12 research outputs found

    Final ethanol yield (mg g<sup>-1</sup> biomass) of lemongrass and palmarosa biomass that was (EX) or was not (NE) previously extracted for essential oils in comparison to two lots of BioEnergy Science Center (BESC) control switchgrass.

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    <p>A) Final ethanol concentration of biomass that was not pretreated in fermentation liquids. B) Final ethanol yield (mg g<sup>-1</sup> biomass) of dilute acid pretreated lemongrass and palmarosa biomass that was (EX) or was not (NE) extracted for essential oils in comparison to lot #1 BESC control switchgrass.</p

    MOESM1 of Switchgrass (Panicum virgatum L.) promoters for green tissue-specific expression of the MYB4 transcription factor for reduced-recalcitrance transgenic switchgrass

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    Additional file 1: Table S1. Sugars (g/g CWR) released by enzymatic hydrolysis from the transgenic switchgrass lines expressing PvMYB4 under the control of each of the three green tissue-specific promoters. Figure S1. Comparison of the deduced amino acid sequences of the rice Lhcb genes and their homologs in switchgrass. Figure S2. Comparison of the deduced amino acid sequences of the rice PEPC gene and its homologs in switchgrass. Figure S3. Comparison of the deduced amino acid sequences of the rice PsbR genes and their homologs in switchgrass. Figure S4. The gene structures of the three rice Lhcb genes (i.e., OsLhcb1-1, OsLhcb1-2, and OsLhcb2-1, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os09g17740 [54, 55, 57], Os1g41710 [54], and Os03g39610 [55], respectively) and their switchgrass homologs with the highest amino acid sequence similarities. Figure S5. The gene structures of the five plant-type rice PEPC genes (i.e., Osppc1, 2a, 2b, 3, and 4, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os02g0244700, Os08g0366000, Os09g0315700, Os01g0758300, and Os01g0208700, respectively [56]) and their switchgrass homologs with the highest amino acid sequence similarities. Figure S6. The gene structures of the three rice PsbR genes (i.e., OsPsbR1, 2 and 3, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os07g05360, Os07g05365, and Os08g10020, respectively [53]) and their switchgrass homologs with the highest amino acid sequence similarities. Figure S7. The in silico expression profiles of the unitranscript entries of the potential switchgrass homologs of OsLhcb1-1, OsLhcb1-2, and OsLhcb2-1, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os09g17740 [54, 55, 57], Os1g41710 [54], and Os03g39610 [55], respectively, in different tissues of non-transformed switchgrass. Figure S8. The in silico expression profiles of the unitranscript entries of the potential switchgrass homologs of Osppc1, 2a, 2b, 3, and 4, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os02g0244700, Os08g0366000, Os09g0315700, Os01g0758300, and Os01g0208700, respectively [56], in different tissues of non-transformed switchgrass. Figure S9. The in silico expression profiles of the unitranscript entries of the potential switchgrass homologs of OsPsbR1, 2, and 3, whose International Rice Genome Sequencing Project (IRGSP) gene IDs are Os07g05360, Os07g05365, and Os08g10020, respectively [53], in different tissues of non-transformed switchgrass. Figure S10. The 764-bp-long promoter sequence of PvLhcb (i.e., Pavirv00047797m) used in the present study. Figure S11. The 1878-bp-long promoter sequence of PvPEPC (i.e., Pavirv00033161m) used in the present study. Figure S12. The 2009-bp-long promoter sequence of PvPsbR (i.e., Pavirv00009702m) used in the present study. Figure S13. Quantitative fluorometric GUS analysis of leaf blade, leaf sheath, stem, and panicles of T0 stable transgenic rice containing each serial deletion of the PvLhcb promoter at the heading stage. Figure S14. Quantitative fluorometric GUS analysis of leaf blade, leaf sheath, stem, and panicles of T0 stable transgenic rice containing each serial deletion of the PvPEPC promoter at the heading stage

    Ethanol and High-Value Terpene Co-Production from Lignocellulosic Biomass of <i>Cymbopogon flexuosus</i> and <i>Cymbopogon martinii</i>

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    <div><p><i>Cymbopogon flexuosus</i>, lemongrass, and <i>C</i>. <i>martinii</i>, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared to <i>Panicum virgatum</i> (switchgrass). Mean biomass yields were 12.83 Mg lemongrass ha<sup>-1</sup> and 15.11 Mg palmarosa ha<sup>-1</sup> during the second harvest year resulting in theoretical biofuel yields of 2541 and 2569 L ethanol ha<sup>-1</sup> respectively compared to reported 1749–3691 L ethanol ha<sup>-1</sup> for switchgrass. Pretreated lemongrass yielded 198 mL ethanol (g biomass)<sup>-1</sup> and pretreated palmarosa yielded 170 mL ethanol (g biomass)<sup>-1</sup>. Additionally, lemongrass yielded 85.7 kg essential oil ha<sup>-1</sup> and palmarosa yielded 67.0 kg ha<sup>-1</sup> with an estimated value of USD 857and857 and 1005 ha<sup>-1</sup>. These data suggest that dual-use crops such as lemongrass and palmarosa may increase the economic viability of lignocellulosic biofuels.</p></div

    MOESM1 of Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure

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    Additional file 1: Figure A.1. Carbohydrate composition of initially screened Populus biomass. Figure A.2. Fermentation products of Avicel-control CBP cultures. Figure A.3. Carbohydrate content in Populus before and after repeat autoclave sterilization. Figure A.4. Lignin content in Populus before and after repeat autoclave sterilization

    DataSheet1_Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery.pdf

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    <p>Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant's sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomic and pyMBMS data across this population, as well as co-expression and co-methylation networks in order to better understand the molecular interactions involved in recalcitrance, and identify target genes involved in lignin biosynthesis/degradation. A Lines Of Evidence (LOE) scoring system is developed to integrate the information in the different layers and quantify the number of lines of evidence linking genes to target functions. This new scoring system was applied to quantify the lines of evidence linking genes to lignin-related genes and phenotypes across the network layers, and allowed for the generation of new hypotheses surrounding potential new candidate genes involved in lignin biosynthesis in P. trichocarpa, including various AGAMOUS-LIKE genes. The resulting Genome Wide Association Study networks, integrated with Single Nucleotide Polymorphism (SNP) correlation, co-methylation, and co-expression networks through the LOE scores are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.</p

    MOESM6 of Working towards recalcitrance mechanisms: increased xylan and homogalacturonan production by overexpression of GAlactUronosylTransferase12 (GAUT12) causes increased recalcitrance and decreased growth in Populus

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    Additional file 6. Glycosyl residue composition of (a) alcohol insoluble residue (AIR) and (b–h) wall fractions from stems of field-grown P. deltoides control and PtGAUT12.1-OE transgenic plants. Wall fractions were prepared by sequential extraction of AIR using increasingly harsh reagents: (b) 50 mM ammonium oxalate, (c) 50 mM Na2CO3, (d) 1 M KOH, (e) 4 M KOH, (f) 100 mM sodium chlorite (chlorite) and (g) 4 M KOH post-chlorite (4 M KOH PC). (h) The insoluble pellet remaining after all the extractions. Glycosyl residue composition was determined by GC–MS of trimetylsilyl (TMS) derivatives. Data are mean ± SE of three biological and two technical replicates, n = 5. *P < 0.05, **P < 0.001
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