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| | 1. |
2011 Oct 28 |
Transcriptome Analysis of Differentially Expressed Genes During Embryo Sac Development in Apomeiotic Non-Parthenogenetic Interspecific Hybrid of Pennisetum glaucum.
Sahu PP, Gupta S, Malaviya DR, Roy AK, Kaushal P, Prasad M
Mol Biotechnol. 2011 Oct 28; [Epub ahead of print] Abstract
Apomixis results in the production of genetically uniform progeny, derived from the fertilization independent development (parthenogenesis) of an unreduced egg cell (apomeiosis). To identify genes involved in the apomeiosis, a comparative transcriptome analysis of differentially expressed genes during embryo sac (ES) development in a sexual Pennisetum glaucum (genotype 81A1) and its apomeiotic (aposporic) non-parthenogenetic interspecific hybrid (BC1GO) was investigated. BC1GO exhibited the partitioned apomeiosis component, whereby the second apomixis component viz., parthenogenesis was completely lacking. A total of 96 non-redundant transcripts were recovered using suppression subtractive hybridization and classified into 11 different categories according to their putative functions. Amongst the identified transcripts, many of them belonged to unknown function (40%) followed by those involved in protein metabolism, stress response, pollen/ovule/embryo development, and translation/protein modification process. A data search of transcriptional profiling in other apomictic species revealed that 75% of the differentially expressed transcripts have not been reported in previous studies. By macroarray analysis, we identified differential expression pattern of 96 transcripts, 45 (47%) of which showed ≥2-fold induction in apomeiotic BC1GO. Further, the obtained results were validated by quantitative real-time polymerase chain reaction to have a comparative expression profiling of eight selected up-regulated transcripts (≥2.5-fold) between BC1GO and 81A1 at different phases of ovule development. In silico mapping demonstrated that 13 transcripts were located onto rice chromosome 2, region syntenic with the apospory locus as reported in Brachiaria brizantha and Paspalum notatum. The expression patterns of these transcripts showed a significant difference at differentiating megaspore mother cell and gametogenesis stages thereby suggesting their involvement in floral development during apomeiotic (Panicum-type aposporous) ES development. [Pubmed: 22033774] | | 2. |
2011 Nov 28 |
Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia.
Gladden JM, Eichorst SA, Hazen TC, Simmons BA, Singer SW
Biotechnol Bioeng. 2011 Nov 28; [Epub ahead of print] Abstract
Bacteria modulate glycoside hydrolase expression in response to the changes in the composition of lignocellulosic biomass. The response of switchgrass-adapted thermophilic bacterial consortia to perturbation with a variety of biomass substrates was characterized to determine if bacterial consortia also responded to changes in biomass composition. Incubation of the switchgrass-adapted consortia with these alternative substrates produced shifts in glycoside hydrolase activities and bacterial community composition. Substantially increased endoglucanase activity was observed upon incubation with microcrystalline cellulose and trifluororacetic acid-pretreated switchgrass. In contrast, culturing the microbial consortia with ionic liquid-pretreated switchgrass increased xylanase activity dramatically. Microbial community analyses of these cultures indicated that the increased endoglucanase activity correlated with an increase in bacteria related to Rhodothermus marinus. Inclusion of simple organic substrates in the culture medium abrogated glycoside hydrolase activity and enriched for bacteria related to Thermus thermophilus. These results demonstrate that the composition of biomass substrates influences the glycoside hydrolase activities and community composition of biomass-deconstructing bacterial consortia. Biotechnol. Bioeng. © 2011 Wiley Periodicals, Inc. [Pubmed: 22125273] | | 3. |
2012 Jan 12 |
Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production.
Fu C, Sunkar R, Zhou C, Shen H, Zhang JY, Matts J, Wolf J, Mann DG, Stewart CN, Tang Y, Wang ZY
Plant Biotechnol J. 2012 Jan 12; [Epub ahead of print] Abstract
Switchgrass (Panicum virgatum L.) has been developed into a dedicated herbaceous bioenergy crop. Biomass yield is a major target trait for genetic improvement of switchgrass. microRNAs have emerged as a prominent class of gene regulatory factors that has the potential to improve complex traits such as biomass yield. A miR156b precursor was overexpressed in switchgrass. The effects of miR156 overexpression on SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes were revealed by microarray and quantitative RT-PCR analyses. Morphological alterations, biomass yield, saccharification efficiency and forage digestibility of the transgenic plants were characterized. miR156 controls apical dominance and floral transition in switchgrass by suppressing its target SPL genes. Relatively low levels of miR156 overexpression were sufficient to increase biomass yield while producing plants with normal flowering time. Moderate levels of miR156 led to improved biomass but the plants were non-flowering. These two groups of plants produced 58%-101% more biomass yield compared with the control. However, high miR156 levels resulted in severely stunted growth. The degree of morphological alterations of the transgenic switchgrass depends on miR156 level. Compared with floral transition, a lower miR156 level is required to disrupt apical dominance. The improvement in biomass yield was mainly because of the increase in tiller number. Targeted overexpression of miR156 also improved solubilized sugar yield and forage digestibility, and offered an effective approach for transgene containment. [Pubmed: 22239253] | | 4. |
2012 Feb 14 |
A thermochemical pretreatment process to produce xylooligosaccharides (XOS), arabinooligosaccharides (AOS) and mannooligosaccharides (MOS) from lignocellulosic biomasses.
