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Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19. [ABSTRACT FROM AUTHOR]

Summary: Hirschmanniella diversa and H. imamuri parasitise the lotus, Nelumbo nucifera. Hirschmanniella spp. are the most important pests of lotus cultivation in Japan, but the distribution and species dominancy are not fully understood. In this study, we aimed to collect Hirschmanniella spp. individuals from lotus roots in the major lotus cultivation areas in Japan and identify them morphologically and molecularly using the 18S, D2-D3 regions of rRNA and mitochondrial cytochrome c oxidase subunit I (mtCOI). Hirschmanniella oryzae , commonly known to cause damage on rice in Japan, was also obtained and analysed for inter- and intraspecies sequence variations. All individuals of the genus Hirschmanniella extracted from lotus roots in 16 fields in ten prefectures were identified as H. diversa morphologically and molecularly. This result revealed that H. diversa is a dominant Hirschmanniella species parasitising lotus in Japan. Meanwhile, intraspecific sequence variations in H. diversa were relatively higher in the mtCOI (1-21 bases, ≦5.3%) than in the 18S rRNA and D2-D3 of 28S rRNA (0.0-0.3% and 0.0-0.4%, respectively) and in those of H. oryzae. Based on the mtCOI sequences, five haplotypes were identified and each haplotype was distributed in relatively close regions or regions in which the same lotus cultivars were grown, although further studies are required to verify this assertion. The morphological and genetic variations were higher in H. diversa than in H. oryzae (no intraspecific sequence variation in mtCOI), suggesting that H. diversa was not a recent invasive species. [ABSTRACT FROM AUTHOR]

Non-coding repeat expansions within RFC1 and NOTCH2NLC genes have lately been linked to multisystem neurodegenerative diseases, which also shed light on yet undiagnosed patients with inherited peripheral neuropathies. The aim of this study was to identify the genetic basis of patients with hereditary sensory and autonomic neuropathy (HSAN). We collected 79 unrelated DNA samples clinically suspected with HSAN from multiple regions of Japan. Mutation screening was first performed using gene panel sequencing and whole-exome sequencing. Pathogenic/likely pathogenic variants were identified from genes of WNK1/HSN2 (6 cases), SCN9A (3 cases), NTRK1 (3 cases), and DNMT1 (2 cases). Subsequently, long-range flanking PCR and repeat-primed PCR were applied to analyze repeat expansions in RFC1 and NOTCH2NLC. Bi-allelic RFC1 repeat expansions were detected from 20 adult-onset HSAN patients, consisting of [(AAGGG)exp/(AAGGG)exp] (8 cases), [(ACAGG)exp/(ACAGG)exp] (8 cases), and [(AAGGG)exp/(ACAGG)exp] (4 cases). GGC repeat expansion in NOTCH2NLC was found in 1 case. Single-nucleotide variant-based haplotype analysis of patients harboring disease-associated repeat expansions in RFC1 revealed distinguishable haplotypes among subgroups with different repeat genotypes. These findings substantially redefine the genetic spectrum of HSAN, where multi-type RFC1 repeat expansions account for 25.3% of all patients, highlighting the necessity of genetic screening, particularly for adult-onset patients. [ABSTRACT FROM AUTHOR]

SUMMARY: Pineapple (Ananas comosus (L.) Merr.) is one of the most economically important tropical fruit species. The major aim of the breeding programs in several countries, including Japan, is quality improvement, mainly for the fresh market. 'Yugafu', a Japanese cultivar with distinctive pipe‐type leaf margin phenotype and white flesh color, is popular for fresh consumption. Therefore, genome sequencing of 'Yugafu' is expected to assist pineapple breeding. Here, we developed a haplotype‐resolved assembly for the heterozygous genome of 'Yugafu' using long‐read sequencing technology and obtained a pair of 25 pseudomolecule sequences inherited from the parental accessions 'Cream pineapple' and 'HI101'. The causative genes for leaf margin and fruit flesh color were identified. Fine mapping revealed a 162‐kb region on CLG23 for the leaf margin phenotype. In this region, 20 kb of inverted repeat was specifically observed in the 'Cream pineapple' derived allele, and the WUSCHEL‐related homeobox 3 (AcWOX3) gene was predicted as the key gene for leaf margin morphogenesis. Dominantly repressed AcWOX3 via RNAi was suggested to be the cause of the pipe‐type leaf margin phenotype. Quantitative trait locus (QTL) analysis revealed that the terminal region of CLG08 contributed to white flesh and low carotenoid content. Carotenoid cleaved dioxygenase 4 (AcCCD4), a key gene for carotenoid degradation underlying this QTL, was predicted as the key gene for white flesh color through expression analysis. These findings could assist in modern pineapple breeding and facilitate marker‐assisted selection for important traits. [ABSTRACT FROM AUTHOR]

Onychodactylus kinneburi is a hynobiid salamander endemic to Japan; it occurs sympatrically with O. japonicus in the Western Chugoku Mountains. Currently, information on the distribution and abundance of O. kinneburi is limited and the necessity for its conservation has not been considered. In this study, we investigated the distribution pattern and genetic diversity of the O. kinneburi population of the Western Chugoku Mountains based on mitochondrial DNA sequences. Onychodactylus kinneburi was widely distributed in the area; however, its genetic diversity was relatively low and its population size seemed to be smaller than that of O. japonicus, which is endangered in the same area. Thus, habitat management and monitoring are likely required to conserve the O. kinneburi population in the Western Chugoku Mountains. [ABSTRACT FROM AUTHOR]

