Phase resetting reveals network dynamics underlying a bacterial cell cycle

Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS)

Picosecond photofragment spectroscopy. II. The overtone initiated unimolecular reaction H_2O_2(v_(OH)=5)→2OH

This paper, second in the series, reports on the picosecond time‐resolved photofragmentation of the overtone (v_(OH)=5) initiated reaction: HOOH+hν→2OH. The hydrogen peroxide is initially excited by way of a picosecond laser pulse to the fourth overtone level of the OH‐stretch local mode. The subsequent unimolecular reaction behavior is obtained by monitoring the laser‐induced fluorescence, caused by the picosecond probe–pulse electronic excitation of the OH radical photoproduct (in a given rotational state). The two pulses are scanned relative to one another in time thereby mapping out the product yield for the given delay‐time interval. The resultant product formation behavior is found to be nonexponential, and may be modeled as a biexponential rise. Furthermore, the quasibiexponential behavior is sensitive to the exact excitation wavelength—slight variations of which result in large changes in the two time constants and the relative amplitudes of the fast and slow components. These experiments give direct evidence for the inhomogeneous nature of the overtone transition on the picosecond time scale, and provide the dissociation rate contribution to the homogeneous width (0.05–0.15 cm^(−1)). The apparent width for the main band feature is about 200 cm^(−1). The rate of product formation (magnitude and form) is interpreted in terms of statistical and nonstatistical theories. The limitations of the applicability of each model is discussed. The fluctuations of the fitting parameters as a function of excitation wavelength may be simulated by a statistical model which considers all possible discrete optical transitions within the simulated laser bandwidth and the details of product formation from each state. For a nonstatistical interpretation, the biexponential form reflects a division of the vibrational phase space, and this is discussed in the spirit of a kinetic model. Finally, experimental results are reported for direct UV initiated photofragmentation. The observed dynamics indicate that a very different type of potential surface (repulsive) is involved, in contrast to the overtone initiated dissociation, which takes place on the ground state surface

Ultrafast resonant optical scattering from single gold nanorods: Large nonlinearities and plasmon saturation

We measure nonlinear optical scattering from individual Au nanorods excited by ultrafast laser pulses on resonance with their longitudinal plasmon mode. Isolating single rods removes inhomogeneous broadening and allows the measurement of a large nonlinearity, much greater than that of nanorod ensembles. Surprisingly, the ultrafast nonlinearity can be attributed entirely to heating of conduction electrons and does not exhibit any response associated with coherent plasmon oscillation. This indicates a previously unobserved damping of strongly driven plasmons.Comment: Revised tex

Structural Responses of Quasi-2D Colloid Fluids to Excitations Elicited by Nonequilibrium Perturbations

We investigate the response of a dense monodisperse quasi-two-dimensional (q2D) colloid suspension when a particle is dragged by a constant velocity optical trap. Consistent with microrheological studies of other geometries, the perturbation induces a leading density wave and trailing wake, and we use Stokesian Dynamics (SD) simulations to parse direct colloid-colloid and hydrodynamic interactions. We go on to analyze the underlying individual particle-particle collisions in the experimental images. The displacements of particles form chains reminiscent of stress propagation in sheared granular materials. From these data, we can reconstruct steady-state dipolar flow patterns that were predicted for dilute suspensions and previously observed in granular analogs to our system. The decay of this field differs, however, from point Stokeslet calculations, indicating that the finite size of the colloids is important. Moreover, there is a pronounced angular dependence that corresponds to the surrounding colloid structure, which evolves in response to the perturbation. Put together, our results show that the response of the complex fluid is highly anisotropic owing to the fact that the effects of the perturbation propagate through the structured medium via chains of colloid-colloid collisions

Real-time picosecond clocking of the collision complex in a bimolecular reaction: The birth of OH from H+CO_2

Picosecond (and femtosecond) photofragment spectroscopy has recently provided time-resolved, state-to-state dynamics of molecular photofragmentation. The focus of these experiments was on unimolecular reactions, where two main issues are fundamental to the dynamics: the nature of the "half-collision" and the degree to which statistical theories account for the time evolution of product state distributions (PSDs)

Scaling laws governing stochastic growth and division of single bacterial cells

Uncovering the quantitative laws that govern the growth and division of single cells remains a major challenge. Using a unique combination of technologies that yields unprecedented statistical precision, we find that the sizes of individual Caulobacter crescentus cells increase exponentially in time. We also establish that they divide upon reaching a critical multiple ($\approx$1.8) of their initial sizes, rather than an absolute size. We show that when the temperature is varied, the growth and division timescales scale proportionally with each other over the physiological temperature range. Strikingly, the cell-size and division-time distributions can both be rescaled by their mean values such that the condition-specific distributions collapse to universal curves. We account for these observations with a minimal stochastic model that is based on an autocatalytic cycle. It predicts the scalings, as well as specific functional forms for the universal curves. Our experimental and theoretical analysis reveals a simple physical principle governing these complex biological processes: a single temperature-dependent scale of cellular time governs the stochastic dynamics of growth and division in balanced growth conditions.Comment: Text+Supplementar