Mitsuharu Yagi

Length and GC Content Variability of Introns among Teleostean Genomes in the Light of the Metabolic Rate Hypothesis

A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmanns factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼40% to ∼90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from <1% to ∼10%, in each pairwise comparison). The results further support the hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

Influence of the Kuroshio on Mesoscale Convective Systems in the Baiu Frontal Zone over the East China Sea

AbstractTwo mesoscale convective events in the baiu frontal zone (BFZ) were documented, based on intensive atmospheric soundings and oceanic castings in the East China Sea during May 2011, in addition to continuous surface meteorological observations, satellite products, and objective analyses. These events occurred while the BFZ was nearly stagnant and a mesolow was deepening in the zone. Near-surface southerlies associated with the low-level jet transported a warm, humid air mass from south of the BFZ. Enhanced evaporation, which was mainly attributable to the high sea surface temperature of the Kuroshio, augmented the moisture content of the air mass and helped maintain a convectively unstable stratification in the lower troposphere around the BFZ.

On the genome base composition of teleosts: the effect of environment and lifestyle

BackgroundThe DNA base composition is well known to be highly variable among organisms. Bio-physic studies on the effect of the GC increments on the DNA structure have shown that GC-richer DNA sequences are more bendable. The result was the keystone of the hypothesis proposing the metabolic rate as the major force driving the GC content variability, since an increased resistance to the torsion stress is mainly required during the transcription process to avoid DNA breakage. Hence, the aim of the present work is to test if both salinity and migration, suggested to affect the metabolic rate of teleostean fishes, affect the average genomic GC content as well. Moreover, since the gill surface has been reported to be a major morphological expression of metabolic rate, this parameter was also analyzed in the light of the above hypothesis.ResultsTeleosts living in different environments (freshwater and seawater) and with different lifestyles (migratory and non-migratory) were analyzed studying three variables: routine metabolic rate, gill area and genomic GC-content, none of them showing a phylogenetic signal among fish species. Routine metabolic rate, specific gill area and average genomic GC were higher in seawater than freshwater species. The same trend was observed comparing migratory versus non-migratory species. Crossing salinity and lifestyle, the active migratory species living in seawater show coincidentally the highest routine metabolic rate, the highest specific gill area and the highest average genomic GC content.ConclusionsThe results clearly highlight that environmental factors (salinity) and lifestyle (migration) affect not only the physiology (i.e. the routine metabolic rate), and the morphology (i.e. gill area) of teleosts, but also basic genome feature (i.e. the GC content), thus opening to an interesting liaison among the three variables in the light of the metabolic rate hypothesis.

Study on the Propulsion Efficiency of Working Ro-Scull based on the Energy Expenditure

The Japanese boat “Wasen” uses “Ro-Scull” as a human-powered propulsion system. These traditional boats and propulsion system are almost vanished in Japan due to decrease in material Wood, and boat-builder’s aging. “Ro-Scull” is thought to be effective propulsive method compared to other human-powered boat such as canoe and cutter boat. In this study, the authors evaluate propulsive efficiency of “Ro-Scull” based on active metabolic rate (MR). The authors measured MR and metabolic equivalents (Mets) during “Ro-Scull”, walking, and jogging exercise by using indirect calorimeter. MR and Mets during “Ro-Scull” exercise were nearly equal to walking ones. Energy conversion efficiency of “Ro-scull” was 12.3%. These suggest that propulsion efficiency of “Ro-Scull” is efficient, and its exercise can be done for a prolonged time as well as walking. “Ro-Scull” exercise seems to be useful way to become familiar with maritime activities and seamanship.

Distance to Encountered Ships Estimated by Visual Observation during Cruises

Judging the distance between one’s own ship and other ships is more difficult at sea than on land, because landmarks or reference objects are scarce at sea. Although we can now measure the precise distance to an encountered ship using nautical instruments, such as a radar distance indicator or the automatic identification system, ship crews occasionally judge distances by visual observation, particularly in the case of obstacle avoidance. These estimated distances are typically used for making decisions regarding collision risk, and errors might be influenced by experience. In this study, we evaluate errors in the distance to encountered ships estimated by visual observation. Estimated distances were more precise for experienced crew than were those for trainees. There were tendencies to overestimate the distance to encountered ships with increasing ship size, and to underestimate the distance with decreasing actual range. The colour of the ship did not affect the estimated distance. These results may contribute to ensuring safe ship operation.