The present-day genetic structure of macroalgal species reflects both geographical history and oceanic circulation patterns as well as anthropogenic introduction across native ranges. To precisely understand the genetic diversity and how the factors shape the current population structure of Gloiopeltis furcata sensu lato, we determined the mitochondrial 5' end of cytochrome c oxidase subunit I (COI-5P) sequences for 677 individuals sampled from 67 sites spanning almost the entire distribution range in Korea and Japan. Results from the phylogenetic analysis and haplotype distribution revealed eleven distinct lineages within G. furcata s.l. along the Korea-Japan coastal areas and displayed divergent phylogeographic patterns among lineages. Despite the closely related lineages distributed in same habitats as high rocky intertidal zone, they display different phylogeographic patterns among lineages. The populations from the south of Korea-Japan harbored the highest genetic diversity and unique endemism in comparison with other populations in the distribution range. This could be the evidence of southern refugia for G. furcata s.l. in the Northwest (NW) Pacific and the recent migration from native to introduced region. The reason is that an exceptional distribution pattern was found high genetic diversity in Hakodate of Japan where is the northern location in the NW Pacific. Our results imply the contemporary influence on the distribution due to current circulation pattern and anthropogenic effects. These phylogeographic findings provide the important insight into cryptic species diversity and the detailed distribution pattern of Gloiopeltis in the NW Pacific. [ABSTRACT FROM AUTHOR]

Polymorphisms of the myostatin gene (MSTN) have been studied in vertebrates including several aquaculture species, revealing their role in growth. We attempted to identify polymorphisms in MSTN associated with growth traits of juvenile farmed red sea bream Pagrus major, an important cultured fish species in Japan. Polymorphisms in the coding region of MSTN were screened, and six polymorphisms were found among three exons: a deletion in exon 1, a single nucleotide polymorphism (SNP) in exon 2 and four SNPs in exon 3. The deletion in exon 1 eliminated a codon (glutamine) from the region comprising the polyglutamine structure, but all SNPs were synonymous. We analysed the polymorphisms for association with growth phenotype in large and small P. major specimens obtained from commercial production at 50 days post hatching. Two SNPs located in exon 3 (c.+846T>C and c.+1140T>C) were significantly more frequent in the large group, while no SNPs were significantly associated with the small phenotype. Haplotypes were reconstructed using genotype information of the two phenotype groups, and nine haplotypes (Hap_1 to Hap_9) were successfully reconstructed. Hap_6 and Hap_7 were significantly more often observed in small and large groups respectively. Analysis of diplotypes (haplotype combinations) of individual specimens revealed 19 diplotypes. The Hap_7/Hap_7 diplotype was found in 46.7% of large phenotype specimens, significantly more frequently than in the small group (13.5%). These results will be useful for marker‐assisted selection of red sea bream to improve production with respect to growth. [ABSTRACT FROM AUTHOR]

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

We report the complete mitogenome of a rough-toothed dolphin, Steno bredanensis CRI008296, stranded in Korea. Overall, structure and taxonomical position of the mitogenome were analysed, and its determined haplotype indicated that the same subpopulation is distributed between Korea and Japan. [ABSTRACT FROM AUTHOR]

The present investigation was aimed to study the sequence, phylogenetic and haplotype analyses of Toxocara cati based on the ITS region, along with the genetic diversity, demographic history and population-genetic structure. The maximum likelihood tree based on Kimura 2-parameter model was constructed using the complete ITS region of all the nucleotide sequences (n = 57) of Toxocara spp. and other related ascarid worms available in the GenBank™. It placed all the sequences of T. cati into four major clades designated as T. cati genotypes 1-4 (TcG1-G4). A total of 66 signature nucleotides were identified in the ITS region between genotypes. The median-joining haplotype network displayed a total of 24 haplotypes, with China exhibiting the highest number of haplotypes (h = 20) followed by India (h = 4), and Japan and Russia (h = 1). It indicated a clear distinction between all the four genotypes. The pairwise F ST values between all the genotypes indicated huge genetic differentiation (> 0.25) between different T. cati genotypes. Moreover, the gene flow (Nm) between T. cati genotypes was very low. Results of AMOVA revealed higher genetic variation between genotypes (92.82%) as compared to the variation within genotypes (7.18%). The neutrality indices and mismatch distributions for the G1-G4 genotypes, Indian isolates and the overall dataset of T. cati indicated either a constant population size or a slight population increase. The geographical distribution of all the genotypes of T. cati is also reported. This is the first report of genotyping of T. cati on the basis of the ITS region., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Abstract: To develop DNA markers for forensic analysis, we examined the hypervariable region 1 (HVR1) sequences of 447 pure-bred domestic dogs (Canis lupus familiaris) that had been bred and raised in Japan. HVR1 is a 660-bp stretch of mitochondrial (mt) DNA. Among the 447 HVR1 sequences examined, we identified 58 haplotypes from 47 single nucleotide polymorphisms (SNPs) and two insertion-deletion (InDel) polymorphisms. The haplotype diversity inferred from inter-breed analysis (N =154, 88 breeds) was 0.929±0.011. Intra-breed analysis showed that the haplotype diversity of Golden Retrievers (N =53), Labrador Retrievers (N =67), Miniature Dachshunds (N =61), Toy Poodles (N =62), and Welsh Corgis (N =50) was 0.624±0.052, 0.722±0.029, 0.922±0.010, 0.877±0.020, and 0.443±0.084, respectively. The results of this genotype analysis were used to construct a dataset consisting of dog mtDNA HVR1 sequences for use in forensic applications in Japan. [Copyright &y& Elsevier]

