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Azarm A, Koosha M, Dalimi A, Zahraie-Ramazani A, Akhavan AA, Saeidi Z, Mohebali M, Azam K, Vatandoost H, Oshaghi MA. Association Between Wolbachia Infection and Susceptibility to Deltamethrin Insecticide in Phlebotomus papatasi (Diptera: Psychodidae), the Main Vector of Zoonotic Cutaneous Leishmaniasis. Vector Borne Zoonotic Dis 2024; 24:159-165. [PMID: 38016137 DOI: 10.1089/vbz.2023.0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Background: Phlebotomus papatasi (Diptera: Psychodidae) is the main vector of zoonotic cutaneous leishmaniasis. Wolbachia is a symbiotic alphaproteobacteria of arthropods that can be involved in susceptibility or resistance. This study aimed to investigate the relationship between Wolbachia and Deltamethrin susceptibility/resistance in Ph. papatasi. Deltamethrin filter papers (0.00002%) were used to test sand fly field collected from southern Iran. After the test, PCR amplification of the Wolbachia surface protein gene (wsp) was used to measure Wolbachia infection rate in the killed, surviving, and control groups. Result: The rates of infection by Wolbachia strain (wPap, super group A) differed between killed (susceptible) and surviving (resistant) Ph. papatasi specimens. The rate of Wolbachia infection in susceptible individuals was more than twice (2.3) (39% vs. 17%) in resistant individuals with the same genetic background. This difference was highly significant (p < 0.001), indicating a positive association between Wolbachia infection and susceptibility to Deltamethrin. In addition, the results showed that Deltamethrin can act as a PCR inhibitor during detection of Wolbachia in Ph. papatasi. Conclusion: Results of this study show that Wolbachia is associated with Deltamethrin susceptibility level in Ph. papatasi. Also, as Deltamethrin has been identified as a PCR inhibitor, great care must be taken in interpreting Wolbachia infection status in infected populations. The results of this study may provide information for a better understanding of the host-symbiont relationship, as well as application of host symbiosis in pest management.
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Affiliation(s)
- Amrollah Azarm
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Parasitology and Entomology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mona Koosha
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abdolhossein Dalimi
- Department of Medical Parasitology and Entomology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Alireza Zahraie-Ramazani
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Ahmad Akhavan
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Saeidi
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mohebali
- Department of Medical Parasitology and Mycology and School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamal Azam
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Vatandoost
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Chemical Pollutants and Pesticides, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oshaghi
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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2
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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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3
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Irestedt M, Thörn F, Müller IA, Jønsson KA, Ericson PGP, Blom MPK. A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins. Mol Ecol Resour 2022; 22:2672-2684. [PMID: 35661418 PMCID: PMC9542604 DOI: 10.1111/1755-0998.13660] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
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Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Filip Thörn
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Ingo A Müller
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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4
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Pedersen MW, Antunes C, De Cahsan B, Moreno-Mayar JV, Sikora M, Vinner L, Mann D, Klimov PB, Black S, Michieli CT, Braig HR, Perotti MA. Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits. Mol Biol Evol 2021; 39:6481551. [PMID: 34963129 PMCID: PMC8829908 DOI: 10.1093/molbev/msab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.
