Network analysis of the autophagy biochemical network in relation to various autophagy-targeted proteins found among SARS-CoV-2 variants of concern.

Autophagy is an important cellular process that triggers a coordinated action involving multiple individual proteins and protein complexes while SARS-CoV-2 (SARS2) was found to both hinder autophagy to evade host defense and utilize autophagy for viral replication. Interestingly, the possible significant stages of the autophagy biochemical network in relation to the corresponding autophagy-targeted SARS2 proteins from the different variants of concern (VOC) were never established. In this study, we performed the following: autophagy biochemical network design and centrality analyses; generated autophagy-targeted SARS2 protein models; and superimposed protein models for structural comparison. We identified 2 significant biochemical pathways (one starts from the ULK complex and the other starts from the PI3P complex) within the autophagy biochemical network. Similarly, we determined that the autophagy-targeted SARS2 proteins (Nsp15, M, ORF7a, ORF3a, and E) are structurally conserved throughout the different SARS2 VOC suggesting that the function of each protein is preserved during SARS2 evolution. Interestingly, among the autophagy-targeted SARS2 proteins, the M protein coincides with the 2 significant biochemical pathways we identified within the autophagy biochemical network. In this regard, we propose that the SARS2 M protein is the main determinant that would influence autophagy outcome in regard to SARS2 infection.

Liquid-liquid biphasic synthesis of layered zinc hydroxides intercalated with long-chain carboxylate ions and their conversion into ZnO nanostructures.

A method for synthesizing layered zinc hydroxide compounds in high yields is developed using an immiscible liquid-liquid system in one pot. Long-chain carboxylate ions such as heptanoate, decanoate, and dodecanoate were successfully intercalated between zinc hydroxide layers in one process starting from a xylene-water system. Typically, a xylene phase dissolving the respective carboxylic acids was allowed to stand in contact with an aqueous phase dissolving zinc nitrate hexahydrate and urea. During keeping the resultant biphasic system at 80 °C, urea was thermo-hydrolyzed to supply OH(-) in the aqueous phase while the carboxylic acids were continuously transferred from the xylene phase under the distribution law. The aqueous phase was then supersaturated, and a solid phase of layered basic zinc carboxylate was precipitated as films on glass substrates through heterogeneous nucleation and subsequent two-dimensional crystal growth. Crystal structures and morphology of the films were modulated by the kind of the carboxylic acids employed. The layered basic zinc carboxylate films could be converted to nanostructured, mesoporous ZnO films by heating at 450 °C in air. The relationship between the initial solution compositions and the final solid products was systematically examined to discuss reaction mechanisms in the biphasic systems.

Synthesis of inorganic-organic layered compounds using immiscible liquid-liquid systems under the distribution law.

A method for synthesizing inorganic-organic layered compounds is proposed using a biphasic liquid-liquid system in one pot. Layered basic zinc benzoate (LBZB) compounds were chosen, and their formation was investigated starting from a xylene-water system. In a typical synthesis, a xylene phase dissolving benzoic acid was allowed to stand in contact with an equal amount of an aqueous phase dissolving zinc nitrate hexahydrate and urea. A role of urea is to supply OH(-) gradually by hydrolysis at an elevated temperature. The biphasically separated solutions were maintained at 80 °C, and then LBZB was obtained in the aqueous phase. Two kinds of layered structures with a basal spacing of 27.14 and 14.77 Å were formed by changing a C(6)H(5)COOH/Zn molar ratio. Chemical compositions of the 27.14 and the 14.77 Å layered phases were estimated to be Zn(OH)(1.74)(C(6)H(5)COO)(0.26)·0.29H(2)O and Zn(OH)(1.12)(C(6)H(5)COO)(0.88)·0.21H(2)O, respectively. The 27.14 Å phase could also be deposited as a film on substrates by heterogeneous nucleation. The film consisted of standing platelike particles and exhibited a two-dimensional structure, which could be converted to ZnO by heating. The relationship between the initial solution compositions and the final solid products was systematically examined on the basis of distribution law for benzoic acid in the xylene-water system.