Regions believed to be refugia are known to have lineages indigenous to the regions. The Izu Peninsula, where genus Fagus existed during the last glacial period, was focused on to survey chloroplast DNA of Japanese beech ( Fagus crenata Blume) that grew there. DNA sequence analysis of chloroplast genome regions of about 14 kb revealed two new haplotypes, O and E-1, in F. crenata populations in the Izu Peninsula and adjacent regions. Both haplotypes were conceivably derived from haplotype E. The result of the genetic analysis in this study in combination with the result of pollen analyses performed in the past clearly showed that refugia for F. crenata existed in the Izu Peninsula, and that F. crenata now in growth are lineages indigenous to the region. [ABSTRACT FROM AUTHOR]

Abstract: X-chromosomal STR (X-STR) polymorphisms are particularly useful in complex cases of kinship testing involving inheritance through female subjects. An X-chromosomal multiplex amplifying 18 STRs in one single PCR reaction was developed and optimized in this study. The multiplex system included the DXS7424, GATA172D05, HPRTB, DXS8377, GATA31E08, DXS6810, DXS7423, DXS981, DXS6795, DXS6803, DXS6789, DXS6800, DXS6809, DXS7133, DXS7132, DXS9902, DXS101 and DXS6807 loci, which are distributed over the whole X-chromosome. It was designed as a potential first option in determining recombination within the whole X chromosome in kinship testing. Allele frequencies were obtained from samples from 378 male and 175 female Japanese individuals, all unrelated. The sizes of the amplified products ranged from 82 to 297bp. The combined power of discrimination of the 18 loci was 0.999999999999997 in females and 0.9999999992 in males. A case is presented in which this system allowed considerable efficacy in reaching a solution. The present multiplex system amplified the largest number of loci among the X-STR multiplex systems tested, indicating its potential in personal identification and determining kinship. [Copyright &y& Elsevier]

This study deals with mitochondrial phylogenetic information of Japanese flounder in the Pacific coast of Tohoku Japan to estimate the genetic population subdivision that was undetectable by conventional population statistics. We determined complete sequences of mitochondrial NADH dehydrogenase subunit-2 (ND2) and subunit-5 (ND5) genes for 151 individuals from northern (Aomori and Iwate prefectures, 40-41°N) and southern (Miyagi and Fukushima prefectures, 37-38°N) waters. Samples from both waters showed high genetic diversity, including 126 haplotypes. These haplotypes were located at mixed and nested positions on an inferred phylogenetic tree, and traditional F-statistics indicated no significant population divergence (fST = -0.00335, p > 0.05), corroborating our previous study. Three variable sites, however, showed significant base composition heterogeneity between samples from the northern and southern waters (Fisher's exact-test, p < 0.01). Nucleotide substitutions at the three sites converged on an apical clade, which consisted of the five southern individuals, whereas its sister clade consisted only of the three northern individuals. This phylogenetic information corroborates previous ecological studies indicating the presence of separate stocks in the northern and southern waters. [ABSTRACT FROM AUTHOR]

Conclusion: Haplogroup D4b, especially subhaplogroup D4b2, may be one of the modifiers associated with the phenotypic expression of hereditary hearing loss (HL). Objectives: The present study investigated the association between suspected hereditary HL and 12 major mtDNA haplogroups in a Japanese population. Besides the mutations of mitochondrial DNA, many modifiers including environmental factors and genetic polymorphisms are involved in HL. Methods: The subjects comprised 373 unrelated Japanese patients with suspected hereditary HL and 480 controls. Twenty of the 373 patients were excluded from the study because the m.1555A>G or the m.3243A>G mutation had been detected in them. The mitochondrial haplotypes were classified into 12 major Japanese haplogroups (i.e. F, B, A, N9a, N9b, M7a, M7b, G1, G2, D4a, D4b, and D5). The frequency of each haplogroup in patients with HL was compared with that of the controls using the chi-squared test. Results: The frequency of the HL patients carrying the mitochondrial haplogroup D4b was significantly higher than that of the controls (37/353 [10.5%] vs 31/480 [6.5%]; OR 1.70 [95% CI 1.03-2.79, p = 0.036]) and evidence for enhancement was found in subhaplogroup D4b2 (32/353 [9.1%] vs 24/480 [5%], OR 1.89 [95% CI 1.09-3.28, p = 0.021]). [ABSTRACT FROM AUTHOR]