Otieno DO, Ahring BK
Bioresour. Technol. 2012 May;112:285-92. Epub 2012 Feb 14. Abstract
Efficient and high yield production of xylooligosaccharides, arabinooligosaccharide and mannooligosaccharides from biomasses is a significant boost to the nutraceutical and pharmaceutical industry. These organic compounds, also known as prebiotics, promote the growth of intestinal probiotic microorganisms thus improving the hosts' overall immune system. This work aimed at designing a thermochemical pretreatment of biomasses leading to production of high prebiotic yields and assessing the liquor quality based on resultant oligomer-monomer constituents. Four biomasses, namely Miscanthus sinensis, Panicum virgatum, Calamagrostis acutiflora and Bagasse, each having a dry weight xylan content of ⩾20% were used. Identification and quantification using HPLC and ion chromatography systems showed xylooligomer yields of 65.0%, 84.2%, 87.9% and 92.3%, respectively. The xylooligomers also showed a degree of polymerization ranging from 2 to 25. These results demonstrate the potential of a low cost, pretreatment process of biomasses which may be suitable for a commercial scale production of prebiotics. [Pubmed: 22425397] | | 5. |
2012 Mar 07 |
Hydrolytic potential of Trichoderma sp. strains evaluated by microplate-based screening followed by switchgrass saccharification.
Cianchetta S, Galletti S, Burzi PL, Cerato C
Enzyme Microb. Technol. 2012 May 10;50(6-7):304-10. Epub 2012 Mar 07. Abstract
Bioconversion of lignocellulosic biomass to fuel requires a hydrolysis step to obtain fermentable sugars, generally accomplished by fungal enzymes. Large-scale screening of different microbial strains would provide optimal enzyme cocktails for any target feedstock. The aim of this study was to screen a large collection of Trichoderma sp. strains for the hydrolytic potential towards switchgrass (Panicum virgatum L.). Strains were cultivated in a small-scale system and assayed in micro-plates for xylanase and cellulase activities. The population distributions of these traits are reported after growth on switchgrass in comparison with cellulose. The distribution profiles suggest that the growth on switchgrass strongly promotes xylanase production. The IK4 strain displayed the highest xylanase activity after growth on switchgrass (133U/mL). Enzymes (10FPU/g substrate) from IK4 were compared with those from 2 cellulolytic Trichoderma strains and a commercial enzyme in saccharification time-course experiments on untreated and pretreated switchgrass and on an artificial substrate. Samples were analysed by DNS assay and by an oxygraphic method for sugar equivalent or glucose concentration. On the untreated substrate, IK4 enzymes even outperformed a 5-fold load of commercial enzyme, suggesting that xylanase or accessory enzymes are a limiting factor on this type of recalcitrant substrate. On the other substrates, IK4 preparations showed intermediate behaviour if compared with the commercial enzyme at 10FPU/g substrate and at 5-fold load. IK4 also nearly halved the time to release 50% of the hydrolysable sugar equivalents (T(50%)), with respect to the other preparations at the same enzymatic load. DNS assay and oxygraphic method gave highly correlated results for the 3 saccharified substrates. The study suggests that accessory enzymes like xylanase play a key role in improving the performance of cellulase preparations on herbaceous lignocellulosic feedstocks like switchgrass. [Pubmed: 22500897] | | 6. |
2012 Apr 25 |
Model evaluation of plant metal content and biomass yield for the phytoextraction of heavy metals by switchgrass.
Chen BC, Lai HY, Juang KW
Ecotoxicol Environ Saf. 2012 Apr 25; [Epub ahead of print] Abstract
To better understand the ability of switchgrass (Panicum virgatum L.), a perennial grass often relegated to marginal agricultural areas with minimal inputs, to remove cadmium, chromium, and zinc by phytoextraction from contaminated sites, the relationship between plant metal content and biomass yield is expressed in different models to predict the amount of metals switchgrass can extract. These models are reliable in assessing the use of switchgrass for phytoremediation of heavy-metal-contaminated sites. In the present study, linear and exponential decay models are more suitable for presenting the relationship between plant cadmium and dry weight. The maximum extractions of cadmium using switchgrass, as predicted by the linear and exponential decay models, approached 40 and 34μgpot(-1), respectively. The log normal model was superior in predicting the relationship between plant chromium and dry weight. The predicted maximum extraction of chromium by switchgrass was about 56μgpot(-1). In addition, the exponential decay and log normal models were better than the linear model in predicting the relationship between plant zinc and dry weight. The maximum extractions of zinc by switchgrass, as predicted by the exponential decay and log normal models, were about 358 and 254μgpot(-1), respectively. To meet the maximum removal of Cd, Cr, and Zn, one can adopt the optimal timing of harvest as plant Cd, Cr, and Zn approach 450 and 526mgkg(-1), 266mgkg(-1), and 3022 and 5000mgkg(-1), respectively. Due to the well-known agronomic characteristics of cultivation and the high biomass production of switchgrass, it is practicable to use switchgrass for the phytoextraction of heavy metals in situ. [Pubmed: 22541831] | | 7. |
2012 Apr 19 |
Productive performance and urinary excretion of mimosine metabolites by hair sheep grazing in a silvopastoral system with high densities of Leucaena leucocephala.
Barros-Rodríguez M, Solorio-Sánchez J, Ku-Vera J, Ayala-Burgos A, Sandoval-Castro C, Solís-Pérez G
Trop Anim Health Prod. 2012 Apr 19; [Epub ahead of print] Abstract
The aim of this study was to evaluate daily weight gain (DWG), total dry matter (DM) intake, rumen degradability of forage, and urinary excretion of mimosine metabolites by hair sheep in a silvopastoral system with high densities of Leucaena leucocephala. A completely randomized design was carried out with two treatments: treatment 1 (T1) silvopastoral system with leucaena at a density of 35,000 plants/ha and treatment 2 (T2), leucaena at a density of 55,000 plants/ha. Leucaena was associated with tropical grasses Panicum maximum and Cynodon nlemfluensis. Twenty-four male Pelibuey lambs of 23.2 ± 3.4 kg live weight (LW) were used (12 lambs per treatment). Results showed differences (P < 0.05) in DWG of T1 (106.41 ± 11.66 g(-1) sheep(-1)) with respect to that of T2 (81.33 ± 11.81 g(-1) sheep). Voluntary intake was higher in lambs from T1 (83.81 ± 04.07 g DM/kg LW(0.75)) with respect to that from T2 (71.67 ± 8.12 g DM/kg LW(0.75)). There was a difference in color of urine between sheep of T1 and T2, the latter giving positive results for the presence of metabolites derived from mimosine (3-4 dihydroxypyridine and 2-3 dihydroxy pyridone). Rumen degradability of DM of L. leucocephala was higher (P < 0.05) compared to that of P. maximum and C. nlemfluensis (72.94 ± 0.40 vs. 67.06 ± 1.50 and 63.25 ± 1.51 %, respectively). It is concluded that grazing at high densities of L. leucocephala affects daily weight gain of hair sheep, possibly due to ingestion of high amounts of mimosine which may exert an adverse effect on voluntary intake. [Pubmed: 22528536] | | 8. |
2012 Jan 28 |
Sodium hydroxide pretreatment of genetically modified switchgrass for improved enzymatic release of sugars.
