Ryo Hanai

The effects of guanine and cytosine variation on dinucleotide frequency and amino acid composition in the human genome

SummaryOne hundred twelve human DNA sequences were analyzed with respect to dinucleotide frequency and amino acid composition. The variation in guanine and cytosine (G+C) content revealed: (1) at 2–3 and 3-1 doublet positions CG discrimination is attenuated at high G+C, but TA disfavor is enhanced, and (2) several amino acids are subject to G+C change. These findings have been reported in part for collections of sequences from various species. The present study confirms that in a single organism-the human-the G+C effects do exist. Aspects of the argument that connects G+C with protein thermal stability are also discussed.

Phenomenological theory of GC/AT pressure on DNA base composition

SummaryWe present a phenomenological theory expressing the constraints operating on the (G+C) contents of the three codon positions, i.e., first, second, and third bases of codons, by using the smallest number of constraint parameters having clear physical and genetic meaning. Theoretical curves displaying base composition at each of the three codon sites are given. The agreement between the theoretical curves and the data points of 1277 genes is quite good irrespective of the species from which the DNAs originated; the curves might be universal ones and the constraint parameters might have general biological meanings in relation to the DNA/RNA and protein functions.

Doublet preference and gene evolution.

SummaryDoublet preference analysis was carried out on coding and noncoding regions ofEscherichia coli, Saccharomyces cerevisiae, and human mitochondrial and nuclear DNA. The preference pattern in 1–2 and 2–3 doublets inE. coli andS. cerevisiae correlated with that in noncoding regions. The 3-1 doublet preference inE. coli genes with low optimal codon frequency and inS. cerevisiae genes also showed a correlation with each of their noncoding doublet preference. A mechanism to explain these double preference correlations in doublet preference is presented: mutational biases, the origin of the noncoding region doublet preference, evolved so as to maintain the 1–2 and 2–3 doublet preference, which is determined by codon usage. These biases then acted on the 3-1 doublet, which was almost free of coding constraints, resulting in a similar preference in this doublet.

Analysis of the cis-trans isomerization kinetics of l-alanyl-l-proline by the elution-band relaxation method

The elution-band relaxation method has been applied to the analysis of the cis-trans kinetics isomerization of the proline of L-Ala-L-Pro using reversed-phase liquid chromatography. A procedure suitable for cases where neither isomer can be injected separately is described.

Outdoor 3D map generation based on planar feature for autonomous vehicle navigation in urban environment

This paper describes a 3D textured map generation method for autonomous vehicle in urban outdoor environment, where GPS signals can not be reached. Constructed map will be used for short cycle and accurate localization and for obstacle detection using onbody laser scanner.

Real-time navigation for a personal mobility in an environment with pedestrians

This paper describes a navigation system in a dynamic environment for a two-wheeled inverted pendulum mobile robot, PMR. Our system is organized by localization, detection and tracking of pedestrians, and trajectory planner. The localization is robust to effects of moving obstacles and pitching movements of the robot, and the trajectory planner creates a path with a certain smoothness considering movements of pedestrians. In addition, the planner introduces strategies to avoid pedestrians to be friendly to pedestrians around the robot. Besides, our system can run on two laptop PCs in real time. Finally, we show experimental results as well.

Novel third-letter bias in Escherichia coli codons revealed by rigorous treatment of coding constraints

A novel bias in codon third-letter usage was found in Escherichia coli genes with low fractions of optimal codons, by comparing intact sequences with control random sequences. Third-letter usage has been found to be biased according to preference in codon usage and to doublet preference from the following first letter. The present study examines third-letter usage in the context of the nucleotide sequence when these preferences are considered. In order to exclude any influence by these factors, the random sequences were generated such that the amino acid sequence, codon usage, and the doublet frequency in each gene were all preserved. Comparison of intact sequences with these randomly generated sequences reveals that third letters of codons show a strong preference for the purine/pyrimidine pattern of the next codons: purine (R) is preferred to pyrimidine (Y) at the third site when followed by an R-Y-R codon, and pyrimidine is preferred when followed by an R-R-Y, an R-Y-Y or a Y-R-Y codon. This bias is probably related to interactions of tRNA molecules in the ribosome.

Elution-band relaxation method: A method to analyze isomerization kinetics by hplc and application to protein denaturation-renaturation

We present a novel method, the elution-band relaxation method, to analyze quantitatively reversible isomerization kinetics by elution chromatography, taking advantage of the high resolution and speed of high-performance liquid chromatography (HPLC). The kinetic information is obtained by measuring the first temporal moments of chromatograms of molecules undergoing isomerization and analyzing their dependence on the column length or flow rate. The major advantage of this method is that it is applicable to reactions as fast as the time of elution in HPLC, a speed which has not been attained previously in analysis of isomerization reactions based on the chromatographic property of molecules. We describe the method and report an experimental application to the denaturation-renaturation kinetics of bovine pancreatic ribonuclease A as an example.

Vestiges of lost introns in the thermal stability map of DNA

The absence of introns in prokaryotic genes has been explained by intron loss on various bases. Here we report another piece of evidence on intron loss, which was found in the thermal stability map of DNA. We calculated the local melting temperature of cDNA sequences and found that (i) gaps in thermal stability tend to occur near intron positions with a statistical significance, and (ii) one‐third of the gaps far from intron positions can be assigned to lost introns. From these results we conclude that the gaps of thermal stability in protein coding regions are the vestiges of lost introns.

Pedestrian detection using a LRF and a small omni-view camera for outdoor personal mobility robot

This paper describes a pedestrian detection method using a LRF and a small omni-view camera. In outdoor environment, the resolutions of LRFs are too low to recognize human reliably, and high resolution image requires high calculation cost for detecting walking persons. We propose a combination approach using these data. Particle filter based tracking and HOG (Histogram of Oriented Gradients) feature based identification enables to detect pedestrians with high reliability and effectiveness. Although the pedestrian identification from omni-view image needs computational effort for searching large area, LRF based tracking provides the identification process with limited interest regions in advance. We also reports how to construct a discriminative function which is able to cope with various resolution images. Finally, the proposed method was combined with gesture recognition and other robot system, and then an application to taxi service is introduced. The robot could find a person standing 15 meter away, recognized his swinging hand, and moved to the front of him.