Crop depredation by brown bears (Ursus arctos) in Hokkaido, Japan, has increased over the past 2 decades. With increased depredation, the number of permits issued and the removal of conflict animals have also increased. We hypothesized that peripheral areas adjacent to agricultural lands represent attractive sink-like habitat because of the association between abundant high-quality anthropogenic food resources and high levels of human-induced mortality by nuisance control. We used an allopatric distribution of mitochondrial DNA (mtDNA) haplotypes in females to distinguish core from peripheral habitat; nuisance control for female bears was 2x greater in the periphery. Using these definitions, we investigated 85 male mtDNA haplotypes recovered from dead bears from eastern Hokkaido (1996-2008) and classified the birthplace for 64. Of these, 14 of 31 born in core were killed in periphery, whereas 5 of 33 born in periphery died in core. In periphery, the largest proportion of males killed occurred during early summer (mating season); for females, the largest proportion was in late summer (period of greatest crop damage). We also documented a significant increase in the number of males killed in the periphery since late 1990s. Timing of mortalities suggested that males were attracted to the periphery for both mating opportunities and by abundant anthropogenic food resources. Because our results suggest a directional flow of males from core to periphery, we suspected (although did not document) a net loss of residents from core. If reproduction was unable to compensate, unregulated control killing could eventually result in a decline in the numbers of males residing in the core. Our findings demonstrate an important application of mtDNA analyses as well as how source-sink dynamics can differentially affect males and females because of varying behavioral traits such as home range size and dispersal characteristics. [ABSTRACT FROM AUTHOR]

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Association of UDP-glucuronosyltransferase 1A1 ( UGT1A1) genetic polymorphisms * 6 and * 28 with reduced clearance of SN-38 and severe neutropenia in irinotecan therapy was demonstrated in Japanese cancer patients. • The detailed gene structure of CES1 has been characterized. • Possible functional SNPs in the promoter region have been reported. WHAT THIS STUDY ADDS • Association of functional CES1 gene number with AUC ratio [(SN-38 + SN-38G)/irinotecan], an in vivo index of CES activity, was observed in patients with irinotecan monotherapy. • No significant effects of major CES1 SNPs on irinotecan PK were detected. AIMS Human carboxylesterase 1 (CES1) hydrolyzes irinotecan to produce an active metabolite SN-38 in the liver. The human CES1 gene family consists of two functional genes, CES1A1 ( 1A1) and CES1A2 ( 1A2), which are located tail-to-tail on chromosome 16q13-q22.1 ( CES1A2-1A1). The pseudogene CES1A3 ( 1A3) and a chimeric CES1A1 variant ( var1A1) are also found as polymorphic isoforms of 1A2 and 1A1, respectively. In this study, roles of CES1 genotypes and major SNPs in irinotecan pharmacokinetics were investigated in Japanese cancer patients. METHODS CES1A diplotypes [combinations of haplotypes A ( 1A3- 1A1), B ( 1A2- 1A1), C ( 1A3-var1A1) and D ( 1A2-var1A1)] and the major SNPs (−75T>G and −30G>A in 1A1, and −816A>C in 1A2 and 1A3) were determined in 177 Japanese cancer patients. Associations of CES1 genotypes, number of functional CES1 genes ( 1A1, 1A2 and var1A1) and major SNPs, with the AUC ratio of (SN-38 + SN-38G)/irinotecan, a parameter of in vivo CES activity, were analyzed for 58 patients treated with irinotecan monotherapy. RESULTS The median AUC ratio of patients having three or four functional CES1 genes (diplotypes A/B, A/D or B/C, C/D, B/B and B/D; n= 35) was 1.24-fold of that in patients with two functional CES1 genes (diplotypes A/A, A/C and C/C; n= 23) [median (25th–75th percentiles): 0.31 (0.25–0.38) vs. 0.25 (0.20–0.32), P= 0.0134]. No significant effects of var1A1 and the major SNPs examined were observed. CONCLUSION This study suggests a gene-dose effect of functional CES1A genes on SN-38 formation in irinotecan-treated Japanese cancer patients. [ABSTRACT FROM AUTHOR]

We consider testing independence in group-wise selections with some restrictions on combinations of choices. We present models for frequency data of selections for which it is easy to perform conditional tests by Markov chain Monte Carlo (MCMC) methods. When the restrictions on the combinations can be described in terms of a Segre–Veronese configuration, an explicit form of a Gröbner basis consisting of binomials of degree two is readily available for performing a Markov chain. We illustrate our setting with the National Center Test for university entrance examinations in Japan. We also apply our method to testing independence hypotheses involving genotypes at more than one locus or haplotypes of alleles on the same chromosome. [ABSTRACT FROM AUTHOR]

We performed haplotype analysis using nine single nucleotide polymorphisms in the ornithine transcarbamylase gene to explore the ancestral origins of three mutations associated with late-onset phenotype in male patients: p.R40H, p.R277W and p.Y55D. Overall, 8 haplotypes were defined among 14 families carrying p.R40H, 5 families carrying p.R277W and 2 families with p.Y55D mutations. Of nine Japanese families carrying p.R40H, eight exhibited haplotype (HT)1, whereas the other family harbored HT2. Among three Caucasian families, one Spanish and one Australian family bore HT3; one Austrian family had HT4. Two US patients harbored HT2 and HT4. Among families carrying p.R277W, HT5 was found in one Japanese, one Korean and one US family. Two other US families had HT2 and HT6. Two families carrying p.Y55D, both Japanese, shared HT1. These results indicate that the p.R40H mutation has arisen recurrently in all populations studied, although there is evidence for a founder effect in Japan, with most cases probably sharing a common origin, and to a lesser extent in subjects of European ancestry (HT3). It is evident that p.R277W mutation has recurred in discrete populations. The p.Y55D mutation appears to have arisen from a common ancestor, because this transversion (c.163T>G) occurs rarely. [ABSTRACT FROM AUTHOR]

