Education

Ph.D. in Biophysics, Johann-Wolfgang-Goethe-Universität Frankfurt, 1998

Current position

Staff Scientist (Principal Investigator), Lawrence Berkeley National Laboratory, Berkeley, CA (2004-present)
Director of Physical Analysis, Joint BioEnergy Institute, Emeryville, CA (2007-present)
Program Leader, Mesoscale BioImaging Technology Program, Life Sciences Division, LBNL (2014-present)

Publications (since 2010)

1. Sun, L., Singh, S., Joo, M., Vega-Sanchez, M., Ronald, P., Simmons, B. A., Adams, P. and Auer, M. (2016). Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnol Bioeng 113(1): 82-90.
   
2. Gregoire, P., Engelbrektson, A., Hubbard, C. G., Metlagel, Z., Csencsits, R., Auer, M., Conrad, M. E., Thieme, J., Northrup, P. and Coates, J. D. (2014). Control of sulfidogenesis through bio-oxidation of H2S coupled to (per)chlorate reduction. Environ Microbiol Rep 6(6): 558-564.
   
3. Piao, H., Lachman, M., Malfatti, S., Sczyrba, A., Knierim, B., Auer, M., Tringe, S. G., Mackie, R. I., Yeoman, C. J. and Hess, M. (2014). Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Front Microbiol 5: 307.
   
4. Berleman, J. E., Allen, S., Danielewicz, M. A., Remis, J. P., Gorur, A., Cunha, J., Hadi, M. Z., Zusman, D. R., Northen, T. R., Witkowska, H. E. and Auer, M. (2014). The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front Microbiol 5: 474.
   
5. Sarkar, P., Bosneaga, E., Yap, E. G., Jr., Das, J., Tsai, W. T., Cabal, A., Neuhaus, E., Maji, D., Kumar, S., Joo, M., Yakovlev, S., Csencsits, R., Yu, Z., Bajaj, C., Downing, K. H. and Auer, M. (2014). Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ. PLoS One 9(9): e106928.
   
6. Tsai, W. T., Hassan, A., Sarkar, P., Correa, J., Metlagel, Z., Jorgens, D. M. and Auer, M. (2014). From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data. J Vis Exp(90): e51673.
   
7. Dougherty, M. J., Tran, H. M., Stavila, V., Knierim, B., George, A., Auer, M., Adams, P. D. and Hadi, M. Z. (2014). Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size. PLoS One 9(6): e100836.
   
8. Schaudinn, C., Stoodley, P., Hall-Stoodley, L., Gorur, A., Remis, J., Wu, S., Auer, M., Hertwig, S., Guerrero-Given, D., Hu, F. Z., Ehrlich, G. D., Costerton, J. W., Robinson, D. H. and Webster, P. (2014). Death and transfiguration in static Staphylococcus epidermidis cultures. PLoS One 9(6): e100002.
   
9. Oh, J. W., Chung, W. J., Heo, K., Jin, H. E., Lee, B. Y., Wang, E., Zueger, C., Wong, W., Meyer, J., Kim, C., Lee, S. Y., Kim, W. G., Zemla, M., Auer, M., Hexemer, A. and Lee, S. W. (2014). Biomimetic virus-based colourimetric sensors. Nat Commun 5: 3043.
   
10. Ray, J., Keller, K. L., Catena, M., Juba, T. R., Zemla, M., Rajeev, L., Knierim, B., Zane, G. M., Robertson, J. J., Auer, M., Wall, J. D. and Mukhopadhyay, A. (2014). Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. Front Microbiol 5: 77.
    
11. Shamir, E. R., Pappalardo, E., Jorgens, D. M., Coutinho, K., Tsai, W. T., Aziz, K., Auer, M., Tran, P. T., Bader, J. S. and Ewald, A. J. (2014). Twist1-induced dissemination preserves epithelial identity and requires E-cadherin. J Cell Biol 204(5): 839-856.
    
12. Antonellis, P. J., Pollock, L. M., Chou, S. W., Hassan, A., Geng, R., Chen, X., Fuchs, E., Alagramam, K. N., Auer, M. and McDermott, B. M., Jr. (2014). ACF7 is a hair-bundle antecedent, positioned to integrate cuticular plate actin and somatic tubulin. J Neurosci 34(1): 305-312.
    
