Publications by authors named "Hajime Ishida"

58 Publications

Fine-scale genetic structure and demographic history in the Miyako Islands of the Ryukyu Archipelago.

Mol Biol Evol 2021 Jan 11. Epub 2021 Jan 11.

Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan.

The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis (PCA) on genome-wide single nucleotide polymorphisms (SNPs), 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 SNPs 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 7 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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http://dx.doi.org/10.1093/molbev/msab005DOI Listing
January 2021

Early development of the Neanderthal ribcage reveals a different body shape at birth compared to modern humans.

Sci Adv 2020 Oct 7;6(41). Epub 2020 Oct 7.

University of Bordeaux, CNRS, MCC, PACEA, UMR5199, Pessac, France.

Ontogenetic studies provide clues for understanding important paleobiological aspects of extinct species. When compared 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 , and it is likely linked to large energetic requirements.
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http://dx.doi.org/10.1126/sciadv.abb4377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541074PMC
October 2020

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.

Commun Biol 2020 Aug 25;3(1):437. Epub 2020 Aug 25.

Kitasato University School of Medicine, Sagamihara, Japan.

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered 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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http://dx.doi.org/10.1038/s42003-020-01162-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7447786PMC
August 2020

A health crisis during the Japanese Medieval Period: A new paleodemographic perspective.

Int J Paleopathol 2019 09 30;26:145-156. Epub 2019 Mar 30.

Department of Anatomy, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae Ward, Kawasaki, Kanagawa, 216-8511, Japan.

Objective: To test the hypothesis that the "Little Ice Age" (LIA) (in Japan, ˜1440 - 1730 CE) co-occurred with unique age-at-death patterns.

Materials: 810 adult human skeletons from the early Medieval Period (EMP) of Japan, which are contemporaneous with the Medieval Warm Period (10th - mid 13th century AD), and the late Medieval Period (LMP) and Edo Period, which are contemporary with the LIA.

Methods: Age at death and sex was determined for each skeleton and demographic profiles of the Yayoi Period (5th century BC - 3rd century AD), EMP, LMP, and Edo site samples were compared. Paleopathological data from previously published reports were evaluated.

Results: The EMP had the highest mortality among young adults. Longevity increased in the samples (LMP and Edo) contemporaneous with the LIA.

Conclusions: EMP early age-at-death was the result of poor community health, violent death, and frequent large-scale natural catastrophes. The LMP and Edo Period samples have an older age-at-death pattern and higher frequency of stress markers, argued to be a consequence of a colder climate.

Significance: This study is the first to synthesize paleodemographic and paleopathological data on a large scale to assess the possible effects of the Little Ice Age in Japan.

Limitations: Varying skeletal preservation and focus on adult skeletons reduces the ability to evaluate health throughout the life span.

Suggestions For Further Research: Analysis of nonadult remains and multiple health indicators will likely shed more light on the effects of the Little Ice Age in Japan.
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http://dx.doi.org/10.1016/j.ijpp.2019.03.005DOI Listing
September 2019

Validation of a novel digital health monitoring system to measure the volume of voided urine.

Neurourol Urodyn 2019 04 8;38(4):1106-1110. Epub 2019 Mar 8.

Department of Molecular and Cellular Physiology, University of the Ryukyus, Okinawa, Japan.

Aim: To validate a novel digital health monitoring system to measure the volume of voided urine.

Methods: Micturition volume was calculated using our novel digital self-health monitoring system of urine excretion (s-HMSU) in 18 participants (16 women and 2 men; average age, 40.8 years), without a history of voiding symptoms. Participants completed a self-reported questionnaire regarding their medical history and water intake during the period of observation, as well as the Core Lower Urinary Tract Symptom Score (CLSS) questionnaire. To assess the reliability of the voided volumes measured using the s-HMSU, the intraclass correlation coefficient (ICC) was calculated between the volume and the change in body weight before and after micturition.

Results: The CLSS questionnaire confirmed the absence of urinary system diseases in all participants. The medical history was also negative with the exception of hypertension in one participant. The ICC (1,1) between the measured volume of urine excretion using the s-HMSU and the change in body weight was 0.972 (95% confidence interval, 0.957-0.982).

Conclusions: The s-HMSU system provides a reliable measure of voiding volume and is appropriate for home use. It has the potential to facilitate large-scale clinical research to examine the relationship between medical diseases and voiding dysfunction.
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http://dx.doi.org/10.1002/nau.23965DOI Listing
April 2019

The prehistoric peopling of Southeast Asia.

Science 2018 07;361(6397):88-92

Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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http://dx.doi.org/10.1126/science.aat3628DOI Listing
July 2018

Association between the FGFR1 rs13317 single nucleotide polymorphism and orbitale-nasion depth based on cephalometric images.

J Hum Genet 2018 Aug 5;63(8):901-909. Epub 2018 Jun 5.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.