We analyzed sequence variation in chloroplast DNA (cpDNA) to investigate the origin of the cultivated strawberry, Fragaria xananassa. From analysis of two noncoding regions, trnL-trnF and trnR-rrn5, we found three haplotypes (V, C, and X) in F. xananassa. Haplotype V corresponded to the haplotype of F. virginiana and was possessed by cultivars bred over a wide geographic range, including North America, Europe, and Japan. Almost all the North American cultivars analyzed in this study possessed haplotype V, suggesting a founder effect. Haplotype C corresponded to the haplotype of F. chiloensis and was detected mainly in Japanese cultivars. Haplotype X was found in only two English cultivars. This haplotype was positioned as intermediate between haplotypes V and C in a median-joining network and was considered to be representative of the process of differentiation between F. virginiana and F. chiloensis. Results of controlled crosses indicate that cpDNA haplotypes of F. xananassa are maternally inherited. These results verify that F. xananassa is an interspecific hybrid between F. virginiana and F. chiloensis and indicate that traditional cultivars of F. xananassa have been derived from at least three maternal lineages. We demonstrate that the cpDNA variation detected in this study can be used to verify parentage and for extending hypotheses about June yellows, a leaf variegation disorder in strawberry. [ABSTRACT FROM AUTHOR]

Abstract: Based on the hypothesis that a glutamatergic dysfunction is involved in the pathophysiology of schizophrenia, we have been conducting systematic studies on the association between glutamate receptor genes and schizophrenia. Here we report association studies of schizophrenia with polymorphisms in group III metabotropic glutamate receptor genes, GRM4 and GRM7. We selected 8 and 43 common SNPs distributed in the entire gene regions of GRM4 (>111 kb) and GRM7 (>900 kb), respectively. We scanned significant associations with schizophrenia using 100 case-control pairs of Japanese. We identified two neighboring SNPs (rs12491620 and rs1450099) in GRM7 showing highly significant haplotype association with schizophrenia surviving the FDR correction. We then performed additional typing of the two SNPs using the expanded sample set (404 cases and 420 controls) and confirmed the significant association with the disease. We conclude that at least one susceptibility locus for schizophrenia is located within or nearby GRM7, whereas GRM4 is unlikely to be a major susceptibility gene for schizophrenia in the Japanese population. [Copyright &y& Elsevier]

Cytochrome P450 3A4 (CYP3A4) converts an anticancer prodrug, irinotecan, to inactive metabolites such as APC. However, the contribution of CYP3A4 genetic polymorphisms to irinotecan pharmacokinetics (PK) and pharmacodynamics (PD) is not fully elucidated. In paclitaxel-administered cancer patients, an association of CYP3A4* 16B harboring the low activity allele * 16 [554C > G (Thr185Ser)] has been shown with altered metabolite/paclitaxel area under the plasma concentration–time curve (AUC) ratios, suggesting a possible impact of * 16B on the PK of other drugs. In this study, the effects of CYP3A4 haplotypes including * 16B on irinotecan PK/PD were investigated in irinotecan-administered patients. The CYP3A4 genotypes for 177 Japanese cancer patients who received irinotecan were defined in terms of 4 major haplotypes, i.e., * 1A (wild type), * 1G (IVS10 + 12G > A), * 16B [554C > G (Thr185Ser) and IVS10 + 12G > A], and * 18B [878T > C (Leu293Pro) and IVS10 + 12G > A]. Associations of CYP3A4 genotypes with irinotecan PK and severe toxicities (grade 3 diarrhea and grade 3 or 4 neutropenia) were investigated. Area under the concentration–time curve ratios of APC/irinotecan, an in vivo parameter for CYP3A4 activity, were significantly higher in females than in males. The male patients with * 16B showed significantly decreased AUC ratios (APC/irinotecan) with 50% of the median value of the non-* 16B male patients (no * 16B-bearing female patients in this study), whereas no significant alteration in the AUC ratios was observed in the patients with * 18B. A slight trend toward increasing AUC ratios (20%) was detected in both male and female patients bearing * 1G. Multivariate analysis confirmed contributions of CYP3A4* 16B (coefficient ± SE = −0.18 ± 0.077, P = 0.021) and * 1G (0.047 ± 0.021, P = 0.029) to the AUC ratio. However, no significant association was observed between the CYP3A4 genotypes and total clearance of irinotecan or toxicities (severe diarrhea and neutropenia). This study suggested that CYP3A4* 16B was associated with decreased metabolism of irinotecan to APC . However, the clinical impact of CYP3A4 genotypes on total clearance and irinotecan toxicities was not significant. [ABSTRACT FROM AUTHOR]