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Affiliation(s)
- Mikkel W Pedersen
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Catia Antunes
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Binia De Cahsan
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Martin Sikora
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Lasse Vinner
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Darren Mann
- Oxford University Museum of Natural History, Oxford, United Kingdom
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Department of Ecology and Evolutionary Biology, University of Michigan, Museum of Zoology, Ann Arbor, USA
| | - Stuart Black
- Department of Geography and Environmental Science, Wager Building, University of Reading, Reading, United Kingdom
| | - Catalina Teresa Michieli
- Instituto de Investigaciones Arqueológicas y Museo "Prof. Mariano Gambier", Universidad Nacional de San Juan, San Juan, Argentina
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Institute and Museum of Natural Sciences, Faculty of Exact, Physical and Natural Sciences, National University of San Juan, San Juan, Argentina
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
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5
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Rinkert A, Misiewicz TM, Carter BE, Salmaan A, Whittall JB. Bird nests as botanical time capsules: DNA barcoding identifies the contents of contemporary and historical nests. PLoS One 2021; 16:e0257624. [PMID: 34614003 PMCID: PMC8494352 DOI: 10.1371/journal.pone.0257624] [Citation(s) in RCA: 3] [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: 04/21/2021] [Accepted: 09/06/2021] [Indexed: 11/18/2022] Open
Abstract
Bird nests in natural history collections are an abundant yet vastly underutilized source of genetic information. We sequenced the nuclear ribosomal internal transcribed spacer to identify plant species used as nest material in two contemporary (2003 and 2018) and two historical (both 1915) nest specimens constructed by Song Sparrows (Melospiza melodia) and Savannah Sparrows (Passerculus sandwichensis). A total of 13 (22%) samples yielded single, strong bands that could be identified using GenBank resources: six plants (Angiospermae), six green algae (Chlorophyta), and one ciliate (Ciliophora). Two native plant species identified in the nests included Festuca microstachys, which was introduced to the nest collection site by restoration practitioners, and Rosa californica, identified in a nest collected from a lost habitat that existed about 100 years ago. Successful sequencing was correlated with higher sample mass and DNA quality, suggesting future studies should select larger pieces of contiguous material from nests and materials that appear to have been fresh when incorporated into the nest. This molecular approach was used to distinguish plant species that were not visually identifiable, and did not require disassembling the nest specimens as is a traditional practice with nest material studies. The many thousands of nest specimens in natural history collections hold great promise as sources of genetic information to address myriad ecological questions.
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Affiliation(s)
- Alex Rinkert
- Department of Biological Sciences, San José State University, San José, CA, United States of America
- * E-mail:
| | - Tracy M. Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States of America
| | - Benjamin E. Carter
- Department of Biological Sciences, San José State University, San José, CA, United States of America
| | - Aleezah Salmaan
- Department of Biology, Santa Clara University, Santa Clara, CA, United States of America
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, Santa Clara, CA, United States of America
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6
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Impacts of changes in temperature and exposure time on the median lethal concentrations (LC50) of a combination of organophosphate and pyrethroid in the control of Culex quinquefasciatus, say (Diptera: Culicidae). SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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7
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Bist R, Chaudhary B, Bhatt DK. Defensive proclivity of bacoside A and bromelain against oxidative stress and AChE gene expression induced by dichlorvos in the brain of Mus musculus. Sci Rep 2021; 11:3668. [PMID: 33574433 PMCID: PMC7878736 DOI: 10.1038/s41598-021-83289-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/25/2021] [Indexed: 01/22/2023] Open
Abstract
The objective of current study was to evaluate the neuroprotective effects of bacoside A and bromelain against dichlorvos induced toxicity. The healthy, 6-8 weeks old male Swiss mice were administered in separate groups subacute doses of dichlorvos (40 mg/kg bw), bacoside A (5 mg/kg bw) and bromelain (70 mg/kg bw). In order to determination of oxidative stress in different groups, thiobarbituric acid reactive substances (TBARS) and protein carbonyl content (PCC) were studied in the present investigation. Moreover, for toxic manifestation at molecular level the site-specific gene amplification of acetylcholinesterase (AChE) gene was studied in the brain. Nonetheless, the protective effects of bacoside A and bromelain were also evaluated on the TBARS, PCC and AChE gene. The exposure of dichlorvos leads to significant increase in TBARS level (p < 0.01, p < 0.001) and PCC. Besides, the decline in DNA yield, expression of amplified products of AChE gene was observed in the brain of dichlorvos treated group. The bacoside A and bromelain treatments significantly decreased the level of TBARS (p < 0.05, (p < 0.01) and PCC whereas, increase in the DNA yield and expression of amplified AChE gene products were observed in the brain compared to only dichlorvos treated mice. The overall picture which emerged after critical evaluation of results indicated that the dichlorvos induced oxidative stress and alteration in AChE gene expression showed significant improvement owing to the treatments of bacoside A and bromelain. Thus, bacoside A and bromelain are very effective in alleviating neurotoxicity induced by dichlorvos.
