Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry.
Identifieur interne : 001F94 ( Main/Exploration ); précédent : 001F93; suivant : 001F95Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry.
Auteurs : Colin Ruprecht ; Takayuki Tohge ; Alisdair Fernie ; Cara L. Mortimer [Royaume-Uni] ; Amanda Kozlo [Royaume-Uni] ; Paul D. Fraser [Royaume-Uni] ; Norma Funke ; Igor Cesarino ; Ruben Vanholme ; Wout Boerjan ; Kris Morreel ; Ingo Burgert ; Notburga Gierlinger ; Vincent Bulone ; Vera Schneider ; Andrea Stockero ; Juan Navarro-Avi ; Frank Pudel ; Bart Tambuyser ; James Hygate ; Jon Bumstead ; Louis Notley ; Staffan Persson [Allemagne]Source :
- Journal of visualized experiments : JoVE [ 1940-087X ] ; 2014.
Descripteurs français
- KwdFr :
- Aliment pour animaux (MeSH), Biocarburants (MeSH), Biomasse (MeSH), Chromatographie en phase liquide (MeSH), Chromatographie gazeuse-spectrométrie de masse (MeSH), Métabolomique (MeSH), Populus (génétique), Populus (métabolisme), Tabac (génétique), Tabac (métabolisme), Transcription génétique (MeSH).
- MESH :
- génétique : Populus, Tabac.
- métabolisme : Populus, Tabac.
- Aliment pour animaux, Biocarburants, Biomasse, Chromatographie en phase liquide, Chromatographie gazeuse-spectrométrie de masse, Métabolomique, Transcription génétique.
English descriptors
- KwdEn :
- MESH :
- chemical : Biofuels.
- genetics : Populus, Tobacco.
- metabolism : Populus, Tobacco.
- Animal Feed, Biomass, Chromatography, Liquid, Gas Chromatography-Mass Spectrometry, Metabolomics, Transcription, Genetic.
Abstract
The global demand for food, feed, energy and water poses extraordinary challenges for future generations. It is evident that robust platforms for the exploration of renewable resources are necessary to overcome these challenges. Within the multinational framework MultiBioPro we are developing biorefinery pipelines to maximize the use of plant biomass. More specifically, we use poplar and tobacco tree (Nicotiana glauca) as target crop species for improving saccharification, isoprenoid, long chain hydrocarbon contents, fiber quality, and suberin and lignin contents. The methods used to obtain these outputs include GC-MS, LC-MS and RNA sequencing platforms. The metabolite pipelines are well established tools to generate these types of data, but also have the limitations in that only well characterized metabolites can be used. The deep sequencing will allow us to include all transcripts present during the developmental stages of the tobacco tree leaf, but has to be mapped back to the sequence of Nicotiana tabacum. With these set-ups, we aim at a basic understanding for underlying processes and at establishing an industrial framework to exploit the outcomes. In a more long term perspective, we believe that data generated here will provide means for a sustainable biorefinery process using poplar and tobacco tree as raw material. To date the basal level of metabolites in the samples have been analyzed and the protocols utilized are provided in this article.