We investigated the association between steroid responsiveness and single nucleotide polymorphisms of SLC22A4/A5 located within inflammatory bowel disease 5 locus. Our goal is personalized steroid therapy adjusted to match individual variations in drug responsiveness in each inflammatory bowel disease patient. Unrelated Japanese cohorts of 94 patients with Crohn’s, 94 patients with ulcerative colitis, and 257 healthy control subjects were consecutively enrolled in this study. Genotyping and haplotype analysis focusing on steroid responsiveness was performed by using 15 single nucleotide polymorphisms. The G allele of −368T > G in SLC22A5, in which strong linkage disequilibrium was observed and the limited diversity of three haplotypes was estimated, was significantly associated with steroid resistance in Japanese patients with Crohn’s disease ( P = 0.016). Haplotype analysis between −446C > T and −368T > G in the SLC22A5 promoter region showed that the CG allele appeared to be a risk haplotype for steroid resistance (CG: odds ratio, 4.13; 95 percent confidence interval, 1.41–12.1; P = 0.016). This extensive linkage disequilibrium may form a general risk haplotype for steroid resistance in Crohn’s disease in Japanese. Further analyses of the pharmacogenomics of steroid responsiveness are warranted to achieve the goal of individualized steroid therapy against inflammatory bowel disease. [ABSTRACT FROM AUTHOR]

Abstract: The proportion of treatment-resistant schizophrenia (TRS) has been estimated as 20–40% in the schizophrenic patients. Genetic factors are considered to be involved in the development of this condition. Serotonin subtypes are hypothesized to be the candidate genes. In the present study, single marker and haplotype analyses between several mutations of serotonin receptor subtypes (HTR2A, HTR3A and HTR4) and TRS (TRS=101, NON-TRS=239) were performed to determine a possible relationship with the development of TRS. Additionally, we also compared the daily neuroleptic dosage among each genotype. No significant association was observed between TRS and each allele, genotype, and haplotype. However, the daily neuroleptic dosage that patients had been receiving during their maintenance therapy was significantly higher in patients with the T/T genotype of HTR3A polymorphism (rs1062613, p =0.041). The present results support further research to examine the relationship between HTR3A polymorphism and the development of TRS in the Japanese population. [Copyright &y& Elsevier]

Hepatic lipase (HL) plays a major role in the regulation of plasma lipids. Several groups seeking to find association between the gene encoding HL ( LIPC) and plasma concentrations of high-density lipoprotein cholesterol (HDLc) using various methods and populations have reported conflicting results. We have approached the problem of demonstrating a relationship between the LIPC locus and HDLc by means of haplotype association using four single nucleotide polymorphisms (SNPs) (rs12594375G/A, rs8023503C/T, rs4775047C/T, and rs11634134T/A) located in intron 1 of the LIPC gene in two independent Japanese populations consisting of 2,970 and 1,638 individuals, respectively. Significant association between hyperalphalipoproteinemia and a specific haplotype in this intron was detected in both populations. When HDLc levels among the three haplotypic categories were analyzed [haplotype rs8023503C/rs12594375G (haplotype-1; H1) homozygotes (H1H1), haplotype rs8023503T/rs12594375A (haplotype-2; H2) homozygotes (H2H2), and heterozygotes (H1H2)], HDLc levels were lowest among H1H1 [mean ± standard error (SE) = 58.4 ± 0.4 mg/dl], highest among H2H2 (62.5 ± 0.8 mg/dl), and intermediate among H1H2 (59.2 ± 0.4 mg/dl) ( P = 0.00011), indicating that H2 haplotype elevates plasma HDLc levels. This association was validated in the second population ( n = 1,638) ( P = 0.00070). The results provide convincing evidence that the LIPC locus influences HDL metabolism. [ABSTRACT FROM AUTHOR]

The 16q22.1-linked autosomal dominant cerebellar ataxia (16q-ADCA; Online Mendelian Inheritance in Man [OMIN] #117210) is one of the most common ADCAs in Japan. Previously, we had reported that the patients share a common haplotype by founder effect and that a C-to-T substitution (−16C>T) in the puratrophin-1 gene was strongly associated with the disease. However, recently, an exceptional patient without the substitution was reported, indicating that a true pathogenic mutation might be present elsewhere. In this study, we clarified the disease locus more definitely by the haplotype analysis of families showing pure cerebellar ataxia. In addition to microsatellite markers, the single nucleotide polymorphisms (SNPs) that we identified on the disease chromosome were examined to confirm the borders of the disease locus. The analysis of 64 families with the −16C>T substitution in the puratrophin-1 gene revealed one family showing an ancestral recombination event between SNP04 and SNP05 on the disease chromosome. The analysis of 22 families without identifiable genetic mutations revealed another family carrying the common haplotype centromeric to the puratrophin-1 gene, but lacking the −16C>T substitution in this gene. We concluded that the disease locus of 16q-ADCA was definitely confined to a 900-kb genomic region between the SNP04 and the −16C>T substitution in the puratrophin-1 gene in 16q22.1. [ABSTRACT FROM AUTHOR]