13. Remis, J. P., Wei, D., Gorur, A., Zemla, M., Haraga, J., Allen, S., Witkowska, H. E., Costerton, J. W., Berleman, J. E. and Auer, M. (2014). Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environ Microbiol 16(2): 598-610.[Epub ahead of print]
    
14. Eichorst, S. A., Varanasi, P., Stavila, V., Zemla, M., Auer, M., Singh, S., Simmons, B. A. and Singer, S. W. (2013). Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol 15(9): 2573-2587.
    
15. Chiniquy, D., Varanasi, P., Oh, T., Harholt, J., Katnelson, J., Singh, S., Auer, M., Simmons, B., Adams, P. D., Scheller, H. V. and Ronald, P. C. (2013). Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci 4: 83.
    
16. Neng, L., Zhang, W., Hassan, A., Zemla, M., Kachelmeier, A., Fridberger, A., Auer, M. and Shi, X. (2013). Isolation and culture of endothelial cells, pericytes and perivascular resident macrophage-like melanocytes from the young mouse ear. Nat Protoc 8(4): 709-720.
    
17. Varanasi, P., Singh, P., Auer, M., Adams, P. D., Simmons, B. A. and Singh, S. (2013). Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels 6(1): 14.
    
18. Shin, J. B., Krey, J. F., Hassan, A., Metlagel, Z., Tauscher, A. N., Pagana, J. M., Sherman, N. E., Jeffery, E. D., Spinelli, K. J., Zhao, H., Wilmarth, P. A., Choi, D., David, L. L., Auer, M. and Barr-Gillespie, P. G. (2013). Molecular architecture of the chick vestibular hair bundle. Nat Neurosci 16(3): 365-374.
    
19. Berleman, J. and Auer, M. (2013). The role of bacterial outer membrane vesicles for intra- and interspecies delivery. Environ Microbiol 15(2): 347-354.
    
20. Petersen, P. D., Lau, J., Ebert, B., Yang, F., Verhertbruggen, Y., Kim, J. S., Varanasi, P., Suttangkakul, A., Auer, M., Loque, D. and Scheller, H. V. (2012). Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants. Biotechnol Biofuels 5(1): 84.
    
21. Chen, X., Vega-Sanchez, M. E., Verhertbruggen, Y., Chiniquy, D., Canlas, P. E., Fagerstrom, A., Prak, L., Christensen, U., Oikawa, A., Chern, M., Zuo, S., Lin, F., Auer, M., Willats, W. G., Bartley, L., Harholt, J., Scheller, H. V. and Ronald, P. C. (2013). Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification. Mol Plant 6(2): 570-573.
    
22. Yang, F., Mitra, P., Zhang, L., Prak, L., Verhertbruggen, Y., Kim, J. S., Sun, L., Zheng, K., Tang, K., Auer, M., Scheller, H. V. and Loque, D. (2013). Engineering secondary cell wall deposition in plants. Plant Biotechnol J 11(3): 325-335.
    
23. Varanasi, P., Singh, P., Arora, R., Adams, P. D., Auer, M., Simmons, B. A. and Singh, S. (2012). Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour Technol 126: 156-161.
    
24. Zhang, W., Dai, M., Fridberger, A., Hassan, A., Degagne, J., Neng, L., Zhang, F., He, W., Ren, T., Trune, D., Auer, M. and Shi, X. (2012). Perivascular-resident macrophage-like melanocytes in the inner ear are essential for the integrity of the intrastrial fluid-blood barrier. Proc Natl Acad Sci U S A 109(26): 10388-10393.
    
25. Baelum, J., Borglin, S., Chakraborty, R., Fortney, J. L., Lamendella, R., Mason, O. U., Auer, M., Zemla, M., Bill, M., Conrad, M. E., Malfatti, S. A., Tringe, S. G., Holman, H. Y., Hazen, T. C. and Jansson, J. K. (2012). Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14(9): 2405-2416.
    
26. Parsons, H. T., Christiansen, K., Knierim, B., Carroll, A., Ito, J., Batth, T. S., Smith-Moritz, A. M., Morrison, S., McInerney, P., Hadi, M. Z., Auer, M., Mukhopadhyay, A., Petzold, C. J., Scheller, H. V., Loque, D. and Heazlewood, J. L. (2012). Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol 159(1): 12-26.
    