DOI: 10.3791/51393
PubMed: 24894952
PubMed Central: PMC4189316
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Vanholme, Ruben" sort="Vanholme, Ruben" uniqKey="Vanholme R" first="Ruben" last="Vanholme">Ruben Vanholme</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Morreel, Kris" sort="Morreel, Kris" uniqKey="Morreel K" first="Kris" last="Morreel">Kris Morreel</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Burgert, Ingo" sort="Burgert, Ingo" uniqKey="Burgert I" first="Ingo" last="Burgert">Ingo Burgert</name><affiliation><nlm:affiliation>Institute for Building Materials, ETH Zurich; Applied Wood Materials, EMPA.</nlm:affiliation><wicri:noCountry code="subField">EMPA</wicri:noCountry></affiliation></author><author><name sortKey="Gierlinger, Notburga" sort="Gierlinger, Notburga" uniqKey="Gierlinger N" first="Notburga" last="Gierlinger">Notburga Gierlinger</name><affiliation><nlm:affiliation>Institute for Building Materials, ETH Zurich; Applied Wood Materials, EMPA.</nlm:affiliation><wicri:noCountry code="subField">EMPA</wicri:noCountry></affiliation></author><author><name sortKey="Bulone, Vincent" sort="Bulone, Vincent" uniqKey="Bulone V" first="Vincent" last="Bulone">Vincent Bulone</name><affiliation><nlm:affiliation>Division of Glycoscience, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH).</nlm:affiliation><wicri:noCountry code="subField">Royal Institute of Technology (KTH)</wicri:noCountry></affiliation></author><author><name sortKey="Schneider, Vera" sort="Schneider, Vera" uniqKey="Schneider V" first="Vera" last="Schneider">Vera Schneider</name><affiliation><nlm:affiliation>European Research and Project Office GmbH.</nlm:affiliation><wicri:noCountry code="no comma">European Research and Project Office GmbH.</wicri:noCountry></affiliation></author><author><name sortKey="Stockero, Andrea" sort="Stockero, Andrea" uniqKey="Stockero A" first="Andrea" last="Stockero">Andrea Stockero</name><affiliation><nlm:affiliation>European Research and Project Office GmbH.</nlm:affiliation><wicri:noCountry code="no comma">European Research and Project Office GmbH.</wicri:noCountry></affiliation></author><author><name sortKey="Navarro Avi, Juan" sort="Navarro Avi, Juan" uniqKey="Navarro Avi J" first="Juan" last="Navarro-Avi">Juan Navarro-Avi</name><affiliation><nlm:affiliation>ABBA Gaia S.L.</nlm:affiliation><wicri:noCountry code="no comma">ABBA Gaia S.L.</wicri:noCountry></affiliation></author><author><name sortKey="Pudel, Frank" sort="Pudel, Frank" uniqKey="Pudel F" first="Frank" last="Pudel">Frank Pudel</name><affiliation><nlm:affiliation>Pflanzenöltechnologie.</nlm:affiliation><wicri:noCountry code="no comma">Pflanzenöltechnologie.</wicri:noCountry></affiliation></author><author><name sortKey="Tambuyser, Bart" sort="Tambuyser, Bart" uniqKey="Tambuyser B" first="Bart" last="Tambuyser">Bart Tambuyser</name><affiliation><nlm:affiliation>Capax Environmental Services.</nlm:affiliation><wicri:noCountry code="no comma">Capax Environmental Services.</wicri:noCountry></affiliation></author><author><name sortKey="Hygate, James" sort="Hygate, James" uniqKey="Hygate J" first="James" last="Hygate">James Hygate</name><affiliation><nlm:affiliation>Green Fuels.</nlm:affiliation><wicri:noCountry code="no comma">Green Fuels.</wicri:noCountry></affiliation></author><author><name sortKey="Bumstead, Jon" sort="Bumstead, Jon" uniqKey="Bumstead J" first="Jon" last="Bumstead">Jon Bumstead</name><affiliation><nlm:affiliation>Neutral Consulting Ltd.</nlm:affiliation><wicri:noCountry code="no comma">Neutral Consulting Ltd.</wicri:noCountry></affiliation></author><author><name sortKey="Notley, Louis" sort="Notley, Louis" uniqKey="Notley L" first="Louis" last="Notley">Louis Notley</name><affiliation><nlm:affiliation>Neutral Consulting Ltd.</nlm:affiliation><wicri:noCountry code="no comma">Neutral Consulting Ltd.</wicri:noCountry></affiliation></author><author><name sortKey="Persson, Staffan" sort="Persson, Staffan" uniqKey="Persson S" first="Staffan" last="Persson">Staffan Persson</name><affiliation wicri:level="1"><nlm:affiliation>Max Planck Institute for Molecular Plant Physiology; Plant Cell Biology Research Centre, School of Botany, University of Melbourne; Persson@mpimp-golm.mpg.de.</nlm:affiliation><country wicri:rule="url">Allemagne</country><wicri:regionArea>Max Planck Institute for Molecular Plant Physiology; Plant Cell Biology Research Centre, School of Botany</wicri:regionArea><wicri:noRegion>School of Botany</wicri:noRegion><wicri:noRegion>School of Botany</wicri:noRegion><wicri:noRegion>School of Botany</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24894952</idno><idno type="pmid">24894952</idno><idno type="doi">10.3791/51393</idno><idno type="pmc">PMC4189316</idno><idno type="wicri:Area/Main/Corpus">002154</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002154</idno><idno type="wicri:Area/Main/Curation">002154</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002154</idno><idno type="wicri:Area/Main/Exploration">002154</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry.