Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2014-12-30

AUTHORS

Jarrad T. Hampton-Marcell , Angel Frazier , Stephanie M. Moormann , Sarah M. Owens , Jack A. Gilbert

ABSTRACT

Metatranscriptomics has increased our working knowledge of the functional significance and genetic variability of microbial communities, yet there is still limited information concerning how gene expression and regulation in a microbiome influences interactions with hydrocarbon sources. Petroleum hydrocarbon environmental contamination provides a multitude of microenvironment interactions, which result in complex microbial community dynamics. While our understanding of microbial-mediated hydrocarbon metabolic potential is significantly improving, the transcriptional responses of key genotypic markers remain limited. The existence and persistence of microbial hydrocarbon metabolism can only be deciphered through the transcriptional regulation, characterized through metatranscriptomics. This technique is both fast, relatively cheap compared to proteomics and metabolomics, and provides a potential catalogue of interacting elements that can be used to define metabolic relationships between microbes. These metatranscriptomic analyses can also be coupled with metagenomic sequencing and statistical models to provide an in-depth approach to assemblage systems biology. In this work, we detail a standardized method to process and analyze hydrocarbon-associated microbial metatranscriptomes. More... »

PAGES

51-67

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/8623_2014_24

DOI

http://dx.doi.org/10.1007/8623_2014_24

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1020478937


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 Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, 60637, Chicago, IL, USA", 
          "id": "http://www.grid.ac/institutes/grid.170205.1", 
          "name": [
            "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA", 
            "Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hampton-Marcell", 
        "givenName": "Jarrad T.", 
        "id": "sg:person.01247573421.51", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247573421.51"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA", 
          "id": "http://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Frazier", 
        "givenName": "Angel", 
        "id": "sg:person.0645674437.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0645674437.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA", 
          "id": "http://www.grid.ac/institutes/grid.187073.a", 
          "name": [
            "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Moormann", 
        "givenName": "Stephanie M.", 
        "id": "sg:person.013556743337.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013556743337.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Computation Institute, University of Chicago, 5735 South Ellis Avenue, 60637, Chicago, IL, USA", 
          "id": "http://www.grid.ac/institutes/grid.170205.1", 
          "name": [
            "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA", 
            "Computation Institute, University of Chicago, 5735 South Ellis Avenue, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Owens", 
        "givenName": "Sarah M.", 
        "id": "sg:person.0746341376.67", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0746341376.67"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, 60637, Chicago, IL, USA", 
          "id": "http://www.grid.ac/institutes/grid.170205.1", 
          "name": [
            "Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA", 
            "Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, 60637, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gilbert", 
        "givenName": "Jack A.", 
        "id": "sg:person.0727626545.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0727626545.37"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2014-12-30", 
    "datePublishedReg": "2014-12-30", 
