James R. Swartz - Professor

Office: Keck Science Building, Room 185
Phone: (650) 723-5398
E-Mail: jswartz@stanford.edu
Admin. Associate: Roosmery Yang, (650) 726-1807
Group Website: http://swartzgroup.stanford.edu/

Highest Degree

• Ph.D., Massachusetts Institute of Technology, 1978

Major Honors and Awards

• Pfizer Fellowship in Biochemical Engineerin, 1976
• Florasynth Fellowship, Institute of Food Technologist, 1977
• Served on National Research Council Committee on Bioprocess Engineering, 1991
• Keynote Address at Inaugural Meeting of The American Institute of Medical and Biological Engineers, 1992
• Inducted as founding Fellow, The American Institute of Medical and Biological Engineerr, 1993
• James Van Lanen Service Award from the Division of Biochemical Technology, American Chem. Soc., 1993
• Keynote Address at Asia-Pacific Biochemical Engineering Conference, 1994
• Keynote Adress, Biotech 2000 Meeting, Seoul, Korea, 1994
• Co-Chair of Biochemical Engineering X. 1997
• Elected to National Academy of Engineering, 1999
• Opening Keynote Lecture, 2nd International Conference Recombinant Protein Production with Prokaryotic and Eukaryotic Host Cell, Cemobbio, Italy, 2002
• Amgen Award, Society of Industrial Microbiology, 2005
• Distinguished Alumnus Award, S.Dak. School of Mines and Technology, 2005
• Gaden Award, 2006
• Leland T. Edwards Professor in the School of Engineering, 2006
• Member of the National Academy of Engineering (NAE)
• Keynote Lecture, 20th Meeting for the European Society for Animal Cell Tech, 2007, Dresden, Germany, 2007
• Opening Keynote Speaker, Recent Advances in Ferm Tech (RAFT VII), 2007, St. Pete Beach, Florida, 2007

Research Area

Using and Understanding Cell-Free Biology

Swartz Lab General Research Focus

The current and projected research in the Swartz lab balances basic research in microbial metabolism, protein expression, and protein folding with a strong emphasis on compelling applications. The power and versatility of cell-free methods coupled with careful evaluation and engineering of these new systems enables a whole new range of applications and scientific investigation. Fundamental research on: the mechanisms and kinetics of ribosomal function, fundamental bioenergetics, basic mechanisms of protein folding, functional genomics, and metabolic pathway analysis is motivated by a variety of near- and medium term applications spanning medicine, energy, and environmental needs.

Swartz Lab Application Foci

In the medical area , current research addresses the need for patient-specific vaccines to treat cancer. Particularly for lymphomas, there is a strong need to be able to make a new cancer vaccine for each patient. Current technologies are not practical for this demanding task, but cell-free approaches are rapid and inexpensive. We have already demonstrated feasibility in mouse tumor challenge studies and are now expanding the range of applications and working to improve the relevant technologies. Experience with these vaccines has also suggested a new and exciting format for making inexpensive and very potent vaccines for general use.

To address pressing needs for a new and cleaner energy source, we are working towards an organism that can efficiently capture solar energy and convert it into hydrogen. The first task is to develop an oxygen tolerant hydrogenase using cell-free technology to express libraries of mutated enzymes that can be rapidly screened for improved function. Even though these are very complex enzymes, we have produced active hydrogenases with our cell-free methods. We are now perfecting the screening methods for rapid and accurate identification of improved enzymes. After these new enzymes are identified, the project will progress toward metabolic engineering and bioreactor design research to achieve the scales and economies required.

To address environmental needs, we are developing an improved water filters using an amazing membrane protein, Aquaporin Z. It has the ability to reject all other chemicals and ions except water. We have efficiently expressed the protein into lipid bilayer vesicles and are now working to cast these membranes on porous supports to complete the development of a new and powerful water purification technology. The same lessons will be applied toward the development of a new class of biosensors that brings high sensitivity and selectivity.

