)
- Laura Magro
- MMN, Gulliver Laboratory, UMR CNRS 7083, ESPCI Paris, PSL Research University, Paris, France.
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49
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Superb fairy-wrens respond more to alarm calls from mate and kin compared to unrelated individuals. Behav Ecol 2017. [DOI: 10.1093/beheco/arx071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Dou M, Sanjay ST, Dominguez DC, Liu P, Xu F, Li X. Multiplexed instrument-free meningitis diagnosis on a polymer/paper hybrid microfluidic biochip. Biosens Bioelectron 2017; 87:865-873. [PMID: 27657849 PMCID: PMC5125860 DOI: 10.1016/j.bios.2016.09.033] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/30/2016] [Accepted: 09/10/2016] [Indexed: 11/18/2022]
Abstract
Neisseria meningitidis (N. meningitidis), Streptococcus pneumoniae (S. pneumoniae), and Haemophilus influenzae type b (Hib) are three most common pathogens accounting for most bacterial meningitis, a serious global infectious disease with high fatality, especially in developing nations. Because the treatment and antibiotics differ among each type, the identification of the exact bacteria causing the disease is vital. Herein, we report a polymer/paper hybrid microfluidic biochip integrated with loop-mediated isothermal amplification (LAMP) for multiplexed instrument-free diagnosis of these three major types of bacterial meningitis, with high sensitivity and specificity. Results can be visually observed by the naked eye or imaged by a smartphone camera under a portable UV light source. Without using any specialized laboratory instrument, the limits of detection of a few DNA copies per LAMP zone for N. meningitidis, S. pneumoniae and Hib were achieved within 1h. In addition, these three types of microorganisms spiked in artificial cerebrospinal fluid (ACSF) were directly detected simultaneously, avoiding cumbersome sample preparation procedures in conventional methods. Compared with the paper-free non-hybrid microfluidic biochip over a period of three months, the hybrid microfluidic biochip was found to have a much longer shelf life. Hence, this rapid, instrument-free and highly sensitive microfluidic approach has great potential for point-of-care (POC) diagnosis of multiple infectious diseases simultaneously, especially in resource-limited settings.
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Affiliation(s)
- Maowei Dou
- Department of Chemistry, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Sharma T Sanjay
- Department of Chemistry, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Delfina C Dominguez
- College of Health Sciences, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - XiuJun Li
- Department of Chemistry, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA; Biomedical Engineering, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA; Border Biomedical Research Center, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA; Environmental Science and Engineering, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA.
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