F2_Phenotype_and_Genotype_data

Raw morphological data, genetic sex, and CYP1B1 genotypes from F2 individuals

Enzyme Activities of CYP1A and CYP1B1 alleles

Raw and relative enzyme activities of CYP1A and CYP1B1 allele

Morphological data from two medaka populations

Raw morphological data from Tanabe and Maegok populations

How ‘Circumpolar’ is Ainu Music? Musical and Genetic Perspectives on the History of the Japanese Archipelago

<div><p>Understanding the cultural and genetic origins of the Ainu of northern Japan has important implications for understanding the history of the Japanese archipelago. Ethnomusicologists have tended to emphasise connections between Ainu music and a ‘circumpolar’ culture area. However, the ‘dual structure’ model from physical anthropology describes the Ainu as descendants of the first inhabitants of Japan with minimal circumpolar influence. To examine Ainu musical diversity empirically from a comparative perspective, we analysed 680 traditional songs from two Ainu and 33 surrounding East Asian and circumpolar populations. The Ainu repertoire contained a majority (∼50%) of unique stylistic song-types and lower frequencies of types shared with circumpolar (∼40%) and East Asian (∼10%) populations. These frequencies were similar to the corresponding frequencies of mitochondrial DNA types within the Ainu gene pool (∼50%, ∼30% and ∼20%, respectively), consistent with an emerging ‘triple structure’ model of Japanese archipelago history.</p></div

Suppressed autophosphorylation of DNA-PKcs (pT2609) in cells expressing olNbs1 (H170)-Venus protein.

<p>(A) The cells overexpressing olNbs1-Venus (Nos. 101 and 301) and the cells overexpressing olNbs1 (H170)-Venus (Nos. 309 and 2202) were stained with DAPI and immunostained with anti-phosphorylated DNA-PKcs (pT2609) antibody 30 min after the γ-ray irradiation (5 Gy). Fluorescent images of DAPI-stained nuclei, expressed Venus-fusion proteins, foci of phosphorylated DNA-PKcs (pT2609) and merged images of the Venus-fusion proteins and phosphorylated DNA-PKcs (pT2609) are shown. (B) Fractions of pT2609 foci positive cells (>30 foci per cell) in the cells overexpressing olNbs1-Venus (No. 101, n = 48; No. 301, n = 65) and in the cells overexpressing olNbs1 (H170)-Venus (No. 309, n = 41; No. 2202, n = 50) are shown. (C) Fractions of pT2609 foci positive cells (>20 foci per cell) in the cells overexpressing olNbs1-Venus (Nos. 101 and 301) and the cells overexpressing olNbs1 (H170)-Venus (Nos. 309 and 2202) treated with DNA-PK inhibitor (NU7026) or ATM inhibitor (KU55933) were counted 30 min after the γ-ray irradiation (5 Gy). At least 40 cells were counted in each experiment and bars represent standard errors of 3 independent experiments.</p

Accumulation of olNbs1-Venus proteins at DSBs.

<p>(A) Nuclei of the cells overexpressing olNbs1-Venus (No. 301) and the cells overexpressing olNbs1 (H170)-Venus (No. 309) were micro-irradiated with 405 nm laser and accumulation of olNbs1-Venus proteins at the induced DSB sites were visualized. (B) Increase in the Venus fluorescence intensity at the laser-induced DSBs in the cells overexpressing olNbs1-Venus (No. 101, open circles, average in 4 cells; No. 301, open triangles, average in 4 cells) and in the cells expressing olNbs1 (H170)-Venus (No. 309, filled circles, average in 4 cells; No. 2202, filled triangles, average in 3 cells; No. 2502, filled squares, average in 6 cells) were measured after the micro-irradiation and plotted. The Y-axis represents fold increase in the fluorescence intensity determined by dividing by the mean intensity of the irradiated area of nuclei at 1.3 sec after the micro-irradiation. Time points are on the X-axis in sec. (C) Foci of olNbs1 or olNbs1 (H170) and γ-H2AX were visualized by immunostaining in the cells overexpressing olNbs1-Venus (No. 301) and in the cells expressing olNbs1 (H170)-Venus (No.309) at 2 and 12 h after the γ-ray irradiation (5 Gy). Foci in the not-irradiated cells are also shown (0 Gy). (D) Numbers of olNbs1 foci were counted at 30 min, 2, 6 and 12 h after the γ-ray irradiation (5 Gy) in the cells overexpressing olNbs1 -Venus (No. 301) and in the cells overexpressing olNbs1 (H170)-Venus (No. 309). The foci number in the not-irradiated cells were also counted (0 Gy). Bars represent standard errors of the averaged foci number per cell (n > 20 cells). Statistical analyses were performed using Student's <i>t</i> tests (*<i>p</i> < 0.01).</p

A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

<div><p>To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, <i>ring finger protein 213</i>, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome regions with substantial length.</p></div

Delayed DSB repair in cells overexpressing olNbs1 (H170)-Venus protein.

<p>(A) Typical photographs of electrophoresed nuclei of the cells overexpressing olNbs1-Venus (No. 301) and the cells overexpressing olNbs1 (H170)-Venus (No. 309) are shown. Immediately after the γ-rays irradiation (5 Gy) (0 min), electrophoresed nuclei of both No. 301 cell and No. 309 cell showed comet tailing, indicating that DSB were induced by irradiation. Electrophoresed nuclei of No.309 cell still showed comet tailing 30 min after the irradiation, indicating that DSBs remained not repaired, while DSBs in the nuclei of No.301 cell were repaired within 30 min after the irradiation. (B) Tail moment scores were measured 30 min after the γ-ray irradiation (5 Gy) in the cells overexpressing olNbs1-Venus (Nos. 101 and 301) and olNbs1 (H170)-Venus (Nos. 309, 2202 and 2502). Open and filled circles represent average tail moment scores of at least 100 cells of No.101, 301 cells and No.309, 2202 and 2505 cells, respectively. The experiments were repeated three times and averages of the tail moment scores from triplicate experiments are shown in bars. (C) The cells overexpressing olNbs1-Venus (No. 301) and the cells overexpressing olNbs1 (H170)-Venus (No. 309) were irradiated with γ-rays (5 Gy). Induced γ-H2AX and olNbs1 foci were visualized 2 and 12 h after the irradiation by immunostaining. Foci of γ-H2AX and olNbs1 in the not-irradiated cells are also shown (0 Gy). (D) γ-H2AX foci were counted 30 min, 2, 6 and 12 h after the γ-irradiation (5 Gy) in the cells (No. 301) overexpressing olNbs1-Venus and in the cells (No. 309) overexpressing olNbs1 (H170)-Venus. Data were obtained from one representative experiment, and error bars represent standard errors of the means per cell (n > 20 cells). Statistical analyses were performed using a Student <i>t</i> test and * and † represent significant differences between No. 301 cell and No. 309 cell (<i>p</i> < 0.005 and <i>p</i> < 0.001, respectively).</p

Numbers of validated SNPs.

<p>Numbers of validated SNPs.</p

Average numbers of BDC and MB.

<p>Average numbers of BDC and MB.</p