Representative Publications

1. Boyer M.E., Stapleton J.A., Kuchenreuther J.M., Wang C-W, Swartz J.R., “Cell-free synthesis and maturation of [FeFe] hydrogenases”,  Biotechnology and Bioengineering, Vol99, p59-67, 2008.
2. Goerke, A.R. and Swartz J.R., “Development of cell-free protein synthesis platforms for disulfide bonded proteins”, Biotechnology and Bioengineering,Vol99, p 351-367, 2008.
3. Kanter G., Yang J., Voloshin A., Levy S, Swartz J.R. and Levy R., “Cell-free production of scFv Fusion
4. Proteins: An Efficient Approach for Personalized Lymphoma Vaccines”, Blood, 109: 3393-3399, 2007.
5. Knapp K.G., Goerke A.R., and Swartz J.R., “Cell-free synthesis of proteins that require disulfide bonds using glucose as an energy source”, Biotechnology and Bioengineering, Vol97,p901-908, 2007.
6. Cell-free Protein Synthesis: Methods and Protocols, Spirin, AS and Swartz J..R, Ed., Wiley-VCH, Weinheim, Germany, 2007.
7. Spirin A.S. and Swartz J.R., “Cell-free protein synthesis systems: historical landmarks, classification, and general  methods”, Ch 1, p 1-34, in Cell-free Protein Synthesis: Methods and Protocols, Spirin, AS and Swartz J.R., Ed., Wiley-VCH, Weinheim, Germany, 2007.
8. Voloshin A.M. and Swartz J.R., “Large-scale batch reactions for cell-free protein synthesis”, Ch 12, p 207-235,
9. in Cell-free Protein Synthesis: Methods and Protocols, Spirin, A.S. and Swartz J.R., Ed., Wiley-VCH, Weinheim, Germany, 2007.
10. Woodrow, K.A. and Swartz J.R., “A sequential expression system for high-throughput functional genomic analysis”, Proteomics, Vol 7, p3870-3879, 2007.
11. Bundy B.C., Franciszkowicz M.J., and Swartz J.R., “Escherichia coli-based cell-free synthesis of virus-like particles”, Biotechnology and Bioengineering, Early View, Dec 2007.Calhoun, K.A. and J.R. Swartz, “Total amino acid stabilization during cell-free protein synthesis reactions", Journal of Biotechnology, Vol. 123, p193-203, 2006.
12. Zawada, J. and J.R. Swartz, “Effects of growth rate on cell extract performance in cell-free protein synthesis”, Biotechnology and Bioengineering, Vol. 94, p618-624, 2006.
13. Woodrow K.A.., Airen I.O.., and Swartz J.R., Rapid expression of functional genomic libraries. Journal of Proteome Research. Vol. 5, p3288-300, 2006.
14. Swartz J.R., Developing cell-free biology for industrial applications. Journal of Industrial Microbiology & Biotechnology, Vol. 33, p476-85, 2006.
15. Boyer, M., Wang, C.W., and Swartz, J.R., “Simultaneous Expression and Maturation of the Iron-Sulfur Protein, Ferredoxin, in a Cell-free System”, Biotechnol. and Bioeng., Vol. 94, p128-138, 2006.
16. Michel-Reydellet, N., Woodrow K. and Swartz J.R., “Increasing PCR Fragment Stability and Protein Expression in a Cell-free System with Genetically Modified Escherichia coli extracts,” J. of Mol. Microb.&Biotechn., 9:26-34, 2005.
17. Calhoun K.C. and Swartz, J.R.,”An Economical Method for Cell-Free Protein Synthesis Using Glucose and Nucleotide Monophosphates”, Biotechnology Progress, 21:1146-53, 2005.
18. Underwood, K., Swartz, J.R., and J.D. Puglisi, “Quantitative Polysome Analysis Identifies Limitations in Bacterial Cell-free Protein Synthesis”, Biotechnol. and Bioeng., 91:425-435, 2005.
19. Voloshin, A.M. and J.R. Swartz, “Efficient and Scaleable Method for Scaling up Cell-free Protein Synthesis Systems in Batch Mode”, Biotechnol. and Bioeng., 91:516-521, 2005.
20. Zawada, J. and Swartz J. R, “Maintaining rapid growth in moderate-density Escherichia coli fermentations”, Biotechnol. and Bioeng., 89:407-415, 2005.
21. Liu, D., Zawada, J. and Swartz J.R., “Streamlining Escherichia coli S30 Extract Preparation for Economical Cell-free Protein Synthesis”, Biotechnology Progress, 21:460-465, 2005.
22. Calhoun, K.C. and Swartz, J.R., “Energizing Cell-free Protein Synthesis with Glucose Metabolism, Biotechnol. and Bioeng., 90:606-613, 2005.
23. Yang, J., Kanter, G., Voloshin, A., Michel-Reydellet, N., Velkeen, H., Levy, R. and Swartz, J.R., “Rapid Expression of Vaccine Proteins for B Cell Lymphoma in a Cell-free System” Biotechnol. and Bioeng., 89:503-511, 2005.
24. Yang, J., Kanter, G, Voloshin, A., Levy, R., and Swartz, J.R., “Expression of Active Murine Granulocyte-macrophage Colony-stimulating Factor in an Escherichia coli Cell-free System”, Biotechnology Progress, 20:1689-96, 2004.
25. Jewett, M.C. and Swartz, J.R., “Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis”, Biotechnol. and Bioeng., 86:19-26, 2004.
26. Yin, G. and Swartz, J.R., “Enhancing multiple disulfide bonded protein folding in a cell-free system”, Biotechnol. and Bioeng., 86:188-195, 2004.
27. Kim, D-M. and J. Swartz, “Efficient Production of a Bioactive, Multiply-Disulfided Protein Using Modified Extracts of Escherichia coli”, Biotechnol. and Bioeng., 85:122-129, 2004.
28. Knapp, K. and Swartz, J.R., “Cell-free production of active E.coli thioredoxin reductase and glutathione reductase”, FEBS Letters, 559:66-70, 2004.
29. Jewett, M.C. and Swartz, J.R., “Rapid expression and purification of 100 nanomole quantities of active protein using cell-free protein synthesis”  Biotechnology Progress, 20:102-109, 2004.
30. Cell-Free Protein Expression, Swartz, J.R., ed., Springer Verlag, New York, 2003.
31. Swartz, J.R., “Advances in Escherichia coli Production of Therapeutic Proteins”, Current Opinion in Biotechnology, 12:195-201, 2001

Current Students

Ph.D. Students—Undergraduate Institution

• Isoken Airen - University of California, San Diego
• Cem Albayrak - M.I.T.
• Brad Bundy - Brigham Young University
• Kedar Patel - University of Wisconsin
• Jon Kuchenreuther - University of Utah
• Nathan Lassig - University of Utah
• Bertrand Lui - California Institute of Technology
• Pornthep Joe Meethunkij—Yale University
• Phillip Smith - Brigham Young University
• James Stapleton—University of California Berkeley
• Deborah Stoner - University of Washington
• Postdoctoral Fellows—Doctoral Institution
• Jeanne Bonomo, Ph.D. - University of Colorado, Boulder