Phenotypic consequences of logarithmic signaling in MAPK stress response.

How cells respond to dynamic environmental changes is crucial for understanding fundamental biological processes and cell physiology. In this study, we developed an experimental and quantitative analytical framework to explore how dynamic stress gradients that change over time regulate cellular volume, signaling activation, and growth phenotypes. Our findings reveal that gradual stress conditions substantially enhance cell growth compared to conventional acute stress.

Building predictive signaling models by perturbing yeast cells with time-varying stimulations resulting in distinct signaling responses.

This protocol provides a step-by-step approach to perturb single cells with time-varying stimulation profiles, collect distinct signaling responses, and use these to infer a system of ordinary differential equations to capture and predict dynamics of protein-protein regulation in signal transduction pathways. The models are validated by predicting the signaling activation upon new cell stimulation conditions. In comparison to using standard step-like stimulations, application of diverse time-varying cell stimulations results in better inference of model parameters and substantially improves model predictions.

A rate threshold mechanism regulates MAPK stress signaling and survival.

Cells are exposed to changes in extracellular stimulus concentration that vary as a function of rate. However, how cells integrate information conveyed from stimulation rate along with concentration remains poorly understood. Here, we examined how varying the rate of stress application alters budding yeast mitogen-activated protein kinase (MAPK) signaling and cell behavior at the single-cell level.

Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models.

Computationally understanding the molecular mechanisms that give rise to cell signaling responses upon different environmental, chemical, and genetic perturbations is a long-standing challenge that requires models that fit and predict quantitative responses for new biological conditions. Overcoming this challenge depends not only on good models and detailed experimental data but also on the rigorous integration of both. We propose a quantitative framework to perturb and model generic signaling networks using multiple and diverse changing environments (hereafter "kinetic stimulations") resulting in distinct pathway activation dynamics.

Generating kinetic environments to study dynamic cellular processes in single cells.

Cells of any organism are consistently exposed to changes over time in their environment. The kinetics by which these changes occur are critical for the cellular response and fate decision. It is therefore important to control the temporal changes of extracellular stimuli precisely to understand biological mechanisms in a quantitative manner.

From the volcano effect to banding: a minimal model for bacterial behavioral transitions near chemoattractant sources.

Sharp chemoattractant (CA) gradient variations near food sources may give rise to dramatic behavioral changes of bacteria neighboring these sources. For instance, marine bacteria exhibiting run-reverse motility are known to form distinct bands around patches (large sources) of chemoattractant such as nutrient-soaked beads while run-and-tumble bacteria have been predicted to exhibit a 'volcano effect' (spherical shell-shaped density) around a small (point) source of food. Here we provide the first minimal model of banding for run-reverse bacteria and show that, while banding and the volcano effect may appear superficially similar, they are different physical effects manifested under different source emission rate (and thus effective source size).

Statistical signatures of a targeted search by bacteria.

Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena-such as the volcano effect or banding-have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources.

Hydrodynamic Hunters.

The Gram-negative Bdellovibrio bacteriovorus (BV) is a model bacterial predator that hunts other bacteria and may serve as a living antibiotic. Despite over 50 years since its discovery, it is suggested that BV probably collides into its prey at random. It remains unclear to what degree, if any, BV uses chemical cues to target its prey.

A novel method to accurately locate and count large numbers of steps by photobleaching.

Photobleaching event counting is a single-molecule fluorescence technique that is increasingly being used to determine the stoichiometry of protein and RNA complexes composed of many subunits in vivo as well as in vitro. By tagging protein or RNA subunits with fluorophores, activating them, and subsequently observing as the fluorophores photobleach, one obtains information on the number of subunits in a complex. The noise properties in a photobleaching time trace depend on the number of active fluorescent subunits.

Inferring Models of Bacterial Dynamics toward Point Sources.

Experiments have shown that bacteria can be sensitive to small variations in chemoattractant (CA) concentrations. Motivated by these findings, our focus here is on a regime rarely studied in experiments: bacteria tracking point CA sources (such as food patches or even prey). In tracking point sources, the CA detected by bacteria may show very large spatiotemporal fluctuations which vary with distance from the source.

Holographic polymer dispersed liquid crystal enhanced by introducing urethane trimethacrylate.

This work characterizes holographic polymer dispersed liquid crystals (HPDLC) composite material based on a new monomer, urethane trimethacrylate, by fabricating switchable diffraction grating. The highest diffraction efficiency achieved was 90.3%.

All-optical switchable holographic Fresnel lens based on azo-dye-doped polymer-dispersed liquid crystals.

Fabrication of an all-optical switchable holographic liquid crystal (LC) Fresnel lens based on azo-dye-doped polymer-dispersed LCs is reported using a Michelson interferometer. It is found that, upon circularly polarized photoirradiation, the diffraction efficiency of the fabricated Fresnel lens was increased significantly in a reversible manner. We believe this is due to the anisotropy induced by reorientation of the LC molecules coupled with azo-dye molecule orientation due to trans-cis-trans photoisomerization, which modulates the refractive index of the LC-rich regions.

Electrically switchable holographic liquid crystal/polymer Fresnel lens using a Michelson interferometer.

A holographic technique for fabricating an electrically switchable liquid crystal/polymer composite Fresnel lens is reported. A Michelson interferometer is used to produce the required Fresnel pattern, by placing a convex lens into one path of the interferometer. Simplicity of the method and the possibility of fabricating different focal length lenses in a single arrangement are advantages of the method.