Wang Z, Li R, Xu J, Marita JM, Hatfield RD, Qu R, Cheng JJ
Bioresour. Technol. 2012 Apr;110:364-70. Epub 2012 Jan 28. Abstract
Overcoming biomass recalcitrance to bioconversion is crucial for cellulosic biofuels commercialization. In this study, Alamo switchgrass (Panicum virgatum L.) was genetically transformed to suppress the expression of 4-coumarate-CoA ligase (4CL). The transgenic plants were determined to have lignin content reductions of up to 5.8%. The ratios of acid soluble lignin (ASL) to acid insoluble lignin (AIL) and syringyl/guaiacyl (S/G) in transgenic plants were 21.4-64.3% and 11.8-164.5%, respectively, higher than those of conventional biomass. Both conventional and transgenic plants were pretreated with 0.5%, 1%, and 2% (w/v) NaOH for 15, 30, and 60min at 121°C, followed by enzymatic hydrolysis with commercial cellulases and xylanases. At the optimal conditions, the glucan and xylan conversion efficiency in the best transgenic plants were 16% and 18% higher than the conventional plant, respectively. The results show that down-regulation of 4CL gene promoted enzymatic hydrolysis of plant cell walls following a mild alkali pretreatment. [Pubmed: 22330602] | | 9. |
2012 Mar 3 |
Molecular characterisation of dicot-infecting mastreviruses from Australia.
Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A
Virus Res. 2012 Mar 3; [Epub ahead of print] Abstract
Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus. [Pubmed: 22406325] | | 10. |
2012 Feb 11 |
Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research.
Meyer E, Logan TL, Juenger TE
Plant J. 2012 Feb 11; [Epub ahead of print] Abstract
Panicum hallii is an emerging model for genetic studies of agronomic traits in Panicum, presenting a tractable diploid alternative study system to the tetra- or octaploid biofuel crop switchgrass (P. virgatum). To characterize the gene complement in P. hallii var. filipes and enable gene expression analysis in this system we sequenced, assembled, and annotated the transcriptome. Over 300 Mb of normalized cDNA prepared from multiple tissues and treatments was sequenced using 454-Titanium, producing an annotated assembly including 15,422 unique gene names. Comparison with other grass genomes identified putative P. hallii homologs for >14,000 previously characterized genes. We also developed an atlas of gene expression across tissues and stages using RNA-Seq. SOLiD sequencing and quantitative analysis of more than 40 million cDNA tags identified substantial variation in expression profiles among tissues, consistent with known functional differences. Putative homologs were found for all enzymes in the phenylpropanoid pathway leading to lignin biosynthesis, including genes with known effects on biomass conversion efficiency. The resources developed here will enable studies of the genes underlying variation in cell wall composition, drought tolerance, and biomass production in Panicum. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd. [Pubmed: 22324449] | | 11. |
2012 May 13 |
Reference genome sequence of the model plant Setaria.
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM
Nat Biotechnol. 2012 May 13; [Epub ahead of print] Abstract
We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum). [Pubmed: 22580951] | | 12. |
2012 Feb 21 |
Early millet use in northern China.
Yang X, Wan Z, Perry L, Lu H, Wang Q, Zhao C, Li J, Xie F, Yu J, Cui T, Wang T, Li M, Ge Q
Proc. Natl. Acad. Sci. U.S.A. 2012 Mar 6;109(10):3726-30. Epub 2012 Feb 21. Abstract
It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5-11.0 cal kyBP) and Donghulin (11.0-9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place. [Pubmed: 22355109] | | 13. |
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[Herbicide activity of some micromycetes].
Savchuk IaI
Mikrobiol. Z.;74(3):43-8. Abstract
Screening of phytotoxic properties of 5 micromycete strains were made concerning cultivated plants and weeds. All of the strains show phytotoxic activity of different levels. In particular, the cultural filtrates of Penicillium sp. 10-51 and Aspergillus niveus 2411 suppressed the growth of seeds of Galinsoga parviflora, Amaranthus retroflexus and Capsella bursa pastoris. The cultural filtrate of Ulocladium consortiale 960 suppressed the growth of Panicum capillare and Setaria viridis. The greatest phytotoxic activity was shown by the cultural filtrates of Myrothecium cinctum 903 and 910, on the one hand, both of them suppressed the growth of seeds of E. virgata completely, but, on the other hand, they did not take any effect on the seeds of radish. [Pubmed: 22830196] | | 14. |
2012 Jun 4 |
Complete genome sequence of switchgrass mosaic virus, a member of a proposed new species in the genus Marafivirus.
