Biomass Depolymerization projects

Cell Wall 3D Architecture at Nanometer Resolution Using Correlative Raman and Electron Tomography Imaging

A detailed knowledge of the 3D architecture of Type I and Type II plant cell walls is key for a rational design of plants that can be more easily broken down into fermentable sugars. In addition, a model of the cell wall based on experimental data will serve as the framework for understanding and further optimizing chemical and microbial deconstruction regimens. This project uses sophisticated sample preparation and imaging techniques to achieve its goals. In addition, this group’s expertise serves as a resource for other EBI investigators with imaging needs.

project Highlights

2012 Highlights

The goal of this project was to develop realistic structure-based 3D models of plant cell walls using high-resolution 3D images obtained by electron tomography. We found that conventional sample preparation protocols lead to significant extraction of the plant cell wall, whereas samples prepared by high pressure freezing (HPF) and freeze substitution (FS) were close in preservation to the “gold standard” in electron microscopy, i.e. frozen-hydrated samples. We carried out cryogenic sample preparation and electron microscopy of unextracted plant cell walls from Arabidopsis, Miscanthus and Equisetum in their near-native state, yielding unprecedented insight into the 3D architecture of plant cell walls. We have also developed semi-automatic segmentation methods in order to analyze larger plant cell wall volumes and to quantify changes in cell wall architecture and composition during various deconstruction protocols, i.e. selected chemical extraction of cell wall components. The results of this project were presented and favorably received as two oral presentations and as a poster at the 2012 Gordon Research Conference and Seminar (Plant Cell Walls) and at the International Symposium on New Horizons in BioEnergy Research at IIT-Kharagpur, India.

2011 Highlights

Auer’s group completed tomography data collection and standardized 3D image analysis methods in anticipation of developing the first 3D model of plant cell walls using various Arabidopsis samples. The undertaking will enable them to study the architecture of plant cell walls close to their native state at molecular resolution. In addition, the researchers collected tomography data of cell walls from Miscanthus and Equisetum. The research team also completed the development of high-throughput sample preparation and semi-automated image analysis algorithm for rapid analysis of deconstructed biomass.

2010 Highlights

In 2010, Auer’s group succeeded in cutting and imaging frozen-hydrated cryo-sections, resulting in the first images and 3D volumes of unstained plant cell walls.

2009 Highlights

Auer’s group has developed automated computational analysis tools that allow for the segmentation and analysis of a large number of tomograms. This group is also exploring super-resolution optical imaging (PALM) using mEos-CBM fusion proteins that are known to bind to cellulose fibers, and have identified a number of challenges that need to be overcome. The group has also developed a 3D visualization interface that facilitates Raman spectral imaging analysis.



Published in 2012


Deep-Sea Bacteria Enriched by Oil and Dispersant from the Deepwater Horizon Spill, Jacob Baelum, Sharon Borglin, Romy Chakraborty, Julian Fortney, Regina Lamendella, Olivia Mason, Manfred Auer, Marcin Zemla, Markus Bill, Mark Conrad, Stephanie Malfatti, Susannah Tringe, Hoi-Ying Holman, Terry Hazen, Janet Jansson, Environmental Microbiology, doi: 10.1111/j.1462-2920.2012.02780, May 23, 2012.


Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography,  Leandro Loss, Hang Chang, Purbasha Sarkar, George Bebis, Manfred Auer, Bahram Parvin, ACM Conference on Bioinformatics, Computational Biology, and Biomedicine Technology, doi/pdf/10.1890/12-0854.1, October 7, 2012.


Published in 2011

Quantifying Bio-Engineering: the Importance of Biophysics in Biofuel Research, Patanjali Varanasi, Lan Sun, Bernhard Knierim, Elena Bosneaga, Purbasha Sarkar, Seema Singh, Manfred Auer, Biofuel's Engineering Process Technology (Chapter), Marco Aurélio dos Santos Bernardes (Ed.), ISBN: 978-953-307-480-1, InTech, August 2011.

Published in 2010

Chemical Profiling of the Plant Cell Wall Through Raman Microspectroscopy, Ju Han, Seema Singh, Lan Sun, Blake Simmons, Manfred Auer, Bahram Parvin, Information Bridge: DOE Scientific and Technical Information, Record 137, October 2010.

Published in 2009

Plant Cell Walls Throughout Evolution: Towards a Molecular Understanding of Their Design Principles, Purbasha Sarkar, Elena Bosneaga, Manfred Auer, Journal of Experimental Botany, 60(13): pp. 3615-3635, Aug. 17, 2009.




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