Current Understanding of the Structure,Stability and Dynamic Properties of Amyloid Fibrils

Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.     

Comparative study of lipogenic enzymes in several vertebrates

The liver lipogenic enzymes are compared among rats, chickens, frogs and fish. Although the apparent Km values of glucose-6-phosphate dehydrogenase for glucose-6-phosphate are not much different among all the species, those of malic enzyme for malate are much higher in chickens and fish than in rats and frogs. Glucose-6-phosphate dehydrogenase showed very high activities compared with malic enzyme in fish liver, and malic enzyme showed high activities in chicken liver. Although the apparent Km values of acetyl-CoA carboxylase and fatty acid synthetase for substrates are in the same range among all the animals, the activity of acetyl-CoA carboxylase seems to be extremely low in fish and frog livers, and that of fatty acid synthetase is low in frog livers only. In addition, the apparent Km values of α-glycerophosphate acyltransferase of fish liver are very high, and the enzyme activity appears to be extremely low compared to the others. Therefore, the enzymes at the first steps of both fatty acid and glycerolipid syntheses of poikilothermos animals appear to be very low. On the other hand, the Ouchterlony double-diffusion patterns showed that the lipogenic enzymes of chickens, frogs and fish are immunologically different from those of rats, with the exception of acetyl-CoA carboxylase in chickens. Therefore, it is suggested that the fatty acid and glycerolipid forming systems of poikilothermos animals are quite different from those of homoiothermos and the lipogenesis is very low in poikilothermos.     

Stability analysis of networked control systems subject to packet-dropouts and finite-level quantization

This paper is concerned with the stability analysis of a networked control system, wherein communication from the controller to the plant input is through a digital channel subject to packet-dropouts and finite-level quantization. No acknowledgments of receipt are available to the controller. To alleviate the effect of packet-dropouts, the controller transmits tentative plant input sequences. Within this setup, we derive a sufficient condition for small ?^∞ signal ?^∞ stability of the networked control system. This condition requires the maximum number of consecutive packet-dropouts to be bounded. We also elucidate the trade-off which exists between the disturbance attenuation and the step size of the quantizer and the maximum number of consecutive packet-dropouts.     

Determination of γ-glutamyl-valyl-glycine in raw scallop and processed scallop products using high pressure liquid chromatography–tandem mass spectrometry

The determination of the kokumi peptide, γ-glutamyl-valyl-glycine (γ-Glu-Val-Gly) in raw scallop and processed scallop products was carried out using high pressure liquid chromatography–tandem mass spectrometry (LC/MS/MS). The detection of γ-Glu-Val-Gly was achieved using a multiple reaction monitoring (MRM) method. The optimised condition enabled the precise determination of γ-Glu-Val-Gly. Raw scallop contained 0.08 μg/g γ-Glu-Val-Gly, and the γ-Glu-Val-Gly levels in processed scallop products, such as dried-scallop and scallop extract, were measured to be 0.64 and 0.77 μg/g, respectively. This is the first report to confirm the existence of γ-Glu-Val-Gly in foodstuff.     

Robust comprehension of natural language instructions by a domestic service robot

We present a method through which domestic service robots can comprehend natural language instructions. For each action type, a variety of natural language expressions can be used, for example, the instruction, ‘Go to the kitchen’ can also be expressed as ‘Move to the kitchen.’ We are of the view that natural language instructions are intuitive and, therefore, constitute one of the most user-friendly robot instruction methods. In this paper, we propose a method that enables robots to comprehend instructions spoken by a human user in his/her natural language. The proposed method combines action-type classification, which is based on a support vector machine, and slot extraction, which is based on conditional random fields, both of which are required in order for a robot to execute an action. Further, by considering the co-occurrence relationship between the action type and the slots along with the speech recognition score, the proposed method can avoid degradation of the robot’s comprehension accuracy in noisy environments, where inaccurate speech recognition can be problematic. We conducted experiments using a Japanese instruction data-set collected using a questionnaire-based survey. Experimental results show that the robot’s comprehension accuracy is higher in a noisy environment using our method than when using a baseline method with only a 1-best speech recognition result.     

Carbon coating of anatase-type TiO2 through their precipitation in PVA aqueous solution

Fine particles of photocatalytic anatase-type TiO₂ prepared through hydrolysis of titanium-tetraisopropoxide were coated by carbon through their precipitation in poly(vinyl alcohol) (PVA) aqueous solution, followed by heat treatment at high temperatures of 400-1000 °C in a flow of high purity Ar. Without carbon coating, the phase transformation from anatase to rutile started above 600 °C, but it was suppressed up to 800 °C with carbon coating. Suppression of the phase transformation depended on the amount of carbon coated, apparent suppression being observed with carbon content above 5 mass%. The amount of carbon coated on anatase was controlled by changing the concentration of PVA in the solution. In order to have a carbon content of about 5 mass%, a PVA solution with more than 2 mass% had to be used.     