Agindotan BO, Gray ME, Hammond RW, Bradley CA
Arch Virol. 2012 Jun 4; [Epub ahead of print] Abstract
The complete genome sequence of a virus recently detected in switchgrass (Panicum virgatum) was determined and found to be closely related to that of maize rayado fino virus (MRFV), genus Marafivirus, family Tymoviridae. The genomic RNA is 6408 nucleotides long. It contains three predicted open reading frames (ORFs 1-3), encoding proteins of 227 kDa, 43.9 kDa, and 31.5 kDa, compared to two ORFs (1 and 2) for MRFV. The complete genome shares 76 % sequence identity with MRFV. The nucleotide sequence of ORF2 of this virus and the amino acid sequence of its encoded protein are 49 % and 77 % identical, respectively, to those of MRFV. The virus-encoded polyprotein and capsid protein aa sequences are 83 % and 74-80 % identical, respectively, to those of MRFV. Although closely related to MRFV, the amino acid sequence of its capsid protein (CP) forms a clade that is separate from that of MRFV. Based on the International Committee on Taxonomy of Viruses (ICTV) sequence-related criteria for delineation of species within the genus Marafivirus, the virus qualifies as a member of a new species, and the name Switchgrass mosaic virus (SwMV) is proposed. [Pubmed: 22661377] | | 15. |
2012 Jun 10 |
Nitrogen-fixing bacteria, arbuscular mycorrhizal fungi, and the productivity and structure of prairie grassland communities.
Bauer JT, Kleczewski NM, Bever JD, Clay K, Reynolds HL
Oecologia. 2012 Jun 10; [Epub ahead of print] Abstract
Due to their complementary roles in meeting plant nutritional needs, arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (N(2)-fixers) may have synergistic effects on plant communities. Using greenhouse microcosms, we tested the effects of AMF, N(2)-fixers (symbiotic: rhizobia, and associative: Azospirillum brasilense), and their potential interactions on the productivity, diversity, and species composition of diverse tallgrass prairie communities and on the productivity of Panicum virgatum in monoculture. Our results demonstrate the importance of AMF and N(2)-fixers as drivers of plant community structure and function. In the communities, we found a positive effect of AMF on diversity and productivity, but a negative effect of N(2)-fixers on productivity. Both AMF and N(2)-fixers affected relative abundances of species. AMF shifted the communities from dominance by Elymus canadensis to Sorghastrum nutans, and seven other species increased in abundance with AMF, accounting for the increased diversity. N(2)-fixers led to increases in Astragalus canadensis and Desmanthus illinoense, two legumes that likely benefited from the presence of the appropriate rhizobia symbionts. Sorghastrum nutans declined 44 % in the presence of N(2)-fixers, with the most likely explanation being increased competition from legumes. Panicum monocultures were more productive with AMF, but showed no response to N(2)-fixers, although inference was constrained by low Azospirillum treatment effectivity. We did not find interactions between AMF and N(2)-fixers in communities or Panicum monocultures, indicating that short-term effects of these microbial functional groups are additive. [Pubmed: 22684866] | | 16. |
2012 Jun |
Silica and nitrogen modulate physical defense against chewing insect herbivores in bioenergy crops Miscanthus x Giganteus and Panicum virgatum (Poaceae).
Nabity PD, Orpet R, Miresmailli S, Berenbaum MR, DeLucia EH
J. Econ. Entomol. 2012 Jun;105(3):878-83. Abstract
Feedstock crops selected for bioenergy production to date are almost exclusively perennial grasses because of favorable physiological traits that enhance growth, water use, and nutrient assimilation efficiency. Grasses, however, tend to rely primarily on physical defenses, such as silica, to deter herbivores. Silica impedes processing of feedstocks and introduces a trade-off between managing for cost efficiency (i.e., yield) and plant defenses. To test how silica modulates herbivory in two of the most preferred feedstock crops for production across the central United States, miscanthus (Miscanthus x giganteus Greef and Deuter ex Hodkinson and Renvoize) and switchgrass (Panicum virgatum L.), we examined the performance of two immature generalist insect herbivores, fall armyworm (Spodoptera frugiperda (J.E. Smith) and the American grasshopper [Schistocerca americana (Drury)], on grasses grown under silica and nitrogen amendment. Both miscanthus and switchgrass assimilated nitrogen and silica when grown in amended soil that altered the consumption and conversion efficiency of herbivores consuming leaf tissue. The magnitude of nutrient assimilation, however, depended on intrinsic plant traits. Nitrogen increased conversion efficiency for both fall armyworm and American grasshopper but increased consumption rate only for fall armyworm. Silica reduced conversion efficiency and increased consumption rate only for the American grasshopper. Because of this variability, management strategies that reduce silica or increase nitrogen content in feedstock crops to enhance yields may directly influence the ability of bioenergy grasses to deter certain generalist herbivores. [Pubmed: 22812125] | | 17. |
2012 Jun 22 |
Endophytic insect-parasitic fungi translocate nitrogen directly from insects to plants.
Behie SW, Zelisko PM, Bidochka MJ
Science. 2012 Jun 22;336(6088):1576-7. Abstract
Most plants obtain nitrogen through nitrogen-fixing bacteria and microbial decomposition of plant and animal material. Many vascular plants are able to form close symbiotic associations with endophytic fungi. Metarhizium is a common plant endophyte found in a large number of ecosystems. This abundant soil fungus is also a pathogen to a large number of insects, which are a source of nitrogen. It is possible that the endophytic capability and insect pathogenicity of Metarhizium are coupled to provide an active method of nitrogen transfer to plant hosts via fungal mycelia. We used soil microcosms to test the ability of M. robertsii to translocate insect-derived nitrogen to plants. Insects were injected with (15)N-labeled nitrogen, and we tracked the incorporation of (15)N into amino acids in two plant species, haricot bean (Phaseolus vulgaris) and switchgrass (Panicum virgatum), in the presence of M. robertsii. These findings are evidence that active nitrogen acquisition by plants in this tripartite interaction may play a larger role in soil nitrogen cycling than previously thought. [Pubmed: 22723421] | | 18. |
2012 Aug 7 |
Leaching and ponding of viral contaminants following land application of biosolids on sandy-loam soil.