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Affiliation(s)
- Renu Bist
- Department of Zoology, University of Rajasthan, Jaipur, Rajasthan, 302004, India.
| | - Bharti Chaudhary
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan, 304022, India
| | - D K Bhatt
- Department of Zoology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
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8
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Affiliation(s)
- Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo Sanda City Japan
- The Museum of Nature and Human Activities, Hyogo Sanda City Japan
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9
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Patzold F, Zilli A, Hundsdoerfer AK. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS One 2020; 15:e0235222. [PMID: 32639972 PMCID: PMC7343169 DOI: 10.1371/journal.pone.0235222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.
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Affiliation(s)
- Franziska Patzold
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Alberto Zilli
- Division Insects, Department Life Sciences, Natural History Museum, London, United Kingdom
| | - Anna K. Hundsdoerfer
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
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10
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Thongjued K, Chotigeat W, Bumrungsri S, Thanakiatkrai P, Kitpipit T. A new cost-effective and fast direct PCR protocol for insects based on PBS buffer. Mol Ecol Resour 2019; 19:691-701. [PMID: 30758899 DOI: 10.1111/1755-0998.13005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 01/26/2023]
Abstract
Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification. The developed protocol achieved 100% success rates for amplification in six orders: Mantodea, Phasmatodea, Neuroptera, Odonata, Blattodea and Orthoptera. High and moderate success rates were obtained for five other species: Lepidoptera (97.3%), Coleoptera (93.8%), Diptera (90.5%), Hemiptera (81.8%) and Hymenoptera (75.0%). High-quality sequencing data were also obtained from these amplifiable products, allowing confidence in species identification. The method was sensitive down to 1/4th of a 1-mm fragment of leg or body and its success rates with oven-dried, ethanol-preserved, food, bat guano and museum specimens were 100%, 98.6%, 90.0%, 84.0% and 30.0%, respectively. In addition, the pre-PCR solution (PBS with insect tissues) could be used for further DNA extraction if needed. The workflow will be beneficial in the fields of insect taxonomy and ecological studies due to its low cost, simplicity and applicability to highly degraded specimens.
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Affiliation(s)
- Kantima Thongjued
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wilaiwan Chotigeat
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.,Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Sara Bumrungsri
- Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Phuvadol Thanakiatkrai
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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11
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Mitochondrial Gene Sequence ( COI) Reveals the Genetic Structure and Demographic History of Lymantria dispar (Lepidoptera: Erebidae: Lymantriinae) in and around China. INSECTS 2019; 10:insects10050146. [PMID: 31121918 PMCID: PMC6572239 DOI: 10.3390/insects10050146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 11/17/2022]
Abstract
The gypsy moth, Lymantria dispar, is among the most destructive quarantine pests of forests. Here, we reconstructed the genetic structure and determined the population differentiation of gypsy moths across its distribution range at different times. This information could be used to both improve the prevention and detection of gypsy moths in the field. Using 31 newly designed species-specific primers targeting fragments of 216-1102 bp, we identified 103 full-length cytochrome oxidase subunit I (COI) gene sequences from eight fresh samples and 95 L. dispar specimens collected between 1955 and 1996, mainly in China. Combining 103 full-length COI gene sequences with 146 COI gene sequences from Genbank or DNA barcode libraries, we analyzed the genetic differentiation, gene flow and haplotypes between gypsy moth populations in order to reflect the genetic structure and population dynamics of gypsy moths. We discovered 25 previously unknown haplotypes from old gypsy moth specimens. We found that the genetic diversity among gypsy moth populations (collected in the same region at different time points) was relatively high. Furthermore, the genetic structure of Chinese geographical populations (Heilongjiang, Liaoning, Beijing) in different years was distinct. Our results suggested that some gypsy moths in China showed the genetic affinity with European gypsy moths (a sub-species of gypsy moths found mainly in Europe).
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12
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Astaxanthin supplementation reduces dichlorvos-induced cytotoxicity in Saccharomyces cerevisiae. 3 Biotech 2019; 9:88. [PMID: 30800599 DOI: 10.1007/s13205-019-1634-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/11/2019] [Indexed: 01/06/2023] Open
Abstract
This study evaluates the protective effect of astaxanthin against dichlorvos cytotoxicity in yeast Saccharomyces cerevisiae. Dichlorvos induce a dose-dependent cytotoxicity in yeast cells, which is mediated by oxidative stress. Our experimental results showed pre-treatment with astaxanthin enhances cell viability by 20-30% in yeast cells exposed to dichlorvos. A decrease in DCF fluorescence intensity and lipid peroxidation, increased SOD activity, and glutathione levels in astaxanthin-treated cells indicate that astaxanthin protected the cells against dichlorvos-induced oxidative stress. Reduced chromatin condensation and nuclear fragmentation in astaxanthin pre-treated cells also indicate that astaxanthin rescued the cells from dichlorvos-induced apoptosis. Our overall results suggest that dichlorvos induces oxidative stress-mediated cytotoxicity in yeast cells, and that was rescued by astaxanthin pre-treatment.
