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Rayo E, Ulrich GF, Zemp N, Greeff M, Schuenemann VJ, Widmer A, Fischer MC. Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens. Sci Rep 2024; 14:12875. [PMID: 38834639 DOI: 10.1038/s41598-024-63587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, Melitaea diamina, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.
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Affiliation(s)
- Enrique Rayo
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
- Institut Für Veterinärpathologie, University of Zurich, Zurich, Switzerland
| | - Gabriel F Ulrich
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Michael Greeff
- Institute of Agricultural Sciences (IAS), ETH Zurich, Zurich, Switzerland
| | - Verena J Schuenemann
- Department of Environmental Sciences (DUW), University of Basel, Basel, Switzerland
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland.
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Neely WJ, Greenspan SE, Stahl LM, Heraghty SD, Marshall VM, Atkinson CL, Becker CG. Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians. MICROBIAL ECOLOGY 2022; 84:901-910. [PMID: 34671826 DOI: 10.1007/s00248-021-01897-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.
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Affiliation(s)
- Wesley J Neely
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA.
| | - Sasha E Greenspan
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Leigha M Stahl
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Sam D Heraghty
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Vanessa M Marshall
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Carla L Atkinson
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - C Guilherme Becker
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
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Hegde R, Hegde S, Gataraddi S, Kulkarni SS, Gai PB. Novel and PCR ready rapid DNA isolation from Drosophila. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1162-1173. [PMID: 35875860 DOI: 10.1080/15257770.2022.2104313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Isolation of genomic DNA is an initial step in molecular biology techniques. The quality of isolated DNA depends on procedures and chemicals, as well as source and types of the sample used. Several existing procedures are expensive and time consuming. In this study, we isolated high quality genomic DNA with an inexpensive and least time consuming procedure using Drosophila melanogaster flies, larvae, and pupae. METHODS Drosophila melanogaster samples were collected from pre-cultured bottles, and genomic DNA was extracted using a proposed novel and PCR-ready method from three different pools of flies [PF1, PF2, and PF3], similarly from larvae and pupae [PL1, PL2, PL3, PP1, PP2, and PP3, respectively]. Isolated genomic DNA was subjected to PCR amplification with different dilutions using the COI gene and further amplicons were used for RAPD and DNA sequencing. RESULTS The high quality of isolated genomic DNA was confirmed by 0.8% agarose gel electrophoresis and the purity and quantity of the DNA isolated from single fly, larva and pupa was similar to the purity and quantity of the DNA isolated using the NucleoSpinR Tissue kit method. Isolated genomic DNA was successfully amplified when the template was diluted in the ratio of 1:10. Further successful RAPD amplification and sequencing analysis of the COI gene confirms the efficiency of the downstream application of the proposed novel method. CONCLUSION The present Novel and PCR ready rapid DNA isolation method will be potentially beneficial, and it can be successfully used for quick isolation of high molecular weight DNA from Drosophila flies larvae and pupae for DNA barcoding, identification of new species, genotyping, RAPD analysis, etc. Moreover, it can also be easily scaled up for bulk preparations.
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Affiliation(s)
- Rajat Hegde
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka, India
| | - Smita Hegde
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka, India
| | | | | | - Pramod B Gai
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka, India
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Galán-Puchades MT, Solano J, González G, Osuna A, Pascual J, Bueno-Marí R, Franco S, Peracho V, Montalvo T, Fuentes MV. Molecular detection of Leishmania infantum in rats and sand flies in the urban sewers of Barcelona, Spain. Parasit Vectors 2022; 15:211. [PMID: 35710435 PMCID: PMC9201797 DOI: 10.1186/s13071-022-05309-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background Classically, dogs have been considered to be the only reservoir of leishmaniasis in urban areas. However, in a previous study, we found a 33.3% prevalence of Leishmania infantum in the spleens of Norway rats (Rattus norvegicus) sampled in the underground sewer system of the city of Barcelona (Spain). The aim of the present study was to verify, using molecular methods, the potential reservoir role of these rats in the same sewer system. Methods A sensitive real-time PCR (qPCR) assay, DNA sequencing and phylogenetic analysis were carried out to identify and quantify the presence of L. infantum DNA in sand fly individuals captured in the same underground sewer system of Barcelona as in our previous study and in the spleens and ears of rats captured in the same sewer system. Results Leishmania infantum DNA was found in 14 of the 27 (51.9%) sand flies identified as Phlebotomus perniciosus, and 10 of the 24 (41.7%) rats studied were infected. Leishmania infantum was found in the spleens (70%) and in the ears (40%) of the infected rats. Quantitative results revealed the presence of high loads of L. infantum in the rats studied (> 3 × 106 parasites/g ear tissue) and among the sand flies (> 34 × 106 parasites in 1 individual). Conclusions The molecular methods used in this study demonstrated a high prevalence of L. infantum in the underground
sewer populations of both R. norvegicus and P. perniciosus. These results suggest that sewer rats, in addition to dogs, are likely to act as reservoirs of leishmaniasis in cities, where sewer systems seem to offer the ideal scenario for the transmission of leishmaniasis. Therefore, to achieve the WHO 2030 target on the elimination of leishmaniasis as a public health problem successfully, an efficient control strategy against leishmaniasis in rats and sand flies should be implemented, particularly in the sewer systems of urban areas of endemic countries. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05309-4.
