1
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Rapid and zero-cost DNA extraction from soft-bodied insects for routine PCR-based applications. PLoS One 2022; 17:e0271312. [PMID: 35839213 PMCID: PMC9286237 DOI: 10.1371/journal.pone.0271312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Nucleic acid extraction is the first and foremost step in molecular biology studies. Extraction of DNA from small, soft-bodied insects is often time-consuming and costly. A fast, easy, and cost-effective DNA extraction method with greater yield and purity of DNA would aid in the rapid diagnostics, screening of large populations, and other routine PCR-based applications. The present study evaluated and standardized a rapid and zero-cost DNA extraction from soft-bodied small insects for routine molecular studies. Five rapid DNA extraction methods viz. extraction in sterile distilled water (SDW), 1X phosphate-buffered saline (PBS, pH 7.4), 1.4 M sodium chloride (NaCl), 20 mM ethylenediaminetetraacetic acid (EDTA, pH 8.0), and elution from blotted nitrocellulose membrane (NCM) were compared with standard CTAB extraction buffer and DNeasy® Blood and Tissue Kit methods. The average yield, purity, storage stability, time, and cost of extraction were assessed for all the methods and compared. A method of DNA extraction by simply crushing the soft-bodied insects in SDW was ideal in terms of yield, purity, storability, and performing routine PCR-based applications including detection of pathogens from vector species. The extraction could be accomplished in 2.5 min only with zero-reagent cost. The method would be useful in rapid molecular diagnostics and screening large populations of soft-bodied insects.
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2
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Smith AD, Kamiński MJ, Kanda K, Sweet AD, Betancourt JL, Holmgren CA, Hempel E, Alberti F, Hofreiter M. Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing. Sci Rep 2021; 11:12635. [PMID: 34135378 PMCID: PMC8209150 DOI: 10.1038/s41598-021-91896-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.
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Affiliation(s)
- Aaron D Smith
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA.
| | - Marcin J Kamiński
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Zoological Museum, Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warszawa, Poland
| | - Kojun Kanda
- USDA Systematic Entomology Laboratory, C/O Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Andrew D Sweet
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Arkansas State University, State University, AR, 72467, USA
| | | | - Camille A Holmgren
- Department of Geography and Planning, SUNY Buffalo State College, Buffalo, NY, USA
| | - Elisabeth Hempel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Museum Für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Federica Alberti
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Reiss-Engelhorn-Museen, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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3
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Successful extraction of insect DNA from recent copal inclusions: limits and perspectives. Sci Rep 2021; 11:6851. [PMID: 33767248 PMCID: PMC7994385 DOI: 10.1038/s41598-021-86058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.
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4
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Peris D, Janssen K, Barthel HJ, Bierbaum G, Delclòs X, Peñalver E, Solórzano-Kraemer MM, Jordal BH, Rust J. DNA from resin-embedded organisms: Past, present and future. PLoS One 2020; 15:e0239521. [PMID: 32986737 PMCID: PMC7521698 DOI: 10.1371/journal.pone.0239521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
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Affiliation(s)
- David Peris
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - H. Jonas Barthel
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics and Biodiversity Research Institute (IRBio), Faculty of Earth Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Peñalver
- Geological and Mining Institute of Spain (Geominero Museum), Valencia, Spain
| | - Mónica M. Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Bjarte H. Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Jes Rust
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
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5
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Abstract
Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.
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Affiliation(s)
- Brian Thomas
- Mass Spectrometry Group, Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
| | - Stephen Taylor
- Mass Spectrometry Group, Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
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6
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Abstract
The purpose of this Milankovitch review is to explain the significance of Quaternary DNA studies and the importance of the recent methodological advances that have enabled the study of late Quaternary remains in more detail, and the testing of new assumptions in evolutionary biology and phylogeography to reconstruct the past. The topic is wide, and this review is not intended to be an exhaustive account of all the aDNA work performed in the last three decades on late-Quaternary remains. Instead, it is a selection of relevant studies aimed at illustrating how aDNA has been used to reconstruct not only environments of the past, but also the history of many species including our own.
