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Gandhi H, Jain M, Gupta S, Singh AK, Kumar A, Sohal JS. Comparative evaluation of various in-house protocols on diagnostic performance for paratuberculosis IS900 PCR. Mol Biol Rep 2023; 50:943-947. [PMID: 36371554 DOI: 10.1007/s11033-022-07984-z] [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: 08/08/2022] [Accepted: 09/23/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Paratuberculosis is a worldwide endemic infectious disease of ruminants that results in high economic losses. Public health concerns are also being raised with human Crohn's disease. Therefore, control is becoming priority for governments. Control is largely dependent on "Test and Cull" or "Test and Segregate" policy. Hence, it is critical to assure the infection before making the decision. Commercial kits are costly especially in view of resource limited areas. Present study analyzed the performance various in house DNA isolation methods and PCR master mix combinations to optimize a protocol for confirmation of paratuberculosis bacilli shedding in feces. METHODS AND RESULTS Present study included five protocols of fecal DNA isolation (chemical, bio-chemical, physio-chemical and physical) and three reaction mixes (based on Qiagen, Genei and Thermo 2X master mixes) in nine different combinations using additives and tested their performance for IS900 PCR. Spiked fecal samples were used to select the best combination of DNA isolation method and PCR master mix (PRM). Selected combination was used to test reference (positive and negative) fecal samples and field samples. Findings revealed that combination physical method of DNA isolation and Genei based PRM (with additives; betaine DMSO and BSA) had lowest limit of detection. Sensitivity was 83% and specificity was 100% in comparison to fecal culture. High prevalence (23%) was reported for paratuberculosis on field samples. CONCLUSION Optimized protocol has acceptable sensitivity and can easily be adopted in resource-limited laboratories. High prevalence of paratuberculosis needs immediate implementation of the control strategies.
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Affiliation(s)
- Harshita Gandhi
- Amity Institute of Microbial Technology, Amity University Rajasthan, Kant-Kalwar, NH11C, Delhi- Jaipur, 303 002, Jaipur, Rajasthan, India
| | - Mukta Jain
- Biogenix Inc Pvt. Ltd, Amausi Industrial Area, 226008, Nadarganj, Lucknow, UP, India
| | - Saurabh Gupta
- Department of of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, NH-2, Post- Chaumunha, 281 406, Mathura, India.
| | - Amit Kumar Singh
- Amity Institute of Microbial Technology, Amity University Rajasthan, Kant-Kalwar, NH11C, Delhi- Jaipur, 303 002, Jaipur, Rajasthan, India
| | - Amit Kumar
- Department of Immunology & Defense Mechanism, Sardar Vallabh Bhai Patel University of Agriculture & Technology (SVPUAT), 250 110, Modipurum, Meerut, India
| | - Jagdip Singh Sohal
- Centre for Vaccines and Diagnostic Research, GLA University, NH-2, 281 406, Chaumunha, Mathura, India.
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Zaiko A, Greenfield P, Abbott C, von Ammon U, Bilewitch J, Bunce M, Cristescu ME, Chariton A, Dowle E, Geller J, Ardura Gutierrez A, Hajibabaei M, Haggard E, Inglis GJ, Lavery SD, Samuiloviene A, Simpson T, Stat M, Stephenson S, Sutherland J, Thakur V, Westfall K, Wood SA, Wright M, Zhang G, Pochon X. Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment. Mol Ecol Resour 2021; 22:519-538. [PMID: 34398515 DOI: 10.1111/1755-0998.13485] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/21/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia.,Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Cathryn Abbott
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Jaret Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Michael Bunce
- Environmental Protection Authority, Wellington, New Zealand
| | | | - Anthony Chariton
- Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Eddy Dowle
- School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jonathan Geller
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | | | | | - Emmet Haggard
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Graeme J Inglis
- National Institute of Water & Atmospheric Research Ltd (NIWA), Christchurch, New Zealand
| | - Shane D Lavery
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Tiffany Simpson
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Michael Stat
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Judy Sutherland
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Vibha Thakur
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kristen Westfall
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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Mantellatto AMB, González S, Duarte JMB. Molecular identification of Mazama species (Cervidae: Artiodactyla) from natural history collections. Genet Mol Biol 2020; 43:e20190008. [PMID: 32215543 PMCID: PMC7197991 DOI: 10.1590/1678-4685-gmb-2019-0008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/02/2019] [Indexed: 11/21/2022] Open
Abstract
Natural history museum collections constitute an invaluable patrimony of
biological diversity for analysing the taxa distribution and evolution. However,
it is very common to discover taxonomic misidentification in museum collections
based on incorrect data. The aim of this research was to identify brocket deer
species (Mazama genus) using molecular markers. We collected
199 samples, performed DNA extraction and species identification using a
specific mitochondrial marker based on a fragment of cytochrome b
(Cytb) for Neotropical deer. We achieved the amplification
and sequencing of 77 specimens and verified that 26% of the skulls were wrongly
identified. Moreover, in the museum collections 57% of the specimens were only
identified as Mazama sp, and we were able to identify them by
molecular methods to the species level. Our findings clearly demonstrate the
importance of integrating molecular analyses to identify Mazama
species, since using only external morphology can result in a high probability
of errors. We recommend the selection of non-convergent morphological
characters, which together with the use of DNA collected from museum specimens
should contribute to more accurate taxonomic identifications.
