Extraction of DNA from Paleofeces View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2012

AUTHORS

Melanie Kuch , Hendrik Poinar

ABSTRACT

Paleofeces are the nonmineralized remains of dung from extant and extinct fauna. They represent a surprisingly large proportion of fossil remains recovered from cave sites across the world. Paleofeces contain the DNA of the defecator as well as the DNA of ingested plant and animal remains. To successfully extract DNA from paleofeces, a balance must be achieved between the minimization of DNA loss during extraction and the removal of coeluates that would otherwise inhibit the Taq DNA polymerase during downstream applications. Here we present a simplified version of a protocol to extract DNA from paleofecal remains. More... »

PAGES

37-42

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_5

DOI

http://dx.doi.org/10.1007/978-1-61779-516-9_5

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1003990320

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22237519


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Extinction, Biological", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Feces", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Paleontology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Silicon Dioxide", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "McMaster University", 
          "id": "https://www.grid.ac/institutes/grid.25073.33", 
          "name": [
            "McMaster Ancient DNA Centre, McMaster University, Hamilton, ON, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kuch", 
        "givenName": "Melanie", 
        "id": "sg:person.01311102275.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01311102275.09"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "McMaster University", 
          "id": "https://www.grid.ac/institutes/grid.25073.33", 
          "name": [
            "McMaster Ancient DNA Centre, McMaster University, Hamilton, ON, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Poinar", 
        "givenName": "Hendrik", 
        "id": "sg:person.0676355246.40", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676355246.40"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1073/pnas.95.8.4630", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001973451"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.061014798", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005588411"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.genet.37.110801.143214", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014567048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2003.08.039", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036204299"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2003.08.039", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036204299"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1080/10420949809386438", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038519467"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1006/jcis.1996.0421", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041974497"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-294x.2000.01106.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043150740"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/382275a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045140965", 
          "https://doi.org/10.1038/382275a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.281.5375.402", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051953666"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ac0516638", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1054997531"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ac0516638", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1054997531"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/scientificamerican0587-90", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1056542222", 
          "https://doi.org/10.1038/scientificamerican0587-90"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1084114", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062448079"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/000112383", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069095463"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/000113244", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069096078"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1077284558", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012", 
    "datePublishedReg": "2012-01-01", 
    "description": "Paleofeces are the nonmineralized remains of dung from extant and extinct fauna. They represent a surprisingly large proportion of fossil remains recovered from cave sites across the world. Paleofeces contain the DNA of the defecator as well as the DNA of ingested plant and animal remains. To successfully extract DNA from paleofeces, a balance must be achieved between the minimization of DNA loss during extraction and the removal of coeluates that would otherwise inhibit the Taq DNA polymerase during downstream applications. Here we present a simplified version of a protocol to extract DNA from paleofecal remains.", 
    "editor": [
      {
        "familyName": "Shapiro", 
        "givenName": "Beth", 
        "type": "Person"
      }, 
      {
        "familyName": "Hofreiter", 
        "givenName": "Michael", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-61779-516-9_5", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-61779-515-2", 
        "978-1-61779-516-9"
      ], 
      "name": "Ancient DNA", 
      "type": "Book"
    }, 
    "name": "Extraction of DNA from Paleofeces", 
    "pagination": "37-42", 
    "productId": [
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-61779-516-9_5"
        ]
      }, 
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "1302c0c905bd87e24232b5721d49581c23768a4c29226253b0478eb81c7e7c94"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1003990320"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22237519"
        ]
      }
    ], 
    "publisher": {
      "location": "Totowa, NJ", 
      "name": "Humana Press", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-61779-516-9_5", 
      "https://app.dimensions.ai/details/publication/pub.1003990320"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-15T12:29", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8663_00000245.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-1-61779-516-9_5"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_5'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_5'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_5'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-516-9_5'


 

This table displays all metadata directly associated to this object as RDF triples.