The fibroblast growth factor receptor 1 (FGFR1) gene plays an important role in craniofacial morphogenesis. In our previous study, an association between FGFR1 single nucleotide polymorphisms (SNPs) and craniofacial morphology was demonstrated in Japanese and Korean subjects. The present study aimed to evaluate the relationship between a common FGFR1 SNP (rs13317) with craniofacial morphology, increasing the number of measurements and examining Egyptian subjects (n = 191) in addition to the Japanese (n = 211) and Korean (n = 226) subjects. Genotyping for rs13317 was performed using the TaqMan assay, and its associations with 81 craniofacial measurements derived from lateral and posteroanterior cephalograms were analyzed by multiple regression analysis controlling sex and facial size. The results from each of the populations were then statistically combined. In the Egyptian subjects, rs13317 was significantly associated with the nasion-orbitale depth (P = 0.00040), and a suggestive association was also observed in the Japanese (P = 0.037) and Korean subjects (P = 0.045). The combined analysis revealed that only the nasion-orbitale depth showed a significant association (P = 0.000062) and that several measurements showed a suggestive association. Our results strongly indicate that rs13317 is associated with a smaller depth between the nasion and orbitale, representing a relative protrusion of the cheekbones and retrusion of the nasal root. A similar characteristic is also observed in individuals with Pfeiffer syndrome, which is caused by a dysfunctional FGFR1 mutation.
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http://dx.doi.org/10.1038/s10038-018-0471-6DOI Listing
August 2018

Interferon regulatory factor 6 variants affect nasolabial morphology in East Asian populations.

Arch Oral Biol 2018 Jan 9;85:142-147. Epub 2017 Oct 9.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan. Electronic address:

Objective: The interferon regulatory factor 6 gene (IRF6) is one of the most conspicuous genes among a large number of candidate risk genes for non-syndromic cleft lip with or without cleft palate, which is considered to be a multifactorial defect. Variants of IRF6 are also suggested to affect normal craniofacial variations, especially in the area of the nose and the upper lip. In the present study, we used lateral cephalograms to establish the relationship between IRF6 and sagittal nasolabial morphology in healthy East Asian subjects.

Design: Genomic DNA was extracted from 215 Japanese and 226 Korean individuals, and genotyped for five IRF6 single nucleotide polymorphisms (SNPs): rs17389541, rs642961, rs2013162, rs2235371, and rs7802. These SNPs were tested by multiple regression analyses for their association with craniofacial measurements obtained from lateral cephalometrics.

Results: We detected a significant association between the derived variants, rs2013162 and rs2235371 and the distances between a facial bone plane indicated by distance from Nasion and Point A (NA plane) to soft tissue landmarks; the Subalare (NA-Sbal) and the Subnasale (NA-Sn) in the sagittal plane.

Conclusion: Our results indicate that IRF6 variants play an important role in the normal range of variation in nasolabial soft-tissue morphology.
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http://dx.doi.org/10.1016/j.archoralbio.2017.10.005DOI Listing
January 2018

Spatial relationships of the bronchial arteries to the left recurrent laryngeal nerve in the sub-aortic arch area.

Surg Today 2018 Mar 25;48(3):346-351. Epub 2017 Sep 25.

Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903-0215, Japan.

Purpose: To safely perform lymphadenectomy in the sub-aortic arch area during esophagectomy for esophageal cancer, we investigated the spatial relationships between the bronchial arteries (BAs) and the left recurrent laryngeal nerve (LRLN).

Methods: For this macro-anatomical study, 72 cadavers were used.

Results: Of the 195 dissected BAs, 15 (7.7%) arteries ran dorsally across the LRLN. Such a running pattern of the BA was found in 15 (20.8%) of the 72 cadavers. Fourteen (93.3%) of the 15 arteries ran anteriorly along the left side of the esophagus, and 13 (86.7%) passed further to the lateral side of the left main bronchus to reach the ventral surface of the tracheobronchus; we named this running pattern "Type III". Of the 51 arteries with the Type III pattern, 25.5% ran across the dorsal side of the LRLN.

Conclusion: Approximately 20% of the cadavers had BAs running dorsally to the LRLN in the sub-aortic arch area. Most of these arteries had the Type III pattern. One-quarter of the BAs with the Type III pattern showed this running pattern. Care must be practiced to safely perform lymphadenectomy for esophageal cancer in patients with Type III BAs.
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http://dx.doi.org/10.1007/s00595-017-1593-8DOI Listing
March 2018

An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression.

PLoS One 2017 26;12(6):e0178373. Epub 2017 Jun 26.

Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.

Humans show various responses to the environmental stimulus in individual levels as "physiological variations." However, 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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178373PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484468PMC
September 2017

Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands.

Hum Genet 2017 04 14;136(4):387-397. Epub 2017 Feb 14.

Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0674, Japan.

