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November 23, 2012

Nanoscale Architecture of Plant Cell Walls Determines Their Accessibility and Digestibility by Enzymes
Plant cell walls are complex nanocomposites containing networks of cellulose fibrils and complex “matrixing” polymers. There is little agreement about which plant cell wall features most affect digestibility by microbes and cellulolytic enzymes. The overall performance of biomass saccharification may be attributed to the synergistic action of many complementary enzymes, which makes it difficult to study one factor at a time. Traditional solution methods have suffered from the classical ensemble average limitation presented by analysis of these mixtures of complex biomass, and the bulk data measurements gathered are therefore sometimes inconclusive and in part contradictory. Our imaging data support the hypothesis that ideal pretreatments should maximize lignin removal and minimize polysaccharide modification, thereby retaining the essentially native microfibrillar structure and improving accessibility.

October 16, 2012

New Developments in High-performance Proteomics Identify Important Networks and Pathways in Populus
This large scale dataset features the first systems-wide survey of protein expression across different Populus organs and strongly testifies to the credibility of the approach; instead of quantitatively comparing a few proteins, a systems view of all the changes associated with a given cellular perturbation can now be made. Most large-scale proteome analyses with Populus are performed on isolated organs, this method combines state-of-the-art sample preparation methodology to generate a high-coverage proteome atlas of the principal organ types from Populus.

October 10, 2012

Methods in Molecular Biology
Of the twenty-one chapters in Volume 908 of “Methods in Molecular Biology” released in August 2012, thirteen chapters covered the science of BESC.

October 10, 2012

Industrial Biotechnology Special Issue on Advances in Biomass Characterization
The August 2012 issue of Industrial Biotechnology will feature five articles by BESC scientists and one article featuring JBEI research. The featured cover art highlights the work of BESC researchers Marcus Foston and Arthur J. Ragauskas at the Georgia Institute of Technology.

September 28, 2012

Down-Regulation of the Caffeic acid O-methyltransferase Gene in Switchgrass Reveals a Novel Monolignol Analog
The more facile breakdown of cell walls of COMT-deficient plants is associated with increased concentrations of phenolic acid and aldehyde inhibitors of microbial fermentation, and a monolignol analog of sinapyl alcohol that is not integrated into the cell walls.

September 28, 2012

3-Dimensional Chemical Imaging of Populus Tension Wood by Time-of-Flight Secondary Ion Mass Spectrometry
This demonstrates the usefulness of 3D TOF-SIMS to the study of biomass recalcitrance by using tension wood samples as a model substrate to investigate how chemical spatial and lateral heterogeneity affects recalcitrance. Spatial distribution of major cell wall components in biomass is critical to bioconversion and can provide useful information in the future in determining the effects of pretreatment or genetic variation.

August 22, 2012

BESC Reports Successful Genetic Manipulation of Caldicellulosiruptor
This technology is being established in BESC partner labs and will allow the metabolic engineering of these bacteria for the direct conversion of lignocellulose to biofuels such as ethanol and butanol.

August 14, 2012

Discovery of plant glucuronoxylan synthesis gene lays groundwork for improved biofuel processing
The ability to selectively manipulate polysaccharide methylation may provide new opportunities to modulate biopolymer interactions in the plant cell wall of bioenergy crops such as switchgrass. This work extends the portfolio of BESC structural targets that can be modified either alone or in combination to increase the economic value of lignocellulosic biomass.

July 23, 2012

BESC Reports Clostridium thermocellum Ethanol Stress Responses
Largest responses were related to nitrogen uptake and metabolism Likely important for redirecting the cells physiology to overcome inhibition and allow growth to resume. Study suggests possible avenues for metabolic engineering and provides comprehensive, integrated systems biology datasets Useful for future metabolic modeling, synthetic biology and strain development endeavors.

May 29, 2012

dbCAN: a web resource for automated carbohydrate-active enzymes (CAZymes) annotation
Developed a community web resource, dbCAN (http://www.bioenergycenter.org/besc/redirect/dbcan.html), to provide a capability for automated CAZyme signature domain-based annotation for any given protein dataset (e.g. proteins from a newly sequenced genome). Defined a signature domain and constructed a hidden Markov model (HMM) for every CAZyme family, which is not publically available through any existing tools.

May 25, 2012

BESC Reports Genome Sequences for Clostridium thermocellum
Access to these genome sequences will help shed light on the mechanism of action of the cellulosome and cellulose-degrading capabilities in these and other cellulolytic organisms.

May 25, 2012

Caldicellulosiruptor pan genomes and proteomes reveal thermophilic deconstruction of plant biomass
Celluloytic ability is linked to modular, multi-domain enzymes (not cellulosomes). Weakly cellulolytic species lost this ability through deletion of a key genomic locus. The strongly cellulolytic Caldicellulosiruptor species possess novel cellulose-binding adhesins. Biogeography influences phylogeny and synteny among co-located species, but does not predict the ability to hydrolyze crystalline cellulose.

May 15, 2012

Genome for the Model Plant Setaria

Sequencing and Analysis of a Reference Genome for the Model Plant Setaria
The high quality whole genome assembly of the diploid S. italica is proving valuable as a framework in assisting with the genome assembly of other polyploid sequenced grasses, notably switchgrass. Comparison between the genomes of S. italica and S. viridis, switchgrass, sorghum and rice have revealed both shared and unique properties of the independent adaptations of several grasses to life on earth. Phylogenetic analysis of five nuclear genes shows that millet and switchgrass lineages underwent independent polyploidization events, both of which occurred after the divergence of Panicum from Setaria. The completed genome sequence enables the further development of Setaria as a model plant, improves our understanding of cell wall composition, plant structure and development and traits that are pertinent to the development of biofuel crops.

May 01, 2012

Metagenome of Microbial Community Decomposing Wood Biomass
Imagery shows differential digestion of cellulose over lignin under anaerobic conditions. Identified Magnetospirillum-like bacteria as dominant community members—possible role of de-toxification. Distinct differences between decay community and other cellulose-digesting microbiomes.

April 04, 2012

High-Performance Computing Delineates Chemistry of Lignin Synthesis
The synthesis of lignin involves oxidative radical-radical coupling of monolignols. In a BESC collaboration, we used density functional theory to characterize these reactions.

January 17, 2012

Unusual “C-lignin” polymer discovered in certain plant seeds
This discovery shows the natural capability that native plants have in producing specific lignin polymers. It supports the radical coupling polymerization hypothesis. This lignin may be new source for carbon fiber manufacturing Selected as the cover story for an upcoming issue in the Proceedings of the National Academy of Sciences and as an “editor’s choice” story in an upcoming volume of Science magazine

January 11, 2012

BESC Knowledge Base (BESCKB)
This integration is the key to gain comprehensive, systems level understanding of cellular processes involved in plant biomass formation, degradation and biofuel production. Data available through BESCKB include genomic, pathways, Omics data, resequencing data, and various assay results related to biomass properties, structure and composition. Tools available through knowledgebase include annotation, visualization, comparative analysis, integration, data mining, and various navigation tools.

BioEnergy Science Center one of three DOE Bioenergy Research Centers established by the U.S. Department of Energy.