Emergence of cooperative bistability and robustness of gene regulatory networks

Gene regulatory networks (GRNs) are complex systems in which many genes regulate mutually to adapt the cell state to environmental conditions. In addition to function, the GRNs possess several kinds of robustness. This robustness means that systems do not lose their functionality when exposed to disturbances such as mutations or noise, and is widely observed at many levels in living systems. Both function and robustness have been acquired through evolution. In this respect, GRNs utilized in living systems are rare among all possible GRNs. In this study, we explored the fitness landscape of GRNs and investigated how robustness emerged in highly-fit GRNs. We considered a toy model of GRNs with one input gene and one output gene. The difference in the expression level of the output gene between two input states, “on” and “off”, was considered as fitness. Thus, the determination of the fitness of a GRN was based on how sensitively it responded to the input. We employed the multicanonical Monte Carlo method, which can sample GRNs randomly in a wide range of fitness levels, and classified the GRNs according to their fitness. As a result, the following properties were found: (1) Highly-fit GRNs exhibited bistability for intermediate input between “on” and “off”. This means that such GRNs responded to two input states by using different fixed points of dynamics. This bistability emerges necessarily as fitness increases. (2) These highly-fit GRNs were robust against noise because of their bistability. In other words, noise robustness is a byproduct of high fitness. (3) GRNs that were robust against mutations were not extremely rare among the highly-fit GRNs. This implies that mutational robustness is readily acquired through the evolutionary process. These properties are universal irrespective of the evolutionary pathway, because the results do not rely on evolutionary simulation.Nagata S., Kikuchi M..(2020) Emergence of cooperative bistability and robustness of gene regulatory networks. PLoS Computational Biology 16(6): 1007969. doi: 10.1371/journal.pcbi.1007969

A MATHEMATICAL THEORY FOR BLOOD FLOW DYNAMICS IN THE ARTERIAL SYSTEM analysis of rotation angle and dynamical equations for forces and moments operating on artreial wall.

We have established a mathematical model of arterial system. This paper expand theoretical analysis of the mechanical dynamical structure of the arterial wall. The general deformation theory of dynamical analysis was applied to establish the balancing equations of the forces and moments that operate on the arterial wall surface. To generalyze the dynamical problem，we brought the shell theory of the curved surface into the analysis of the arterial wall surface. To associate and identify the directions of the forces and moments before and after the deformation， we firstly analyzed the relative rotation angles between each lines of the micro surface elements around the 3 axies which were founded on the elements. Utilyzing these parameters of the relative rotation， movements， we induced the balancing equations of the forces. Since we Assume more general case， we also studied the balancing equations of bending，twisting moments and transverse shear. Then we have obtained 6 equilibrium equation in 3 directions. This paper is one of the vital points of the mathematical expansion of our theory. [The constructive dynamic analysis of the arterial wall] -1 The rotation angle of the arterial wall and the equilibrium equations for the stress and moments operating on the wall

Enhanced extraction of heavy metals in the two-step process with the mixed culture of Lactobacillus bulgaricus and Streptococcus thermophilus

For biological extraction of heavy metals from chromated copper arsenate (CCA) treated wood, different bacteria were investigated. The extraction rates of heavy metals using Lactobacillus bulgaricus and Streptococcus thermophilus were highest. The chemical extraction rates were depended on the amounts of pyruvic acid and lactic acid. Especially, the extraction rates using mixed pyruvic acid and lactic acid were increased compared to those of sole one. They were also enhanced in the mixed culture of L. bulgaricus and S. thermophilus. To improve the extraction of CCA, a two-step processing procedure with the mixed culture of L. bulgaricus and S. thermophilus was conducted. A maximum of 93% of copper, 86.5% of chromium, and 97.8% of arsenic were extracted after 4 days. These results suggest that a two-step process with the mixed culture of L. bulgaricus and S. thermophilus is most effective to extract heavy metals from CCA treated wood

Isolation and characterization of an arsenate-reducing bacterium and its application for arsenic extraction from contaminated soil

A Gram-negative anaerobic bacterium, Citrobacter sp. NC-1, was isolated from soil contaminated with arsenic at levels as high as 5,000 mg As kg−1. Strain NC-1 completely reduced 20 mM arsenate within 24 h and exhibited arsenate-reducing activity at concentrations as high as 60 mM. These results indicate that strain NC-1 is superior to other dissimilatory arsenate-reducing bacteria with respect to arsenate reduction, particularly at high concentrations. Strain NC-1 was also able to effectively extract arsenic from contaminated soils via the reduction of solid-phase arsenate to arsenite, which is much less adsorptive than arsenate. To characterize the reductase systems in strain NC-1, arsenate and nitrate reduction activities were investigated using washed-cell suspensions and crude cell extracts from cells grown on arsenate or nitrate. These reductase activities were induced individually by the two electron acceptors. This may be advantageous during bioremediation processes in which both contaminants are present