Crohn's disease (CD) involves chronic inflammation in the gastrointestinal tract due to dysregulation of the host immune response to the gut microbiome. Even though the host-microbiome interactions are likely contributors to the development of CD, a few studies have detected genetic variants that change bacterial compositions and increase CD risk. We focus on one of the well-replicated susceptible genes, tumor necrosis factor superfamily member 15 (TNFSF15), and apply statistical analyses for personal profiles of genotypes and salivary microbiota collected from CD cases and controls in the Ryukyu Islands, southernmost islands of the Japanese archipelago. Our association test confirmed the susceptibility of TNFSF15 in the Ryukyu Islands. We found that the recessive model was supported to fit the observed genotype frequency of risk alleles slightly better than the additive model, defining the genetic effect on CD if a pair of the chromosomes in an individual consists of all risk alleles. The combined analysis of haplotypes and salivary microbiome from a small set of samples showed a significant association of the genetic effect with the increase of Prevotella, which led to a significant increase of CD risk. However, the genetic effect on CD disappeared if the abundance of Prevotella was low, suggesting the genetic contribution to CD is conditionally independent given a fixed amount of Prevotella. Although our statistical power is limited due to the small sample size, these results support an idea that the genetic susceptibility of TNFSF15 to CD may be confounded, in part, by the increase of Prevotella.
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http://dx.doi.org/10.1007/s00439-017-1764-0DOI Listing
April 2017

Contribution of FGFR1 Variants to Craniofacial Variations in East Asians.

PLoS One 2017 27;12(1):e0170645. Epub 2017 Jan 27.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.

FGFR1 plays an important role in the development of the nervous system as well as the regulation of the skeletal development and bone homeostasis. Mutations in FGFR1 genes affect skull development, specifically suture and synchondrosis, resulting in craniosynostosis and facial abnormalities. We examined subjects with normal skull morphology for genetic polymorphisms that might be associated with normal craniofacial variations. Genomic DNA was obtained from 216 Japanese and 227 Korean subjects. Four FGFR1 SNPs, namely, rs881301, rs6996321, rs4647905, and rs13317, were genotyped. These SNPs were tested for association with craniofacial measurements obtained from lateral and posteroanterior cephalometries, in which principle component analysis was performed to compress the data of the craniofacial measurements. We observed that SNPs rs13317 and rs6996321 were correlated with the overall head size and midfacial development, indicating that FGFR1 SNPs played crucial roles in the normal variation of human craniofacial morphology. Subjects with the derived alleles of SNPs rs13317 and rs6996321 had a small face and a facial pattern associated with a retruded midface and relatively wide-set eyes. These facial features were similar to but were milder than those of individuals with Pfeiffer syndrome, which is caused by a dysfunctional mutation in FGFR1.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170645PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5271310PMC
August 2017

A new anatomical classification of the bronchial arteries based on the spatial relationships to the esophagus and the tracheobronchus.

Surg Today 2017 Jul 23;47(7):883-890. Epub 2016 Nov 23.

Department of Digestive and General Surgery, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, Okinawa, 903-0215, Japan.

Purpose: To reveal the patterns of the mediastinal course of the bronchial arteries (BAs).

Methods: The BAs were dissected to determine the positional relationships of their mediastinal courses with the tracheobronchus and the esophagus in 72 adult cadavers.

Results: The mediastinal courses of the 227 BAs found in this study were classified into 4 types. There were 61 and 163 BAs passing the right side (Type I) and the left side (Type II reaching dorsal surface (n = 98), or Type III reaching ventral surface (n = 65) of the tracheobronchus) of the esophagus, respectively. Three BAs originated from the subclavian artery (Type IV). All Type I BAs were right BAs, whereas 91.8% of the Type II BAs were left BAs. However, 43.1 and 56.9% of the Type III BAs were the right and left BAs, respectively.

Conclusion: The classification of the mediastinal course of the BAs determined by the spatial relationships to the tracheobronchus and the esophagus may be clinically useful, because each category of this classification can be determined during esophagectomy and indicates whether the BA is a right or left BA.
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http://dx.doi.org/10.1007/s00595-016-1450-1DOI Listing
July 2017

The allele frequency of ALDH2*Glu504Lys and ADH1B*Arg47His for the Ryukyu islanders and their history of expansion among East Asians.

Am J Hum Biol 2017 Mar 1;29(2). Epub 2016 Nov 1.

Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Kanagawa, 252-0373, Japan.

Objectives: A cline of frequencies of the derived allele of the ALDH2 gene, which causes a deficiency of an enzyme and "facial flushing" in humans who drink alcohol, has been known among the people of the Japanese archipelago. This cline is conventionally explained by admixture with immigrants from the Asian continent occurring during the Yayoi period. Previous studies lack sufficient data from the peripheral regions of the indigenous Jomon people, and those data the ADH1B gene that is involved in the Class I ADH gene cluster and contains another variant leading to a functional change.