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7
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Georgiou R, Gueriau P, Sahle CJ, Bernard S, Mirone A, Garrouste R, Bergmann U, Rueff JP, Bertrand L. Carbon speciation in organic fossils using 2D to 3D x-ray Raman multispectral imaging. SCIENCE ADVANCES 2019; 5:eaaw5019. [PMID: 31497643 PMCID: PMC6716953 DOI: 10.1126/sciadv.aaw5019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/25/2019] [Indexed: 05/30/2023]
Abstract
The in situ two-dimensional (2D) and 3D imaging of the chemical speciation of organic fossils is an unsolved problem in paleontology and cultural heritage. Here, we use x-ray Raman scattering (XRS)-based imaging at the carbon K-edge to form 2D and 3D images of the carbon chemistry in two exceptionally preserved specimens, a fossil plant dating back from the Carboniferous and an ancient insect entrapped in 53-million-year-old amber. The 2D XRS imaging of the plant fossil reveals a homogeneous chemical composition with micrometric "pockets" of preservation, likely inherited from its geological history. The 3D XRS imaging of the insect cuticle displays an exceptionally well preserved remaining chemical signature typical of polysaccharides such as chitin around a largely hollowed-out inclusion. Our results open up new perspectives for in situ chemical speciation imaging of fossilized organic materials, with the potential to enhance our understanding of organic specimens and their paleobiology.
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Affiliation(s)
- Rafaella Georgiou
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
| | - Pierre Gueriau
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Institute of Earth Sciences, University of Lausanne, Géopolis, CH-1015 Lausanne, Switzerland
| | - Christoph J. Sahle
- ESRF–The European Synchrotron, 71, avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Sylvain Bernard
- Muséum National d’Histoire Naturelle, Sorbonne Université, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Alessandro Mirone
- ESRF–The European Synchrotron, 71, avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Romain Garrouste
- Institut de Systématique Evolution Biodiversité (ISYEB), UMR 7205 MNHN/CNRS/Sorbonne Univ./EPHE/Univ. Antilles, Muséum National d’Histoire Naturelle, 57 rue Cuvier, CP 50, F-75005 Paris, France
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jean-Pascal Rueff
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique–Matière et Rayonnement, LCPMR, F-75005 Paris, France
| | - Loïc Bertrand
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
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8
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Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol 2019; 27:105-117. [DOI: 10.1016/j.tim.2018.11.003] [Citation(s) in RCA: 421] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/06/2018] [Accepted: 11/05/2018] [Indexed: 01/18/2023]
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9
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Kumar VP, Rajpoot A, Mukesh, Shukla M, Kumar D, Goyal SP. Illegal trade of Indian Pangolin (Manis crassicaudata): Genetic study from scales based on mitochondrial genes. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2016. [DOI: 10.1016/j.ejfs.2016.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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11
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Affiliation(s)
- Anna Linderholm
- Research Laboratory for Archaeology; University of Oxford; Dyson Perrins Building South Parks Road Oxford OX1 3Q UK
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12
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Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130371. [PMID: 25487324 PMCID: PMC4275880 DOI: 10.1098/rstb.2013.0371] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Erika Hagelberg
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Christine Keyser
- Institut de Médecine Légale, Laboratoire AMIS, Université de Strasbourg, CNRS UMR 5288, Strasbourg, France
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13
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Species identification through mitochondrial rRNA genetic analysis. Sci Rep 2014; 4:4089. [PMID: 24522485 PMCID: PMC5379257 DOI: 10.1038/srep04089] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 01/27/2014] [Indexed: 12/22/2022] Open
Abstract
Inter-species and intraspecific variations in mitochondrial DNA (mtDNA) were observed in a bioinformatics analysis of the mitochondrial genomic sequences of 11 animal species. Some highly conserved regions were identified in the mitochondrial 12S and 16S ribosomal RNA (rRNA) genes of these species. To test whether these sequences are universally conserved, primers were designed to target the conserved regions of these two genes and were used to amplify DNA from 21 animal tissues, including two of unknown origin. By sequencing these PCR amplicons and aligning the sequences to a database of non-redundant nucleotide sequences, it was confirmed that these amplicons aligned specifically to mtDNA sequences from the expected species of origin. This molecular technique, when combined with bioinformatics, provides a reliable method for the taxonomic classification of animal tissues.
