A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement

Cells polarize their movement or growth toward external directional cues in many different contexts. For example, budding yeast cells grow toward potential mating partners in response to pheromone gradients. Directed growth is controlled by polarity factors that assemble into clusters at the cell membrane. The clusters assemble, disassemble, and move between different regions of the membrane before eventually forming a stable polarity site directed toward the pheromone source. Pathways that regulate clustering have been identified but the molecular mechanisms that regulate cluster mobility are not well understood. To gain insight into the contribution of chemical noise to cluster behavior we simulated clustering within the reaction-diffusion master equation (RDME) framework to account for molecular-level fluctuations. RDME simulations are a computationally efficient approximation, but their results can diverge from the underlying microscopic dynamics. We implemented novel concentration-dependent rate constants that improved the accuracy of RDME-based simulations of cluster behavior, allowing us to efficiently investigate how cluster dynamics might be regulated. Molecular noise was effective in relocating clusters when the clusters contained low numbers of limiting polarity factors, and when Cdc42, the central polarity regulator, exhibited short dwell times at the polarity site. Cluster stabilization occurred when abundances or binding rates were altered to either lengthen dwell times or increase the number of polarity molecules in the cluster. We validated key results using full 3D particle-based simulations. Understanding the mechanisms cells use to regulate the dynamics of polarity clusters should provide insights into how cells dynamically track external directional cues.

Metabolomic Markers of Storage Temperature and Time in Pasteurized Milk

The current date labeling system for pasteurized milk is based on the predicted growth of spoilage microorganisms, but inherent inaccuracies and the inability to account for environmental factors (e.g., temperature fluctuations) contribute to household and retail food waste. Improved shelf-life estimation can be achieved by monitoring milk quality in real-time. In this study, we identify and quantify metabolites changing over storage temperature and time, the main factors affecting milk stability. Pasteurized 2% fat milk was stored at 4, 10, 15, and 20 °C. Metabolite change was analyzed using untargeted and targeted nuclear magnetic resonance (NMR) metabolomics approaches. Several metabolites correlated significantly to storage time and temperature. Citric acid decreased linearly over time at a temperature-dependent rate. Ethanol, formic acid, acetic acid, lactic acid, and succinic acid increased non-linearly after an initial period of minimal increase. Butyric acid exhibited strong inverse temperature dependencies. This study provides the first analysis of the effect of time and temperature on the concentration of key metabolites during milk storage. Candidate molecules for shelf-life monitoring have been identified, and the results improve our understanding of molecular changes during milk storage. These results will inform the development of real-time shelf-life indicators for milk, helping to reduce milk waste.

Atmospheric Reaction of Hydrazine Plus Hydroxyl Radical. I. Reliable Pathways

Understanding the mechanism of hydrazine oxidation reaction by OH radical accompanied by the rate constants of all possible pathways is important. They are key parameters to explain the fate of hydrazine in the atmosphere. To reach the mentioned parameters, higher-level calculations by using quantum chemical methods have been implemented comprehensively for reliable channels such as H-abstraction, SN2, and addition/elimination reactions. To estimate the barrier energies of H-abstraction channels accurately, large numbers of the CCSD(T)/X calculations (where X denotes the augmented Dunning and Pople double zeta or triple zeta basis sets) have been applied to the optimized geometries of the MP2/aug-cc-pVTZ, MP2/maug-cc-pVTZ, and M062X/maug-cc-pVTZ levels. Contributions of excited states on the computed potential energy surface have been considered by the MR-MP2 (multi-reference) method in conjunction with the large augmented quadruple zeta, aug-cc-pVQZ, basis sets. The direct dynamic calculations have been carried out using the accurate energies of the CCSD(T) method and the partition functions of the second-order MØller-Plesset perturbation theory, and also by the validated M06-2X method with the aug-cc-pVTZ, and maug-cc-pVTZ basis sets. Finally, The VTST and TST theories have been used to calculate the temperature dependence of rate constants of the considered pathways. Also, the pressure-dependent rate constants of the barrierless pathways have been investigated by the strong collision master equation/RRKM theory.