A Comparison of the Use of In Vitro–Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1998-11

AUTHORS

K.D. McMahon, D.A. Stahl, L. Raskin

ABSTRACT

Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro–transcribed and native rRNA indicated that, when in vitro–transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro–transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments. More... »

PAGES

362-371

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s002489900122

DOI

http://dx.doi.org/10.1007/s002489900122

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1018541404

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/9852515


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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA, US", 
          "id": "http://www.grid.ac/institutes/grid.35403.31", 
          "name": [
            "Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McMahon", 
        "givenName": "K.D.", 
        "id": "sg:person.01007375500.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007375500.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Civil Engineering, Northwestern University, Technological Institute, Evanston, IL 60208, USA, US", 
          "id": "http://www.grid.ac/institutes/grid.16753.36", 
          "name": [
            "Department of Civil Engineering, Northwestern University, Technological Institute, Evanston, IL 60208, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stahl", 
        "givenName": "D.A.", 
        "id": "sg:person.01316025700.58", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316025700.58"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA, US", 
          "id": "http://www.grid.ac/institutes/grid.35403.31", 
          "name": [
            "Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA, US"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Raskin", 
        "givenName": "L.", 
        "id": "sg:person.0707350364.49", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707350364.49"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1007/978-1-4684-7609-5_5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043177342", 
          "https://doi.org/10.1007/978-1-4684-7609-5_5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02529981", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035990758", 
          "https://doi.org/10.1007/bf02529981"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4757-0611-6_1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001841887", 
          "https://doi.org/10.1007/978-1-4757-0611-6_1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf00874140", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008888891", 
          "https://doi.org/10.1007/bf00874140"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4757-0322-1_7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1089798111", 
          "https://doi.org/10.1007/978-1-4757-0322-1_7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf00871644", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030686887", 
          "https://doi.org/10.1007/bf00871644"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "1998-11", 
    "datePublishedReg": "1998-11-01", 
    "description": "Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro\u2013transcribed and native rRNA indicated that, when in vitro\u2013transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro\u2013transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.", 
    "genre": "article", 
    "id": "sg:pub.10.1007/s002489900122", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1081458", 
        "issn": [
          "0095-3628", 
          "1432-184X"
        ], 
        "name": "Microbial Ecology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3-4", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "36"
      }
    ], 
    "keywords": [
      "SSU rRNA", 
      "native rRNA", 
      "population abundance", 
      "small subunit rRNA", 
      "SSU rDNA gene", 
      "total SSU rRNA", 
      "quantification of microorganisms", 
      "higher-order structure", 
      "subunit rRNA", 
      "rDNA gene", 
      "community structure", 
      "quantitative hybridization", 
      "microbial populations", 
      "rRNA", 
      "membrane hybridization", 
      "hybridization signals", 
      "oligonucleotide probes", 
      "vitro-transcribed", 
      "denaturation conditions", 
      "absolute quantification", 
      "quantitative membrane hybridizations", 
      "order structure", 
      "abundance", 
      "hybridization", 
      "genes", 
      "clones", 
      "microorganisms", 
      "population", 
      "probe", 
      "structure", 
      "environment", 
      "quantification", 
      "signals", 
      "shift", 
      "location", 
      "conditions", 
      "differences", 
      "percentage", 
      "comparison", 
      "use", 
      "time", 
      "standards", 
      "target location"
    ], 
    "name": "A Comparison of the Use of In Vitro\u2013Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment", 
    "pagination": "362-371", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1018541404"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s002489900122"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "9852515"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s002489900122", 
      "https://app.dimensions.ai/details/publication/pub.1018541404"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-05-20T07:20", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_271.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/s002489900122"
  }
]
 

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/s002489900122'

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/s002489900122'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s002489900122'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s002489900122'


 