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14
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Smejkal GB, Poinar GO, Righetti PG. Will amber inclusions provide the first glimpse of a Mesozoic proteome? Expert Rev Proteomics 2014; 6:1-4. [DOI: 10.1586/14789450.6.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Abstract
Ancient biomolecules including DNA, proteins, and lipids are often preserved in archaeological skeletons or artifacts such as potsherds from cooking vessels. Techniques for analyzing these molecules have improved dramatically in recent years, though challenges remain in ensuring that results are authentic and not confused by the presence of contaminating modern biomolecules. Ancient DNA (aDNA) can be used to identify the sex, kinship relationships, and population affinities of human skeletons, and also to detect the presence of disease-causing organisms such as the plague and tuberculosis bacteria. Stable isotope ratios in collagen and other skeletal proteins enable past diets to be studied, and similar work with lipids from potsherds have revealed that dairying in Europe began 2,000 years earlier than previously thought. Biomolecular archaeology has therefore developed into a mature discipline that is making a significant contribution to different aspects of our understanding of the human past.
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Affiliation(s)
- Keri A. Brown
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom;,
| | - Terence A. Brown
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom;,
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16
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Penney D, Wadsworth C, Fox G, Kennedy SL, Preziosi RF, Brown TA. Absence of ancient DNA in sub-fossil insect inclusions preserved in 'Anthropocene' Colombian copal. PLoS One 2013; 8:e73150. [PMID: 24039876 PMCID: PMC3770633 DOI: 10.1371/journal.pone.0073150] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in ‘Anthropocene’ Colombian copal, dated to ‘post-Bomb’ and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.
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Affiliation(s)
- David Penney
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
| | - Caroline Wadsworth
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Graeme Fox
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Sandra L. Kennedy
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Richard F. Preziosi
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Terence A. Brown
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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17
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Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci 2012; 279:4724-33. [PMID: 23055061 PMCID: PMC3497090 DOI: 10.1098/rspb.2012.1745] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/14/2012] [Indexed: 12/26/2022] Open
Abstract
Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10(-6) per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R(2) = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
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Affiliation(s)
- Morten E. Allentoft
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Matthew Collins
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - David Harker
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - James Haile
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
| | - Charlotte L. Oskam
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
| | - Marie L. Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Paula F. Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
- Museu da Ciência, University of Coimbra, Laboratorio Chimico, Largo Marquês de Pombal, 3000-272 Coimbra, Portugal
| | - Jose A. Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - M. Thomas P. Gilbert
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Guojie Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, People's Republic of China
| | - R. Paul Scofield
- Canterbury Museum, Rolleston Avenue, Christchurch 8050, New Zealand
| | - Richard N. Holdaway
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Palaecol Research Ltd, 167 Springs Road, Hornby, Christchurch 8042, New Zealand
| | - Michael Bunce
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
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Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons. Methods Mol Biol 2012; 830:283-99. [PMID: 22139668 DOI: 10.1007/978-1-61779-461-2_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons' identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.
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Brushkov AV, Bezrukov VV, Griva GI, Muradyan KK. The effects of the relict microorganism B. sp. on development, gas exchange, spontaneous motor activity, stress resistance, and survival of Drosophila melanogaster. ADVANCES IN GERONTOLOGY 2012. [DOI: 10.1134/s2079057012010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
Museum and archival collections of parasites are available throughout the world but, although they represent a huge diversity of species and forms, they tend to be used solely for reference to morphology, if at all. As biochemical techniques begin to overcome the problems associated with ancient, degraded and formalin-fixed tissues, the value of such collections increases. Molecular data are now available for rare, elusive and extinct species, as well as those densely sampled for epidemiological, biogeographical or clinical collections. Here, Elisabeth Herniou, Auriol Pearce and Tim Littlewood describe some of the advances and pitfalls associated with retrieving DNA from formalin-fixed helminth material and suggest just some of the new ways that parasitologists can tap into these resources.
