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| 1.
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Sato, Takehiro ; Adachi, Noboru ; Kimura, Ryosuke ; Hosomichi, Kazuyoshi ; Yoneda, Minoru ; Oota, Hiroki ; Tajima, Atsushi ; Toyoda, Atsushi ; Kanazawa-Kiriyama, Hideaki ; Matsumae, Hiromi ; Koganebuchi, Kae ; Shimizu, K Kentaro ; Shinoda, Ken-ichi ; Hanihara, Tsunehiko ; Weber, Andrzej ; Kato, Hirofumi ; Ishida, Hajime
概要:
Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights int
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o the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.
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| 2.
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Miyazato, Minoru ; Ashikari, Asuka ; Nakamura, Koshi ; Nakamura, Takehiro ; Yamashiro, Kiyoto ; Uema, Tsugumi ; Uehara, Moriyuki ; Masuzaki, Hiroaki ; Saito, Seiichi ; Maeda, Shiro ; Ishida, Hajime ; Matsushita, Masayuki
概要:
Purpose:To evaluate the effect of a mobile digital intervention on voiding patterns, we performed 24-h voided volume mon
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itoring in individuals with metabolic disorders.\nMethods:Participants with metabolic disorders were grouped into either the intervention group (n = 17), who had access to a smartphone app (CARADA), or the non-intervention group (n = 11), who did not. Urine monitoring was conducted for 24 h using a novel digital self-health monitoring system for urine excretion (s-HMSU). Body weight, abdominal circumference, blood pressure, and biomarkers were measured.\nResults:Physical findings and blood test results at baseline and 6 months indicated no significant between-group differences. Night-time frequency did not change between baseline and 6 months in the intervention group but significantly worsened at 6 months in the non-intervention group, as compared to baseline (1.0 ± 0.7 vs. 1.5 ± 0.5, p < 0.05). The change in night-time frequency over 6 months did not differ between the intervention and non-intervention groups. Furthermore, the change in hours of undisturbed sleep over 6 months did not differ between the two groups. However, compared with baseline, nocturnal polyuria index tended to worsen at 6 months in the non-intervention group.\nConclusion:Our study results suggest that mobile digital intervention might be useful for behavioral therapy to improve night-time frequency and urine production and that s-HMSU might be beneficial for confirming the prevention of progress in individuals with metabolic disorders, which can aid in modifying lifestyle.
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| 3.
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Koganebuchi, Kae ; Sato, Kimitoshi ; Fujii, Kiyotaka ; Kumabe, Toshihiro ; Haneji, Kuniaki ; Toma, Takashi ; Ishida, Hajime ; Joh, Keiichiro ; Soejima, Hidenobu ; Mano, Shuhei ; Ogawa, Motoyuki ; Oota, Hiroki
概要:
Background:Ring finger protein 213 (RNF213) is a susceptibility gene of moyamoya disease (MMD). A previous case–control
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study and a family analysis demonstrated a strong association of the East Asian-specific variant, R4810K (rs112735431), with MMD. Our aim is to uncover evolutionary history of R4810K in East Asian populations.\nMethods:The RNF213 locus of 24 MMD patients in Japan were sequenced using targeted-capture sequencing. Based on the sequence data, we conducted population genetic analysis and estimated the age of R4810K using coalescent simulation.\nResults:The diversity of the RNF213 gene was higher in Africans than non-Africans, which can be explained by bottleneck effect of the out-of-Africa migration. Coalescent simulation showed that the risk variant was born in East Asia 14,500–5100 years ago and came to the Japanese archipelago afterward, probably in the period when the known migration based on archaeological evidences occurred.\nConclusions:Although clinical data show that the symptoms varies, all sequences harboring the risk allele are almost identical with a small number of exceptions, suggesting the MMD phenotypes are unaffected by the variants of this gene and rather would be more affected by environmental factors.
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| 4.
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Matsunami, Masatoshi ; Koganebuchi, Kae ; Imamura, Minako ; Ishida, Hajime ; Kimura, Ryosuke ; Maeda, Shiro
概要:
The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped
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into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis on genome-wide single-nucleotide polymorphisms, genetic differentiation was observed among the island groups of the Ryukyu Archipelago. However, a detailed population structure analysis of the Ryukyu Archipelago has not yet been completed. We obtained genomic DNA samples from 1,240 individuals living in the Miyako Islands, and we genotyped 665,326 single-nucleotide polymorphisms to infer population history within the Miyako Islands, including Miyakojima, Irabu, and Ikema islands. The haplotype-based analysis showed that populations in the Miyako Islands were divided into three subpopulations located on Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema. The results of haplotype sharing and the D statistics analyses showed that the Irabu/Ikema subpopulation received gene flows different from those of the Miyakojima subpopulations, which may be related with the historically attested immigration during the Gusuku period (900 − 500 BP). A coalescent-based demographic inference suggests that the Irabu/Ikema population firstly split away from the ancestral Ryukyu population about 41 generations ago, followed by a split of the Miyako southwest population from the ancestral Ryukyu population (about 16 generations ago), and the differentiation of the ancestral Ryukyu population into two populations (Miyako northeast and Okinawajima populations) about seven generations ago. Such genetic information is useful for explaining the population history of modern Miyako people and must be taken into account when performing disease association studies.
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| 5.