</title><author><name sortKey="Ruprecht, Colin" sort="Ruprecht, Colin" uniqKey="Ruprecht C" first="Colin" last="Ruprecht">Colin Ruprecht</name><affiliation><nlm:affiliation>Max Planck Institute for Molecular Plant Physiology.</nlm:affiliation><wicri:noCountry code="no comma">Max Planck Institute for Molecular Plant Physiology.</wicri:noCountry></affiliation></author><author><name sortKey="Tohge, Takayuki" sort="Tohge, Takayuki" uniqKey="Tohge T" first="Takayuki" last="Tohge">Takayuki Tohge</name><affiliation><nlm:affiliation>Max Planck Institute for Molecular Plant Physiology.</nlm:affiliation><wicri:noCountry code="no comma">Max Planck Institute for Molecular Plant Physiology.</wicri:noCountry></affiliation></author><author><name sortKey="Fernie, Alisdair" sort="Fernie, Alisdair" uniqKey="Fernie A" first="Alisdair" last="Fernie">Alisdair Fernie</name><affiliation><nlm:affiliation>Max Planck Institute for Molecular Plant Physiology.</nlm:affiliation><wicri:noCountry code="no comma">Max Planck Institute for Molecular Plant Physiology.</wicri:noCountry></affiliation></author><author><name sortKey="Mortimer, Cara L" sort="Mortimer, Cara L" uniqKey="Mortimer C" first="Cara L" last="Mortimer">Cara L. Mortimer</name><affiliation wicri:level="4"><nlm:affiliation>School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London.</nlm:affiliation><country>Royaume-Uni</country><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName><orgName type="university">Université de Londres</orgName></affiliation></author><author><name sortKey="Kozlo, Amanda" sort="Kozlo, Amanda" uniqKey="Kozlo A" first="Amanda" last="Kozlo">Amanda Kozlo</name><affiliation wicri:level="4"><nlm:affiliation>School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London.</nlm:affiliation><country>Royaume-Uni</country><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName><orgName type="university">Université de Londres</orgName></affiliation></author><author><name sortKey="Fraser, Paul D" sort="Fraser, Paul D" uniqKey="Fraser P" first="Paul D" last="Fraser">Paul D. Fraser</name><affiliation wicri:level="4"><nlm:affiliation>School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London.</nlm:affiliation><country>Royaume-Uni</country><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName><orgName type="university">Université de Londres</orgName></affiliation></author><author><name sortKey="Funke, Norma" sort="Funke, Norma" uniqKey="Funke N" first="Norma" last="Funke">Norma Funke</name><affiliation><nlm:affiliation>Max Planck Institute for Molecular Plant Physiology.</nlm:affiliation><wicri:noCountry code="no comma">Max Planck Institute for Molecular Plant Physiology.</wicri:noCountry></affiliation></author><author><name sortKey="Cesarino, Igor" sort="Cesarino, Igor" uniqKey="Cesarino I" first="Igor" last="Cesarino">Igor Cesarino</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Vanholme, Ruben" sort="Vanholme, Ruben" uniqKey="Vanholme R" first="Ruben" last="Vanholme">Ruben Vanholme</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Morreel, Kris" sort="Morreel, Kris" uniqKey="Morreel K" first="Kris" last="Morreel">Kris Morreel</name><affiliation><nlm:affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</nlm:affiliation><wicri:noCountry code="subField">UGhent</wicri:noCountry></affiliation></author><author><name sortKey="Burgert, Ingo" sort="Burgert, Ingo" uniqKey="Burgert I" first="Ingo" last="Burgert">Ingo Burgert</name><affiliation><nlm:affiliation>Institute for Building Materials, ETH Zurich; Applied Wood Materials, EMPA.</nlm:affiliation><wicri:noCountry code="subField">EMPA</wicri:noCountry></affiliation></author><author><name sortKey="Gierlinger, Notburga" sort="Gierlinger, Notburga" uniqKey="Gierlinger N" first="Notburga" last="Gierlinger">Notburga Gierlinger</name><affiliation><nlm:affiliation>Institute for Building Materials, ETH Zurich; Applied Wood Materials, EMPA.</nlm:affiliation><wicri:noCountry code="subField">EMPA</wicri:noCountry></affiliation></author><author><name sortKey="Bulone, Vincent" sort="Bulone, Vincent" uniqKey="Bulone V" first="Vincent" last="Bulone">Vincent Bulone</name><affiliation><nlm:affiliation>Division of Glycoscience, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH).</nlm:affiliation><wicri:noCountry code="subField">Royal Institute of Technology (KTH)</wicri:noCountry></affiliation></author><author><name sortKey="Schneider, Vera" sort="Schneider, Vera" uniqKey="Schneider V" first="Vera" last="Schneider">Vera Schneider</name><affiliation><nlm:affiliation>European Research and Project Office GmbH.</nlm:affiliation><wicri:noCountry code="no comma">European Research and Project Office GmbH.