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Affiliation(s)
- E A Herniou
- The Natural History Museum, Department of Zoology, Cromwell Road, London, UK SW7 5BD
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Timmann C, Meyer CG. Malaria, mummies, mutations: Tutankhamun's archaeological autopsy. Trop Med Int Health 2010; 15:1278-80. [PMID: 20723182 DOI: 10.1111/j.1365-3156.2010.02614.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The cause of death of the Egyptian pharoah Tutankhamun has now for decades been matter of speculation and various hypotheses. A recent article in the Journal of the American Medical Association (JAMA) provided new evidence and suggested malaria, together with Köhler’s disease, as the most probable cause of death of the boy king. We are sceptical towards this elucidation of the cause of death of King Tut and discuss alternative and differential diagnoses, among them, in particular, sickle cell disease and Gauche’s disease.
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Affiliation(s)
- Christian Timmann
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Strasse 74, Hamburg, Germany
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22
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Ho SYW, Gilbert MTP. Ancient mitogenomics. Mitochondrion 2009; 10:1-11. [PMID: 19788938 DOI: 10.1016/j.mito.2009.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 09/21/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.
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Affiliation(s)
- Simon Y W Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra ACT 0200, Australia.
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Xu Z, Zhang F, Xu B, Tan J, Li S, Jin L. Improving the sensitivity of negative controls in ancient DNA extractions. Electrophoresis 2009; 30:1282-5. [PMID: 19294688 DOI: 10.1002/elps.200800473] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Much attention has been paid on ancient DNA (aDNA) studies, and negative control was used as one of the stringent quality assurance criteria in order to detect potential contamination. However, the results of some aDNA studies showed the evidence of contamination despite their negative controls failed to do so. Using lambda DNA to mock extraneous contaminating DNA, our study showed that aDNA had a property of improving the efficiency of extraction including contaminating DNA, while negative controls had low sensitivity to detect contamination. To circumvent this problem, carrier DNA such as poly(dA) is suggested to be introduced into aDNA extraction.
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Affiliation(s)
- Zhi Xu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, PR China
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24
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PCR-based methodology for the authentication of grouper (Epinephelus marginatus) in commercial fish fillets. Food Control 2009. [DOI: 10.1016/j.foodcont.2008.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Valdiosera C, García N, Dalén L, Smith C, Kahlke RD, Lidén K, Angerbjörn A, Arsuaga JL, Götherström A. Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA. Biol Lett 2008; 2:601-3. [PMID: 17148299 PMCID: PMC1833985 DOI: 10.1098/rsbl.2006.0515] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, we have used a technique designed to target short fragments containing informative mitochondrial substitutions to extend the temporal limits of DNA recovery and study the molecular phylogeny of Ursus deningeri. We present a cladistic analysis using DNA recovered from 400 kyr old U. deningeri remains, which demonstrates U. deningeri's relation to Ursus spelaeus. This study extends the limits of recovery from skeletal remains by almost 300 kyr. Plant material from permafrost environments has yielded DNA of this age in earlier studies, and our data suggest that DNA in teeth from cave environments may be equally well preserved.
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Affiliation(s)
- Cristina Valdiosera
- Centro UCM-ISCIII de Evolución y Comportamiento Humanos, C/Sinesio Delgado 4, 28029 Madrid, Spain.
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Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM. New developments in ancient genomics. Trends Ecol Evol 2008; 23:386-93. [PMID: 18501471 DOI: 10.1016/j.tree.2008.04.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 03/27/2008] [Accepted: 04/04/2008] [Indexed: 11/29/2022]
Abstract
Ancient DNA research is on the crest of a 'third wave' of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.
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Affiliation(s)
- Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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27
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Martín-González A, Wierzchos J, Gutiérrez JC, Alonso J, Ascaso C. Morphological Stasis of Protists in Lower Cretaceous Amber. Protist 2008; 159:251-7. [DOI: 10.1016/j.protis.2007.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 08/05/2007] [Indexed: 01/26/2023]
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Gewin V. Amber collectors hit on oldest mushroom find. Nature 2007. [DOI: 10.1038/news070611-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.
