Yufang Wang

Princeton University, Princeton, NJ, United States

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Publications (7)29.68 Total impact

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    ABSTRACT: Gene expression is stochastic, and noise that arises from the stochastic nature of biochemical reactions propagates through active regulatory links. Thus, correlations in gene-expression noise can provide information about regulatory links. We present what to our knowledge is a new approach to measure and interpret such correlated fluctuations at the level of single microcolonies, which derive from single cells. We demonstrated this approach mathematically using stochastic modeling, and applied it to experimental time-lapse fluorescence microscopy data. Specifically, we investigated the relationships among LuxO, LuxR, and the small regulatory RNA qrr4 in the model quorum-sensing bacterium Vibrio harveyi. Our results show that LuxR positively regulates the qrr4 promoter. Under our conditions, we find that qrr regulation weakly depends on total LuxO levels and that LuxO autorepression is saturated. We also find evidence that the fluctuations in LuxO levels are dominated by intrinsic noise. We furthermore propose LuxO and LuxR interact at all autoinducer levels via an unknown mechanism. Of importance, our new method of evaluating correlations at the microcolony level is unaffected by partition noise at cell division. Moreover, the method is first-order accurate and requires less effort for data analysis than single-cell-based approaches. This new correlation approach can be applied to other systems to aid analysis of gene regulatory circuits.
    Biophysical Journal 06/2011; 100(12):3045-53. · 3.67 Impact Factor
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    ABSTRACT: Quorum-sensing is the mechanism by which bacteria communicate and synchronize group behaviors. Quantitative information on parameters such as the copy number of particular quorum-sensing proteins should contribute strongly to understanding how the quorum-sensing network functions. Here, we show that the copy number of the master regulator protein LuxR in Vibrio harveyi can be determined in vivo by exploiting small-number fluctuations of the protein distribution when cells undergo division. When a cell divides, both its volume and LuxR protein copy number, N, are partitioned with slight asymmetries. We measured the distribution functions describing the partitioning of the protein fluorescence and the cell volume. The fluorescence distribution is found to narrow systematically as the LuxR population increases, whereas the volume partitioning is unchanged. Analyzing these changes statistically, we determined that N = 80-135 dimers at low cell density and 575 dimers at high cell density. In addition, we measured the static distribution of LuxR over a large (3000) clonal population. Combining the static and time-lapse experiments, we determine the magnitude of the Fano factor of the distribution. This technique has broad applicability as a general in vivo technique for measuring protein copy number and burst size.
    Biophysical Journal 05/2010; 98(9):2024-31. · 3.67 Impact Factor
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    ABSTRACT: Cell-to-cell communication in bacteria is a process known as quorum sensing that relies on the production, detection, and response to the extracellular accumulation of signaling molecules called autoinducers. Often, bacteria use multiple autoinducers to obtain information about the vicinal cell density. However, how cells integrate and interpret the information contained within multiple autoinducers remains a mystery. Using single-cell fluorescence microscopy, we quantified the signaling responses to and analyzed the integration of multiple autoinducers by the model quorum-sensing bacterium Vibrio harveyi. Our results revealed that signals from two distinct autoinducers, AI-1 and AI-2, are combined strictly additively in a shared phosphorelay pathway, with each autoinducer contributing nearly equally to the total response. We found a coherent response across the population with little cell-to-cell variation, indicating that the entire population of cells can reliably distinguish several distinct conditions of external autoinducer concentration. We speculate that the use of multiple autoinducers allows a growing population of cells to synchronize gene expression during a series of distinct developmental stages.
    PLoS Biology 04/2009; 7(3):e68. · 12.69 Impact Factor
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    ABSTRACT: We investigated the binding interaction between the bacteriophage lambda-repressor CI and its target DNA using total internal reflection fluorescence microscopy. Large stepwise changes in the intensity of the red fluorescent protein fused to CI were observed as it associated with and dissociated from individually labeled single-molecule DNA targets. The stochastic association and dissociation were characterized by Poisson statistics. Dark and bright intervals were measured for thousands of individual events. The exponential distribution of the intervals allowed direct determination of the association and dissociation rate constants (k(a) and k(d), respectively). We resolved in detail how k(a) and k(d) varied as a function of three control parameters: the DNA length L, the CI dimer concentration, and the binding affinity. Our results show that although interactions with nonoperator DNA sequences are observable, CI binding to the operator site is not dependent on the length of flanking nonoperator DNA.
    Biophysical Journal 02/2009; 96(2):609-20. · 3.67 Impact Factor
  • Biophysical Journal 01/2009; 96(3). · 3.67 Impact Factor
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    Yufang Wang, Y Zhang, N P Ong
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    ABSTRACT: Recently, several groups have designed and synthesized single-molecule devices based on DNA that can switch between different configurations in response to sequential addition of fuel DNA strands. There is considerable interest in improving the speed of these "nanomotors." One approach is the use of rationally designed DNA catalysts to promote hybridization of complementary oligonucleotides. A particularly simple and robust DNA device reported by Li and Tan is comprised of a single-strand 17-base oligomer that folds into a chairlike quadruplex structure. We have identified the key rate-limiting barrier in this device as the tendency for one of the fuel strands B to fold into the quadruplex configuration of the device strand. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of B and shown that the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst remains effective even after repeated cycling
    Physical Review E 12/2005; 72(5 Pt 1):051918. · 2.31 Impact Factor
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    Yufang Wang, Y Zhang, N. P. Ong
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    ABSTRACT: We demonstrate a catalytic control method for speeding up the single-molecule DNA motor introduced by Li and Tan [Nano Lett. {\bf 2}, 315 (2002)]. A key rate-limiting barrier in the reaction part of the cycle is the tendency for the second fuel strand $B$ to fold into the chair-like configuration of the original motor strand $M$. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of $B$. Introduction of the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst shows robust behavior for more than one cycle. The experimental data can be understood with a model with intermediate products. This technique provides dynamic control of the restoration rate of the motor without affecting the straightening rate. Comment: 6 pages, 5 figures New figure (Fig. 6) and appendix added. Text revised
    12/2004;