Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague
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{"title"=>"Yersinia pestis DNA from Skeletal Remains from the 6thCentury AD Reveals Insights into Justinianic Plague", "type"=>"journal", "authors"=>[{"first_name"=>"Michaela", "last_name"=>"Harbeck", "scopus_author_id"=>"6602787426"}, {"first_name"=>"Lisa", "last_name"=>"Seifert", "scopus_author_id"=>"55754977200"}, {"first_name"=>"Stephanie", "last_name"=>"Hänsch", "scopus_author_id"=>"55389563000"}, {"first_name"=>"David M.", "last_name"=>"Wagner", "scopus_author_id"=>"7401982601"}, {"first_name"=>"Dawn", "last_name"=>"Birdsell", "scopus_author_id"=>"26530764900"}, {"first_name"=>"Katy L.", "last_name"=>"Parise", "scopus_author_id"=>"56003005700"}, {"first_name"=>"Ingrid", "last_name"=>"Wiechmann", "scopus_author_id"=>"6602663653"}, {"first_name"=>"Gisela", "last_name"=>"Grupe", "scopus_author_id"=>"7003537958"}, {"first_name"=>"Astrid", "last_name"=>"Thomas", "scopus_author_id"=>"35390067300"}, {"first_name"=>"Paul", "last_name"=>"Keim", "scopus_author_id"=>"7007034048"}, {"first_name"=>"Lothar", "last_name"=>"Zöller", "scopus_author_id"=>"7007064195"}, {"first_name"=>"Barbara", "last_name"=>"Bramanti", "scopus_author_id"=>"6602574670"}, {"first_name"=>"Julia M.", "last_name"=>"Riehm", "scopus_author_id"=>"35488808200"}, {"first_name"=>"Holger C.", "last_name"=>"Scholz", "scopus_author_id"=>"7202371399"}], "year"=>2013, "source"=>"PLoS Pathogens", "identifiers"=>{"pui"=>"369039720", "sgr"=>"84878478933", "pmid"=>"23658525", "scopus"=>"2-s2.0-84878478933", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "doi"=>"10.1371/journal.ppat.1003349", "issn"=>"15537366"}, "id"=>"674a1747-61f1-3240-84e9-377f00c162cd", "abstract"=>"Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.", "link"=>"http://www.mendeley.com/research/yersinia-pestis-dna-skeletal-remains-6thcentury-ad-reveals-insights-justinianic-plague", "reader_count"=>146, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>28, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>40, "Student > Postgraduate"=>7, "Student > Master"=>14, "Other"=>4, "Student > Bachelor"=>24, "Lecturer"=>3, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>28, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>40, "Student > Postgraduate"=>7, "Student > Master"=>14, "Other"=>4, "Student > Bachelor"=>24, "Lecturer"=>3, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>10, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>20, "Medicine and Dentistry"=>10, "Agricultural and Biological Sciences"=>71, "Arts and Humanities"=>13, "Design"=>1, "Social Sciences"=>8, "Computer Science"=>1, "Immunology and Microbiology"=>5, "Earth and Planetary Sciences"=>3, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>10}, "Social Sciences"=>{"Social Sciences"=>8}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>71}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>20}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>3}, "Arts and Humanities"=>{"Arts and Humanities"=>13}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>5, "Norway"=>1, "Guatemala"=>1, "United Kingdom"=>4, "Madagascar"=>1, "Australia"=>1, "Germany"=>2, "Spain"=>2}, "group_count"=>3}

