Conversations in Science
for K-12 Educators

A program conceived and organized by the Wisconsin Initiative for Science Literacy at the University of Wisconsin-Madison, with the collaboration of the Madison Metropolitan School District and the Edgewood Sonderegger Science Center.

Single Molecule Approaches for the “New Biology”

David C. Schwartz, Ph.D
Kellett Professor of Chemistry and Genetics at the University of Wisconsin-Madison.

Reduction of experimental scale terminates at the single molecule level. Single molecules are the ultimate analyte, since they represent the pinnacle of miniaturization, and when systematically analyzed as ensembles, offer the greatest advantages for the generation large-scale data sets. Such large and often complex data sets have become the currency of modern biological analysis. In this regard, our laboratory has pioneered the first single molecule system for large-scale genome analysis--Optical Mapping. This system uses automated fluorescence microscopy, and on-line analysis to image and analyze thousands of individual of "biochemically marked" DNA molecules. The analysis files are then directly piped to a database, where further analysis or linking with public resources is enabled. This linkage brings biological annotation into a single molecule context. Downstream systems then allow users to visualize data and analysis as an integral part of their research efforts. Through such integration, the Optical Mapping System has emerged as a general platform for the large-scale analysis of single molecule phenomena, and has made single molecules a practical substrate for chemical and biological research.
Single molecule approaches are enabling researchers to understand mechanistic details and events that commonly evade traditional means that employ bulk analysis techniques, which obscure valuable distributions. With some notable exceptions, the single molecule approaches currently in use are quite toilsome and very low throughput. Given the modern requirements for large and complex datasets, a critical need for high-throughput single molecule approaches has emerged within the biological community. This need has emerged due to the recent appreciation of what large, complex datasets offer, when optimally interfaced with powerful analysis and experimental systems. In this regard, high-throughput, single molecule systems provide the necessary platform for whole genome analysis that is applicable to a broad range of biological problems. High-resolution, whole genome analysis has been gaining favor because we now have the means to grapple with the complexities of “real” biological systems, both locally and in terms of meaningful populations.
In this talk, I plan to present our single molecule platforms, and their application to a broad range of biological problems, both current and future.

About the Presenter:

David C. Schwartz is a professor in the Departments of Genetics and Chemistry at the University of Wisconsin-Madison. Dr. Schwartz is also a member of the Biotechnology Center and Director of the Genomic Sciences Training Program. He received a Ph.D. from Columbia University in 1985. While a graduate student, he invented pulsed field gel electrophoresis. After receiving his Ph.D., Dr. Schwartz was a staff associate at the Carnegie Institution, and from 1989 to 1999, he was a professor at New York University.

Dr. Schwartz has received numerous scientific honors, including the Lucille P. Markey Scholar Award, Presidential Young Investigator Award, Beckman Young Investigator Award, and the American Society for Biochemistry and Molecular Biology-Amgen Prize.

Dr. Schwartz’s research focuses on discovery and elucidation of new single molecule effects, and their application to problems in biology and genetics through the reation/analysis of massively large, complex data sets (surface science, imaging, nano/microfluidics, polymer dynamics, nanochemistry, transcription, genome evolution, population genomics, single cell genomics, epigenetics, cancer).

Suggestions for reading:

Jendrejack, R. M., Dimalanta, E. T., Schwartz, D. C., Graham, M. D., and de Pablo, J. J. “DNA Dynamics in a Microchannel”. Phys. Rev. Lett. 91: 2003.

Jendrejack, R. M., Schwartz, D. C., Graham, M. D., de Pablo, J. J. , “Effect of Confinement on DNA Dynamics in Microfluidic Devices”. J. Chem. Phys. 119: 1165-1173, 2003.

Lim, A., Dimalanta, E. T., Potamousis, K. D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., Perna, N. T., Burland, V., Mau, B., Blattner, F. R., Anantharaman, T., R., Mishra, B., Schwartz, D. C. “Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome”, Genome Res. 11: 1584-1593, 2001.

Perna, N., Plunkett III, G., Burland, V., Mau, B., Glasner, J., Rose, D., Mayhew, G., Evans, P., Gregor, J., Kirkpatrick, H., Posfai, G, Hackett, J., Klink, S., Boutin, A., Shao, Y., Miller, L., Grotbeck, E., Davis, N., Lim, A., Dimalanta, E., Potamousis, K., Apodaca, J., Anantharaman, T., Lin, J., Yen, G., Schwartz, D., Welch, R., Blattner, F. “Genome sequence of enterohemorrhagic Escherichia coli 0157:H7”, Nature 409: 529-533, 2001.

Giacalone, J., Delobette, S., Gibaja, V., Ni, L., Skiadas, J., Qi, R., Edington, J., Lai, Z., Gebauer, D., Zhao, H., Anantharaman, T., Mishra, B., Brown, L. G., Saxena, R., Page, D. C., Schwartz, D.C., “Optical mapping of BAC clones from the human Y chromosome DAZ locus”, Genome Research 10: 1421-1429, 2000.

Lai, Z., Jing, J., Aston, C., Clarke, V., Apodaca, J., Dimalanta, E., Carucci, D. Gardner, M., Mishra, B., Anantharaman, T., Paxia, S., Hoffman, S., Venter, J., Huff, E., Schwartz, D.C., “A shotgun optical map of the entire Plasmodium falciparum genome”, Nature Genetics, 23: 309-313, 1999.

Skiadas, J., Aston, C., Samad, A., Anantharaman, T., Mishra, B., Schwartz, D.C., “Optical PCR: Genomic Analysis by Long-Range PCR and Optical Mapping”, Mammalian Genome, 10: 1005-1009, 1999.

Lin, J., Qi, R., Aston, C., Jing, J., Anantharaman, T. S., Mishra, B., White, O., Venter, J. C., Schwartz, D. C., “Whole Genome Shotgun Optical Mapping of Deinococcus radiodurans”, Science, 285: 1558-1562, 1999.

Aston, C., Mishra, B., Schwartz, D. C., “Optical Mapping and its potential for large-scale sequencing projects”, Trends in Biotechnology, vol. 17: 297-302, 1999.

Jing, J., Reed, J., Huang, J., Hu, X., Clarke, V., Edington, J., Houseman, D., Anantharaman, T., Huff, E., Mishra, B., Porter, B., Shenker, A., Wolfson, E., Hiort, C., Kantor, K., Aston, C., Schwartz, D., “Automated High Resolution Optical Mapping Using Arrayed, Fluid Fixed, DNA Molecules”, Proc. Natl. Acad. Sci. USA, 95: 8046-8051, 1998.

Aston, C., Hiort, C., Schwartz, D., "Optical Mapping: An approach for fine mapping" in Methods in Enzymology, Academic Press, New York, vol. 303, chap. 4, 55-73, 1999.

Reed, J., Singer, E., Kresbach, G., and Schwartz, D. C. “A quantitative study of Optical Mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays”, Analytical Biochemistry, 259: 80-88, 1998.

Anantharaman, T. S., Mishra, B., Schwartz, D.C., “Genomics via Optical Mapping III: Contiging genomic DNA and variations”, Courant Technical Report #760, Courant Institute, NY (March 1998).

Wang, W., Lin, J., Schwartz, D.C., “Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet”, Biophys. Journal, 75: 513-520, 1998.

Ananthraman, T. S., Mishra, B., Schwartz, D. C., “Genomics via Optical Mapping II: Ordered Restriction Maps”, Journal of Computational Biology, 4, No.2: 91-118, 1997.