27. Ewald, A. J., Huebner, R. J., Palsdottir, H., Lee, J. K., Perez, M. J., Jorgens, D. M., Tauscher, A. N., Cheung, K. J., Werb, Z. and Auer, M. (2012). Mammary collective cell migration involves transient loss of epithelial features and individual cell migration within the epithelium. J Cell Sci 125(Pt 11): 2638-2654.
    
28. Knierim, B., Luef, B., Wilmes, P., Webb, R. I., Auer, M., Comolli, L. R. and Banfield, J. F. (2012). Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities. Environ Microbiol Rep 4(1): 36-41.
    
29. Carlson, H. K., Iavarone, A. T., Gorur, A., Yeo, B. S., Tran, R., Melnyk, R. A., Mathies, R. A., Auer, M. and Coates, J. D. (2012). Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria. Proc Natl Acad Sci U S A 109(5): 1702-1707.
    
30. Chhabra, S. R., Butland, G., Elias, D. A., Chandonia, J. M., Fok, O. Y., Juba, T. R., Gorur, A., Allen, S., Leung, C. M., Keller, K. L., Reveco, S., Zane, G. M., Semkiw, E., Prathapam, R., Gold, B., Singer, M., Ouellet, M., Szakal, E. D., Jorgens, D., Price, M. N., Witkowska, H. E., Beller, H. R., Arkin, A. P., Hazen, T. C., Biggin, M. D., Auer, M., Wall, J. D. and Keasling, J. D. (2011). Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Appl Environ Microbiol 77(21): 7595-7604.
    
31. Wrighton, K. C., Thrash, J. C., Melnyk, R. A., Bigi, J. P., Byrne-Bailey, K. G., Remis, J. P., Schichnes, D., Auer, M., Chang, C. J. and Coates, J. D. (2011). Evidence for direct electron transfer by a gram-positive bacterium isolated from a microbial fuel cell. Appl Environ Microbiol 77(21): 7633-7639.
    
32. Yin, L., Verhertbruggen, Y., Oikawa, A., Manisseri, C., Knierim, B., Prak, L., Jensen, J. K., Knox, J. P., Auer, M., Willats, W. G. and Scheller, H. V. (2011). The cooperative activities of CSLD2, CSLD3, and CSLD5 are required for normal Arabidopsis development. Mol Plant 4(6): 1024-1037.
    
33. Miroshnikova, Y. A., Jorgens, D. M., Spirio, L., Auer, M., Sarang-Sieminski, A. L. and Weaver, V. M. (2011). Engineering strategies to recapitulate epithelial morphogenesis within synthetic three-dimensional extracellular matrix with tunable mechanical properties. Phys Biol 8(2): 026013.
    
34. Vega-Sanchez, M. E., Verhertbruggen, Y., Christensen, U., Chen, X., Sharma, V., Varanasi, P., Jobling, S. A., Talbot, M., White, R. G., Joo, M., Singh, S., Auer, M., Scheller, H. V. and Ronald, P. C. (2012). Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice. Plant Physiol 159(1): 56-69.
    
35. Bharadwaj, R., Wong, A., Knierim, B., Singh, S., Holmes, B. M., Auer, M., Simmons, B. A., Adams, P. D. and Singh, A. K. (2011). High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresour Technol 102(2): 1329-1337.
    
36. Hazen, T. C., Dubinsky, E. A., DeSantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh, N., Jansson, J. K., Probst, A., Borglin, S. E., Fortney, J. L., Stringfellow, W. T., Bill, M., Conrad, M. E., Tom, L. M., Chavarria, K. L., Alusi, T. R., Lamendella, R., Joyner, D. C., Spier, C., Baelum, J., Auer, M., Zemla, M. L., Chakraborty, R., Sonnenthal, E. L., D'Haeseleer, P., Holman, H. Y., Osman, S., Lu, Z., Van Nostrand, J. D., Deng, Y., Zhou, J. and Mason, O. U. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001): 204-208.
    
37. Remis, J. P., Costerton, J. W. and Auer, M. (2010). Biofilms: structures that may facilitate cell-cell interactions. ISME J 4(9): 1085-1087.
    
38. Kent, M. S., Cheng, G., Murton, J. K., Carles, E. L., Dibble, D. C., Zendejas, F., Rodriquez, M. A., Tran, H., Holmes, B., Simmons, B. A., Knierim, B., Auer, M., Banuelos, J. L., Urquidi, J. and Hjelm, R. P. (2010). Study of enzymatic digestion of cellulose by small angle neutron scattering. Biomacromolecules 11(2): 357-368.