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Affiliation(s)
- Régis Debruyne
- Muséum National d'Histoire Naturelle, Département Histoire de la Terre, UMR 5143 CNRS, Paléobiodiversité, 57, rue Cuvier, 75231 Paris Cedex 05, France
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Dahms HU, Ying X, Pfeiffer C. Antifouling potential of cyanobacteria: a mini-review. BIOFOULING 2006; 22:317-27. [PMID: 17110355 DOI: 10.1080/08927010600967261] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cyanobacteria produce a variety of bioactive metabolites that may have allelochemical functions in the natural environment, such as in the prevention of fouling by colonising organisms. Chemical compounds from cyanobacteria are also of biotechnological interest, especially for clinical applications, because of their antibiotic, algicidal, cytotoxic, immunosupressive and enzyme inhibiting activities. Cyanobacterial metabolites have the potential for use in antifouling technology, since they show antibacterial, antialgal, antifungal and antimacrofouling properties which could be expoited in the prevention of biofouling on man-made substrata in the aquatic environment. Molecules with antifouling activity represent a number of types including fatty acids, lipopeptides, amides, alkaloids, terpenoids, lactones, pyrroles and steroids. The isolation of biogenic compounds and the determination of their structure may provide leads for future development of, for example, environmentally friendly antifouling paints. An advantage of exploring the efficacy of cyanobacterial products is that the organisms can be grown in mass culture, which can be manipulated to achieve optimal production of bioactive substances. Phycotoxins and related products from cyanobacteria may serve as materials for antimicro- and antimacrofouling applications. A survey of antibiotic compounds with antifouling potential revealed more than 21 different antifouling substances from 27 strains of cyanobacteria.
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Affiliation(s)
- Hans-Uwe Dahms
- Department of Biology, Hong Kong University of Science & Technology, Kowloon, Hong Kong.
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34
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Mulligan CJ. Isolation and analysis of DNA from archaeological, clinical, and natural history specimens. Methods Enzymol 2005; 395:87-103. [PMID: 15865963 DOI: 10.1016/s0076-6879(05)95007-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. Novel methods exist for the isolation, purification, and analysis of aDNA because these DNA templates are likely to be damaged, fragmented and?or associated with non-nucleic acid material. However, contamination of ancient specimens and DNA extracts with modern DNA is more widespread than is generally acknowledged and remains a significant problem in aDNA analysis. Studies of human aDNA are uniquely sensitive to contamination due to the continual presence of potential contamination sources. Meticulous authentication of results and careful selection of polymorphic markers capable of distinguishing between aDNA and probable DNA contaminants are critical to a successful aDNA study.
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Affiliation(s)
- Connie J Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida 32611, USA
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Pruvost M, Grange T, Geigl EM. Minimizing DNA contamination by using UNG-coupled quantitative real-time PCR on degraded DNA samples: application to ancient DNA studies. Biotechniques 2005; 38:569-75. [PMID: 15884675 DOI: 10.2144/05384st03] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PCR analyses of ancient and degraded DNA suffer from their extreme sensitivity to contamination by modern DNA originating, in particular, from carryover contamination with previously amplified or cloned material. Any strategy for limiting carryover contamination would also have to be compatible with the particular requirements of ancient DNA analyses. These include the need (i) to amplify short PCR products due to template fragmentation; (ii) to clone PCR products in order to track possible base misincorporation resulting from damaged templates; and (iii) to avoid incomplete decontamination causing artifactual sequence transformation. Here we show that the enzymatic decontamination procedures based upon dUTP- and uracil-N-glycosylase (UNG) can be adapted to meet the specific requirements of ancient DNA research. Thus, efficiency can be improved to vastly reduce the amplification of fragments < or = 100 bp. Secondly, the use of an Escherichia coli strain deficient in both UNG and dUTPase allows for the cloning of uracil-containing PCR products and offers protection from plasmid DNA contamination, and, lastly, PCR products amplified from UNG-degraded material are free of misleading sequence modifications.
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Abstract
Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.
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Affiliation(s)
- Martin B Hebsgaard
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK OX1 3PS
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37
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Abstract
In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.
