Hydrophobic effects on protein/nucleic acid interaction: enhancement of substrate binding by mutating tyrosine 45 to tryptophan in ribonuclease Tl

Hydrophobic effects on binding of ribonuclease Tl to guaninebases of several ribonucleotides have been proved by mutatinga hydrophobic residue at the recognition site and by measuringthe effect on binding. Mutation of a hydrophobic surface residueto a more hydrophobic residue (Tyr45 – Trp) enhances thebinding to ribonucleotides, including mononucleotide inhibitorand product, and a synthetic substrate-analog trinudeotide aswell as the binding to dinucleotide substrates and RNA. Enhancementson binding to non-substrate ribonucleotides by the mutationhave been observed with free energy changes ranging from –2.2 to – 3 .9 kJ/mol. These changes are in good agreementwith that of substrate binding, –2.3 kJ/mol, which iscalculated from Michaelis constants obtained from kinetic studies.It is shown, by comparing the observed and calculated changesin binding free energy with differences in the observed transferfree energy changes of the amino acid side chains from organicsolvents to water, that the enhancement observed on guaninebinding comes from the difference in the hydrophobic effectsof the side chains of tyrosine and tryptophan. Furthermore,a linear relationship between nucleolytic activities and hydrophobicityof the residues (Ala, Phe, Tyr, Trp) at position 45 is observed.The mutation could not change substantially the base specificityof RNase Tl, which exhibits a prime requirement for guaninebases of substrates.     

Autoxidation of ethyl eicosapentaenoate and docosahexaenoate

The extent of oxidation of ethyl esters of eicosapentaenoic (EPA) and docosahexaenoic acids (DHA) was compared quantitatively with that of ethyl linoleate (Lo) and ethyl linolenate (Ln) by oxygen uptake and formation of conjugated diene, hydroperoxide and secondary oxidation products. EPA and DHA esters were oxidized rapidly even at 5 C in the dark after an induction period of 3–4 days, while the induction periods of Ln and Lo esters were 20 days and more than 60 days, respectively. Oxygen uptake of EPA and DHA esters after the induction period was 5.2 and 8.5 times faster than that of ethyl Ln, respectively. Hydroperoxides of EPA and DHA esters are much less stable than those of ethyl Lo. The peroxide value is not necessarily a good indication of oxidation in these polyenoic acids because a considerable amount of secondary products is formed at the early stage of oxidation. Polymers were found to be major secondary products in these polyenoic esters.     

The oxidative coupling of methane on alkali- and alkaline earth-phosphate catalysts

The oxidative coupling of methane has been tested over alkali- and alkaline earth-phosphate catalysts at 700 and 775 °C with and without the introduction of a small quantity of tetrachloromethane (TCM) to the feedstream. In general, the conversion of methane was enhanced by the addition of TCM but the effect on selectivity was dependent on the catalyst being examined. The selectivity to C₂ and higher hydrocarbons and that to oxidation products have been shown to have a dependence on the cation radius/charge ratio.     

A low wall-loading DEMO reactor design with high priority for early and reliable realization of a tokamak fusion reactor over the cost performance

Based on scientific databases adopted for designing ITER plasmas and on the advancement of fusion nuclear technology from the recent R&D program, a low wall-loading DEMO fusion reactor has been designed, where high priority has been given to the early and reliable realization of a tokamak fusion plasma over the cost performance. Since the major radius of this DEMO reactor is chosen to be 10 m, plasma ignition is achievable with a low fusion power of 0.8 GW and an operation period of 4–5 hours is available only with inductive current drive. The low ignition power makes it possible to adopt a first wall with an austenitic stainless steel, for which significant databases and operating experience exists, due to its use in the presence of neutron irradiation in fission reactors. In step with development of advanced materials, a step-wise increase of the fusion power seems to be feasible and realistic, because this DEMO reactor has the potential to produce a fusion power of 5 GW.     