151 TRIPLES      23 PREDICATES      49 URIs      27 LITERALS      15 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-61779-516-9_5 schema:about N0874efde4ced4228acf111192844db95
2 N8987f73878874241b3ca8455188fc963
3 N9a59c47704a347a9872efe4dd0295f4f
4 Nebcdfcecfead41fab89268256baadb4a
5 Nee16ad8679014974829738a93e8acae1
6 Nf2a7ebea906b4fc39e5d6366a565ad7c
7 anzsrc-for:06
8 anzsrc-for:0604
9 schema:author Nabd70ae71f1e4f6faad101e03f5a8da5
10 schema:citation sg:pub.10.1038/382275a0
11 sg:pub.10.1038/scientificamerican0587-90
12 https://app.dimensions.ai/details/publication/pub.1077284558
13 https://doi.org/10.1006/jcis.1996.0421
14 https://doi.org/10.1016/j.cub.2003.08.039
15 https://doi.org/10.1021/ac0516638
16 https://doi.org/10.1046/j.1365-294x.2000.01106.x
17 https://doi.org/10.1073/pnas.061014798
18 https://doi.org/10.1073/pnas.95.8.4630
19 https://doi.org/10.1080/10420949809386438
20 https://doi.org/10.1126/science.1084114
21 https://doi.org/10.1126/science.281.5375.402
22 https://doi.org/10.1146/annurev.genet.37.110801.143214
23 https://doi.org/10.2144/000112383
24 https://doi.org/10.2144/000113244
25 schema:datePublished 2012
26 schema:datePublishedReg 2012-01-01
27 schema:description Paleofeces are the nonmineralized remains of dung from extant and extinct fauna. They represent a surprisingly large proportion of fossil remains recovered from cave sites across the world. Paleofeces contain the DNA of the defecator as well as the DNA of ingested plant and animal remains. To successfully extract DNA from paleofeces, a balance must be achieved between the minimization of DNA loss during extraction and the removal of coeluates that would otherwise inhibit the Taq DNA polymerase during downstream applications. Here we present a simplified version of a protocol to extract DNA from paleofecal remains.
28 schema:editor Ne24a2ad9605e493080c956a2e91dc06e
29 schema:genre chapter
30 schema:inLanguage en
31 schema:isAccessibleForFree false
32 schema:isPartOf Nbe6557925b3246a6bb1f184b13ed5ff1
33 schema:name Extraction of DNA from Paleofeces
34 schema:pagination 37-42
35 schema:productId N22e483c88d9941258191afa167c7749d
36 Na38fa7bf29dd4682ba7b5bb9d9aa3201
37 Na68f3a4baafa481eb7d9f1fc0a8e4654
38 Nd5106547c9814dd4883ac51764a9b66b
39 schema:publisher N8cd869cc02104e96be1a6255a09f40f3
40 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003990320
41 https://doi.org/10.1007/978-1-61779-516-9_5
42 schema:sdDatePublished 2019-04-15T12:29
43 schema:sdLicense https://scigraph.springernature.com/explorer/license/
44 schema:sdPublisher N67b86d5849374624b5c955fb0f6c4a7c
45 schema:url http://link.springer.com/10.1007/978-1-61779-516-9_5
46 sgo:license sg:explorer/license/
47 sgo:sdDataset chapters
48 rdf:type schema:Chapter
49 N0874efde4ced4228acf111192844db95 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
50 schema:name Feces
51 rdf:type schema:DefinedTerm
52 N1444f3d69153410687d9b99e33b8cef7 rdf:first sg:person.0676355246.40
53 rdf:rest rdf:nil
54 N22e483c88d9941258191afa167c7749d schema:name dimensions_id
55 schema:value pub.1003990320
56 rdf:type schema:PropertyValue
57 N67b86d5849374624b5c955fb0f6c4a7c schema:name Springer Nature - SN SciGraph project
58 rdf:type schema:Organization
59 N8598a9840b5a4dd1b0fc039fefab2747 schema:familyName Hofreiter
60 schema:givenName Michael
61 rdf:type schema:Person
62 N8987f73878874241b3ca8455188fc963 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
63 schema:name Animals
64 rdf:type schema:DefinedTerm
65 N8cd869cc02104e96be1a6255a09f40f3 schema:location Totowa, NJ
66 schema:name Humana Press
67 rdf:type schema:Organisation
68 N9a59c47704a347a9872efe4dd0295f4f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name DNA
70 rdf:type schema:DefinedTerm
71 Na38fa7bf29dd4682ba7b5bb9d9aa3201 schema:name pubmed_id
72 schema:value 22237519
73 rdf:type schema:PropertyValue
74 Na68f3a4baafa481eb7d9f1fc0a8e4654 schema:name readcube_id
75 schema:value 1302c0c905bd87e24232b5721d49581c23768a4c29226253b0478eb81c7e7c94
76 rdf:type schema:PropertyValue
77 Nabd70ae71f1e4f6faad101e03f5a8da5 rdf:first sg:person.01311102275.09
78 rdf:rest N1444f3d69153410687d9b99e33b8cef7