Wong K, Harrigan T, Xagoraraki I
J. Environ. Manage. 2012 Aug 7;112C:79-86. Epub 2012 Aug 7. Abstract
Much of the land available for application of biosolids is cropland near urban areas. Biosolids are often applied on hay or grassland during the growing season or on corn ground before planting or after harvest in the fall. In this study, mesophilic anaerobic digested (MAD) biosolids were applied at 56,000 L/ha on a sandy-loam soil over large containment lysimeters seeded to perennial covers of orchardgrass (Dactylis glomerata L.), switchgrass (Panicum virgatum), or planted annually to maize (Zea mays L.). Portable rainfall simulators were to maintain the lysimeters under a nearly saturated (90%, volumetric basis) conditions. Lysimeter leachate and surface ponded water samples were collected and analyzed for somatic phage, adenoviruses, and anionic (chloride) and microbial (P-22 bacteriophage) tracers. Neither adenovirus nor somatic phage was recovered from the leachate samples. P-22 bacteriophage was found in the leachate of three lysimeters (removal rates ranged from 1.8 to 3.2 log(10)/m). Although the peak of the anionic tracer breakthrough occurred at a similar pore volume in each lysimeter (around 0.3 pore volume) the peak of P-22 breakthrough varied between lysimeters (<0.1, 0.3 and 0.7 pore volume). The early time to peak breakthrough of anionic and microbial tracers indicated preferential flow paths, presumably from soil cracks, root channels, worm holes or other natural phenomena. The concentration of viral contaminants collected in ponded surface water ranged from 1 to 10% of the initial concentration in the applied biosolids. The die off of somatic phage and P-22 in the surface water was fit to a first order decay model and somatic phage reached background level at about day ten. In conclusion, sandy-loam soils can effectively remove/adsorb the indigenous viruses leached from the land-applied biosolids, but there is a potential of viral pollution from runoff following significant rainfall events when biosolids remain on the soil surface. [Pubmed: 22885066] | | 19. |
2012 Jul 28 |
Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions.
McClendon SD, Baath T, Petzold CJ, Adams PD, Simmons BA, Singer SW
Biotechnol Biofuels. 2012 Jul 28;5(1):54. Epub 2012 Jul 28. Abstract
ABSTRACT: BACKGROUND: Thermophilic fungi have attracted increased interest for their ability to secrete enzymes that deconstruct biomass at high temperatures. However, development of thermophilic fungi as enzyme producers for biomass deconstruction has not been thoroughly investigated. Comparing the enzymatic activities of thermophilic fungal strains that grow on targeted biomass feedstocks has the potential to identify promising candidates for strain development. Thielavia terrestris and Thermoascus aurantiacus were chosen for characterization based on literature precedents. RESULTS: Thermoascus aurantiacus and Thielavia terrestris were cultivated on various biomass substrates and culture supernatants assayed for glycoside hydrolase activities. Supernatants from both cultures possessed comparable glycoside hydrolase activities when incubated with artificial biomass substrates. In contrast, saccharifications of crystalline cellulose and ionic liquid-pretreated switchgrass (Panicum virgatum) revealed that T. aurantiacus enzymes released more glucose than T. terrestris enzymes over a range of protein mass loadings and temperatures. Temperature-dependent saccharifications demonstrated that the T. aurantiacus proteins retained higher levels of activity compared to a commercial enzyme mixture sold by Novozymes, Cellic CTec2, at elevated temperatures. Enzymes secreted by T. aurantiacus released glucose at similar protein loadings to CTec2 on dilute acid, ammonia fiber expansion, or ionic liquid pretreated switchgrass. Proteomic analysis of the T. aurantiacus culture supernatant revealed dominant glycoside hydrolases from families 5, 7, 10, and 61, proteins that are key enzymes in commercial cocktails. CONCLUSIONS: T. aurantiacus produces a complement of secreted proteins capable of higher levels of saccharification of pretreated switchgrass than T. terrestris enzymes. The T. aurantiacus enzymatic cocktail performs at the same level as commercially available enzymatic cocktail for biomass deconstruction, without strain development or genetic modifications. Therefore, T. aurantiacus provides an excellent platform to develop a thermophilic fungal system for enzyme production for the conversion of biomass to biofuels. [Pubmed: 22839529] | | 20. |
2012 Jul 26 |
Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass.
Young HA, Sarath G, Tobias CM
BMC Plant Biol. 2012 Jul 26;12(1):117. Epub 2012 Jul 26. Abstract
ABSTRACT: BACKGROUND: Karyotypes can provide information about taxonomic relationships, genetic aberrations, and the evolutionary origins of species. However, differentiation of the tiny chromosomes of switchgrass (Panicum virgatum L.) and creation of a standard karyotype for this bioenergy crop has not been accomplished due to lack of distinguishing features and polyploidy. RESULTS: A cytogenetic study was conducted on a dihaploid individual (2n=2X=18) of switchgrass to establish a chromosome karyotype. Size differences, condensation patterns, and arm-length ratios were used as identifying features and fluorescence in-situ hybridization (FISH) assigned 5S and 45S rDNA loci to chromosomes 7 and 2 respectively. Both a maize CentC and a native switchgrass centromeric repeat (PviCentC) that shared 73% sequence identity demonstrated a strong signal on chromosome 3. However, only the PviCentC probe labeled the centromeres of all chromosomes. Unexpected PviCentC and 5S rDNA hybidization patterns were consistent with severe reduction or total deletion of these repeats in one subgenome. These patterns were maintained in tetraploid and octoploid individuals. The 45S rDNA repeat produced the expected number of loci in dihaploid, tetraploid and octoploid individuals. Differences observed at the 5S rDNA loci between the upland and lowland ecotypes of switchgrass provided a basis for distinguishing these subpopulations. CONCLUSION: Collectively, these results provide a quantitative karyotype of switchgrass chromosomes. FISH analyses indicate genetic divergence between subgenomes and allow for the classification of switchgrass plants belonging to divergent genetic pools. Furthermore, the karyotype structure and cytogenetic analysis of switchgrass provides a framework for future genetic and genomic studies. [Pubmed: 22834676] | | 21. |
2012 Jul 14 |
Photosynthetic responses of a C(3) and three C (4) species of the genus Panicum (s.l.) with different metabolic subtypes to drought stress.
