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Suzuki-Hashido N.,Kyoto University | Suzuki-Hashido N.,Japan Society for the Promotion of Science | Hayakawa T.,Kyoto University | Hayakawa T.,Japan Society for the Promotion of Science | And 11 more authors.
PLoS ONE | Year: 2015

Bitter taste receptors (TAS2R proteins) allow mammals to detect and avoid ingestion of toxins in food. Thus, TAS2Rs play an important role in food choice and are subject to complex natural selection pressures. In our previous study, we examined nucleotide variation in TAS2R38, a gene expressing bitter taste receptor for phenylthiocarbamide (PTC), in 333 Japanese macaques (Macaca fuscata) from 9 local populations in Japan. We identified a PTC "non-taster" TAS2R38 allele in Japanese macaques that was caused by a loss of the start codon. This PTC non-taster allele was only found in a limited local population (the Kii area), at a frequency of 29%. In this study, we confirmed that this allele was present in only the Kii population by analyzing an additional 264 individuals from eight new populations. Using cellular and behavioral experiments, we found that this allele lost its receptor function for perceiving PTC. The nucleotide sequences of the allele including flanking regions (of about 10 kb) from 23 chromosomes were identical, suggesting that a non-taster allele arose and expanded in the Kii population during the last 13,000 years. Genetic analyses of noncoding regions in Kii individuals and neighboring populations indicated that the high allele frequency in the Kii population could not be explained by demographic history, suggesting that positive selection resulted in a rapid increase in PTC non-tasters in the Kii population. The loss-of-function that occurred at the TAS2R38 locus presumably provided a fitness advantage to Japanese macaques in the Kii population. Because TAS2R38 ligands are often found in plants, this functional change in fitness is perhaps related to feeding habit specificity. These findings should provide valuable insights for elucidating adaptive evolutionary changes with respect to various environments in wild mammals. Copyright: © 2015 Suzuki-Hashido et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Hayakawa T.,Kyoto University | Hayakawa T.,Japan Society for the Promotion of Science | Suzuki-Hashido N.,Kyoto University | Suzuki-Hashido N.,Japan Society for the Promotion of Science | And 5 more authors.
Molecular Biology and Evolution | Year: 2014

Genome studies of mammals in the superorder Euarchontoglires (a clade that comprises the orders Primates, Dermoptera, Scandentia, Rodentia, and Lagomorpha) are important for understanding the biological features of humans, particularly studies of medical model animals such as macaques and mice. Furthermore, the dynamic ecoevolutionary signatures of Euarchontoglires genomes may be discovered because many species in this clade are characterized by their successful adaptive radiation to various ecological niches. In this study, we investigated the evolutionary trajectory of bitter taste receptor genes (TAS2Rs) in 28 Euarchontoglires species based on homology searches of 39 whole-genome assemblies. The Euarchontoglires species possessed variable numbers of intact TAS2Rs, which ranged from 16 to 40, and their last common ancestor had at least 26 intact TAS2Rs. The gene tree showed that there have been at least seven lineage-specific events involving massive gene duplications. Gene duplications were particularly evident in the ancestral branches of anthropoids (the anthropoid cluster), which may have promoted the adaptive evolution of anthropoid characteristics, such as a trade-off between olfaction and other senses and the development of herbivorous characteristics. Subsequent whole-gene deletions of anthropoid cluster TAS2Rs in hominoid species suggest ongoing ectopic homologous recombination in the anthropoid cluster. These findings provide insights into the roles of adaptive sensory evolution in various ecological niches and important clues related to the molecular mechanisms that underlie taste diversity in Euarchontoglires mammalian species, including humans. © The Author 2014.

Yamashita I.,Osaka Prefecture University | Teranishi M.,Hiroshima Institute of Technology | Yoshioka M.,Osaka Prefecture University | Murayama T.,Juntendo University | Kimori Y.,National Institute of Natural science
2015 10th Asian Control Conference: Emerging Control Techniques for a Sustainable World, ASCC 2015 | Year: 2015

In general, an image degraded by blurring or defocusing is restored by deconvolution using a substantially constant PSF. However, in the case of a confocal laser microscope, there is a problem that the PSF varies according to the depth of focus. In order to overcome this problem, we adopt the iterative approach to estimate the PSF by a blind deconvolution. In order to confirm the effectiveness of our approach, we make some experiments. © 2015 IEEE.

Tatematsu K.,Japan National Institute for Basic Biology | Toyokura K.,Japan National Institute for Basic Biology | Toyokura K.,Kyoto University | Toyokura K.,Kobe University | And 6 more authors.
Plant Journal | Year: 2015

Summary In Arabidopsis leaf primordia, the expression of HD-Zip III, which promotes tissue differentiation on the adaxial side of the leaf primordia, is repressed by miRNA165/166 (miR165/166). Small RNAs, including miRNAs, can move from cell to cell. In this study, HD-Zip III expression was strikingly repressed by miR165/166 in the epidermis and parenchyma cells on the abaxial side of the leaf primordia compared with those on the adaxial side. We also found that the MIR165A locus, which was expressed in the abaxial epidermis, was sufficient to establish the rigid repression pattern of HD-Zip III expression in the leaf primordia. Ectopic expression analyses of MIR165A showed that the abaxial-biased miR165 activity in the leaf primordia was formed neither by a polarized distribution of factors affecting miR165 activity nor by a physical boundary inhibiting the cell-to-cell movement of miRNA between the adaxial and abaxial sides. We revealed that cis-acting factors, including the promoter, backbone, and mature miRNA sequence of MIR165A, are necessary for the abaxial-biased activity of miR165 in the leaf primordia. We also found that the abaxial-determining genes YABBYs are trans-acting factors that are necessary for the miR165 activity pattern, resulting in the rigid determination of the adaxial-abaxial boundary in leaf primordia. Thus, we proposed a molecular mechanism in which the abaxial-biased patterning of miR165 activity is confined. Significance Statement In this paper, we propose a molecular mechanism for determination of activity pattern of miR165/166 in leaf primordia, which depends on both mature miRNA sequence and MIRNA backbone. We consider that our finding will provide an insight into the roles of MIRNA transcript sequences in the mechanisms for determination of miRNA distribution to confine small RNA-meditated gene expression in plants. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Tatematsu K.,Japan National Institute for Basic Biology | Toyokura K.,Kobe University | Okada K.,Ryukoku University | Okada K.,National Institute of Natural science
Plant Signaling and Behavior | Year: 2015

MiRNAs might move cell to cell and act as mobile signals in plant development, while the regulatory mechanisms of miRNA cell-to-cell movement are still unclear. Recently, in Arabidopsis leaf primordia, we revealed that miR165 from the MIR165A gene, which is expressed in the abaxial epidermal cells of leaf primordia, acts non-cell-autonomously in inner cells on the abaxial side. We proposed that not only mature miR165 sequence but also the MIR165A primary transcript sequence are required for the confinement of miR165 activity to the abaxial side of leaf primordia. The deletion analysis of the MIR165A genomic fragment showed that with a lack of the 3’ region of MIR165A its activity is not confined in leaf primordia, suggesting that the full-length primary transcript of MIR165A is important for the regulatory mechanism of miRNA activity. © 2015 Taylor & Francis Group, LLC.

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