On the possible patterns of inputs for block sorting in the Burrows-Wheeler transformation

Block sorting in the Burrows-Wheeler transformation is to sort all of the n circular shifts of a string of length n lexicographically. We introduce a notion called the width of a sequence of n strings of length n and show that the values of widths are very different between the two types of sequences of strings; (1) a sequence of n randomly generated strings of length n, and (2) the sequence of n circular shifts of a randomly generated string of length n.     

Basic constructs of the SIM operating system

The basic constructs of SIMPOS (Sequential Inference Machine Programming and Operating System) are explained. SIMPOS is an operating system for a super-personal computer (SIM), based on logic programming language (a modified Prolog, called KL0). Our design principle is simplicity both in concept and structure. The entire system will be constructed using these basic constructs.     

Colorimetric microdetermination of sulphites in foods by use of the modified rankine apparatus. IV.

Summary Detection and determination of traces of sulphites in foods was attempted by use of the modified Rankine apparatus and pararosaniline colorimetry. Replacement of alkaline titration reported previously by pararosaniline colorimetry lowered the absolute detection limit from 30 g (titration method) to 2 g. In view of clean analysis, in the color developing system, 0.1 N-sodium hydroxide was used in place of mercuric chloride solution commonly used as an absorbant of sulphites. In order to prevent oxidative decomposition of sulphites during operation, nitrogen gas was used as carrier instead of air. Dimedone and sodium azide were used for the elimination of aldehydes and nitrites, respecitvely, in the sample, which will disturb the color development of sulphites with pararosaniline-formaldehyde reagents. With this improved method, it was possible to determine the residual sulphites in frozen peeled shrimps, sugared beans and other foods with low sulphite contents accurately.

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Colorimetrische Mikrobestimmung von Sulfiten in Lebensmitteln bei Anwendung der modifizierten IV. Rankine Apparatur

Zusammenfassung Geringe Sulfitmengen in Lebensmitteln (geschälte Garnelen, gezuckerte Bohnen) können colorimetrisch bestimmt werden. Die neuentwickelte Methode beruht auf einer Kombination von colorimetrischer Bestimmung mittels p-Rosanilin und der Bestimmungsmethode nach Rankine. Auf diese Weise lassen sich Gehalte von 2 g noch genau bestimmen. Bei der Farbentwicklung wurde das giftige Quecksilbertetrachlorid durch 0.1 n-NaOH ersetzt, anstelle von Luft Stickstoff als Trägergas verwendet und somit eine Oxydation des Sulfits während der Bestimmung vermieden. Da Nitrit und Aldehyde die Farbentwicklung stören, wurde ihr Einfluß durch Dimedon und Natriumazid ausgeschaltet.

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Studies on the Analyses of Sulphites in Foods (IV)     

Helium gas permeability of montmorillonite/epoxy nanocomposites

Helium gas permeability of silicate clay (montmorillonite) particles/epoxy nanocomposites was examined. The incorporation of increasing amounts of montmorillonite particles reduced the helium gas permeability. Based on Fick’s law, gas permeation behavior of the nanocomposite was evaluated. With the increase of montmorillonite loading, gas diffusivity decreased, while gas solubility increased. Helium diffusion behavior is in agreement to the numerical results based on the Hatta–Taya–Eshelby theory. It has been revealed that dispersion of nanoscale platelets in polymer is effective in improving gas barrier property.     

On the computational power of insertion-deletion systems

Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecular biology. The genetic mechanism and development based on these evolutionary transformations have been formulated as a formal system with two operations of insertion and deletion, called insertion-deletion systems (Kari and Thierrin, 1996; Kari et al., 1997).We investigate the generative power of insertion-deletion systems (InsDel systems), and show that the family INS ¹ ₁ DEL ¹ ₁ is equal to the family of recursively enumerable languages. This gives a positive answer to an open problem posed in Kari et al. (1997) where it was conjectured contrary. This revised version was published online in June 2006 with corrections to the Cover Date.