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Suwimonteerabutr J, Chaicumpa W, Saengjaruk P, Tapchaisri P, Chongsa-nguan M, Kalambaheti T, Ramasoota P, Sakolvaree Y, Virakul P. Evaluation of a monoclonal antibody-based dot-blot ELISA for detection of Leptospira spp in bovine urine samples. Am J Vet Res 2005; 66:762-6. [PMID: 15934602 DOI: 10.2460/ajvr.2005.66.762] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To evaluate the efficacy of a novel monoclonal antibody (MAb)-based dot-blot ELISA for detection of Leptospira antigens in urine samples of cattle. SAMPLE POPULATION Blood and urine samples of 45 test cattle from 5 farms in Chonburi province and 20 control cattle from 2 farms in Khon Kaen province in Thailand. PROCEDURE Blood and urine samples were assayed (microscopic agglutination test and urine antigen test) for Leptospira infection by use of an MAb-based dot-blot ELISA, and results for the ELISA were compared with those for dark-field microscopy (DFM), microbial culture, and a polymerase chain reaction (PCR) assay. RESULTS All urine samples with positive results for DFM, microbial culture, PCR assay, or > 1 of these tests also had positive results when tested by use of the MAb-based dot-blot ELISA, except for 1 sample that had positive results only for the PCR assay. Detection limits of the dot-blot ELISA were 10(3) leptospires/mL of urine and 9.3 ng of Leptospira homogenate. Comparison revealed that the diagnostic sensitivity, specificity, efficacy (accuracy), positive predictive value, and negative predictive value for the ELISA were in agreement with results for DFM (100%, 72.72%, 80%, 57.14%, and 100%, respectively), microbial culture (100%, 61.54%, 66.62%, 28.57%, and 100%, respectively), and PCR assay (95.45%, 100%, 91.77%, 100%, and 95.83%, respectively). CONCLUSIONS AND CLINICAL RELEVANCE The MAb-based dot-blot ELISA is suitable as a tool for detecting leptospires in urine samples of cattle.
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Affiliation(s)
- Junpen Suwimonteerabutr
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Inagaki F, Okada H, Tsapin AI, Nealson KH. Microbial survival: the paleome: a sedimentary genetic record of past microbial communities. ASTROBIOLOGY 2005; 5:141-153. [PMID: 15815165 DOI: 10.1089/ast.2005.5.141] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular genetic methods were used to analyze the remnants of microbial ecosystems contained within an ancient oceanic microbial habitat that was recovered from a continental drilled core of black shale approximately 100 million years in age. Bacterial ribosomal RNA genes were vertically amplified from the six different depths of a black shale core associated with a phosphate-rich stratum, defined as one of the mid-Cretaceous oceanic anoxic events (OAEs). Although the black shale core was recovered from a terrestrial coring effort, the recovered 16S rRNA gene sequences showed affinity to microbial communities previously seen in deep-sea sedimentary environments (i.e., the microbial assemblage was easily recognizable as a marine community). In particular, a number of 16S rRNA gene clones of oceanic sulfate-reducing bacteria within the delta-Proteobacteria predominated at the OAE layer. The recovered bacterial DNA signatures are consistent with the interpretation that the sequences are derived from the past microbial communities buried in either sea-bottom or subseafloor environments during the sedimentation process and, after ceasing growth, preserved until the present.
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Affiliation(s)
- Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Project, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic Analyses from Ancient DNA. Annu Rev Genet 2004; 38:645-79. [PMID: 15568989 DOI: 10.1146/annurev.genet.37.110801.143214] [Citation(s) in RCA: 654] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.
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Affiliation(s)
- Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, D-04013 Leipzig, Germany.