Reduction and unusual recovery in the reversible hydrogen storage capacity of V1−xTix during hydrogen cycling

The effect of the vanadium content on the cyclic stability of V–Ti binary alloys was investigated. V_1−xTi_x, x = 0.2 and 0.5 samples were hydrogenated and dehydrogenated at 410 K and 553 K respectively, for more than 100 times. During hydrogen cycling, reduction in the reversible hydrogen storage capacity was clearly observed from both samples. No prominent V-effect was found. In fact, the reduction rates of two samples were similar; both samples showed a ∼25% reduction in the reversible hydrogen storage capacity after 100 cycles. In addition, the shape of the pressure–composition-isotherm (PCT) curves was significantly altered over the testing cycle period; the absorption and desorption plateaus got markedly inclined and the hysteresis became evidently smaller. We found that even after the hydrogen storage capacity of V_1−xTi_x was significantly reduced, at low enough temperature V_1−xTi_x was able to absorb hydrogen as much as it did at the first cycle. Furthermore, the reversible hydrogen storage capacity of V_0.8Ti_0.2 at 410 K was recovered to a certain degree after hydrogenating the sample at low temperatures.     

A new approach to species determination for yeast strains: DNA microarray-based comparative genomic hybridization using a yeast DNA microarray with 6000 genes

DNA-DNA hybridization is known as the superior method in the elucidation of relationships between closely related taxa, such as species and strain. For species determination we propose a new DNA-DNA hybridization method: the DNA microarray-based comparative genomic hybridization (CGH) method, using a yeast DNA microarray with approximately 6000 genes. The genome from a yeast strain as a sample strain (Sample) was labelled with Cy3-dye and hybridized to a single DNA microarray, together with the Cy5-labelled genome of S. cerevisiae S288C as a reference strain (Reference). The log2 ratio values [log2[Cy3(Sample)/Cy5(Reference)]: Ratio] of signal intensities of all the gene spots were estimated and divided into the following groups: Ratio < or = -1; -1 < Ratio < 1; 1 < or = Ratio. The hybridization profiles of the genomes of type strains belonging to the genus Saccharomyces were significantly different from that of S. cerevisiae S288C. The Ratio-based grouping allowed us to discriminate between some species from S. cerevisiae more clearly. Furthermore, cluster analysis discriminated between closely related species and strains. Using this method, we were able to not only perform species determination but also to obtain information on alternation in gene copy number of such gene amplifications and deletions with single-gene resolution. These observations indicated that DNA microarray-based CGH is a powerful system for species determination and comparative genome analysis.     

Correlation of the structures of agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses

Correlations between the chemical structures of agricultural fungicides and mRNA expression levels following exposure of Saccharomyces cerevisiae to toxic doses of thiuram, zineb, maneb, TPN, and PCP were examined. Structurally, thiuram, zineb, and maneb are dithiocarbamate fungicides, whereas TPN and PCP are not. To characterize chemical toxicity, genes expression was classified according to the functional groups used by the MIPS database. However, no correlations between the classification scheme and chemical structures were found. Hierarchical clustering of gene expression profiles was performed to characterize the effects of the five chemicals. According to this analysis the similarity of gene expression profiles depended on the similarity of chemical structures. These results suggest that DNA microarray technology has potential for predicting the major chemicals which will cause environmental toxicity and will provide information on new biomonitoring methods.     

Band analysis of temperature-dependent near-infrared spectra of oleic acid in the pure liquid state by the analytic geometric approach

The applicability of the band-stripping and complementary matching method has been demonstrated by the analysis of temperature-dependent near-infrared (NIR) absorption spectra in the 7500-6500 cm(-1) region of oleic acid (cis-9-octadecenoic acid) in the pure liquid state. This method is based on first derivative-second derivative pair (D1-D2) plots and a new concept called the complementary band, cBDi, created by subtracting all the rest of the bands, exclusive of the ith estimated band, eBDi, from an experimental spectrum. The degree of coincidence of both band shapes provides a suitable measure for the quality of fit for each individual component band. It has been confirmed from the present analysis of the NIR spectra of oleic acid measured over a temperature range of 16-79 degrees C that the change of the peak intensity of the component band at around 6915 cm(-1) due to the first overtone of an O-H stretching vibration of the monomer has two transition points around 35 and 55 degrees C. Moreover, the present study has provided new insight into the analysis of temperature-dependent spectral variations of oleic acid. Among the three temperature ranges, 16-35 degrees C, 35-55 degrees C, and 55-79 degrees C, in the first range the band near 6915 cm(-1) shows a slight increase and in the second range it has a linear intensity change with a slope of 0.002 a.u./degree C. In the third range, a rapid increase of the peak intensity is observed. This band exists even at 15 degrees C (just below the melting point) and shows a shift from 6910 to 6915 cm(-1) and a band narrowing from 85 to 80 cm(-1) (full width at half-height) over a temperature range of 16 to 79 degrees C. Furthermore, it has been found that there are two broad bands at around 6835 and 6778.