Methods: We focused on the southwestern-most people from the Ryukyu Islands (n = 218) and those from northern Kyushu (n = 21) where the Yayoi immigrants likely arrived. We investigated both the Class I ADH and ALDH2 loci, as well as neutral genetic markers.

Results: In the Ryukyu Islands, the frequencies of the ancestral alleles in both loci were always higher than those in mainland Japan, while the frequencies of ADH1B were less than those of the derived allele. A haplotype block was not observed in ALDH2 but was in Class I ADH.

Discussion: Our data suggest that the derived allele of ALDH2 came with the Yayoi immigrants from the Asian continent to the Japanese archipelago. However, the derived allele of ADH1B is unlikely to be related to the Yayoi migration. Therefore, we postulate that the expansion of the derived allele of ADHIB in East Asia could be traced back to the last glacial period.
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http://dx.doi.org/10.1002/ajhb.22933DOI Listing
March 2017

Growth hormone receptor gene variant and three-dimensional mandibular morphology.

Angle Orthod 2017 Jan 26;87(1):68-73. Epub 2016 Jul 26.

Objective: To examine the relationship between three-dimensional mandibular morphology and growth hormone receptor (GHR) gene variants in a healthy Japanese population.

Materials And Methods: The subjects, who were unrelated Japanese orthodontic patients, consisted of 64 men and 114 women. Using the Taqman genotyping assay, GHR gene rs6184 and rs6180 variants were detected in genomic DNA extracted from saliva. Mandibular volume and length were measured from cone-beam computed tomography images that were analyzed using Analyze image-processing software. The relationship between GHR gene variants and three-dimensional mandibular morphology was statistically examined.

Results: Statistical significance for the relationship between the distance between the left and right coronoid processes and rs6180 was noted (P < .05).

Conclusion: Our results indicate that the GHR variant rs6180 is associated with the distance between the left and right coronoid process in the Japanese subjects.
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http://dx.doi.org/10.2319/02316-154.1DOI Listing
January 2017

Whole-body patterns of the range of joint motion in young adults: masculine type and feminine type.

J Physiol Anthropol 2016 Oct 1;35(1):23. Epub 2016 Oct 1.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Uehara 207, Nishihara, Okinawa, 903-0215, Japan.

Background: Understanding the whole-body patterns of joint flexibility and their related biological and physical factors contributes not only to clinical assessments but also to the fields of human factors and ergonomics. In this study, ranges of motion (ROMs) at limb and trunk joints of young adults were analysed to understand covariation patterns of different joint motions and to identify factors associated with the variation in ROM.

Methods: Seventy-eight healthy volunteers (42 males and 36 females) living on Okinawa Island, Japan, were recruited. Passive ROM was measured at multiple joints through the whole body (31 measurements) including the left and right side limbs and trunk.

Results: Comparisons between males and females, dominant and non-dominant sides, and antagonistic motions indicated that body structures influence ROMs. In principal component analysis (PCA) on the ROM data, the first principal component (PC1) represented the sex difference and a similar covariation pattern appeared in the analysis within each sex. Multiple regression analysis showed that this component was associated with sex, age, body fat %, iliospinale height, and leg extension strength.

Conclusions: The present study identified that there is a spectrum of "masculine" and "feminine" types in the whole-body patterns of joint flexibility. This study also suggested that body proportion and composition, muscle mass and strength, and possibly skeletal structures partly explain such patterns. These results would be important to understand individual variation in susceptibility to joint injuries and diseases and in one's suitable and effective postures and motions.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045662PMC
http://dx.doi.org/10.1186/s40101-016-0112-8DOI Listing
October 2016

Trial application of oxygen and carbon isotope analysis in tooth enamel for identification of past-war victims for discriminating between Japanese and US soldiers.

Forensic Sci Int 2016 Apr 13;261:166.e1-5. Epub 2016 Feb 13.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 1 Chihara, Nishihara aza, Nakagamigun, Okinawaken 903-0213, Japan. Electronic address:

Stable isotope analysis has undergone rapid development in recent years and yielded significant results in the field of forensic sciences. In particular, carbon and oxygen isotopic ratios in tooth enamel obtained from human remains can provide useful information for the crosschecking of morphological and DNA analyses and facilitate rapid on-site prescreening for the identification of remains. This study analyzes carbon and oxygen isotopic ratios in the tooth enamel of Japanese people born between 1878 and 1930, in order to obtain data for methodological differentiation of Japanese and American remains from the Second World War. The carbon and oxygen isotopic ratios in the tooth enamel of the examined Japanese individuals are compared to previously reported data for American individuals (born post WWII), and statistical analysis is conducted using a discrimination method based on a logistic regression analysis. The discrimination between the Japanese and US populations, including Alaska and Hawaii, is found to be highly accurate. Thus, the present method has potential as a discrimination technique for both populations for use in the examination of mixed remains comprising Japanese and American fallen soldiers.
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http://dx.doi.org/10.1016/j.forsciint.2016.02.010DOI Listing
April 2016

Geographic variation in nasal cavity form among three human groups from the Japanese Archipelago: Ecogeographic and functional implications.