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13
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Lalonde MML, Marcus JM. Entomological time travel: reconstructing the invasion history of the buckeye butterflies (genus Junonia) from Florida, USA. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01948-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Yeates DK, Zwick A, Mikheyev AS. Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections. CURRENT OPINION IN INSECT SCIENCE 2016; 18:83-88. [PMID: 27939715 DOI: 10.1016/j.cois.2016.09.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.
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Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia.
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun 904-0412, Japan
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15
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Werblow A, Flechl E, Klimpel S, Zittra C, Lebl K, Kieser K, Laciny A, Silbermayr K, Melaun C, Fuehrer HP. Direct PCR of indigenous and invasive mosquito species: a time- and cost-effective technique of mosquito barcoding. MEDICAL AND VETERINARY ENTOMOLOGY 2016; 30:8-13. [PMID: 26663040 PMCID: PMC4982094 DOI: 10.1111/mve.12154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/29/2014] [Accepted: 02/17/2015] [Indexed: 06/05/2023]
Abstract
Millions of people die each year as a result of pathogens transmitted by mosquitoes. However, the morphological identification of mosquito species can be difficult even for experts. The identification of morphologically indistinguishable species, such as members of the Anopheles maculipennis complex (Diptera: Culicidae), and possible hybrids, such as Culex pipiens pipiens/Culex pipiens molestus (Diptera: Culicidae), presents a major problem. In addition, the detection and discrimination of newly introduced species can be challenging, particularly to researchers without previous experience. Because of their medical importance, the clear identification of all relevant mosquito species is essential. Using the direct polymerase chain reaction (PCR) method described here, DNA amplification without prior DNA extraction is possible and thus species identification after sequencing can be achieved. Different amounts of tissue (leg, head; larvae or adult) as well as different storage conditions (dry, ethanol, -20 and -80 °C) and storage times were successfully applied and showed positive results after amplification and gel electrophoresis. Overall, 28 different indigenous and non-indigenous mosquito species were analysed using a gene fragment of the COX1 gene for species differentiation and identification by sequencing this 658-bp fragment. Compared with standard PCR, this method is time- and cost-effective and could thus improve existing surveillance and control programmes.
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Affiliation(s)
- A Werblow
- Institute for Ecology, Evolution and Diversity, Goethe University (GU); Senckenberg Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung (SGN), Frankfurt am Main, Germany
| | - E Flechl
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Klimpel
- Institute for Ecology, Evolution and Diversity, Goethe University (GU); Senckenberg Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung (SGN), Frankfurt am Main, Germany
| | - C Zittra
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K Lebl
- Institute for Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K Kieser
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Laciny
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K Silbermayr
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - C Melaun
- Institute for Ecology, Evolution and Diversity, Goethe University (GU); Senckenberg Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung (SGN), Frankfurt am Main, Germany
| | - H-P Fuehrer
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
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16
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Krehenwinkel H, Pekar S. An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider. PLoS One 2015; 10:e0136337. [PMID: 26309219 PMCID: PMC4550360 DOI: 10.1371/journal.pone.0136337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/01/2015] [Indexed: 11/19/2022] Open
Abstract
Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.
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Affiliation(s)
- Henrik Krehenwinkel
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August Thienemann Strasse 2, 24306, Plön, Germany
- University of California, Department of Environmental Science, Policy, and Management, 130 Mulford Hall, Berkeley, United States of America
- * E-mail:
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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17
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Willows-Munro S, Schoeman MC. Influence of killing method on Lepidoptera DNA barcode recovery. Mol Ecol Resour 2014; 15:613-8. [PMID: 25229871 DOI: 10.1111/1755-0998.12331] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 11/30/2022]
Abstract
The global DNA barcoding initiative has revolutionized the field of biodiversity research. Such large-scale sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study, we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). Previous studies have suggested that chemicals, such as ethyl acetate and formaldehyde, degraded DNA and as such may not be appropriate for the collection of insects for DNA-based research. All Lepidoptera collected produced DNA barcodes of good quality, and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis.