    "description": "Metatranscriptomics has increased our working knowledge of the functional significance and genetic variability of microbial communities, yet there is still limited information concerning how gene expression and regulation in a microbiome influences interactions with hydrocarbon sources. Petroleum hydrocarbon environmental contamination provides a multitude of microenvironment interactions, which result in complex microbial community dynamics. While our understanding of microbial-mediated hydrocarbon metabolic potential is significantly improving, the transcriptional responses of key genotypic markers remain limited. The existence and persistence of microbial hydrocarbon metabolism can only be deciphered through the transcriptional regulation, characterized through metatranscriptomics. This technique is both fast, relatively cheap compared to proteomics and metabolomics, and provides a potential catalogue of interacting elements that can be used to define metabolic relationships between microbes. These metatranscriptomic analyses can also be coupled with metagenomic sequencing and statistical models to provide an in-depth approach to assemblage systems biology. In this work, we detail a standardized method to process and analyze hydrocarbon-associated microbial metatranscriptomes.", 
    "editor": [
      {
        "familyName": "McGenity", 
        "givenName": "Terry J.", 
        "type": "Person"
      }, 
      {
        "familyName": "Timmis", 
        "givenName": "Kenneth N.", 
        "type": "Person"
      }, 
      {
        "familyName": "Nogales", 
        "givenName": "Balbina", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/8623_2014_24", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-3-662-50449-9", 
        "978-3-662-50450-5"
      ], 
      "name": "Hydrocarbon and Lipid Microbiology Protocols", 
      "type": "Book"
    }, 
    "keywords": [
      "microbial community dynamics", 
      "microbial metatranscriptomes", 
      "metatranscriptomic libraries", 
      "metatranscriptomic analysis", 
      "transcriptional regulation", 
      "microbe system", 
      "transcriptional response", 
      "microbial communities", 
      "metabolic potential", 
      "community dynamics", 
      "genetic variability", 
      "metagenomic sequencing", 
      "gene expression", 
      "systems biology", 
      "metatranscriptomics", 
      "functional significance", 
      "microenvironment interactions", 
      "hydrocarbon metabolism", 
      "genotypic markers", 
      "metabolic relationships", 
      "regulation", 
      "influence interactions", 
      "metatranscriptomes", 
      "proteomics", 
      "microbes", 
      "sequencing", 
      "biology", 
      "environmental contamination", 
      "expression", 
      "limited information", 
      "metabolism", 
      "interaction", 
      "metabolomics", 
      "library", 
      "markers", 
      "persistence", 
      "community", 
      "multitude", 
      "analysis", 
      "understanding", 
      "response", 
      "variability", 
      "dynamics", 
      "contamination", 
      "potential", 
      "elements", 
      "significance", 
      "standardized method", 
      "catalogue", 
      "depth approach", 
      "knowledge", 
      "source", 
      "existence", 
      "relationship", 
      "statistical model", 
      "information", 
      "system", 
      "preparation", 
      "approach", 
      "model", 
      "work", 
      "method", 
      "technique", 
      "hydrocarbon sources", 
      "microbiome influences interactions", 
      "Petroleum hydrocarbon environmental contamination", 
      "hydrocarbon environmental contamination", 
      "complex microbial community dynamics", 
      "microbial-mediated hydrocarbon metabolic potential", 
      "hydrocarbon metabolic potential", 
      "key genotypic markers", 
      "microbial hydrocarbon metabolism", 
      "potential catalogue", 
      "assemblage systems biology", 
      "hydrocarbon-associated microbial metatranscriptomes", 
      "Petroleum Hydrocarbon Microbe Systems", 
      "Hydrocarbon Microbe Systems"
    ], 
    "name": "Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems", 
    "pagination": "51-67", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1020478937"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/8623_2014_24"
        ]
      }
    ], 
    "publisher": {
      "name": "Springer Nature", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/8623_2014_24", 
      "https://app.dimensions.ai/details/publication/pub.1020478937"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2021-12-01T20:08", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/chapter/chapter_383.jsonl", 
    "type": "Chapter", 
    "url": "https://doi.org/10.1007/8623_2014_24"
  }
]
 

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.10.1007/8623_2014_24'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/8623_2014_24'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/8623_2014_24'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/8623_2014_24'


 