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Affiliation(s)
- María Teresa Galán-Puchades
- Parasite and Health Research Group, Department of Pharmacy, Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Valencia, Spain.
| | - Jennifer Solano
- Molecular Biochemistry and Parasitology Research Group, Department of Parasitology, Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Gloria González
- Molecular Biochemistry and Parasitology Research Group, Department of Parasitology, Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Antonio Osuna
- Molecular Biochemistry and Parasitology Research Group, Department of Parasitology, Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Jordi Pascual
- Pest Surveillance and Control, Agència de Salut Pública de Barcelona (ASPB), 08023, Barcelona, Spain
| | - Rubén Bueno-Marí
- Parasite and Health Research Group, Department of Pharmacy, Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Valencia, Spain.,Department of Research and Development, Laboratorios Lokímica, 46980, Paterna, Valencia, Spain
| | - Sandra Franco
- Pest Surveillance and Control, Agència de Salut Pública de Barcelona (ASPB), 08023, Barcelona, Spain
| | - Víctor Peracho
- Pest Surveillance and Control, Agència de Salut Pública de Barcelona (ASPB), 08023, Barcelona, Spain
| | - Tomás Montalvo
- Pest Surveillance and Control, Agència de Salut Pública de Barcelona (ASPB), 08023, Barcelona, Spain.,Biomedical Research Center Network for Epidemiology and Public Health CIBERESP Epidemiology and Public Health, 08023, Barcelona, Spain
| | - Màrius V Fuentes
- Parasite and Health Research Group, Department of Pharmacy, Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Valencia, Spain
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Senne NA, Santos HA, Araújo TR, Paulino PG, Mendonça LP, Moreira HVS, Camilo TA, da Costa Angelo I. Robust comparative performance of genomic DNA extraction methods from non-engorged phlebotomine sandflies. MEDICAL AND VETERINARY ENTOMOLOGY 2022; 36:203-211. [PMID: 35229900 DOI: 10.1111/mve.12567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/17/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The present study is a comparative analysis of DNeasy Blood & Tissue Qiagen® kit (Qiagen®, Hilden, Alemanha), salting out, HotShot and phenol-chloroform protocols to extract DNA from sandflies. In addition, a comparative test using sandflies with and without eyes evaluated the potential inhibitory effect in the cPCR. An inhibition test was performed using an exogenous DNA added to the qPCR. The genomic DNA quality of each sample was evaluated by cPCR based on the cytochrome c oxidase subunit I (cox1) gene. The DNA extraction protocols showed the following percentage of amplification: HotShot (91.6% [55/60]), salting out (71.6% [43/60]), phenol-chloroform (95% [57/60]) and kit DNeasy Blood & Tissue Qiagen® (73.3% [44/60]). The phenol-chloroform method achieved a significantly higher frequency of cox1 gene amplification. The pigment present in the phlebotomine's eyes seems to inhibit cPCR reactions since the frequency of amplification of the cox1 gene increased in the sandflies without eyes (p < 0.0001). The HotShot method showed the highest inhibitory potential. These manual extraction techniques can be an inexpensive and effective alternative to study vector-pathogen interactions.
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Affiliation(s)
- Nathália Alves Senne
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Huarrisson Azevedo Santos
- Departamento de Epidemiologia e Saúde Pública, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Thamires Rezende Araújo
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Patrícia Gonzaga Paulino
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Leo Paulis Mendonça
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Haika Victória Sales Moreira
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Tays Araújo Camilo
- Programa de Pós-Graduação em Ciências Biológicas, Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Isabele da Costa Angelo
- Departamento de Epidemiologia e Saúde Pública, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
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Leonel JAF, Vioti G, Alves ML, da Silva DT, Meneghesso PA, Benassi JC, Spada JCP, Galvis-Ovallos F, Soares RM, Oliveira TMFDS. DNA extraction from individual Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) specimens: Which is the method with better results? Exp Parasitol 2020; 218:107981. [PMID: 32871144 DOI: 10.1016/j.exppara.2020.107981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) are a group of small insects of great concern for Public Health. These dipterous are intensely studied worldwide due to their involvement in the transmission of several pathogens, mainly Leishmania spp. parasites. Nowadays, the molecular tools have been included in Phlebotomine sand flies studies and has shown to be powerful tools in bioecology studies of these dipterous. Thereby, when molecular approaches are employed, there is a great concern regarding the amount and quality of the DNA obtained for analysis. Here, seven methods of DNA extraction, between commercial kits and in house extraction protocols were evaluated. We considered measure of DNA concentration and purity ratios using a spectrophotometer to check the performance of each protocol. In addition, the quality evaluation of the DNA extracted was performed by endogenous gene PCR on samples. The results of the seven evaluated DNA extraction protocols and their implications are discussed.
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Affiliation(s)
- João Augusto Franco Leonel
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Geovanna Vioti
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Maria Luana Alves
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Diogo Tiago da Silva
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Pedro Armando Meneghesso
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Julia Cristina Benassi
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Julio Cesar Pereira Spada
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Fredy Galvis-Ovallos
- Laboratory of Entomology in Public Health, School of Public Health, University of São Paulo - USP, São Paulo, São Paulo state, Brazil
| | - Rodrigo Martins Soares
- Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil
| | - Trícia Maria Ferreira de Sousa Oliveira
- Laboratory of Applied Preventive Veterinary Medicine, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil; Post-graduate Program in Experimental Epidemiology Applied to Zoonoses, Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo - USP, Pirassununga, São Paulo state, Brazil.
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