Memories of late professor Hideaki Yamada, a giant in enzyme engineering, and successive activities stemmed from his philosophy

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Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis

Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental response

Log-aesthetic Curves as Similarity Geometric Analogue of Euler's Elasticae

In this paper we consider the log-aesthetic curves and their generalization which are used in CAGD. We consider those curves under similarity geometry and characterize them as stationary integrable flow on plane curves which is governed by the Burgers equation. We propose a variational formulation of those curves whose Euler-Lagrange equation yields the stationary Burgers equation. Our result suggests that the log-aesthetic curves and their generalization can be regarded as the similarity geometric analogue of Euler's elasticae

Basics and applications of gut bacterial lipid-metabolizing enzymes- A tribute to the late Professor Hideaki Yamada

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Drop on a Bent Fibre

Inspired by the huge droplets attached on cypress tree leaf tips after rain, we find that a bent fibre can hold significantly more water in the corner than a horizontally placed fibre (typically up to three times or more). The maximum volume of the liquid that can be trapped is remarkably affected by the bending angle of the fibre and surface tension of the liquid. We experimentally find the optimal included angle ($\sim {36}{^\circ}$) that holds the most water. Analytical and semi-empirical models are developed to explain these counter-intuitive experimental observations and predict the optimal angle. The data and models could be useful for designing microfluidic and fog harvesting devices