Strengths of Exaggerated Tsunami-Originated Placenames : Disaster Subculture in Sanriku Coast, Japan

Disaster-originated placename is a kind of disaster subculture that is used for a practical purpose of identifying a location while reminding the past disaster experience. They are expected to transmit the risks and knowledge of high-risk low-frequency natural hazards, surviving over time and generations. This paper compares the perceptions to tsunami-originated placenames in local communities having realistic and exaggerated origins in Sanriku Coast, Japan. The reality of tsunami-originated placenames is first assessed by comparing the tsunami run-ups indicated in the origins and that of the tsunami in the Great East Japan Earthquake 2011 using GIS and digital elevation model. Considerable proportions of placenames had exaggerated origins, but the group interviews to local communities revealed that origins indicating unrealistic tsunami run-ups were more believed than that of the more realistic ones. We discuss that accurate hazard information will be discredited if it contradicts to the people’s everyday life and the desire for safety, and even imprecise and ambiguous information can survive if it is embedded to a system of local knowledge that consistently explains the various facts in a local area that requires explanation

Trace analysis of nitrite ion in seawater using ion chromatography

An ion chromatographic method of separating and detecting nitrite in sea water is described. The system includes precolumn, new hydrophilic separation column, suppressor and two-valve system. Nitrite was diverted, trapped and separeted in a 2.6-ml sample loop using 6- and 4-port valves. The eluent used was 14.4 mM sodium hydrogen carbonate at flow-rate oflml/min while the scanvenger was 14 mM sulfuric acid. Nitrite recovery achieved was 100±2%. The minimum detection limit was 0.15 ppm with the signal-to-noise set 2.5 Nitrite recovery obtained using different mixing ratios of sodium hydrogen carbonate and sodium carbonate were lower. Eluent ph and compoosition affected both peak heights and retention timed of nitrite and other anions

Ion chromatography of inorganic anions in brine samples

An ion chromatographic method for separating and detecting anions in brine samples is described. Nitrite, bromide, nitrate, and sulfate ions in brine samples are well separated when chloride ion concentration in the sample solution is below 2000 ppm. However, at higher chloride concentrations, nitrite and chloride peaks are not resolved. Low level nitrite ion in the brine sample is separated from a major chloride ion by a heart-cutting and recycling system. After elution, the unresolved portion, including the nitrite ion, is cut and trapped in a 10-mL sample collecting loop and reinjected on the column by using 6- and 4-port valve systems. The detection limit of nitrite spiked in the seawater samples is 0.5 ppm

Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations

Threonine synthase (ThrS) catalyzes the final chemical reaction of l-threonine biosynthesis from its precursor, <i>O</i>-phospho-l-homoserine. As the phosphate ion generated in its former half reaction assists its latter reaction, ThrS is recognized as one of the best examples of product-assisted catalysis. In our previous QM/MM study, the chemical reactions for the latter half reactions, which are critical for the product-assisted catalysis, were revealed. However, accurate free energy changes caused by the conformational ensembles and entrance of water molecules into the active site are unknown. In the present study, by performing long-time scale MD simulations, the free energy changes by the divalent anions (phosphate or sulfate ions) and conformational states of the intermediate states were theoretically investigated. We found that the calculated free energy double differences are in good agreement with the experimental results. We also revealed that the phosphate ion contributes to forming hydrogen bonds that are suitable for the main reaction progress. This means that the conformation of the active site amino acid residues and the substrate, and hence, the tunable catalysis, are controlled by the product phosphate ion, and this clearly demonstrates a molecular mechanism of the product-assisted catalysis in ThrS

A QM/MM Study of the l‑Threonine Formation Reaction of Threonine Synthase: Implications into the Mechanism of the Reaction Specificity

Threonine synthase catalyzes the most complex reaction among the pyridoxal-5′-phosphate (PLP)-dependent enzymes. The important step is the addition of a water molecule to the Cβ–Cα double bond of the PLP−α-aminocrotonate aldimine intermediate. Transaldimination of this intermediate with Lys61 as a side reaction to form α-ketobutyrate competes with the normal addition reaction. We previously found that the phosphate ion released from the <i>O</i>-phospho-l-homoserine substrate plays a critical role in specifically promoting the normal reaction. In order to elucidate the detailed mechanism of this “product-assisted catalysis”, we performed comparative QM/MM calculations with an exhaustive search for the lowest-energy-barrier reaction pathways starting from PLP−α-aminocrotonate aldimine intermediate. Satisfactory agreements with the experiment were obtained for the free energy profile and the UV/vis spectra when the PLP pyridine N1 was unprotonated and the phosphate ion was monoprotonated. Contrary to an earlier proposal, the base that abstracts a proton from the attacking water was the ε-amino group of Lys61 rather than the phosphate ion. Nevertheless, the phosphate ion is important for stabilizing the transition state of the normal transaldimination to form l-threonine by making a hydrogen bond with the hydroxy group of the l-threonine moiety. The absence of this interaction may account for the higher energy barrier of the side reaction, and explains the mechanism of the reaction specificity afforded by the phosphate ion product. Additionally, a new mechanism, in which a proton temporarily resides at the phenolate O3′ of PLP, was proposed for the transaldimination process, a prerequisite step for the catalysis of all the PLP enzymes