</wicri:noCountry></affiliation></author><author><name sortKey="Stockero, Andrea" sort="Stockero, Andrea" uniqKey="Stockero A" first="Andrea" last="Stockero">Andrea Stockero</name><affiliation><nlm:affiliation>European Research and Project Office GmbH.</nlm:affiliation><wicri:noCountry code="no comma">European Research and Project Office GmbH.</wicri:noCountry></affiliation></author><author><name sortKey="Navarro Avi, Juan" sort="Navarro Avi, Juan" uniqKey="Navarro Avi J" first="Juan" last="Navarro-Avi">Juan Navarro-Avi</name><affiliation><nlm:affiliation>ABBA Gaia S.L.</nlm:affiliation><wicri:noCountry code="no comma">ABBA Gaia S.L.</wicri:noCountry></affiliation></author><author><name sortKey="Pudel, Frank" sort="Pudel, Frank" uniqKey="Pudel F" first="Frank" last="Pudel">Frank Pudel</name><affiliation><nlm:affiliation>Pflanzenöltechnologie.</nlm:affiliation><wicri:noCountry code="no comma">Pflanzenöltechnologie.</wicri:noCountry></affiliation></author><author><name sortKey="Tambuyser, Bart" sort="Tambuyser, Bart" uniqKey="Tambuyser B" first="Bart" last="Tambuyser">Bart Tambuyser</name><affiliation><nlm:affiliation>Capax Environmental Services.</nlm:affiliation><wicri:noCountry code="no comma">Capax Environmental Services.</wicri:noCountry></affiliation></author><author><name sortKey="Hygate, James" sort="Hygate, James" uniqKey="Hygate J" first="James" last="Hygate">James Hygate</name><affiliation><nlm:affiliation>Green Fuels.</nlm:affiliation><wicri:noCountry code="no comma">Green Fuels.</wicri:noCountry></affiliation></author><author><name sortKey="Bumstead, Jon" sort="Bumstead, Jon" uniqKey="Bumstead J" first="Jon" last="Bumstead">Jon Bumstead</name><affiliation><nlm:affiliation>Neutral Consulting Ltd.</nlm:affiliation><wicri:noCountry code="no comma">Neutral Consulting Ltd.</wicri:noCountry></affiliation></author><author><name sortKey="Notley, Louis" sort="Notley, Louis" uniqKey="Notley L" first="Louis" last="Notley">Louis Notley</name><affiliation><nlm:affiliation>Neutral Consulting Ltd.</nlm:affiliation><wicri:noCountry code="no comma">Neutral Consulting Ltd.</wicri:noCountry></affiliation></author><author><name sortKey="Persson, Staffan" sort="Persson, Staffan" uniqKey="Persson S" first="Staffan" last="Persson">Staffan Persson</name><affiliation wicri:level="1"><nlm:affiliation>Max Planck Institute for Molecular Plant Physiology; Plant Cell Biology Research Centre, School of Botany, University of Melbourne; Persson@mpimp-golm.mpg.de.</nlm:affiliation><country wicri:rule="url">Allemagne</country><wicri:regionArea>Max Planck Institute for Molecular Plant Physiology; Plant Cell Biology Research Centre, School of Botany</wicri:regionArea><wicri:noRegion>School of Botany</wicri:noRegion><wicri:noRegion>School of Botany</wicri:noRegion><wicri:noRegion>School of Botany</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of visualized experiments : JoVE</title><idno type="eISSN">1940-087X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animal Feed (MeSH)</term><term>Biofuels (MeSH)</term><term>Biomass (MeSH)</term><term>Chromatography, Liquid (MeSH)</term><term>Gas Chromatography-Mass Spectrometry (MeSH)</term><term>Metabolomics (MeSH)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>Tobacco (genetics)</term><term>Tobacco (metabolism)</term><term>Transcription, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Aliment pour animaux (MeSH)</term><term>Biocarburants (MeSH)</term><term>Biomasse (MeSH)</term><term>Chromatographie en phase liquide (MeSH)</term><term>Chromatographie gazeuse-spectrométrie de masse (MeSH)</term><term>Métabolomique (MeSH)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Tabac (génétique)</term><term>Tabac (métabolisme)</term><term>Transcription génétique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Biofuels</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term><term>Tobacco</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term><term>Tabac</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Populus</term><term>Tobacco</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Populus</term><term>Tabac</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animal Feed</term><term>Biomass</term><term>Chromatography, Liquid</term><term>Gas Chromatography-Mass Spectrometry</term><term>Metabolomics</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Aliment pour animaux</term><term>Biocarburants</term><term>Biomasse</term><term>Chromatographie en phase liquide</term><term>Chromatographie gazeuse-spectrométrie de masse</term><term>Métabolomique</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The global demand for food, feed, energy and water poses extraordinary challenges for future generations. It is evident that robust platforms for the exploration of renewable resources are necessary to overcome these challenges. Within