Am J Hum Biol 2016 05 8;28(3):343-51. Epub 2015 Sep 8.

Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan.

Objectives: Geographic variation in human nasal form has often been interpreted as a climatic adaptation, owing to the nasal air-conditioning function. The aim of this study was to further address morphofunctional issues of the nasal cavity, using three human groups from subarctic, temperate, and subtropical regions of the Japanese Archipelago: prehistoric Okhotsk, early-modern Honshu and Okinawa groups.

Methods: Using three-dimensional coordinates of craniometric landmarks surrounding the nasal cavity, we compared linear measurements regarding nasal cavity form among the three groups and also conducted 3D geometric morphometrics.

Results: Both linear measurements and morphometric analyses corroborate the previously reported covariation pattern of nasal cavity shape with climate, where humans from a cold/dry climate tend to possess a relatively tall, narrow, and deep nasal cavity compared with those from a warm/humid environment. The northern Okhotsk group had overall larger cranial airways, which may be attributable to their large facial skeleton. However, the ratio of nasal/bimaxillary breadth was significantly lower in the Okhotsk group, indicating that maxillary size does not necessarily constrain the nasal breadth. In addition, despite the presence of obvious geographic clines in anterior nasal shape, posterior choanal shape lacked the north-south geographic cline. This suggests a certain level of morphofunctional independence between the anterior and posterior nasal openings.

Conclusions: The observed geographic variations must, however, be partly considered as a reflection of different ancestral traits and population histories of the three groups. Nevertheless, the results indicate that intergroup variations in nasal cavity morphology can be largely explained by climatic conditions. Am. J. Hum. Biol. 28:343-351, 2016. © 2015 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajhb.22786DOI Listing
May 2016

Weaning age in an expanding population: stable carbon and nitrogen isotope analysis of infant feeding practices in the Okhotsk culture (5th-13th centuries AD) in Northern Japan.

Am J Phys Anthropol 2015 Aug 27;157(4):544-55. Epub 2015 Mar 27.

Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8561, Japan.

Objective: The Okhotsk people were sedentary hunter-gatherer-fishers who lived and prospered in Sakhalin, Hokkaido, and the Kurile Islands during the 5th to 13th centuries AD. They expanded rapidly along the northeastern coast of Hokkaido. We reconstructed infant feeding practices of the Moyoro population of the Okhotsk culture in eastern Hokkaido, Japan.

Methods: Stable isotope ratios in 58 subadult human skeletons were measured.

Results: The results suggest that complementary foods with a relatively low carbon isotope ratio were consumed during and after weaning, as observed in ethnographic descriptions of northern human populations such as the Ainu and isotopically suggested in ancient northern hunter-gatherer-fisher populations. Nitrogen isotope ratios of subadults showed that the age at the end of weaning in the Moyoro population was 1.8 (1.4-2.2 in 95% credible interval) years, which is earlier than that in other northern hunter-gatherer-fisher populations.

Conclusions: Because weaning age is one of the most important determinants of fertility, a shorter breastfeeding period suggests increased fertility. Furthermore, better nutrition would further promote the population increase, and thus populations of the Okhotsk culture could expand into new regions. These findings are consistent with recent emerging evidence of great contributions of the Okhotsk to the formation of later Ainu populations and culture.
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http://dx.doi.org/10.1002/ajpa.22740DOI Listing
August 2015

Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.

Mol Biol Evol 2015 Jun 10;32(6):1533-43. Epub 2015 Mar 10.

Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan

Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000-3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.
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http://dx.doi.org/10.1093/molbev/msv045DOI Listing
June 2015

Common polymorphisms in WNT10A affect tooth morphology as well as hair shape.

Hum Mol Genet 2015 May 22;24(9):2673-80. Epub 2015 Jan 22.

Department of Orthodontics, School of Dentistry, Showa University, Kitasenzoku 2-1-1, Ota-ku, Tokyo 145-8515, Japan

Hair and teeth are appendages of ectodermal origin, and there are common molecular backgrounds involved in their formation. To date, it has been revealed that a non-synonymous polymorphism in EDAR has effects on the morphological variation in both hair and teeth. Previous association studies have confirmed that single-nucleotide polymorphisms (SNPs) in/near THADA, FRAS1, WNT10A, NAF1 and FGFR2 are associated with hair morphology. In this study, we thus examined whether these SNPs are also associated with dental characteristics. We measured metric dental traits including crown size and also evaluated non-metric dental traits using plaster casts obtained from subjects (272 Japanese and 226 Koreans). DNA samples were prepared from the subjects and genotyped for the hair morphology-associated SNPs. We observed a significant association of crown size with an SNP in WNT10A (rs7349332), but not with SNPs in other genes. Therefore, we further examined four SNPs within and around WNT10A, among which rs10177996 had the strongest association with dental traits. World distribution of the derived allele in rs10177996, which is associated with larger teeth, showed that Eurasians have a higher allele frequency than Africans. Together with previous studies on hair morphology, this study demonstrated that common variations in WNT10A have pleiotropic effects on the morphology of ectodermal appendages.
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http://dx.doi.org/10.1093/hmg/ddv014DOI Listing
May 2015

Size and placement of developing anterior teeth in immature Neanderthal mandibles from Dederiyeh Cave, Syria: implications for emergence of the modern human chin.

