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  • 1
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    Ancient DNA: do it right or not at all (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-09-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, A -- Poinar, H N -- New York, N.Y. -- Science. 2000 Aug 18;289(5482):1139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10970224" target="_blank"〉PubMed〈/a〉
    Keywords: Cloning, Molecular ; *Dna ; DNA Primers ; *Fossils ; Humans ; Polymerase Chain Reaction/*standards ; Publishing ; Reproducibility of Results ; Research/*standards
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Preservation of DNA from endangered species (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poinar, H N -- Eglinton, G -- New York, N.Y. -- Science. 2000 Aug 4;289(5480):726; author reply 726-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10950715" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Specimen Banks ; *Conservation of Natural Resources ; *Dna ; Specimen Handling
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Ancient biomolecules from deep ice cores reveal a forested southern Greenland (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-07
    Description: It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694912/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694912/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Willerslev, Eske -- Cappellini, Enrico -- Boomsma, Wouter -- Nielsen, Rasmus -- Hebsgaard, Martin B -- Brand, Tina B -- Hofreiter, Michael -- Bunce, Michael -- Poinar, Hendrik N -- Dahl-Jensen, Dorthe -- Johnsen, Sigfus -- Steffensen, Jorgen Peder -- Bennike, Ole -- Schwenninger, Jean-Luc -- Nathan, Roger -- Armitage, Simon -- de Hoog, Cees-Jan -- Alfimov, Vasily -- Christl, Marcus -- Beer, Juerg -- Muscheler, Raimund -- Barker, Joel -- Sharp, Martin -- Penkman, Kirsty E H -- Haile, James -- Taberlet, Pierre -- Gilbert, M Thomas P -- Casoli, Antonella -- Campani, Elisa -- Collins, Matthew J -- 076905/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2007 Jul 6;317(5834):111-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ancient Genetics, University of Copenhagen, Denmark. ewillerslev@bi.ku.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17615355" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/*analysis/history/isolation & purification ; Animals ; Bayes Theorem ; Climate ; DNA/*analysis/history/isolation & purification ; *Ecosystem ; Fossils ; Geography ; Greenland ; History, Ancient ; Ice Cover/*chemistry ; *Invertebrates/classification/genetics ; *Plants/classification/genetics ; Polymerase Chain Reaction ; Time ; *Trees
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Neandertal genetics (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-08-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, A -- Poinar, H N -- Paabo, S -- Radovcic, J -- Debenath, A -- Caparros, M -- Barroso-Ruiz, C -- Bertranpetit, J -- Nielsen-Marsh, C -- Hedges, R E -- Sykes, B -- New York, N.Y. -- Science. 1997 Aug 22;277(5329):1021-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9289843" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA Primers ; DNA, Mitochondrial/*genetics ; Europe ; Haplotypes ; Hominidae/*genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-17
    Description: DNA from excrements can be amplified by means of the polymerase chain reaction. However, this has not been possible with ancient feces. Cross-links between reducing sugars and amino groups were shown to exist in a Pleistocene coprolite from Gypsum Cave, Nevada. A chemical agent, N-phenacylthiazolium bromide, that cleaves such cross-links made it possible to amplify DNA sequences. Analyses of these DNA sequences showed that the coprolite is derived from an extinct sloth, presumably the Shasta ground sloth Nothrotheriops shastensis. Plant DNA sequences from seven groups of plants were identified in the coprolite. The plant assemblage that formed part of the sloth's diet exists today at elevations about 800 meters higher than the cave.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poinar, H N -- Hofreiter, M -- Spaulding, W G -- Martin, P S -- Stankiewicz, B A -- Bland, H -- Evershed, R P -- Possnert, G -- Paabo, S -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):402-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Evolutionary Anthropology and Zoological Institute, University of Munich, Luisenstrasse 14, D-80333 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665881" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cloning, Molecular ; DNA, Mitochondrial/chemistry/*isolation & purification ; DNA, Plant/chemistry/*isolation & purification ; DNA, Ribosomal/chemistry/*isolation & purification ; *Diet ; Feces/*chemistry ; *Fossils ; Maillard Reaction ; Molecular Sequence Data ; Plants/classification/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; *Sloths/genetics ; Thiazoles