the multinational framework MultiBioPro we are developing biorefinery pipelines to maximize the use of plant biomass. More specifically, we use poplar and tobacco tree (Nicotiana glauca) as target crop species for improving saccharification, isoprenoid, long chain hydrocarbon contents, fiber quality, and suberin and lignin contents. The methods used to obtain these outputs include GC-MS, LC-MS and RNA sequencing platforms. The metabolite pipelines are well established tools to generate these types of data, but also have the limitations in that only well characterized metabolites can be used. The deep sequencing will allow us to include all transcripts present during the developmental stages of the tobacco tree leaf, but has to be mapped back to the sequence of Nicotiana tabacum. With these set-ups, we aim at a basic understanding for underlying processes and at establishing an industrial framework to exploit the outcomes. In a more long term perspective, we believe that data generated here will provide means for a sustainable biorefinery process using poplar and tobacco tree as raw material. To date the basal level of metabolites in the samples have been analyzed and the protocols utilized are provided in this article.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24894952</PMID><DateCompleted><Year>2015</Year><Month>03</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1940-087X</ISSN><JournalIssue CitedMedium="Internet"><Issue>87</Issue><PubDate><Year>2014</Year><Month>05</Month><Day>16</Day></PubDate></JournalIssue><Title>Journal of visualized experiments : JoVE</Title><ISOAbbreviation>J Vis Exp</ISOAbbreviation></Journal><ArticleTitle>Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.3791/51393</ELocationID><Abstract><AbstractText>The global demand for food, feed, energy and water poses extraordinary challenges for future generations. It is evident that robust platforms for the exploration of renewable resources are necessary to overcome these challenges. Within the multinational framework MultiBioPro we are developing biorefinery pipelines to maximize the use of plant biomass. More specifically, we use poplar and tobacco tree (Nicotiana glauca) as target crop species for improving saccharification, isoprenoid, long chain hydrocarbon contents, fiber quality, and suberin and lignin contents. The methods used to obtain these outputs include GC-MS, LC-MS and RNA sequencing platforms. The metabolite pipelines are well established tools to generate these types of data, but also have the limitations in that only well characterized metabolites can be used. The deep sequencing will allow us to include all transcripts present during the developmental stages of the tobacco tree leaf, but has to be mapped back to the sequence of Nicotiana tabacum. With these set-ups, we aim at a basic understanding for underlying processes and at establishing an industrial framework to exploit the outcomes. In a more long term perspective, we believe that data generated here will provide means for a sustainable biorefinery process using poplar and tobacco tree as raw material. To date the basal level of metabolites in the samples have been analyzed and the protocols utilized are provided in this article.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ruprecht</LastName><ForeName>Colin</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Plant Physiology.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tohge</LastName><ForeName>Takayuki</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Plant Physiology.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fernie</LastName><ForeName>Alisdair</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Plant Physiology.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mortimer</LastName><ForeName>Cara L</ForeName><Initials>CL</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kozlo</LastName><ForeName>Amanda</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fraser</LastName><ForeName>Paul D</ForeName><Initials>PD</Initials><AffiliationInfo><Affiliation>School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Funke</LastName><ForeName>Norma</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Plant Physiology.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cesarino</LastName><ForeName>Igor</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vanholme</LastName><ForeName>Ruben</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Boerjan</LastName><ForeName>Wout</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morreel</LastName><ForeName>Kris</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, VIB; Department of Plant Biotechnology and Bioinformatics, UGhent.