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Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry

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Organization
Project
Biotechnology for a sustainable economy (Bio-Economy)
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.
Keywords
Environmental Sciences, Issue 87, botany, plants, Biorefining, Poplar, Tobacco tree, Arabidopsis, suberin, lignin, cell walls, biomass, long-chain hydrocarbons, isoprenoids, Nicotiana glauca, systems biology, MASS-SPECTROMETRY, LIQUID-CHROMATOGRAPHY, NICOTIANA-GLAUCA, IDENTIFICATION, METABOLOMICS, BIOFUELS

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Citation

Please use this url to cite or link to this publication:

Chicago
Ruprecht, Colin, Takayuki Tohge, Alisdair Fernie, Cara L Mortimer, Amanda Kozlo, Paul D Fraser, Norma Funke, et al. 2014. “Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry.” Journal of Visualized Experiments 87.
APA
Ruprecht, C., Tohge, T., Fernie, A., Mortimer, C. L., Kozlo, A., Fraser, P. D., Funke, N., et al. (2014). Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry. JOURNAL OF VISUALIZED EXPERIMENTS, 87.
Vancouver
1.
Ruprecht C, Tohge T, Fernie A, Mortimer CL, Kozlo A, Fraser PD, et al. Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry. JOURNAL OF VISUALIZED EXPERIMENTS. 2014;87.
MLA
Ruprecht, Colin, Takayuki Tohge, Alisdair Fernie, et al. “Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry.” JOURNAL OF VISUALIZED EXPERIMENTS 87 (2014): n. pag. Print.
@article{5669817,
  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.},
  articleno    = {e51393},
  author       = {Ruprecht, Colin and Tohge, Takayuki and Fernie, Alisdair and Mortimer, Cara L and Kozlo, Amanda and Fraser, Paul D and Funke, Norma and Cesarino, Igor and Vanholme, Ruben and Boerjan, Wout and Morreel, Kris and Burgert, Ingo and Gierlinger, Notburga and Bulone, Vincent and Schneider, Vera and Stockero, Andrea and Navarro, Juan Pedro and Pudel, Frank and Tambuyser, Bart and Hygate, James and Bumstead, Jon and Notley, Louis and Persson, Staffan},
  issn         = {1940-087X},
  journal      = {JOURNAL OF VISUALIZED EXPERIMENTS},
  language     = {eng},
  pages        = {7},
  title        = {Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry},
  url          = {http://dx.doi.org/10.3791/51393},
  volume       = {87},
  year         = {2014},
}

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