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Kim S, Soltis DE, Soltis PS, Suh Y. DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae). AMERICAN JOURNAL OF BOTANY 2004; 91:615-620. [PMID: 21653417 DOI: 10.3732/ajb.91.4.615] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We report a partial ndhF sequence (1528 bp) of Magnolia latahensis and a partial rbcL sequence (699 bp) of Persea pseudocarolinensis from the Clarkia fossil beds of Idaho, USA (Miocene; 17-20 million years [my] BP). The ndhF sequence from M. latahensis was identical to those of extant M. grandiflora, M. schiediana, M. guatemalensis, and M. tamaulipana. Parsimony analysis of the ndhF sequence of M. latahensis and previously reported ndhF sequences for Magnoliaceae placed M. latahensis within Magnolia as a member of the Theorhodon clade. This result is reasonable considering that: (1) the morphology of M. latahensis is very similar to that of extant M. grandiflora, and (2) a recent molecular phylogenetic study of Magnoliaceae showed that the maximum sequence divergence of ndhF among extant species is very low (1.05% in subfamily Magnolioideae) compared with other angiosperm families. We reanalyzed the previously reported rbcL sequence of M. latahensis with sequences for all major lineages of extant Magnoliales and Laurales. This sequence is sister to Liriodendron, rather than grouped with a close relative of M. grandiflora as predicted by morphology and the results of the ndhF analysis, possibly due to a few erroneous base calls in the sequences. The rbcL sequence of P. pseudocarolinensis differed from rbcL of extant Persea species by 3-6 nucleotides and from rbcL of extant Sassafras albidum by two nucleotides. Phylogenetic analyses of rbcL sequences for all major lineages of Magnoliales and Laurales placed the fossil P. pseudocarolinensis within Lauraceae and as sister to S. albidum. These results reinforce the suggestion that Clarkia and other similar sites hold untapped potential for molecular analysis of fossils.
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Affiliation(s)
- Sangtae Kim
- Department of Botany, University of Florida, Gainesville, Florida 32611 USA
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Baker GC, Tow LA, Cowan DA. PCR-based detection of non-indigenous microorganisms in 'pristine' environments. J Microbiol Methods 2003; 53:157-64. [PMID: 12654487 DOI: 10.1016/s0167-7012(03)00021-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in 'pristine' environments. For 'pristine' environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions.
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Affiliation(s)
- Gillian C Baker
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, South Africa.
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Capelli C, Tschentscher F, Pascali VL. "Ancient" protocols for the crime scene? Similarities and differences between forensic genetics and ancient DNA analysis. Forensic Sci Int 2003; 131:59-64. [PMID: 12505472 DOI: 10.1016/s0379-0738(02)00396-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide a short overview on some current issues in the fields of forensic genetics and ancient DNA (aDNA) analysis. We discuss about the existence of the possible points of contact between the two disciplines, in terms of open problems and the inherent approach to their solution. We mainly focus on the problem of results authentication, its theoretical and technical aspects.
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Affiliation(s)
- C Capelli
- Immunohematology Laboratory, Department of Forensic Medicine, Catholic University, Largo F. Vito, 1 00168 Rome, Italy.
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Goldstein DB, Chikhi L. Human migrations and population structure: what we know and why it matters. Annu Rev Genomics Hum Genet 2002; 3:129-52. [PMID: 12142358 DOI: 10.1146/annurev.genom.3.022502.103200] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The increasingly obvious medical relevance of human genetic variation is fueling the development of a rich interface between medical genetics and the study of human genetic history. A key feature of this interface is a step increase in the size and diversity of genetic data sets, permitting a range of new questions to be addressed concerning our evolutionary history. Similarly, methodologies first developed to study genetic history are being tailored to address medical challenges, including mapping genes that influence diseases and variable drug reactions. In this paper we do not attempt a comprehensive review of human genetic history. Rather we briefly outline some of the complications and challenges in the study of human genetic history, drawing particular attention to new opportunities created by the explosive growth in genetic information and technologies. First we discuss the complexity of human migration and demographic history, taking both a genetic and archaeological perspective. Then we show how these apparently academic issues are becoming increasingly important in medical genetics, focusing on association studies, the common disease/common variant hypothesis, the evaluation of variable drug response, and inferences about gene function from patterns of genetic variation. Finally we describe some of the inferential approaches available for interpreting human genetic variation, focusing both on current limitations and future developments.
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Affiliation(s)
- David B Goldstein
- Department of Biology, University College London, Darwin Building, London WC1E 6BT, United Kingdom.
