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| == '''Update''' == | | ==Dave Savage == |
| I will be starting my own lab at UC Berkeley this summer and have openings for postdocs interested in synthetic biology and metabolism. Please visit the [http://savagelab.org Savage Lab website] for more details.
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| == A bit about me ==
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| [[Image:savage_headshot.jpg|right|thumb|200px|Frame|]] | | [[Image:savage_headshot.jpg|right|thumb|200px|Frame|]] |
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| I grew up in rural Iowa and studied chemistry and computer science at [http://www.gac.edu Gustavus Adolphus College]. I moved west for graduate school at UCSF to study membrane protein structure and function in the lab of [http://www.msg.ucsf.edu/stroud/index.htm Bob Stroud]. Currently, I am a postdoctoral fellow in the lab of [http://openwetware.org/wiki/Silver_Lab Pamela Silver] at Harvard Medical School, where I am developing the cyanbacterium Synechococcus as a model synthetic biology chassis for interrogating carbon fixation. In my free time, I enjoy spending time with my wife [http://ccib.mgh.harvard.edu/hunglab-people.htm Sarah], running, cooking, trying to garden in New England, and snowboarding.
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| == Research Interests ==
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| [[Image:Carboxysome.png|thumb|left|150px|Frame|Molecular model of the carboxysome]]
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| '''Current work'''. Photosynthetic cyanobacteria are major players in the global carbon cycle and I am developing one such cyano, Synechococcus elongatus, as a model synthetic biology chassis. One aspect of this is to investigate how carboxysomes, massive protein microcompartments similar to viral capsids, facilitate carbon fixation in a manner reminiscent of organelles. In other work, I am investigating the role of circadian rhythm in metabolism and how metabolism can be rewired to produce hydrocarbons directly from light.
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| '''Future work'''. My central interest is how microbes transform their chemical environment and how biological catalysis can be used to improve the molecular diversity and environmental footprint of industrial chemistries. This is a broad topic and I am interested in a variety of model organisms (E. coli, S. cerevisiae, S. elongatus, et al.) and techniques, notably quantitative microscopy, metabolomics, and protein structure. In the future, I intend to continue work in Synechococcus as a model photosynthetic organism and to investigate ways in which protein microcompartments such as the carboxysome can be used for synthetic biology purposes. Moving beyond photosynthetic systems, I intend to develop novel biological tools, such as biosensors, and instrumentation to elucidate the engineering design principles of how metabolic networks are controlled and regulated and have evolved. Finally, I'm interested in how biological systems can be both rationally designed and evolved to produce chemicals relavant to society.
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| == Publications ==
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| Engineering of the aquaporin selectivity filter. Savage, D.F., O’Connell III, J.D., Stroud R.M. (2010) In press at PNAS.
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| Engineered synthesis and export of hydrophillic products from cyanobacteria. Niederholt meyer, H., Wolfstaedter, B., Savage, D.F., Silver, P., Way, J.C. (2010) Appl. Environ. Microbiol, 76:3462-6. [[media:Niederholtmeyer_Way_Appl_Environ_Microbiol_2010.pdf|[PDF]]]
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| Spatially ordered dynamics of the bacterial carbon fixation machinery. Savage, D.F., Afonso, B., Chen, A., Silver, P.A. (2010) Science, 327:1258-61. [[media:Savage_Silver_Science_2010.pdf|[PDF]]]