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Kataoka, Keiichi ; Fujita, Hironori ; Isa, Mutsumi ; Gotoh, Shimpei ; Arasaki, Akira ; Ishida, Hajime ; Kimura, Ryosuke
概要:
Morphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribut
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ion of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR 370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between the EDAR polymorphism and tooth root traits by using computed tomography images and identified that the effects of the EDAR variant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction–diffusion system. The computational study suggested that the complicated effects of the EDAR polymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction–diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.
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| 6.
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Gakuhari, Takashi ; Nakagome, Shigeki ; Rasmussen, Simon ; Allentoft, Morten E. ; Sato, Takehiro ; Korneliussen, Thorfinn ; Chuinneagain, Blanaid Ni ; Matsumae, Hiromi ; Koganebuchi, Kae ; Schmidt, Ryan ; Mizushima, Souichiro ; Kondo, Osamu ; Shigehara, Nobuo ; Yoneda, Minoru ; Kimura, Ryosuke ; Ishida, Hajime ; Masuyama, Tadayuki ; Yamada, Yasuhiro ; Tajima, Atsushi ; Shibata, Hiroki ; Toyoda, Atsushi ; Tsurumoto, Toshiyuki ; Wakebe, Tetsuaki ; Shitara, Hiromi ; Hanihara, Tsunehiko ; Willerslev, Eske ; Sikora, Martin ; Oota, Hiroki
概要:
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered
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with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.
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| 7.
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Gakuhari, Takashi ; Nakagome, Shigeki ; Rasmussen, Simon ; Allentoft, Morten E. ; Sato, Takehiro ; Korneliussen, Thorfinn ; Chuinneagain, Blanaid Ni ; Matsumae, Hiromi ; Koganebuchi, Kae ; Schmidt, Ryan ; Mizushima, Souichiro ; Kondo, Osamu ; Shigehara, Nobuo ; Yoneda, Minoru ; Kimura, Ryosuke ; Ishida, Hajime ; Masuyama, Tadayuki ; Yamada, Yasuhiro ; Tajima, Atsushi ; Shibata, Hiroki ; Toyoda, Atsushi ; Tsurumoto, Toshiyuki ; Wakebe, Tetsuaki ; Shitara, Hiromi ; Hanihara, Tsunehiko ; Willerslev, Eske ; Sikora, Martin ; Oota, Hiroki
概要:
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered
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with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.
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| 8.
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Garcia-Martinez, Daniel ; Bastir, Markus ; Gomez-Olivencia, Asier ; Maureille, Bruno ; Golovanova, Liubov ; Doronichev, Vladimir ; Akazawa, Takeru ; Kondo, Osamu ; Ishida, Hajime ; Gascho, Dominic ; Zollikofer, Christoph P. E. ; de Leon, Marcia Ponce ; Heuze, Yann
概要:
Ontogenetic studies provide clues for understanding important paleobiological aspects of extinct species. When compared
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to that of modern humans, the adult Neanderthal thorax was shorter, deeper, and wider. This is related to the wide Neanderthal body and is consistent with their hypothetical large requirements for energy and oxygen. Whether these differences were already established at birth or appeared later during development is unknown. To delve into this question, we use virtual reconstruction tools and geometric morphometrics to recover the 3D morphology of the ribcages of four Neanderthal individuals from birth to around 3 years old: Mezmaiskaya 1, Le Moustier 2, Dederiyeh 1, and Roc de Marsal. Our results indicate that the comparatively deep and short ribcage of the Neanderthals was already present at birth, as were other skeletal species-specific traits. This morphology possibly represents the plesiomorphic condition shared with Homo erectus, and it is likely linked to large energetic requirements.
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| 9.
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Ito, Tsuyoshi ; Kimura, Ryosuke ; Ryukoden, Azusa ; Tsuchiya, Nanae ; Murayama, Sadayuki ; Ishida, Hajime
概要:
Using computed tomography, we examined the surface and internal morphologies of the upper face of people living on the R
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yukyu Islands and mainland Japanese, focusing on the nasal root protrusion and eyeball position. The results showed that the nasal root protrusion on the surface was influenced by a combination of changes in both hard and soft tissues, such as skeletal nasal protrusion, eyeball recession, and skin thickness. The eyeball position became more posterior as the orbital cavity height and depth increased. Compared with people originating from mainland Japan, Ryukyu Islanders had a more prominent nasal root at both surface and skeletal levels, and a lower orbital rim relative to its internal height. However, a significant difference in the eyeball position and skin thickness was not detected. Therefore, the skeletal nasal root protrusion, not soft tissue configuration, is likely to account for the difference in the surface nasal root protrusion between the two populations. These findings will contribute to a better understanding of the association between hard and soft tissue configurations and the diversification of human facial features at the individual and population levels.
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| 10.
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Akiyama, Tokiho ; Katsumura, Takafumi ; Nakagome, Shigeki ; Lee, Sang-il ; Joh, Keiichiro ; Soejima, Hidenobu ; Fujimoto, Kazuma ; Kimura, Ryosuke ; Ishida, Hajime ; Hanihara, Tsunehiko ; Yasukouchi, Akira ; Satta, Yoko ; Higuchi, Shigekazu ; Oota, Hiroki
概要:
Humans show various responses to the environmental stimulus in individual levels as “physiological variations.” However,
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it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P < 0.05). The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P < 0.05), and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.
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