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  • {"files"=>["https://ndownloader.figshare.com/files/1051898"], "description"=>"<p>This global phylogeny for <i>Y. pestis</i> is based upon <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat-1003349-g001\" target=\"_blank\">figures 1A</a> and S3B in Cui et al. <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Cui1\" target=\"_blank\">[11]</a>. It includes four major branches (0–4) and is rooted with <i>Y. pseudotuberculosis</i>, the ancestor of <i>Y. pestis </i><a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Achtman3\" target=\"_blank\">[28]</a>. The identities of many of the major nodes defined by Cui et al. <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Cui1\" target=\"_blank\">[11]</a> are presented in blue text. Circles represent specific populations; populations highlighted in gray have, to date, only been found in Asia <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Morelli1\" target=\"_blank\">[10]</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Cui1\" target=\"_blank\">[11]</a>. Note that the location where strain Angola was isolated, which is the sole representative of population 0.PE3, is unknown. The phylogenetic position of Mongolian strain MNG 2972 is indicated with the blue box (see text). Five previously identified <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Morelli1\" target=\"_blank\">[10]</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Cui1\" target=\"_blank\">[11]</a> key SNPs were utilized in the current study: s545, which occurs along the branch between nodes N06 and N07 (not shown); s87 and s89; which occur along the branch between N04 and N05; s82, which occurs along the branch between the branching point of strain MNG 2972 and N04; and s463, which occurs along the branch between the branching point of strain MNG 2972 and N03. It is known that these SNPs occur along these specific branches but the exact position and order of these SNPs along each branch is unknown. Sample A120 possesses ancestral states for SNPs s87, s89, and s545; and derived states for SNPs s82 and s463. Thus, the position of sample A120 in this phylogeny is along the branch between the branching point of strain MNG 2972 and N04, along branch N04-N05, along the branch from N04 to 0.ANT1 (red branches), or along one of the sub-branches within 0.ANT.1 (not shown). The phylogenetic positions of strains from the second pandemic <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Bos1\" target=\"_blank\">[3]</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Haensch1\" target=\"_blank\">[12]</a> are indicated with the yellow boxes according to Cui et al. <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Cui1\" target=\"_blank\">[11]</a>. The basal node for the 1.ORI group, which caused the third pandemic, is N14 <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Cui1\" target=\"_blank\">[11]</a>.</p>", "links"=>[], "tags"=>["genetics", "microbiology", "anthropology", "Biological anthropology", "phylogeny"], "article_id"=>696474, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Michaela Harbeck", "Lisa Seifert", "Stephanie Hänsch", "David M. Wagner", "Dawn Birdsell", "Katy L. Parise", "Ingrid Wiechmann", "Gisela Grupe", "Astrid Thomas", "Paul Keim", "Lothar Zöller", "Barbara Bramanti", "Julia M. Riehm", "Holger C. Scholz"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1003349.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_phylogeny_for_Y_pestis_/696474", "title"=>"Global phylogeny for <i>Y.</i><i>pestis</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-02 01:47:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1051899"], "description"=>"<p>DNA sequences longer than 50 nt are deposited in GenBank (accession numbers are given), SNP positions are indicated by bold letters and a dot in the bottom line. The Y in s82 indicates that either a C or a T was observed at this position, a common artifact attributable to DNA degradation <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-Paabo1\" target=\"_blank\">[23]</a>, whereas lower case letters indicate poor quality nucleotides.</p>", "links"=>[], "tags"=>["genetics", "microbiology", "anthropology", "Biological anthropology", "alignment", "amplified", "sequences"], "article_id"=>696475, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Michaela Harbeck", "Lisa Seifert", "Stephanie Hänsch", "David M. Wagner", "Dawn Birdsell", "Katy L. Parise", "Ingrid Wiechmann", "Gisela Grupe", "Astrid Thomas", "Paul Keim", "Lothar Zöller", "Barbara Bramanti", "Julia M. Riehm", "Holger C. Scholz"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1003349.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Partial_Munich_and_total_Mainz_alignment_of_amplified_consensus_sequences_regarding_several_SNPs_/696475", "title"=>"Partial (Munich) and total (Mainz) alignment of amplified consensus sequences regarding several SNPs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-02 01:47:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1051900"], "description"=>"<p>Abbreviations: anc: ancestral, der: derived, pos: positive, <i>pla</i>: plasminogen activator gene, -: not tested, neg: no amplicon.</p>", "links"=>[], "tags"=>["genetics", "microbiology", "anthropology", "Biological anthropology", "molecular", "assays", "carried", "samples", "a120", "adna"], "article_id"=>696476, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Michaela Harbeck", "Lisa Seifert", "Stephanie Hänsch", "David M. Wagner", "Dawn Birdsell", "Katy L. Parise", "Ingrid Wiechmann", "Gisela Grupe", "Astrid Thomas", "Paul Keim", "Lothar Zöller", "Barbara Bramanti", "Julia M. Riehm", "Holger C. Scholz"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1003349.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_molecular_assays_carried_out_on_samples_from_individual_A120_in_two_independent_aDNA_laboratories_/696476", "title"=>"Results of molecular assays carried out on samples from individual A120 in two independent aDNA laboratories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-02 01:47:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1051901"], "description"=>"1<p>estimated age by archaeological evidence <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003349#ppat.1003349-GutsmiedlSchmann1\" target=\"_blank\">[20]</a> for the multiple burial,</p>2<p>estimated age by radiocarbon dating determined for the particular individual (cal 2 sigma),</p>3<p>neg = no amplicon, pos = amplification results, - = not tested.</p>", "links"=>[], "tags"=>["genetics", "microbiology", "anthropology", "Biological anthropology", "medieval", "aschheim-bajuwarenring", "corresponding", "activator"], "article_id"=>696477, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Michaela Harbeck", "Lisa Seifert", "Stephanie Hänsch", "David M. Wagner", "Dawn Birdsell", "Katy L. Parise", "Ingrid Wiechmann", "Gisela Grupe", "Astrid Thomas", "Paul Keim", "Lothar Zöller", "Barbara Bramanti", "Julia M. Riehm", "Holger C. Scholz"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1003349.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Individuals_from_the_Early_Medieval_Cemetery_Aschheim_Bajuwarenring_Germany_that_were_analyzed_in_this_study_and_corresponding_results_of_screening_for_a_portion_of_the_Y_pestis_specific_plasminogen_activator_gene_pla_/696477", "title"=>"Individuals from the Early Medieval Cemetery Aschheim-Bajuwarenring (Germany) that were analyzed in this study and corresponding results of screening for a portion of the <i>Y. pestis</i> specific <i>plasminogen activator gene</i> (<i>pla</i>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-02 01:47:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1051902"], "description"=>"1<p>To minimize the size of PCR amplicons and maximize specificity, we utilized short locked nucleic acid (LNA) probes in our assay. These probes are modified TaqMan probes that were developed by Exiqon (Vedbaek, Denmark) and can be used when high affinity probes as specific as possible are required. The “+” in the sequence of the probe indicates the positions of the LNA labeling.</p>", "links"=>[], "tags"=>["genetics", "microbiology", "anthropology", "Biological anthropology", "molecular", "assays", "carried", "munich", "laboratories"], "article_id"=>696478, "categories"=>["Biological Sciences", "Sociology"], "users"=>["Michaela Harbeck", "Lisa Seifert", "Stephanie Hänsch", "David M. Wagner", "Dawn Birdsell", "Katy L. Parise", "Ingrid Wiechmann", "Gisela Grupe", "Astrid Thomas", "Paul Keim", "Lothar Zöller", "Barbara Bramanti", "Julia M. Riehm", "Holger C. Scholz"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1003349.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Design_of_molecular_assays_carried_out_in_the_Munich_laboratories_conc_8202_8202_concentration_/696478", "title"=>"Design of molecular assays carried out in the Munich laboratories (conc = concentration).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-02 01:47:58"}

PMC Usage Stats | Further Information

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Relative Metric

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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-08-27 19:06:57 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.ppat.1003349)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'