Abstract: Allele frequencies and haplotypes for 16 Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y GATA H4, and DYS385a/b, were determined in 161 unrelated Japanese males using AmpFlSTR® Yfiler™ PCR Amplification Kit. This population was demonstrated 153 haploytpes, of which 146 were unique, six were found in two individuals, and one was found in three individuals. The haplotypes diversity calculated from the 16 Y-STR loci was 0.9994 and the discrimination capacity was 0.9503. [Copyright &y& Elsevier]

Abstract: The regulator of the G-protein signaling 4 (RGS4) has been implicated in the susceptibility to schizophrenia. RGS4 interacts with ErbB3 that acts as receptors for neuregulin 1 and these proteins may play a role in the pathogenesis of schizophrenia via glutamatergic dysfunction. Recently, two meta-analysis studies provided different interpretations for the genetic association between RGS4 and schizophrenia. We attempted to confirm this association in a case-control study of 1918 Japanese patients with schizophrenia and 1909 Japanese control subjects. Four widely studied single nucleotide polymorphisms (SNPs) were genotyped, and none showed association with schizophrenia. SNP 1 (rs10917670), p =0.92; SNP 4 (rs951436), p =0.91; SNP 7 (rs951439), p =0.27; and SNP 18 (rs2661319), p =0.43. A haplotype block constructed by these SNPs spans the 5′ flanking region to the 5′ mid-region of the RGS4 gene. Previous meta-analysis showed that both two major haplotypes of this block were risk haplotypes. The two common haplotypes were observed in the Japanese population. However, neither haplotype was significantly associated with schizophrenia. We conclude that the common haplotypes and SNPs of the RGS4 gene identified thus far are unlikely to contribute to the genetic susceptibility to schizophrenia in the Japanese population. [Copyright &y& Elsevier]

Background: Methamphetamine (MAP) is one of the most frequently used illegal substances in Japan, and family and twin studies have suggested that genetic factors contribute to psychostimulant dependence, including MAP dependence. Organic cation transporter 3 (OCT3) has been reported to be involved in the disposition of MAP as well as MAP-induced behavioral changes in animals. Moreover, SLC22A3 (which encodes OCT3) is a candidate gene for MAP dependence because it is located within a chromosomal region associated with substance dependence. Methods: Using 96 healthy control subjects, linkage disequilibrium (LD) within the SLC22A3 was investigated, and 5 single-nucleotide polymorphisms (SNPs) were selected as haplotype tag SNPs to search for an association with MAP dependence. Single-marker analyses and haplotype analyses of these SNPs were performed in 213 subjects with MAP dependence and 443 healthy controls. Results: SLC22A3 polymorphisms were not significantly associated with MAP dependence in any of the single-marker and haplotype analyses. When subjects with MAP dependence were divided into polysubstance and single-MAP users, genotype and allele frequency of SNP2 ( p=0.024, p=0.011, respectively), allele frequency of SNP3 ( p=0.037), and haplotypic frequencies for these 2 SNPs ( p=0.0438) differed significantly between groups. Conclusions: These results suggest that polymorphisms of SLC22A3 are related to the development of polysubstance use in Japanese patients with MAP dependence. [ABSTRACT FROM AUTHOR]

We have investigated cpDNA haplotype distribution in 24 populations of Fagus crenata in the southwest of Kanto District, Japan, and clarified the extent of intermixing of haplotypes in the contact zone by additional fine-scale analysis of two areas. Two cpDNA haplotypes belonging to different lineages were detected, and their distribution had geographical structure. Intermixed populations with the two haplotypes were limited to a narrow area. The geographical boundary between the haplotypes extended from Hakone to the west of the Kanto Mountains through the northern foot of Mt Fuji. No relationship was observed between the boundary location and the current topography of the southwest of Kanto District. [ABSTRACT FROM AUTHOR]

Aquaporin 4 (AQP4) has an important role in water homeostasis of human brain and a dysfunction of AQP4 could induce pathological conditions in neuronal activity. Several genome scan studies for schizophrenia found a suggestive linkage on 18q, where human AQP4 (18q11.2–12.1) is located nearby. A case-control study was performed which comprised 261 schizophrenia subjects and 278 controls from the Japanese population with four SNP markers. We found strong linkage disequilibrium (LD) and an LD block in the AQP4 gene but found no association between AQP4 and schizophrenia, both single SNP and haplotype analyses. The present study shows that AQP4 is not directly associated with schizophrenia in these Japanese patients. [ABSTRACT FROM AUTHOR]

Abstract: We report here the characterization of a Japanese family with maternally transmitted nonsyndromic hearing loss. Fourteen of 21 matrilineal relatives in this family exhibited early or late-onset/progressive but noncongenital hearing impairment with a wide range of severity, ranging from severe to normal hearing. The age-of-onset varies from 3 to 30 years. Sequence analysis of the complete mitochondrial genome in one matrilineal relative of this family revealed the presence of T7511C mutation and other variants. However, the levels of heteroplasmy of T7511C mutation did not correlate with the severity and age-of-onset of hearing loss in this family. Furthermore, none of other mtDNA variants are evolutionarily conserved and implicated to have significantly functional consequence. The absence of the ND1 T3308C and tRNAAla T5655C mutations in this Japanese family but the presence of these mtDNA mutations in an African family with a high penetrance seems to account for different penetrance between two pedigrees. Incomplete penetrance in this family indicates the involvement of modulatory factors in the phenotypic expression of hearing impairment associated with the T7511C mutation. Here, two known variants G79A and G109A in the GJB2 gene were identified in the hearing-impaired and normal hearing matrilineal relatives of this Japanese family. However, the lack of correlation in the severity and age-of-onset in hearing impairment with homozygous or heterozygous G79A or G109A or combination of both variants in the GJB2 gene in those subjects with hearing impairment and normal hearing indicates that those variants of GJB2 gene may not be a modifier of the phenotypic effects of the T7511C mutation in those subjects. Thus, the phenotypic variability in this family is due to the involvement of other modifier factor(s). [Copyright &y& Elsevier]