Alfonso SU, Brüggemann W
Photosynth Res. 2012 Jul 14; [Epub ahead of print] Abstract
Young plants of Panicum bisulcatum (C(3)), Zuloagaea bulbosa [NADP-malic enzyme (ME)-C(4)], P. miliaceum (NAD-ME-C(4)) and Urochloa maxima [phosphoenolpyruvate carboxykinase (PCK)-C(4)] were subjected to drought stress (DS) in soil for 6 days. The C(3) species showed severe wilting symptoms at higher soil water potential (-1.1 MPa) and relative leaf water content (77 %) than in the case of the C(4) species (-1.5 to -1.7 MPa; 58-64 %). DS decreased photosynthesis, both under atmospheric and under saturating CO(2). Stomatal limitation of net photosynthesis (P (N)) in the C(3), but not in the C(4) species was indicated by P (N)/C (o) curves. Chlorophyll fluorescence of photosystem II, resulting from different cell types in the four species, indicated NADPH accumulation and non-stomatal limitation of photosynthesis in all four species, even under high CO(2). In the NAD-ME-C(4) and the PCK-C(4) species, DS plants showed increased violaxanthin de-epoxidase rates. Biochemical analyses of carboxylating enzymes and in vitro enzyme activities of the C(4) enzymes identified the most likely non-stomatal limiting steps of photosynthesis. In P. bisulcatum, declining RubisCO content and activity would explain the findings. In Z. bulbosa, all photosynthesis enzymes declined significantly; photosynthesis is probably limited by the turnover rate of the PEPC reaction. In P. miliaceum, all enzyme levels remained fairly constant under DS, but photosynthesis can be limited by feedback inhibition of the Calvin cycle, resulting in asp inhibition of PEPC. In U. maxima, declines of in vivo PEPC activity and feedback inhibition of the Calvin cycle are the main candidates for non-stomatal limitation of photosynthesis under DS. [Pubmed: 22797823] | | 22. |
2012 Jul 5 |
Model analysing the antioxidant responses of leaves and roots of switchgrass to NaCl-salinity stress.
Wang Q, Wu C, Xie B, Liu Y, Cui J, Chen G, Zhang Y
Plant Physiol. Biochem. 2012 Jul 5;58C:288-296. Epub 2012 Jul 5. Abstract
Salinity is a major environmental stress and a substantial constraint on plant production. The objective of this research was to better understand the mechanisms of the antioxidant responses of leaves and roots to NaCl-salinity stress in switchgrass (Panicum virgatum L.). The effects of NaCl-salinity stress (1, 3, 5, 10 and 15gNaCl/kgdrysoil) on lipid peroxidation and antioxidant defences in switchgrass leaves and roots were investigated, and a model analysis was conducted. The results of the correlation analyses indicated that CAT, POD and SOD were more important than APX, GSH and MDA, whereas the model analyses suggested that the latter three biochemical indices were more sensitive than the former three indices to NaCl-salinity in switchgrass. The connective models of APX, GSH, MDA, CAT, SOD and POD between leaves and roots were obtained, respectively. The new models can be used to closely predict the biochemical index values in switchgrass roots or leaves. [Pubmed: 22871483] | | 23. |
2012 Jul 3 |
A RIBOSOME-BINDING, 3' TRANSLATIONAL ENHANCER HAS A T-SHAPED STRUCTURE AND ENGAGES IN A LONG DISTANCE RNA:RNA INTERACTION.
Gao F, Kasprzak W, Stupina VA, Shapiro BA, Simon AE
J Virol. 2012 Jul 3; [Epub ahead of print] Abstract
Many plant RNA viruses contain elements in their 3' UTRs that enhance translation. The PTE (Panicum mosaic virus-like translational enhancer) of Pea enation mosaic virus (PEMV) binds to eIF4E, but how this affects translation from the 5' end is unknown. We have discovered a three-way branched element just upstream of the PEMV PTE that engages in a long-distance kissing-loop interaction with a coding sequence hairpin that is critical for translation of a reporter construct and accumulation of the viral genome in vivo. Loss of the long-distance interaction was more detrimental than elimination of the adjacent PTE, indicating that the RNA:RNA interaction supports additional translation functions besides relocating the PTE to the 5' end. The branched element is predicted by molecular modeling and molecular dynamics to form a T-shaped structure (TSS) that is similar to the ribosome-binding TSS of Turnip crinkle virus (TCV). The PEMV element binds to plant 80S ribosomes with a K(d) = 0.52 μM and 60S subunits with a K(d) = 0.30 μM. Unlike the TCV TSS, the PEMV element also binds 40S subunits (K(d) = 0.36 μM). Mutations in the element that suppressed translation either reduced ribosome binding or the RNA:RNA interaction, suggesting that ribosome binding is important for function. This novel, multifunctional element is designated a kl-TSS (kissing-loop T-shaped structure) to distinguish it from the TCV TSS. The kl-TSS has sequence and structural features conserved with the upper portion of most PTE-type elements, which, with the exception of the PEMV PTE, can engage in similar long-distance RNA:RNA interactions. [Pubmed: 22761367] | | 24. |
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Switchgrass biochar affects two aridisols.