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Eigenheer AL, Young S, Blomquist GJ, Borgeson CE, Tillman JA, Tittiger C. Isolation and molecular characterization of Musca domestica delta-9 desaturase sequences. INSECT MOLECULAR BIOLOGY 2002; 11:533-542. [PMID: 12421411 DOI: 10.1046/j.1365-2583.2002.00362.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We have isolated fatty acyl-CoA desaturase cDNA (Mdomd9) and genomic sequences from the housefly, Musca domestica. Two approximately 1.66 kb cDNAs were recovered. They had identical coding regions and 3' untranslated regions (UTRs), but differed in their 5' UTRs. The open reading frame encodes a 380 amino acid (aa) protein with 82% identity to Drosophila melanogaster desat1, and significant (> 50%) identity with other insect delta-9 desaturases. Functional analyses in a yeast expression system confirmed the cDNA encodes a delta9 desaturase. Northern analysis indicated two transcripts of 1.7 and 2.9 kb that hybridized specifically to the open reading frame. PCR amplification of genomic templates revealed three intron sites that are conserved among other insect species. Southern analysis of genomic DNA indicated at least two desaturase gene copies per haploid genome. There is a high degree of polymorphism, most of which appears to be due to variable intron sequences; curiously, individual flies had varying morphs of intron II and intron III. Together, the data suggest that there are more delta9 desaturase alleles within the population studied than there are loci within the genome, and support other studies suggesting that insect fatty acyl-CoA desaturases are a dynamically evolving gene family.
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Affiliation(s)
- A L Eigenheer
- Department of Biochemistry, University of Nevada, Reno, NV 89557, USA
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Limburg PA, Weider LJ. 'Ancient' DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database. Proc Biol Sci 2002; 269:281-7. [PMID: 11839197 PMCID: PMC1690889 DOI: 10.1098/rspb.2001.1868] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent work on the diapausing egg banks of zooplankton, such as Daphnia (Crustacea: Anomopoda), indicates that these eggs can remain viable for decades while, theoretically, DNA can remain intact for even longer periods (i.e. centuries or millennia). We isolated diapausing eggs of Daphnia from a 30 m long sediment core taken from a hypereutrophic, northern German lake (Belauer See), with some eggs found in dated core material as old as 4500 years. Using microsatellite markers, we analysed the genetic structure of the resting eggs dated as old as ca. 200 years, and found that, although levels of heterozygosity remained remarkably stable, significant genetic differentiation (Nei's D = 0.36; F(ST) = 0.15) between recent and 'ancient' resting eggs (including allele frequency shifts and private alleles) was detected. These shifts represent either species-level changes in this complex (i.e. species-specific characters of ephippia are not always robust), or intraspecific shifts in genetic variation, or a combination of both. This study demonstrates that the egg banks of aquatic zooplankton can serve as repositories of both genetic (intrapopulational) and ecological (interspecific) information. The use of molecular markers, such as microsatellites, on diapausing egg/seed banks may open new avenues of enquiry related to tracking the long-term genetic (and/or species) shifts that are associated with long-term environmental changes.
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Affiliation(s)
- Petra A Limburg
- Max Planck Institute for Limnology, August-Thienemann-Strasse 2, 24306 Plön, Germany
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Asensio L, González I, Fernández A, Rodríguez MA, Lobo E, Hernández PE, García T, Martín R. Application of random amplified polymorphic DNA (RAPD) analysis for identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets. J Food Prot 2002; 65:432-5. [PMID: 11848581 DOI: 10.4315/0362-028x-65.2.432] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A random amplified polymorphic DNA (RAPD) method was developed for the specific identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets. Using two different reaction primers (S1 and L1), RAPD analysis produced clear fingerprints from which the three fish species could be easily identified. This approach is rapid and reliable and offers the potential to detect fraudulent or unintentional mislabeling of these species in routine seafood authentication analysis.
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Affiliation(s)
- Luis Asensio
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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Blatter RH, Jacomet S, Schlumbaum A. Little Evidence for the Preservation of a Single-Copy Gene in Charred Archaeological Wheat. ACTA ACUST UNITED AC 2002. [DOI: 10.1080/1358612021000010677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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