Am J Phys Anthropol 2015 Mar 11;156(3):482-8. Epub 2014 Nov 11.

Division of Human Evolution Studies, Graduate School of Medicine, Hokkaido University, Hokkaido, 060-8638, Japan.

Evolutionary and functional significance of the human chin has long been explored from various perspectives including masticatory biomechanics, speech, and anterior tooth size. Recent ontogenetic studies have indicated that the spatial position of internally forming anterior teeth partially constrains adult mandibular symphyseal morphology. The present study therefore preliminarily examined the size and placement of developing anterior teeth in immature Neanderthal mandibles of Dederiyeh 1 and 2, compared with similarly-aged modern humans (N = 16) and chimpanzees (N = 7) whose incisors are comparatively small and large among extant hominids, respectively. The Dederiyeh 1 mandible is described as slightly presenting a mental trigone and attendant mental fossa, whereas Dederiyeh 2 completely lacks such chin-associated configurations. Results showed that, despite symphyseal size being within the modern human range, both Dederiyeh mandibles accommodated overall larger anterior dentition and displayed a remarkably wide bicanine space compared to those of modern humans. Dederiyeh 2 had comparatively thicker deciduous incisor roots and more enlarged permanent incisor crypts than Dederiyeh 1, but both Dederiyeh individuals exhibited a total dental size mostly intermediate between modern humans and chimpanzees. These findings potentially imply that the large deciduous/permanent incisors collectively distended the labial alveolar bone, obscuring an incipient mental trigone. It is therefore hypothesized that the appearance of chin-associated features, particularly of the mental trigone and fossa, can be accounted for partly by developmental relationships between the sizes of the available mandibular space and anterior teeth. This hypothesis must be, however, further addressed with more referential samples in future studies.
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http://dx.doi.org/10.1002/ajpa.22665DOI Listing
March 2015

Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago.

Mol Biol Evol 2014 Nov 1;31(11):2929-40. Epub 2014 Aug 1.

Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan

The Ryukyu Islands are located to the southwest of the Japanese archipelago. Archaeological evidence has revealed the existence of prehistoric cultural differentiation between the northern Ryukyu islands of Amami and Okinawa, and the southern Ryukyu islands of Miyako and Yaeyama. To examine a genetic subdivision in the Ryukyu Islands, we conducted genome-wide single nucleotide polymorphism typing of inhabitants from the Okinawa Islands, the Miyako Islands, and the Yaeyama Islands. Principal component and cluster analyses revealed genetic differentiation among the island groups, especially between Okinawa and Miyako. No genetic affinity was observed between aboriginal Taiwanese and any of the Ryukyu populations. The genetic differentiation observed between the inhabitants of the Okinawa Islands and the Miyako Islands is likely to have arisen due to genetic drift rather than admixture with people from neighboring regions. Based on the observed genetic differences, the divergence time between the inhabitants of Okinawa and Miyako islands was dated to the Holocene. These findings suggest that the Pleistocene inhabitants, whose bones have been found on the southern Ryukyu Islands, did not make a major genetic contribution, if any, to the present-day inhabitants of the southern Ryukyu Islands.
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http://dx.doi.org/10.1093/molbev/msu230DOI Listing
November 2014

Comparative analysis of facial morphology between Okinawa Islanders and mainland Japanese using three-dimensional images.

Am J Hum Biol 2014 Jul-Aug;26(4):538-48. Epub 2014 May 17.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan.

Objectives: Differences in facial height and breadth between Okinawa Islanders and mainland Japanese have been reported in previous craniometric and somatometric studies. This study using three-dimensional (3D) images aimed to identify more detailed characteristics of facial morphology in each population.

Methods: Using a hand-held 3D scanner, we obtained 60 facial surface images each from Okinawa Islanders and mainland Japanese. Twenty-one landmarks were plotted on a computer and 27 measurements of distances and angles between the landmarks were taken. Statistical analyses such as t test, principal component analysis (PCA), regression analysis, and discriminant analysis were performed to identify sex and regional differences, the patterns of facial features, factors explaining the facial patterns, and other features.

