Transient-Mediated fate determination in a transcriptional circuit of HIV

Leor S. Weinberger (University of California, San Diego), Roy D. Dar (University of Tennessee), and
Michael L. Simpson (Center for Nanophase Materials Sciences, Oak Ridge National Laboratory)


One of the greatest challenges in the characterization of complex nanoscale systems is gaining a mechanistic understanding of underlying processes that cannot be directly imaged. Recent research at the CNMS1 explored a novel technique of discovering the details of these interactions through the measurement of the structure of stochastic fluctuations that occur in neighboring nanoscale system components that can be directly imaged. In this work [Nature Genetics, 40(4), 466-470 (2008)], in collaboration with a researcher at the University of California, San Diego, these techniques were used to discover key operational details of a biochemical switch that determines the fate of HIV-infected cells.


A recent report from the Basic Energy Sciences Advisory Committee has identified understanding the role of stochastic fluctuation in biological systems as key to realizing the “dreams of nanoscience.”2 Like the systems envisioned emerging from nanoscience, the genetic and biochemical processes that generate the complex and versatile behavior of cells are highly functional, densely packed, information processing systems that operate in highly fluctuating environments. It is of great interest to researchers interested in the future design of complex synthetic nanoscale systems to learn how complex cellular functionality is maintained within, and in some cases even enhanced by, this highly noisy environment. The functional role of fluctuations is especially pronounced in decision circuits that choose between two divergent fates, such as the HIV developmental switch at the center of this research. Especially notable in this study is that while the results of decisions were visible, the mechanism of decision making could not be directly imaged. Instead, the mechanistic understanding was found in the structure of fluctuations. This work suggests that a variety of nanoscale phenomenon that cannot be directly imaged may be probed by looking into the noise.

Experiments carried out in the Center for Nanophase Materials Sciences, Oak Ridge National Laboratory by Roy D. Dar (University of Tennessee Graduate Student in Physics) and Michael L. Simpson. Coauthor and collaborator Leor S. Weinberger was a Lewis Thomas Fellow at Princeton University and is presently a faculty member in the Biochemistry Department at the University of California, San Diego (UCSD).

1Austin, D. W., M. S. Allen, J. M. McCollum, R. D. Dar, J. R. Wilgus, G. S. Sayler, N. F. Samatova, C. D. Cox, and M. L. Simpson, “Gene Network Shaping of Inherent Noise Spectra,” Nature 439, 608-611 (2006).

2See Chapter 5, Realizing the Dream Of Nanoscience: Energy And Information On The Nanoscale
From Directing Matter and Energy: Five Challenges for Science and the Imagination, A Report from the Basic Energy Sciences Advisory Committee

(A) Snapshots from the time-lapse fluorescent microscopy of immune cells expressing HIV genes and a green fluorescent protein (GFP) reporter. (B) Time course of GFP fluorescence in the cells showing the very large stochastic fluctuations in which the decision making takes place. Mechanistic details about the function of the biochemical switch were found by detailed analysis of these fluctuations.