Ippolito JA, Novak JM, Busscher WJ, Ahmedna M, Rehrah D, Watts DW
J. Environ. Qual.;41(4):1123-30. Abstract
The use of biochar has received growing attention because of its ability to improve the physicochemical properties of highly weathered Ultisols and Oxisols, yet very little research has focused on its effects in Aridisols. We investigated the effect of low or high temperature (250 or 500°C) pyrolyzed switchgrass () biochar on two Aridisols. In a pot study, biochar was added at 2% w/w to a Declo loam (Xeric Haplocalcids) or to a Warden very fine sandy loam (Xeric Haplocambids) and incubated at 15% moisture content (by weight) for 127 d; a control (no biochar) was also included. Soils were leached with 1.2 to 1.3 pore volumes of deionized HO on Days 34, 62, 92, and 127, and cumulative leachate Ca, K, Mg, Na, P, Cu, Fe, Mn, Ni, Zn, NO-N, NO-N, and NH-N concentrations were quantified. On termination of the incubation, soils were destructively sampled for extractable Cr, Cu, Fe, K, Mg, Mn, Na, Ni, P, Zn, NO-N, and NH-N, total C, inorganic C, organic C, and pH. Compared with 250°C, the 500°C pyrolysis temperature resulted in greater biochar surface area, elevated pH, higher ash content, and minimal total surface charge. For both soils, leachate Ca and Mg decreased with the 250°C switchgrass biochar, likely due to binding by biochar's functional group sites. Both biochars caused an increase in leachate K, whereas the 500°C biochar increased leachate P. Both biochars reduced leachate NO-N concentrations compared with the control; however, the 250°C biochar reduced NO-N concentrations to the greatest extent. Easily degradable C, associated with the 250°C biochar's structural make-up, likely stimulated microbial growth, which caused NO-N immobilization. Soil-extractable K, P, and NO-N followed a pattern similar to the leachate observations. Total soil C content increases were linked to an increase in organic C from the biochars. Cumulative results suggest that the use of switchgrass biochar prepared at 250°C could improve environmental quality in calcareous soil systems by reducing nutrient leaching potential. [Pubmed: 22751054] | | 25. |
2012 Jun 26 |
A simplified protocol for genetic transformation of switchgrass (Panicum virgatum L.).
Ramamoorthy R, Kumar PP
Plant Cell Rep. 2012 Jun 26; [Epub ahead of print] Abstract
The increasing interest in renewable energy has attracted more research attention on biofuels. In order to generate sustainable amount of biomass feedstock from dedicated biofuel crops such as switchgrass they need to be genetically improved. Genetic transformation is one of the techniques to achieve this goal. The aim of our study was to devise a simplified protocol for switchgrass genetic transformation. We have used NB(0) as the basal medium and mature seeds of the cultivar Alamo as the starting material. The nutrient medium used and scutellum-derived callus are fashioned after rice genetic transformation protocols. We obtained friable calluses, which were similar to the type II calluses in other monocotyledonous species. Calluses were amenable for Agrobacterium-mediated genetic transformation with at least 6 % transformation efficiency. The concentration of hygromycin was optimized for successful selection of transgenic calluses. The Green Fluorescent Protein gene was used to monitor and demonstrate successful genetic transformation. Compared to the previously published methods for genetic transformation of switchgrass, our protocol is simpler and equally efficient. KEY MESSAGE: An efficient, simplified switchgrass genetic transformation method with NB(0) basal medium and mature seeds as inoculum was developed. The appropriate concentrations of hormones and selection agent are described. [Pubmed: 22733209] | | 26. |
2012 Jan 07 |
Two-temperature stage biphasic CO2-H2O pretreatment of lignocellulosic biomass at high solid loadings.
Luterbacher JS, Tester JW, Walker LP
Biotechnol. Bioeng. 2012 Jun;109(6):1499-507. Epub 2012 Jan 07. Abstract
Most biomass pretreatment processes for monosaccharide production are run at low-solid concentration (<10 wt%) and use significant amounts of chemical catalysts. Biphasic CO(2) -H(2) O mixtures could provide a more sustainable pretreatment medium while using high-solid contents. Using a stirred reactor for high solids (40 wt%, biomass water mixture) biphasic CO(2)-H(2) O pretreatment of lignocellulosic biomass allowed us to explore the effects of particle size and mixing on mixed hardwood and switchgrass pretreatment. Subsequently, a two-temperature stage pretreatment was introduced. After optimization, a short high-temperature stage at 210°C (16 min for hardwood and 1 min for switchgrass) was followed by a long low-temperature stage at 160°C for 60 min. Glucan to glucose conversion yields of 83% for hardwood and 80% for switchgrass were obtained. Total molar sugar yields of 65% and 55% were obtained for wood and switchgrass, respectively, which consisted of a 10% points improvement over those obtained during our previous study despite a 10-fold increase in particle size. These yields are similar to those obtained with other major pretreatment technologies for wood and within 10% of major technologies for switchgrass despite the absence of chemical catalysts, the use of large particles (0.95 cm) and high solid contents (40 wt%). [Pubmed: 22222713] | | 27. |
2012 May 30 |
Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN.
Kim S, Lowman S, Hou G, Nowak J, Flinn B, Mei C
Biotechnol Biofuels. 2012 May 30;5(1):37. Epub 2012 May 30. Abstract
ABSTRACT: BACKGROUND: Switchgrass is one of the most promising bioenergy crop candidates for the US. It gives relatively high biomass yield and can grow on marginal lands. However, its yields vary from year to year and from location to location. Thus it is imperative to develop a low input and sustainable switchgrass feedstock production system. One of the most feasible ways to increase biomass yields is to harness benefits of microbial endophytes. RESULTS: We demonstrate that one of the most studied plant growth promoting bacterial endophytes, Burkholderia phytofirmans strain PsJN, is able to colonize and significantly promote the growth of switchgrass cv. Alamo under in vitro, growth chamber, and greenhouse conditions. In several in vitro experiments, the average fresh weight of PsJN-inoculated plants was approximately 50% higher than non-inoculated plants. When one-month-old seedlings were grown in a growth chamber for 30 days, the PsJN-inoculated Alamo plants had significantly higher shoot and root biomass compared to controls. Biomass yield (dry weight) averaged from five experiments was 54.1% higher in the inoculated treatment compared to noninoculated control. Similar results were obtained in greenhouse experiments with transplants grown in 4-gallon pots for two months. The inoculated plants exhibited more early tillers and persistent growth vigor with 48.6% higher biomass than controls. We also found that PsJN could significantly promote growth of switchgrass cv. Alamo under sub-optimal conditions. However, PsJN-mediated growth promotion in switchgrass is genotype specific. CONCLUSIONS: Our results show B. phytofirmans strain PsJN significantly promotes growth of switchgrass cv. Alamo under different conditions, especially in the early growth stages leading to enhanced production of tillers. This phenomenon may benefit switchgrass establishment in the first year. Moreover, PsJN significantly stimulated growth of switchgrass cv. Alamo under sub-optimal conditions, indicating that the use of the beneficial bacterial endophytes may boost switchgrass growth on marginal lands and significantly contribute to the development of low input and sustainable feedstock production system. [Pubmed: 22647367] | | 28. |
2012 May |
Xylose isomerase improves growth and ethanol production rates from biomass sugars for both Saccharomyces pastorianus and Saccharomyces cerevisiae.