Results: Okinawa Islanders showed lower facial and nasal heights than mainland Japanese. Furthermore, we identified larger protrusions of the glabella and nasal root in Okinawa Islanders than in mainland Japanese. In the PCA, we observed components of facial shape patterns. These components mainly represented facial size (PC1), facial depth (PC2), the prominence of the glabella and nasal root (PC3), and facial breadth (PC4). We identified that the population difference is strongly associated with PC3.

Conclusions: This study quantitatively identified differences in the facial morphology between Okinawa Islanders and mainland Japanese using 3D digital images, with special emphases on the differences in the nasal height and the prominence of the glabella and nasal root.
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http://dx.doi.org/10.1002/ajhb.22560DOI Listing
January 2015

The role of polymorphisms associated with early tooth eruption in dental and occlusal traits in East Asian populations.

Korean J Orthod 2014 Mar 19;44(2):96-102. Epub 2014 Mar 19.

Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.

Objective: A recent study suggested that rs6504340, a polymorphism within the homeobox B (HOXB) gene cluster, is associated with the susceptibility for malocclusions in Europeans. The resulting malocclusions require orthodontic treatment. The aim of this study was to investigate the association of rs6504340 and other dentition-implicated polymorphisms with dental and occlusal traits in Korean and Japanese populations.

Methods: The study participants included 223 unrelated Koreans from the Busan area and 256 unrelated Japanese individuals from the Tokyo metropolitan area. DNA samples were extracted from saliva specimens. Genotyping for rs6504340 and four single nucleotide polymorphisms (SNPs) that have been shown to be associated with the timing of first tooth eruption and the number of teeth at 1 year of age (rs10506525, rs1956529, rs9674544, and rs8079702) was performed using TaqMan assays. The Index of Orthodontic Treatment Need (IOTN), overjet, overbite, arch length discrepancy, crown sizes, and length and width of the dental arches were measured. Spearman's correlation coefficients were calculated to evaluate relationships between rs6504340 and these dental/occlusal traits.

Results: We evaluated the aesthetic components and dental health components of the IOTN in the Korean and Japanese populations and found that neither rs6504340 nor the other four SNPs showed any association with dental and occlusal traits in these East Asian populations.

Conclusions: These negative results suggest that further research is needed to identify the genetic determinants of malocclusions in order to reach a consensus.
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http://dx.doi.org/10.4041/kjod.2014.44.2.96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971131PMC
March 2014

A genome-wide association study of third molar agenesis in Japanese and Korean populations.

J Hum Genet 2013 Dec 31;58(12):799-803. Epub 2013 Oct 31.

Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan.

Tooth agenesis is the most common developmental anomaly of human dentition, occurring most often in the third molar (wisdom tooth). It is affected by genetic variation, so this study aimed to identify susceptibility genes associated with third molar agenesis. Examination of panoramic radiographs and medical history about third molar extraction were used to diagnose third molar agenesis. We then conducted a genome-wide association study of 149 cases with at least one-third molar agenesis and 338 controls from Japan and Korea using the Illumina HumanOmniExpress BeadChip. After rigorous quality-control filtering, approximately 550 000 single-nucleotide polymorphisms (SNPs) were analyzed in association tests with the status. We identified three SNPs showing evidence of association at P<1 × 10(-5) and 69 SNPs showing evidence of association at P<1 × 10(-4). SNP rs1469622, which maps to an intron of THSD7B (thrombospondin, type I, domain containing 7B) on chromosome 2, showed the strongest association (combined odds ratio=1.88, 95% confidence interval=1.43-2.47, P=7.5 × 10(-6)). The identified SNPs may be considered candidates for future replication studies in independent samples.
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http://dx.doi.org/10.1038/jhg.2013.106DOI Listing
December 2013

Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers.

DNA Res 2014 Feb 7;21(1):15-25. Epub 2013 Sep 7.

1Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan.

Analysis of microbiota in various biological and environmental samples under a variety of conditions has recently become more practical due to remarkable advances in next-generation sequencing. Changes leading to specific biological states including some of the more complex diseases can now be characterized with relative ease. It is known that gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), mainly Crohn's disease and ulcerative colitis, exhibiting symptoms in the gastrointestinal tract. Recent studies also showed increased frequency of oral manifestations among IBD patients, indicating aberrations in the oral microbiota. Based on these observations, we analyzed the composition of salivary microbiota of 35 IBD patients by 454 pyrosequencing of the bacterial 16S rRNA gene and compared it with that of 24 healthy controls (HCs). The results showed that Bacteroidetes was significantly increased with a concurrent decrease in Proteobacteria in the salivary microbiota of IBD patients. The dominant genera, Streptococcus, Prevotella, Neisseria, Haemophilus, Veillonella, and Gemella, were found to largely contribute to dysbiosis (dysbacteriosis) observed in the salivary microbiota of IBD patients. Analysis of immunological biomarkers in the saliva of IBD patients showed elevated levels of many inflammatory cytokines and immunoglobulin A, and a lower lysozyme level. A strong correlation was shown between lysozyme and IL-1β levels and the relative abundance of Streptococcus, Prevotella, Haemophilus and Veillonella. Our data demonstrate that dysbiosis of salivary microbiota is associated with inflammatory responses in IBD patients, suggesting that it is possibly linked to dysbiosis of their gut microbiota.
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http://dx.doi.org/10.1093/dnares/dst037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3925391PMC
February 2014

[Lead content of bones excavated from archaeological sites in Hokkaido].