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Burgert</LastName><ForeName>Ingo</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Institute for Building Materials, ETH Zurich; Applied Wood Materials, EMPA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gierlinger</LastName><ForeName>Notburga</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Institute for Building Materials, ETH Zurich; Applied Wood Materials, EMPA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bulone</LastName><ForeName>Vincent</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Division of Glycoscience, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH).</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schneider</LastName><ForeName>Vera</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>European Research and Project Office GmbH.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stockero</LastName><ForeName>Andrea</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>European Research and Project Office GmbH.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Navarro-Aviñó</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>ABBA Gaia S.L.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pudel</LastName><ForeName>Frank</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Pflanzenöltechnologie.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tambuyser</LastName><ForeName>Bart</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Capax Environmental Services.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hygate</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Green Fuels.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bumstead</LastName><ForeName>Jon</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Neutral Consulting Ltd.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Notley</LastName><ForeName>Louis</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Neutral Consulting Ltd.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Persson</LastName><ForeName>Staffan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Plant Physiology; Plant Cell Biology Research Centre, School of Botany, University of Melbourne; Persson@mpimp-golm.mpg.de.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D059040">Video-Audio Media</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>05</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Vis Exp</MedlineTA><NlmUniqueID>101313252</NlmUniqueID><ISSNLinking>1940-087X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D056804">Biofuels</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>J Vis Exp. 2016 Jun 30;(112):</RefSource><PMID Version="1">27387492</PMID><Note>[Corrected from Navarro, Juan Pedro] [Corrected to Navarro-Aviñó, Juan.]</Note></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000821" MajorTopicYN="N">Animal Feed</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056804" MajorTopicYN="N">Biofuels</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018533" MajorTopicYN="Y">Biomass</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002853" MajorTopicYN="N">Chromatography, Liquid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008401" MajorTopicYN="N">Gas Chromatography-Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055432" MajorTopicYN="N">Metabolomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014026" MajorTopicYN="N">Tobacco</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>6</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>6</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>3</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24894952</ArticleId><ArticleId IdType="doi">10.3791/51393</ArticleId><ArticleId IdType="pmc">PMC4189316</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Plant Physiol. 2010 Aug;153(4):1464-78</Citation><ArticleIdList><ArticleId IdType="pubmed">20554692</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2013 Jun 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sortKey="Boerjan, Wout" sort="Boerjan, Wout" uniqKey="Boerjan W" first="Wout" last="Boerjan">Wout Boerjan</name><name sortKey="Bulone, Vincent" sort="Bulone, Vincent" uniqKey="Bulone V" first="Vincent" last="Bulone">Vincent Bulone</name><name sortKey="Bumstead, Jon" sort="Bumstead, Jon" uniqKey="Bumstead J" first="Jon" last="Bumstead">Jon Bumstead</name><name sortKey="Burgert, Ingo" sort="Burgert, Ingo" uniqKey="Burgert I" first="Ingo" last="Burgert">Ingo Burgert</name><name sortKey="Cesarino, Igor" sort="Cesarino, Igor" uniqKey="Cesarino I" first="Igor" last="Cesarino">Igor Cesarino</name><name sortKey="Fernie, Alisdair" sort="Fernie, Alisdair" uniqKey="Fernie A" first="Alisdair" last="Fernie">Alisdair Fernie</name><name sortKey="Funke, Norma" sort="Funke, Norma" uniqKey="Funke N" first="Norma" last="Funke">Norma Funke</name><name sortKey="Gierlinger, Notburga" sort="Gierlinger, Notburga" uniqKey="Gierlinger N" first="Notburga" last="Gierlinger">Notburga Gierlinger</name><name 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