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Affiliation(s)
- Sandi Willows-Munro
- School of Life Science, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa
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18
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Hebert PDN, Dewaard JR, Zakharov EV, Prosser SWJ, Sones JE, McKeown JTA, Mantle B, La Salle J. A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection. PLoS One 2013; 8:e68535. [PMID: 23874660 PMCID: PMC3707885 DOI: 10.1371/journal.pone.0068535] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/27/2013] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity – insects.
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Affiliation(s)
- Paul D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada.
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Torralba-Burrial A, Ocharan FJ. Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain). Zookeys 2013:37-58. [PMID: 23794917 PMCID: PMC3689041 DOI: 10.3897/zookeys.306.5289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/29/2013] [Indexed: 11/12/2022] Open
Abstract
Odonata are represented from the Iberian Peninsula by 79 species. However, there exists a significant gap in accessible knowledge about these species,especially regarding their distribution. This data paper describes the specimen-based Odonata data of the Arthropod Collection of the Department of Biología de Organismos y Sistemas (BOS), University of Oviedo, Spain. The specimens were mainly collected from the Iberian Peninsula (98.63% of the data records), especially the northern region. The earliest specimen deposited in the collection dates back to 1950, while the 1980's and 2000's are the best-represented time periods. Between 1950 and 2009, 16, 604 Odonata specimens were deposited and are documented in the dataset. Approximately 20% of the specimens belong to the families Coenagrionidae and Calopterygidae. Specimens include the holotype and paratypes of the Iberian subspecies Calopteryx haemorrhoidalis asturica Ocharan, 1983 and Sympetrum vulgatum ibericum Ocharan, 1985. The complete dataset is also provided in Darwin Core Archive format.
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Affiliation(s)
- Antonio Torralba-Burrial
- Universidad de Oviedo, Cluster de Energía, Medioambiente y Cambio Climático, Plaza de Riego 4, 33071, Oviedo, Spain
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Strutzenberger P, Brehm G, Fiedler K. DNA barcode sequencing from old type specimens as a tool in taxonomy: a case study in the diverse genus Eois (Lepidoptera: Geometridae). PLoS One 2012. [PMID: 23185414 PMCID: PMC3504115 DOI: 10.1371/journal.pone.0049710] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this study we report on the sequencing of the COI barcode region from 96 historical specimens (92 type specimens +4 non-types) of Eois. Eois is a diverse clade of tropical geometrid moths and is the target of a number of ongoing studies on life-histories, phylogeny, co-evolution with host plants or parasitoids, and diversity patterns across temporal and spatial dimensions. The unequivocal application of valid names is crucial for all aspects of biodiversity research as well as monitoring and conservation efforts. The availability of barcodes from historical type specimens has the potential to facilitate the much-needed acceleration of species description. We performed non-destructive DNA extraction on the abdomens of Eois specimens between 79 and 157 years of age. We used six primer combinations (recovering between 109 and 130 bp each) to target the full-length barcode sequence of each specimen. We were able to obtain sequences for 91 of 96 specimens (success rate 94.8%). Sequence length ranged from 121 bp to full barcode sequences (658 bp), the average sequence length was ∼500 bp. We detected a moderately strong and statistically significant negative correlation between specimen age and total sequence length, which is in agreement with expectations. The abdomen proved to be an exceedingly valuable source of DNA in old specimens of Lepidoptera. Barcode sequences obtained in this study are currently being used in an effort towards a step-wise taxonomic revision of Eois. We encourage that DNA barcodes obtained from types specimens should be included in all species descriptions and revisions whenever feasible.
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Affiliation(s)
- Patrick Strutzenberger
- Department of Tropical Ecology and Animal Biodiversity, University of Vienna, Vienna, Austria.
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Martinsson S, Kjaerandsen J, Sundberg P. Towards a molecular phylogeny of the fungus gnat genus Boletina (Diptera: Mycetophilidae). ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00474.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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