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| A general protocol for the crystallization of membrane proteins for X-ray structural investi gation. Newby, Z.E., O'Connell 3rd, J.D., Gruswitz, F., Hays, F.A., Harries, W.E., Harwood, I.M., Ho, J.D., Lee, J.K., Savage, D.F., Miercke, L.J., Stroud, R.M. (2009) Nat Protoc. 4:619-37. [[media:Newby_Stroud_Nat_Protoc_2009.pdf|[PDF]]]
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| Defossiling fuel: How synthetic biology can transform biofuel production. Savage, D.F., Way, J., Silver, P.A. (2008) ACS Chem. Biol. 3:13-6. [[media:Savage_Silver_ACS_Chem_Biol_2008.pdf|[PDF]]]
| | [http://mcb.berkeley.edu/index.php?option=com_mcbfaculty&name=savaged Assistant Professor of Biochemistry, Biophysics, and Structural Biology]<br> |
| | Departments of [http://mcb.berkeley.edu/index.php Molecular & Cell Biology] and [http://chemistry.berkeley.edu/ Chemistry]<br> |
| | [http://berkeley.edu/ University of California, Berkeley]<br> |
| | Member in the [http://www.energybiosciencesinstitute.org/ Energy Biosciences Institute] |
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| Structural basis of aquaporin inhibition by mercury. Savage, D.F. and Stroud, R.M. (2007) J. Mol. Biol. 368: 607-17. [[media:Savage_Stroud_J_Mol_Biol_2007.pdf|[PDF]]]
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| Cell-free complements in vivo expression of the E. coli membrane proteome. Savage, D.F., Anderson C.L, Robles-Colmenares, Y., Newby, Z.A., Stroud R.M. (2007) Protein Sci. 16:966-76. [[media:Savage_Stroud_Protein_Sci_2007.pdf|[PDF]]]
| | ===Research Interests=== |
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| Substrate twinning activates the signal recognition particle and its receptor. Egea P.F., Shan S.O., Napetschnig J., Savage D.F., Walter P., Stroud R.M. (2004) Nature, 426:215-221. [[media:Egea_Stroud_Nature_2004.pdf|[PDF]]]
| | The molecules used to build cells, and much of human infrastructure, are synthesized by the chemical reactions of metabolism. In understanding metabolism better, we open the door to new ways of curing disease and environmentally friendly chemistry. Work in our lab focuses on defining how metabolic reactions function in the context of the cellular system in order to elucidate the so-called design principles of metabolic function. To do so, we take an interdisciplinary approach, combining biochemistry, biophysics, and systems biology, with an eye towards building synthetic biology tools.<br><br> |
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| Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family. Lee, J.K., Khademi, S., Harries, W., Savage, D., Miercke, L, Stroud, R.M. (2004) J. Synchrotron Radiat. 11:86-88
| | Please visit the [http://savagelab.org Savage Lab] website for more information. |
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| Architecture and selectivity in aquaporins: 2.5Å x-ray structure of aquaporin Z. Savage, D. F., Egea, P.F., Robles, Y.C., O’Connell III, J.D., and Stroud, R.M. (2003) PLoS Biology, 1:334-340. [[media:Savage_Stroud_PLoS_Biol_2003.pdf|[PDF]]]
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| Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. Stroud, R.M., Savage, D.F., Miercke, L.J., Lee, J.K., Khademi, S., Harries, W. (2003). FEBS Letters, 555:79-84. [[media:Stroud_Harries_FEBS_Lett_2003.pdf|[PDF]]]
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| Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA: ACP transacylase. Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J.W., O'Connell 3rd, J.D., Khosla, C., and Stroud, R.M. (2003) Structure, 11:147-154. [[media:Keatinge-Clay_Stroud_Structure_2003.pdf|[PDF]]]
| | ===Contact Info=== |
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| == Contact info ==
| | David Savage, Ph.D. <br> |
| Dave Savage<br>
| | Energy Biosciences Building<br> |
| Department of Systems Biology<br>
| | 2151 Berkeley Way<br> |
| Harvard Medical School<br>
| | UC Berkeley<br> |
| 200 Longwood Ave. WAB 536<br>
| | Berkeley, CA 94720-5230<br> |
| Boston, MA 02115<br>
| | USA<br> |
| <br> | | E:dsavage * berkeley * edu<br> |
| E david_savage -*AT*- hms.harvard.edu<br> | | P: 510.643.7847<br> |
| T 617.432.6402<br>
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| C 415.637.4450<br>
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