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

181 TRIPLES      23 PREDICATES      102 URIs      95 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/8623_2014_24 schema:about anzsrc-for:06
2 anzsrc-for:0605
3 schema:author N7a51fc149f3a4e9bb37b1a3ad19ad02e
4 schema:datePublished 2014-12-30
5 schema:datePublishedReg 2014-12-30
6 schema:description Metatranscriptomics has increased our working knowledge of the functional significance and genetic variability of microbial communities, yet there is still limited information concerning how gene expression and regulation in a microbiome influences interactions with hydrocarbon sources. Petroleum hydrocarbon environmental contamination provides a multitude of microenvironment interactions, which result in complex microbial community dynamics. While our understanding of microbial-mediated hydrocarbon metabolic potential is significantly improving, the transcriptional responses of key genotypic markers remain limited. The existence and persistence of microbial hydrocarbon metabolism can only be deciphered through the transcriptional regulation, characterized through metatranscriptomics. This technique is both fast, relatively cheap compared to proteomics and metabolomics, and provides a potential catalogue of interacting elements that can be used to define metabolic relationships between microbes. These metatranscriptomic analyses can also be coupled with metagenomic sequencing and statistical models to provide an in-depth approach to assemblage systems biology. In this work, we detail a standardized method to process and analyze hydrocarbon-associated microbial metatranscriptomes.
7 schema:editor N8d9dbe5c8b9144f99290d94ef9333730
8 schema:genre chapter
9 schema:inLanguage en
10 schema:isAccessibleForFree false
11 schema:isPartOf Naf380d4b8d514bfcb06f79820252311b
12 schema:keywords Hydrocarbon Microbe Systems
13 Petroleum Hydrocarbon Microbe Systems
14 Petroleum hydrocarbon environmental contamination
15 analysis
16 approach
17 assemblage systems biology
18 biology
19 catalogue
20 community
21 community dynamics
22 complex microbial community dynamics
23 contamination
24 depth approach
25 dynamics
26 elements
27 environmental contamination
28 existence
29 expression
30 functional significance
31 gene expression
32 genetic variability
33 genotypic markers
34 hydrocarbon environmental contamination
35 hydrocarbon metabolic potential
36 hydrocarbon metabolism
37 hydrocarbon sources
38 hydrocarbon-associated microbial metatranscriptomes
39 influence interactions
40 information
41 interaction
42 key genotypic markers
43 knowledge
44 library
45 limited information
46 markers
47 metabolic potential
48 metabolic relationships
49 metabolism
50 metabolomics
51 metagenomic sequencing
52 metatranscriptomes
53 metatranscriptomic analysis
54 metatranscriptomic libraries
55 metatranscriptomics
56 method
57 microbe system
58 microbes
59 microbial communities
60 microbial community dynamics
61 microbial hydrocarbon metabolism
62 microbial metatranscriptomes
63 microbial-mediated hydrocarbon metabolic potential
64 microbiome influences interactions
65 microenvironment interactions
66 model
67 multitude
68 persistence
69 potential
70 potential catalogue
71 preparation
72 proteomics
73 regulation
74 relationship
75 response
76 sequencing
77 significance
78 source
79 standardized method
80 statistical model
81 system
82 systems biology
83 technique
84 transcriptional regulation
85 transcriptional response
86 understanding
87 variability
88 work
89 schema:name Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems
90 schema:pagination 51-67
91 schema:productId N1835b9a4372646e3b05b1d9aff75564e
92 Nb9d80732effb4c0ca738472932f76352
93 schema:publisher N47abcd17048c44a2874e4645c58ad9cd
94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020478937
95 https://doi.org/10.1007/8623_2014_24
96 schema:sdDatePublished 2021-12-01T20:08
97 schema:sdLicense https://scigraph.springernature.com/explorer/license/
98 schema:sdPublisher N6ca811dec3604344b9823b15e74e893e
99 schema:url https://doi.org/10.1007/8623_2014_24
100 sgo:license sg:explorer/license/
101 sgo:sdDataset chapters
102 rdf:type schema:Chapter
