User:DavidSavage

Update
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 Savage Lab website for more details.

A bit about me


I grew up in rural Iowa and studied chemistry and computer science at Gustavus Adolphus College. I moved west for graduate school at UCSF to study membrane protein structure and function in the lab of Bob Stroud. Currently, I am a postdoctoral fellow in the lab of 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 Sarah, running, cooking, trying to garden in New England, and snowboarding.

Research Interests
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.

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.

Publications
Engineering of the aquaporin selectivity filter. Savage, D.F., O’Connell III, J.D., Stroud R.M. (2010) In press at PNAS.

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]]]

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]]]

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]]]

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]]]

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]]]

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]]]

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]]]

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

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]]]

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]]]

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
Dave Savage Department of Systems Biology Harvard Medical School 200 Longwood Ave. WAB 536 Boston, MA 02115 E david_savage -*AT*- hms.harvard.edu T 617.432.6402 C 415.637.4450