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

146 TRIPLES      22 PREDICATES      76 URIs      62 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s002489900122 schema:about anzsrc-for:06
2 anzsrc-for:0605
3 schema:author Na9f8d25666774403a249e238ef2c07ed
4 schema:citation sg:pub.10.1007/978-1-4684-7609-5_5
5 sg:pub.10.1007/978-1-4757-0322-1_7
6 sg:pub.10.1007/978-1-4757-0611-6_1
7 sg:pub.10.1007/bf00871644
8 sg:pub.10.1007/bf00874140
9 sg:pub.10.1007/bf02529981
10 schema:datePublished 1998-11
11 schema:datePublishedReg 1998-11-01
12 schema:description Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro–transcribed and native rRNA indicated that, when in vitro–transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro–transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.
13 schema:genre article
14 schema:inLanguage en
15 schema:isAccessibleForFree false
16 schema:isPartOf N288502e380c646ba967baa12772618c4
17 Nbd011e18056d4211a3fde175c9360ef3
18 sg:journal.1081458
19 schema:keywords SSU rDNA gene
20 SSU rRNA
21 absolute quantification
22 abundance
23 clones
24 community structure
25 comparison
26 conditions
27 denaturation conditions
28 differences
29 environment
30 genes
31 higher-order structure
32 hybridization
33 hybridization signals
34 location
35 membrane hybridization
36 microbial populations
37 microorganisms
38 native rRNA
39 oligonucleotide probes
40 order structure
41 percentage
42 population
43 population abundance
44 probe
45 quantification
46 quantification of microorganisms
47 quantitative hybridization
48 quantitative membrane hybridizations
49 rDNA gene
50 rRNA
51 shift
52 signals
53 small subunit rRNA
54 standards
55 structure
56 subunit rRNA
57 target location
58 time
59 total SSU rRNA
60 use
61 vitro-transcribed
62 schema:name A Comparison of the Use of In Vitro–Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment
63 schema:pagination 362-371
64 schema:productId N0e0090cb1bee4733a63b65f1645a247b
65 Nf27490638d36492a991d1b293c476759
66 Nf9252e41f6824e39bbb55181cf8f49cf
67 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018541404
68 https://doi.org/10.1007/s002489900122
69 schema:sdDatePublished 2022-05-20T07:20
70 schema:sdLicense https://scigraph.springernature.com/explorer/license/
71 schema:sdPublisher Nc54a6fc0a3354194a0cb3947948aff16
72 schema:url https://doi.org/10.1007/s002489900122
73 sgo:license sg:explorer/license/
74 sgo:sdDataset articles
75 rdf:type schema:ScholarlyArticle
76 N0e0090cb1bee4733a63b65f1645a247b schema:name pubmed_id
77 schema:value 9852515
78 rdf:type schema:PropertyValue
79 N288502e380c646ba967baa12772618c4 schema:volumeNumber 36
80 rdf:type schema:PublicationVolume
81 N526511f299cd4af7b7d0e69f2ec60b91 rdf:first sg:person.01316025700.58
82 rdf:rest Nb23d78260707443083d4d4219aabf169
83 Na9f8d25666774403a249e238ef2c07ed rdf:first sg:person.01007375500.45
84 rdf:rest N526511f299cd4af7b7d0e69f2ec60b91
85 Nb23d78260707443083d4d4219aabf169 rdf:first sg:person.0707350364.49
86 rdf:rest rdf:nil
87 Nbd011e18056d4211a3fde175c9360ef3 schema:issueNumber 3-4
88 rdf:type schema:PublicationIssue
89 Nc54a6fc0a3354194a0cb3947948aff16 schema:name Springer Nature - SN SciGraph project
90 rdf:type schema:Organization
91 Nf27490638d36492a991d1b293c476759 schema:name doi
92 schema:value 10.1007/s002489900122
93 rdf:type schema:PropertyValue
94 Nf9252e41f6824e39bbb55181cf8f49cf schema:name dimensions_id
95 schema:value pub.1018541404
96 rdf:type schema:PropertyValue
97 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
98 schema:name Biological Sciences
99 rdf:type schema:DefinedTerm
100 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
101 schema:name Microbiology
102 rdf:type schema:DefinedTerm
103 sg:journal.1081458 schema:issn 0095-3628
104 1432-184X
105 schema:name Microbial Ecology
106 schema:publisher Springer Nature
107 rdf:type schema:Periodical
108 sg:person.01007375500.45 schema:affiliation grid-institutes:grid.35403.31
109 schema:familyName McMahon
110 schema:givenName K.D.
111 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007375500.45
112 rdf:type schema:Person
113 sg:person.01316025700.58 schema:affiliation grid-institutes:grid.16753.36
114 schema:familyName Stahl
115 schema:givenName D.A.
116 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316025700.58
117 rdf:type schema:Person
118 sg:person.0707350364.49 schema:affiliation grid-institutes:grid.35403.31
119 schema:familyName Raskin
120 schema:givenName L.
121 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707350364.49
122 rdf:type schema:Person
123 sg:pub.10.1007/978-1-4684-7609-5_5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043177342
124 https://doi.org/10.1007/978-1-4684-7609-5_5
125 rdf:type schema:CreativeWork
126 sg:pub.10.1007/978-1-4757-0322-1_7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1089798111
127 https://doi.org/10.1007/978-1-4757-0322-1_7
128 rdf:type schema:CreativeWork
129 sg:pub.10.1007/978-1-4757-0611-6_1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001841887
130 https://doi.org/10.1007/978-1-4757-0611-6_1
131 rdf:type schema:CreativeWork
132 sg:pub.10.1007/bf00871644 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030686887
133 https://doi.org/10.1007/bf00871644
134 rdf:type schema:CreativeWork
135 sg:pub.10.1007/bf00874140 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008888891
136 https://doi.org/10.1007/bf00874140
137 rdf:type schema:CreativeWork
138 sg:pub.10.1007/bf02529981 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035990758
139 https://doi.org/10.1007/bf02529981
140 rdf:type schema:CreativeWork
141 grid-institutes:grid.16753.36 schema:alternateName Department of Civil Engineering, Northwestern University, Technological Institute, Evanston, IL 60208, USA, US
142 schema:name Department of Civil Engineering, Northwestern University, Technological Institute, Evanston, IL 60208, USA, US
143 rdf:type schema:Organization
144 grid-institutes:grid.35403.31 schema:alternateName Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA, US
145 schema:name Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 North Mathews Avenue, Urbana, IL 61801, USA, US
146 rdf:type schema:Organization
 




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


...