79 Nac587e13b7d247a4b60b4fc9737fc664 schema:familyName Shapiro
80 schema:givenName Beth
81 rdf:type schema:Person
82 Nbaf67d603c9744e4a0c757b058af4172 rdf:first N8598a9840b5a4dd1b0fc039fefab2747
83 rdf:rest rdf:nil
84 Nbe6557925b3246a6bb1f184b13ed5ff1 schema:isbn 978-1-61779-515-2
85 978-1-61779-516-9
86 schema:name Ancient DNA
87 rdf:type schema:Book
88 Nd5106547c9814dd4883ac51764a9b66b schema:name doi
89 schema:value 10.1007/978-1-61779-516-9_5
90 rdf:type schema:PropertyValue
91 Ne24a2ad9605e493080c956a2e91dc06e rdf:first Nac587e13b7d247a4b60b4fc9737fc664
92 rdf:rest Nbaf67d603c9744e4a0c757b058af4172
93 Nebcdfcecfead41fab89268256baadb4a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
94 schema:name Silicon Dioxide
95 rdf:type schema:DefinedTerm
96 Nee16ad8679014974829738a93e8acae1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Extinction, Biological
98 rdf:type schema:DefinedTerm
99 Nf2a7ebea906b4fc39e5d6366a565ad7c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name Paleontology
101 rdf:type schema:DefinedTerm
102 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
103 schema:name Biological Sciences
104 rdf:type schema:DefinedTerm
105 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
106 schema:name Genetics
107 rdf:type schema:DefinedTerm
108 sg:person.01311102275.09 schema:affiliation https://www.grid.ac/institutes/grid.25073.33
109 schema:familyName Kuch
110 schema:givenName Melanie
111 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01311102275.09
112 rdf:type schema:Person
113 sg:person.0676355246.40 schema:affiliation https://www.grid.ac/institutes/grid.25073.33
114 schema:familyName Poinar
115 schema:givenName Hendrik
116 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676355246.40
117 rdf:type schema:Person
118 sg:pub.10.1038/382275a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045140965
119 https://doi.org/10.1038/382275a0
120 rdf:type schema:CreativeWork
121 sg:pub.10.1038/scientificamerican0587-90 schema:sameAs https://app.dimensions.ai/details/publication/pub.1056542222
122 https://doi.org/10.1038/scientificamerican0587-90
123 rdf:type schema:CreativeWork
124 https://app.dimensions.ai/details/publication/pub.1077284558 schema:CreativeWork
125 https://doi.org/10.1006/jcis.1996.0421 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041974497
126 rdf:type schema:CreativeWork
127 https://doi.org/10.1016/j.cub.2003.08.039 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036204299
128 rdf:type schema:CreativeWork
129 https://doi.org/10.1021/ac0516638 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054997531
130 rdf:type schema:CreativeWork
131 https://doi.org/10.1046/j.1365-294x.2000.01106.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1043150740
132 rdf:type schema:CreativeWork
133 https://doi.org/10.1073/pnas.061014798 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005588411
134 rdf:type schema:CreativeWork
135 https://doi.org/10.1073/pnas.95.8.4630 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001973451
136 rdf:type schema:CreativeWork
137 https://doi.org/10.1080/10420949809386438 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038519467
138 rdf:type schema:CreativeWork
139 https://doi.org/10.1126/science.1084114 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062448079
140 rdf:type schema:CreativeWork
141 https://doi.org/10.1126/science.281.5375.402 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051953666
142 rdf:type schema:CreativeWork
143 https://doi.org/10.1146/annurev.genet.37.110801.143214 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014567048
144 rdf:type schema:CreativeWork
145 https://doi.org/10.2144/000112383 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069095463
146 rdf:type schema:CreativeWork
147 https://doi.org/10.2144/000113244 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069096078
148 rdf:type schema:CreativeWork
149 https://www.grid.ac/institutes/grid.25073.33 schema:alternateName McMaster University
150 schema:name McMaster Ancient DNA Centre, McMaster University, Hamilton, ON, Canada
151 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...