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Affiliation(s)
- Aline Meira Bonfim Mantellatto
- Universidade Estadual Paulista "Júlio de Mesquota Filho" (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Núcleo de Pesquisa e Conservação de Cervídeos, Jaboticabal, SP, Brazil.,Universidade Federal do Sul da Bahia, Centro de Formação em Ciências Ambientais, Laboratório de Ecologia e Conservação Marinha, Campus Sosígenes Costa, Porto Seguro, BA, Brazil
| | - Susana González
- Instituto de Investigaciones Biológicas Clemente Estable, Departamento de Biodiversidad y Genética, Montevideo, Uruguay
| | - José Maurício Barbanti Duarte
- Universidade Estadual Paulista "Júlio de Mesquota Filho" (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Núcleo de Pesquisa e Conservação de Cervídeos, Jaboticabal, SP, Brazil
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Sang S, Friend DS, Allmon WD, Anderson BM. Protoconch enlargement in Western Atlantic turritelline gastropod species following the closure of the Central American Seaway. Ecol Evol 2019; 9:5309-5323. [PMID: 31110681 PMCID: PMC6509377 DOI: 10.1002/ece3.5120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/12/2019] [Accepted: 03/01/2019] [Indexed: 11/18/2022] Open
Abstract
The closure of the late Neogene interoceanic seaways between the Western Atlantic (WA) and Tropical Eastern Pacific (TEP)-commonly referred to as the Central American Seaway-significantly decreased nutrient supply in the WA compared to the TEP. In marine invertebrates, an increase in parental investment is expected to be selectively favored in nutrient-poor marine environments as prolonged feeding in the plankton becomes less reliable. Here, we examine turritelline gastropods, which were abundant and diverse across this region during the Neogene and serve as important paleoenvironmental proxies, and test whether species exhibit decreased planktotrophy in the WA postclosure as compared to preclosure fossils and extant TEP species. We also test for differences in degree of planktotrophy in extant sister species pairs. Degree of planktotrophy was inferred by measuring the size of protoconchs, the species' larval shell that represents egg size. Protoconch size was compared between extant postclosure WA and TEP species and preclosure fossil species. To compare extant sister species, we reconstructed the phylogeny of available WA and TEP species using one nuclear (H3) and three mitochondrial markers (12S, 16S, and COI). Compared to the preclosure fossils, protoconch size increased in WA species but remained the same in the TEP species. In the two extant sister species pairs recovered in the phylogenetic analysis, the WA species are inferred to be nonplanktotrophic while the TEP species are planktotrophic. This suggests that decreased nutrient availability and primary productivity in the WA may have driven this change in developmental mode, and was the primary selective force resulting in postclosure turritelline extinctions.
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Affiliation(s)
- Stephanie Sang
- Department of Earth and Atmospheric SciencesSnee Hall, Cornell UniversityIthacaNew York
- Paleontological Research InstitutionIthacaNew York
- Present address:
Department of Organismal Biology and AnatomyUniversity of ChicagoChicagoIllinois
| | - Dana Suzanne Friend
- Department of Earth and Atmospheric SciencesSnee Hall, Cornell UniversityIthacaNew York
- Paleontological Research InstitutionIthacaNew York
| | - Warren Douglas Allmon
- Department of Earth and Atmospheric SciencesSnee Hall, Cornell UniversityIthacaNew York
- Paleontological Research InstitutionIthacaNew York
| | - Brendan Matthew Anderson
- Department of Earth and Atmospheric SciencesSnee Hall, Cornell UniversityIthacaNew York
- Paleontological Research InstitutionIthacaNew York
- Present address:
Department of Geology and GeographyWest Virginia UniversityMorgantownWest Virginia
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First insights into the metagenome of Egyptian mummies using next-generation sequencing. J Appl Genet 2013; 54:309-25. [PMID: 23553074 DOI: 10.1007/s13353-013-0145-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
Abstract
We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC-124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a "bacterial fingerprint", discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.
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Farell EM, Alexandre G. Bovine serum albumin further enhances the effects of organic solvents on increased yield of polymerase chain reaction of GC-rich templates. BMC Res Notes 2012; 5:257. [PMID: 22624992 PMCID: PMC3466135 DOI: 10.1186/1756-0500-5-257] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While being a standard powerful molecular biology technique, applications of the PCR to the amplification of high GC-rich DNA samples still present challenges which include limited yield and poor specificity of the reaction. Organic solvents, including DMSO and formamide, have been often employed as additives to increase the efficiency of amplification of high GC content (GC > 60%) DNA sequences. Bovine serum albumin (BSA) has been used as an additive in several applications, including restriction enzyme digestions as well as in PCR amplification of templates from environmental samples that contain potential inhibitors such as phenolic compounds. FINDINGS Significant increase in PCR amplification yields of GC-rich DNA targets ranging in sizes from 0.4 kb to 7.1 kb were achieved by using BSA as a co-additive along with DMSO and formamide. Notably, enhancing effects of BSA occurs in the initial PCR cycles with BSA additions having no detrimental impact on PCR yield or specificity. When a PCR was set up such that the cycling parameters paused after every ten cycles to allow for supplementation of BSA, combining BSA and organic solvent produced significantly higher yields relative to conditions using the solvent alone. The co-enhancing effects of BSA in presence of organic solvents were also obtained in other PCR applications, including site-directed mutagenesis and overlap extension PCR. CONCLUSIONS BSA significantly enhances PCR amplification yield when used in combination with organic solvents, DMSO or formamide. BSA enhancing effects were obtained in several PCR applications, with DNA templates of high GC content and spanning a broad size range. When added to the reaction buffer, promoting effects of BSA were seen in the first cycles of the PCR, regardless of the size of the DNA to amplify. The strategy outlined here provides a cost-effective alternative for increasing the efficiency of PCR amplification of GC-rich DNA targets over a broad size range.
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Affiliation(s)
- Eric M Farell
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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