Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes.

Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination. Amplicon size was designed to be less than 60 bp to make the method more useful for analyzing degraded DNA samples. All DNA samples collected from eight Japanese individuals (four male, four female) were evaluated correctly using our method. The detection limit for accurate sex determination was determined to be 20 pg of DNA. We compared our new method with commercial short tandem repeat analysis kits using DNA samples artificially fragmented by ultraviolet irradiation. Our novel method was the most robust for highly fragmented DNA samples. To deal with allelic dropout resulting from deamination, we adopted "bidirectional analysis," which analyzed samples from both sense and antisense strands. This new method was applied to 14 Jomon individuals (3500-year-old bone samples) whose sex had been identified morphologically. We could correctly identify the sex of 11 out of 14 individuals. These results show that our method is reliable for the sex determination of highly degenerated samples

Sex Differences in Intestinal Microbiota and Their Association with Some Diseases in a Japanese Population Observed by Analysis Using a Large Dataset

In recent years, many studies have focused on the relationship between intestinal microbiota and human health, but the impact of sex has not yet been sufficiently investigated. In this study, sex differences in the intestinal microbiota of a Japanese population were investigated by age group, using a large dataset constructed for a cross-sectional study. α-diversity analysis indicated that the impact of sex differences varied among the 20s–50s age groups but tended to be smaller among the 60s–70s age groups. Fusobacterium, Megamonas, Megasphaera, Prevotella, and Sutterella were more common among males, whereas Alistipes, Bacteroides, Bifidobacterium, Odoribacter, and Ruthenibacterium were common among females. Next, intestinal bacteria potentially associated with 12 diseases were investigated for each sex. The results indicate that many of these differ between males and females, and among age groups. Thus, sex and age should be considered for studies on intestinal microbiota and disease association, prevention, and treatment approaches that target them

Sex Differences in Intestinal Microbiota and Their Association with Some Diseases in a Japanese Population Observed by Analysis Using a Large Dataset

In recent years, many studies have focused on the relationship between intestinal microbiota and human health, but the impact of sex has not yet been sufficiently investigated. In this study, sex differences in the intestinal microbiota of a Japanese population were investigated by age group, using a large dataset constructed for a cross-sectional study. α-diversity analysis indicated that the impact of sex differences varied among the 20s–50s age groups but tended to be smaller among the 60s–70s age groups. Fusobacterium, Megamonas, Megasphaera, Prevotera, and Sutterella were more common among males, whereas Alistipes, Bacteroides, Bifidobacterium, Odoribacter, and Ruthenibacterium were common among females. Next, intestinal bacteria potentially associated with 12 diseases were investigated for each sex. The results indicate that many of these differ between males and females, and among age groups. Thus, sex and age should be considered for studies on intestinal microbiota and disease association, prevention, and treatment approaches that target them

JNK functions in the non-canonical Wnt pathway to regulate convergent extension movements in vertebrates

Recent genetic studies in Drosophila identified a novel non-canonical Wnt pathway, the planar cell polarity (PCP) pathway, that signals via JNK to control epithelial cell polarity in Drosophila. Most recently, a pathway regulating convergent extension movements during gastrulation in vertebrate embryos has been shown to be a vertebrate equivalent of the PCP pathway. However, it is not known whether the JNK pathway functions in this non-canonical Wnt pathway to regulate convergent extension movements in vertebrates. In addition, it is not known whether JNK is in fact activated by Wnt stimulation. Here we show that Wnt5a is capable of activating JNK in cultured cells, and present evidence that the JNK pathway mediates the action of Wnt5a to regulate convergent extension movements in Xenopus. Our results thus demonstrate that the non-canonical Wnt/JNK pathway is conserved in both vertebrate and invertebrate and define that JNK has an activity to regulate morphogenetic cell movements

Sex determination by PowerPlex^® ESX17 Fast using UV-irradiated template DNA.

<p>A and C show female and male DNA with no UV irradiation, respectively. B and D show UV irradiation-exposed female (0.5 J) and male (0.2 J) DNA, respectively. The results were reproduced in three independent assays.</p

Assessment of the quality of mock forensic samples.

<p>Black and white columns show 129/41 bp and 305/41 bp Q-ratios, respectively. The Q-ratios correlate with the amount of UV radiation. Both female and male mock forensic samples with no UV exposure produced Q-ratios close to 1. Mock forensic samples subjected to high levels of UV irradiation yielded 129/41 bp and 305/41 bp ratios in the ranges of 0.00–0.38 and 0.00–0.038, respectively. Mean values ± SD are from triplicate assays.</p

DNA sexing of Jomon samples by our method.

<p>A and B show the results of sex determination using the sense and antisense primer sets, respectively. M indicates the 10-bp ladder marker. The results were reproduced in three independent assays. Typical results of bidirectional analysis are shown because amounts of template DNA were not constant among ancient samples.</p

Sensitivity measurement by PCR-APLP using a dilution series of female and male DNA.

<p>Lanes 1–6 correspond to a serial dilution of female DNA, lanes 7–12 to a serial dilution of male DNA, and lane 13 to the negative control. A and B show results of sensitivity analysis using the sense and antisense primer sets, respectively. M indicates the 10-bp ladder marker. The results were reproduced in three independent assays.</p

Robustness evaluation of a PCR-APLP method using UV-irradiated template DNA.

<p>A and B show the results of robustness analysis using the sense and antisense primer sets, respectively. Lanes 1–5 correspond to female DNA damaged by 0, 0.5, 1.0, 5.0, and 10 J UV irradiation; lanes 6–10 to male DNA damaged by 0, 0.5, 1.0, 5.0, and 10 J UV irradiation; and lane 11 to the negative control. Lanes 1 and 6 are female and male positive controls, respectively. M indicates the 10-bp ladder markers. The results were reproduced in three independent assays.</p