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    A draft genome of Yersinia pestis from victims of the Black Death (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-14
    Description: Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690193/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690193/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bos, Kirsten I -- Schuenemann, Verena J -- Golding, G Brian -- Burbano, Hernan A -- Waglechner, Nicholas -- Coombes, Brian K -- McPhee, Joseph B -- DeWitte, Sharon N -- Meyer, Matthias -- Schmedes, Sarah -- Wood, James -- Earn, David J D -- Herring, D Ann -- Bauer, Peter -- Poinar, Hendrik N -- Krause, Johannes -- R24 HD044943/HD/NICHD NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Oct 12;478(7370):506-10. doi: 10.1038/nature10549.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993626" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Bacterial/genetics ; Contig Mapping ; Dental Pulp/microbiology ; Evolution, Molecular ; Genome, Bacterial/*genetics ; History, Medieval ; Humans ; London/epidemiology ; Molecular Sequence Data ; Phylogeny ; Plague/epidemiology/*microbiology/transmission ; Plasmids/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Virulence/genetics ; Yersinia pestis/classification/*genetics/*isolation & purification
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Antibiotic resistance is ancient (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-09-02
    Description: The discovery of antibiotics more than 70 years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to beta-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Costa, Vanessa M -- King, Christine E -- Kalan, Lindsay -- Morar, Mariya -- Sung, Wilson W L -- Schwarz, Carsten -- Froese, Duane -- Zazula, Grant -- Calmels, Fabrice -- Debruyne, Regis -- Golding, G Brian -- Poinar, Hendrik N -- Wright, Gerard D -- MOP-79488/Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Aug 31;477(7365):457-61. doi: 10.1038/nature10388.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21881561" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/enzymology/genetics ; Bayes Theorem ; Crystallography, X-Ray ; DNA, Chloroplast/genetics ; Freezing ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/genetics ; Genes, Plant/genetics ; Geologic Sediments/microbiology ; History, Ancient ; Hydrogen Bonding ; *Metagenomics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Siberia ; Vancomycin Resistance/drug effects/*genetics ; Vertebrates/genetics ; beta-Lactamases/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-22
    Description: We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poinar, Hendrik N -- Schwarz, Carsten -- Qi, Ji -- Shapiro, Beth -- Macphee, Ross D E -- Buigues, Bernard -- Tikhonov, Alexei -- Huson, Daniel H -- Tomsho, Lynn P -- Auch, Alexander -- Rampp, Markus -- Miller, Webb -- Schuster, Stephan C -- HG02238/HG/NHGRI NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2006 Jan 20;311(5759):392-4. Epub 2005 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada. poinarh@mcmaster.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16368896" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Computational Biology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Dogs/genetics ; Elephants/*genetics ; *Fossils ; Gene Library ; Genome ; *Genomics ; Humans ; Mandible/*chemistry ; *Paleontology ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Siberia
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Amino acid racemization and the preservation of ancient DNA (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-05-10
    Description: The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poinar, H N -- Hoss, M -- Bada, J L -- Paabo, S -- New York, N.Y. -- Science. 1996 May 10;272(5263):864-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8629020" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/chemistry ; *Amber/chemistry ; Amino Acids/*chemistry ; Animals ; Aspartic Acid/chemistry ; DNA/*analysis/chemistry ; *Fossils ; History, Ancient ; Humans ; Leucine/chemistry ; *Paleontology ; Stereoisomerism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Protein preservation and DNA retrieval from ancient tissues (1999)
    National Academy of Sciences
    Details
    Publication Date: 1999-07-20
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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