103 N1835b9a4372646e3b05b1d9aff75564e schema:name dimensions_id
104 schema:value pub.1020478937
105 rdf:type schema:PropertyValue
106 N1b651b8efcb449fc8be750099a989e74 rdf:first sg:person.0746341376.67
107 rdf:rest Ndf660d3a63824cebb4b77c8f3d7142ca
108 N28cb902876ac4bb59ee9008f420c1e6b rdf:first sg:person.013556743337.97
109 rdf:rest N1b651b8efcb449fc8be750099a989e74
110 N2c2fc23efb32427d93f9bb4cdc417da3 rdf:first sg:person.0645674437.46
111 rdf:rest N28cb902876ac4bb59ee9008f420c1e6b
112 N3e5be44191234e148fe16fc6566118d9 rdf:first N6069e869044641cbb6485e103ffc3bb9
113 rdf:rest Nc680879cdbea43e8ad01d9e58e3ff146
114 N47abcd17048c44a2874e4645c58ad9cd schema:name Springer Nature
115 rdf:type schema:Organisation
116 N6069e869044641cbb6485e103ffc3bb9 schema:familyName Timmis
117 schema:givenName Kenneth N.
118 rdf:type schema:Person
119 N6ca811dec3604344b9823b15e74e893e schema:name Springer Nature - SN SciGraph project
120 rdf:type schema:Organization
121 N7a51fc149f3a4e9bb37b1a3ad19ad02e rdf:first sg:person.01247573421.51
122 rdf:rest N2c2fc23efb32427d93f9bb4cdc417da3
123 N8d9dbe5c8b9144f99290d94ef9333730 rdf:first Nb8c8a0f7659643c8a5071a1b0d544812
124 rdf:rest N3e5be44191234e148fe16fc6566118d9
125 Naf380d4b8d514bfcb06f79820252311b schema:isbn 978-3-662-50449-9
126 978-3-662-50450-5
127 schema:name Hydrocarbon and Lipid Microbiology Protocols
128 rdf:type schema:Book
129 Nb8c8a0f7659643c8a5071a1b0d544812 schema:familyName McGenity
130 schema:givenName Terry J.
131 rdf:type schema:Person
132 Nb9d80732effb4c0ca738472932f76352 schema:name doi
133 schema:value 10.1007/8623_2014_24
134 rdf:type schema:PropertyValue
135 Nbb523bd10a2e44f597c14473c5af810e schema:familyName Nogales
136 schema:givenName Balbina
137 rdf:type schema:Person
138 Nc680879cdbea43e8ad01d9e58e3ff146 rdf:first Nbb523bd10a2e44f597c14473c5af810e
139 rdf:rest rdf:nil
140 Ndf660d3a63824cebb4b77c8f3d7142ca rdf:first sg:person.0727626545.37
141 rdf:rest rdf:nil
142 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
143 schema:name Biological Sciences
144 rdf:type schema:DefinedTerm
145 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
146 schema:name Microbiology
147 rdf:type schema:DefinedTerm
148 sg:person.01247573421.51 schema:affiliation grid-institutes:grid.170205.1
149 schema:familyName Hampton-Marcell
150 schema:givenName Jarrad T.
151 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01247573421.51
152 rdf:type schema:Person
153 sg:person.013556743337.97 schema:affiliation grid-institutes:grid.187073.a
154 schema:familyName Moormann
155 schema:givenName Stephanie M.
156 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013556743337.97
157 rdf:type schema:Person
158 sg:person.0645674437.46 schema:affiliation grid-institutes:grid.187073.a
159 schema:familyName Frazier
160 schema:givenName Angel
161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0645674437.46
162 rdf:type schema:Person
163 sg:person.0727626545.37 schema:affiliation grid-institutes:grid.170205.1
164 schema:familyName Gilbert
165 schema:givenName Jack A.
166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0727626545.37
167 rdf:type schema:Person
168 sg:person.0746341376.67 schema:affiliation grid-institutes:grid.170205.1
169 schema:familyName Owens
170 schema:givenName Sarah M.
171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0746341376.67
172 rdf:type schema:Person
173 grid-institutes:grid.170205.1 schema:alternateName Computation Institute, University of Chicago, 5735 South Ellis Avenue, 60637, Chicago, IL, USA
174 Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, 60637, Chicago, IL, USA
175 schema:name Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA
176 Computation Institute, University of Chicago, 5735 South Ellis Avenue, 60637, Chicago, IL, USA
177 Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, 60637, Chicago, IL, USA
178 rdf:type schema:Organization
179 grid-institutes:grid.187073.a schema:alternateName Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA
180 schema:name Argonne National Laboratory, 9700 South Cass Avenue, 60439, Argonne, IL, USA
181 rdf:type schema:Organization
 




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


...