Nihon Eiseigaku Zasshi 2013 ;68(1):53-7

Department of Environmental Studies, University of Tokyo.

Objectives: The lead content of excavated bone samples from archaeological sites in Hokkaido was measured to obtain insight into the source of human lead contamination known in the historic Japanese Edo era.

Methods: Fifty-seven rib samples excavated from 11 sites of five different eras in Hokkaido were analyzed for lead (Pb), calcium (Ca), and iron (Fe) contents by ICP mass spectrometry and ICP emission spectrometry.

Results: The Pb/Ca ratio (mg Pb/kg Ca) was low (approximately 2.0) and constant from the Jomon (approximately 5000 BP) to the Satsumon (approximately 750 BP) eras; however, its median increased to 11 in the Modern era. This elevation of Pb/Ca ratio in the bone samples from sites of the Modern era was not considered to be due to a greater bone contamination with soil particles because of similar Fe concentrations in the bone samples from this era to those in other eras. This historic trend of Pb/Ca ratio was similar to that observed in other parts of Japan. The elevated Pb/Ca ratio in the bone samples excavated from sites in the Modern era in other parts of Japan, that is, Edo era, has been ascribed to the usage of face powder containing Pb; however, people inhabiting Hokkaido in those days, the Ainu, were not considered to have the custom of using face powder.

Conclusions: Contamination source(s) other than face powder was postulated in the Modern era of both Hokkaido and other parts of Japan.
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http://dx.doi.org/10.1265/jjh.68.53DOI Listing
September 2014

Association of melanocortin 1 receptor gene (MC1R) polymorphisms with skin reflectance and freckles in Japanese.

J Hum Genet 2012 Nov 2;57(11):700-8. Epub 2012 Aug 2.

Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, Okinawa, Japan.

Most studies on the genetic basis of human skin pigmentation have focused on people of European ancestry and only a few studies have focused on Asian populations. We investigated the association of skin reflectance and freckling with genetic variants of melanocortin 1 receptor (MC1R) gene in Japanese. DNA samples were obtained from a total of 653 Japanese individuals (ages 19-40 years) residing in Okinawa; skin reflectance was measured using a spectrophotometer and freckling status was determined for each individual. Lightness index (L*) and freckling status were not correlated with age, body mass index or ancestry (Ryukyuan or Main Islanders of Japan). Among the 10 nonsynonymous variants that were identified by direct sequencing of the coding region of MC1R, two variants--R163Q and V92M--with the derived allele frequencies of 78.6 and 5.5%, respectively, were most common. Multiple regression analysis showed that the 163Q allele and the presence of nonsynonymous rare variants (allele frequencies <5%) were significantly associated with an increase in sex-standardized skin lightness (L* of CIELAB (CIE 1976 (L*a*b*) color space)) of the inner upper arm. Relative to the 92V allele, the 92M allele was significantly associated with increased odds of freckling. This is the first study to show an association between the 163Q allele and skin reflectance values; this association indicated that light-toned skin may have been subjected to positive selection in East Asian people.
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http://dx.doi.org/10.1038/jhg.2012.96DOI Listing
November 2012

Association of common PAX9 variants with permanent tooth size variation in non-syndromic East Asian populations.

J Hum Genet 2012 Oct 19;57(10):654-9. Epub 2012 Jul 19.

Department of Orthodontics, Pusan National University Dental Hospital, Kyeongsangnamdo, Korea.

Studies on the heredity of dental characteristics in humans have indicated that the variance in many dental traits results from genetic variation. However, the genetic factors that influence commonly occurring dental variants are poorly understood. Paired domain box 9 (PAX9) codes a transcription factor that is important in tooth development. We investigated whether PAX9 polymorphisms are associated with normal variations in tooth agenesis and morphology. The study subjects were 273 Japanese and 223 Korean adults. Single-nucleotide polymorphisms (SNPs) in PAX9 (rs2295222, rs4904155, rs2073244, rs12881240 and rs4904210) were genotyped, and third molar agenesis and mesiodistal and buccolingual diameters were measured. We found that four of the five SNPs were significantly associated with the crown size. However, no SNP was associated with third molar agenesis. In additional analyses on non-metric dental traits, we found significant associations of PAX9 SNPs with shoveling of upper first incisors. In summary, common variants in PAX9 contributed to morphological variation in permanent teeth in humans.
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http://dx.doi.org/10.1038/jhg.2012.90DOI Listing
October 2012