Characterization of amino acid ligases and development of production processes for peptide containing D-amino acid

制度:新 ; 文部省報告番号:甲2399号 ; 学位の種類:博士(工学) ; 授与年月日:2007/3/15 ; 早大学位記番号:新448

Allosteric Regulation of HIV-1 Reverse Transcriptase by ATP for Nucleotide Selection

Background: Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a DNA polymerase that converts viral RNA genomes into proviral DNAs. How HIV-1 RT regulates nucleotide selectivity is a central issue for genetics and the nucleoside analog RT inhibitor (NRTI) resistance of HIV-1. Methodology/Principal Findings: Here we show that an ATP molecule at physiological concentrations acts as an allosteric regulator of HIV-1 RT to decrease the Km value of the substrate, decrease the kcat value, and increase the Ki value of NRTIs for RT. Computer-assisted structural analyses and mutagenesis studies suggested the positions of the ATP molecule and NRTIresistance mutations during a catalytic reaction, which immediately predict possible influences on nucleotide insertion into the catalytic site, the DNA polymerization, and the excision reaction. Conclusions/Significance: These data imply that the ATP molecule and NRTI mutations can modulate nucleotide selectivity by altering the fidelity of the geometric selection of nucleotides and the probability of an excision reaction

Drum Beating and a Martial Art Bojutsu Performed by a Humanoid Robot

Over the past few decades a considerable number of studies have been made on impact dynamics. Zheng and Hemami discussed a mathematical model of a robot that collides with an environment (Zheng & Hemami, 1985). When a robot arm fixed on the ground collides with a hard environment, the transition from the free space to constrained space may bring instabilit

Bayesian Approach to Find a Long-Term Trend in Erratic Polarization Variations Observed in Blazars

We developed a method to separate a long-term trend from observed temporal variations of polarization in blazars using a Bayesian approach. The temporal variation of the polarization vector is apparently erratic in most blazars, while several objects occasionally exhibited systematic variations, for example, an increase of the polarization degree associated with a flare of the total flux. We assume that the observed polarization vector is a superposition of distinct two components, a long-term trend and a short-term variation component responsible for short flares. Our Bayesian model estimates the long-term trend which satisfies the condition that the total flux correlates with the polarized flux of the short-term component. We demonstrate that assumed long-term polarization components are successfully separated by the Bayesian model for artificial data. We applied this method to photopolarimetric data of OJ 287, S5 0716+714, and S2 0109+224. Simple and systematic long-term trends were obtained in OJ 287 and S2 0109+224, while no such a trend was identified in S5 0716+714. We propose that the apparently erratic variations of polarization in OJ 287 and S2 0109+224 are due to the presence of the long-term polarization component. The behavior of polarization in S5 0716+714 during our observation period implies the presence of a number of polarization components having a quite short time-scale of variations.Comment: 12 pages, 7 figures, accepted for publication in PAS

Time-resolved metabolomics reveals metabolic modulation in rice foliage

<p>Abstract</p> <p>Background</p> <p>To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed.</p> <p>Results</p> <p>Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (<it>Oryza sativa </it>L. ssp. <it>japonica</it>) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks.</p> <p>Conclusion</p> <p>Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems.</p