Miller KP, Gowtham YK, Henson JM, Harcum SW
Biotechnol. Prog. 2012 May;28(3):669-80. Abstract
The demand for biofuel ethanol made from clean, renewable nonfood sources is growing. Cellulosic biomass, such as switch grass (Panicum virgatum L.), is an alternative feedstock for ethanol production; however, cellulosic feedstock hydrolysates contain high levels of xylose, which needs to be converted to ethanol to meet economic feasibility. In this study, the effects of xylose isomerase on cell growth and ethanol production from biomass sugars representative of switch grass were investigated using low cell density cultures. The lager yeast species Saccharomyces pastorianus was grown with immobilized xylose isomerase in the fermentation step to determine the impact of the glucose and xylose concentrations on the ethanol production rates. Ethanol production rates were improved due to xylose isomerase; however, the positive effect was not due solely to the conversion of xylose to xylulose. Xylose isomerase also has glucose isomerase activity, so to better understand the impact of the xylose isomerase on S. pastorianus, growth and ethanol production were examined in cultures provided fructose as the sole carbon. It was observed that growth and ethanol production rates were higher for the fructose cultures with xylose isomerase even in the absence of xylose. To determine whether the positive effects of xylose isomerase extended to other yeast species, a side-by-side comparison of S. pastorianus and Saccharomyces cerevisiae was conducted. These comparisons demonstrated that the xylose isomerase increased ethanol productivity for both the yeast species by increasing the glucose consumption rate. These results suggest that xylose isomerase can contribute to improved ethanol productivity, even without significant xylose conversion. [Pubmed: 22866331] | | 29. |
2012 Apr 03 |
Effect of germination temperatures on proteolysis of the gluten-free grains sorghum and millet during malting and mashing.
Chiba Y, Bryce JH, Goodfellow V, MacKinlay J, Agu RC, Brosnan JM, Bringhurst TA, Harrison B
J. Agric. Food Chem. 2012 Apr 11;60(14):3745-53. Epub 2012 Apr 03. Abstract
Our study showed that sorghum and millet followed a similar pattern of changes when they were malted under similar conditions. When the malt from these cereals was mashed, both cereal types produced wide spectra of substrates (sugars and amino acids) that are required for yeast fermentation when malted at either lower or higher temperatures. At the germination temperatures of 20, 25, and 30 °C used in malting both cereal types, production of reducing sugars and that of free amino nitrogen (FAN) were similar. This is an important quality attribute for both cereals because it implies that variation in temperature during the malting of sorghum and millet, especially when malting temperature is difficult to control, and also reflecting temperature variations, experienced in different countries, will not have an adverse effect on the production and release of amino acids and sugars required by yeast during fermentation. Such consistency in the availability of yeast food (substrates) for metabolism during fermentation when sorghum and millet are malted at various temperatures is likely to reduce processing issues when their malts are used for brewing. Although sorghum has gained wide application in the brewing industry, and has been used extensively in brewing gluten-free beer on industrial scale, this is not the case with millet. The work described here provides novel information regarding the potential of millet for brewing. When both cereals were malted, the results obtained for millet in this study followed patterns similar to those of sorghum. This suggests that millet, in terms of sugars and amino acids, can play a role similar to that of sorghum in the brewing industry. This further suggests that millet, like sorghum, would be a good raw material for brewing gluten-free beer. Inclusion of millet as a brewing raw material will increase the availability of suitable materials (raw material sustainability) for use in the production of gluten-free beer, beverages, and other products. The availability of wider range of raw materials will not only help to reduce costs of beer production, but by extension, the benefit of reduced cost of production can be gained by consumers of gluten-free beer as the product would be cheaper and more widely available. [Pubmed: 22440185] | | 30. |
2012 Mar 21 |
Depolymerization and hydrodeoxygenation of switchgrass lignin with formic acid.
Xu W, Miller SJ, Agrawal PK, Jones CW
ChemSusChem. 2012 Apr;5(4):667-75. Epub 2012 Mar 21. Abstract
Organosolv switchgrass lignin is depolymerized and hydrodeoxygenated with a formic acid hydrogen source, 20 wt % Pt/C catalyst, and ethanol solvent. The combination of formic acid and Pt/C is found to promote production of higher fractions of lower molecular weight compounds in the liquid products. After 4 h of reaction, all of the switchgrass lignin is solubilized and 21 wt % of the biomass is shown to be converted into seven prominent molecular species that are identified and quantified. Reaction time is shown to be an important variable in affecting changes in product distributions and bulk liquid product properties. At 20 h of reaction, the lignin is significantly depolymerized to form liquid products with a 76 % reduction in the weighted average molecular weight. Elemental analysis also shows that the resultant liquid products have a 50 % reduction in O/C and 10 % increase in H/C molar ratios compared to the switchgrass lignin after 20 h. [Pubmed: 22438328] |
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