Abstract: Recent studies of the association between the metabotropic glutamate receptor 3 gene (GRM3) and schizophrenia have produced conflicting results, although GRM3 is a promising candidate gene. Fujii et al. found a single nuclear polymorphism (SNP) for within this gene, rs1468412 to have a positive association to schizophrenia in Japanese patients. To investigate this further, we genotyped 7 SNPs around GRM3 including rs1468412, in 752 Chinese patients with schizophrenia and 752 controls using Taqman technology. We did not detect any association between rs1468412 and schizophrenia, however we found differences in the allele frequency distribution of SNP rs2299225 (p=0.0297, odds ration [OR]=1.44, 95% confidence interval 1.05–1.99) between cases and controls. Moreover, the overall frequency of haplotypes constructed from three SNPs including rs2299225 showed significant differences between cases and controls (p=0.0017). Our results partially support the previous studies in other ethnic groups and indicate that the GRM3 gene may play an important role in the etiology of schizophrenia in the Han Chinese. [Copyright &y& Elsevier]

To gather information on intraspecific phylogeography for use in conservation programs for the endangered species Primula sieboldii in Japan, we analyzed sequence variation in five noncoding regions of chloroplast DNA. Twenty-two distinct haplotypes were recognized in total. The distribution of most haplotypes was geographically confined, but one haplotype was widely distributed throughout northern Japan, and several haplotypes were found in geographically distant regions. Three major clades were revealed by phylogenetic analysis of the haplotypes. Clade I was distributed in Kyushu and central Honshu, clade II in western Honshu and Hokkaido, and clade III from central Honshu to Hokkaido. According to analysis of molecular variance, 59.9% of the total cpDNA variation existed among regions, 32.5% among populations within regions, and 7.6% within populations. Therefore, if genetic conservation of the species is valued, transplanting of P. sieboldii among regions should be avoided. Multiple lineages often existed even in geographically narrow areas (e.g., within a 20-km range), so transplantation between adjacent populations in restoration activities should be carefully designed so as not to change the gene pool of local populations significantly. Also, the geographical distribution of cpDNA haplotypes may allow us to confirm the origin of plants collected for commercial purposes. [Copyright &y& Elsevier]

Asthma is caused by bronchial inflammation. This inflammation involves mucus overproduction and hypersecretion. Recently, a mouse model of asthma showed that gob-5 is involved in the pathogenesis of asthma. The gob-5 gene is involved in mucus secretion and its expression is upregulated upon antigen attack in sensitized mice. The observation suggests that human homologue of gob-5, hCLCA1 (human calcium-dependent chloride channel-1), may be involved in human disease. We screened for single-nucleotide polymorphisms (SNPs) in hCLCA1 in the Japanese population. We identified eight SNPs, and performed association studies using 384 child patients with asthma, 480 adult patients with asthma, and 672 controls. In haplotype analysis, we found a different haplotype distribution pattern between controls and childhood asthma (P<0.0001) and between controls and adult asthma (P=0.0031). We identified a high-risk haplotype (CATCAAGT haplotype; P=0.0014) and a low-risk haplotype (TGCCAAGT haplotype; P=0.00010) in cases of childhood asthma. In diplotype analysis, patients who had the CATCAAGT haplotype showed a higher risk for childhood asthma than those who did not (P=0.0011). Individuals who had the TGCCAAGT haplotype showed a lower risk for childhood asthma than those who did not (P<0.0001). Our data suggested that variation of the hCLCA1 gene affects patients'susceptibility for asthma.Genes and Immunity (2004) 5, 540-547. doi:10.1038/sj.gene.6364124 Published online 19 August 2004 [ABSTRACT FROM AUTHOR]

Recently, linkage disequilibrium analyses have been used to detect disease-causing loci based on the common disease-common variant hypothesis. To see what methods can effectively identify the genes, we have to apply them to the practical data obtained from the human population. We extensively performed linkage disequilibrium and haplotype analyses on adenine phosphoribosyltransferase (APRT) genes in both control and deficient subjects. To examine the power to detect disease-causing loci, we analyzed SNPs, STRPs, and VNTR within and around theAPRTgene. When only SNPs were used,Pvalues did not necessarily show significant difference, even at loci close to the mutation site forAPRT*Jthat is exclusively observed among Japanese. However, the examination of the same samples with haplotypes based on the haplotype block data gave sufficient significance. In the case of STRP and VNTR, some single-marker loci showed significant difference. Our study suggested that the use of haplotype analysis based on the haplotype-block structure is more powerful than single-marker locus analysis for the detection of disease-related loci. [ABSTRACT FROM AUTHOR]

Epidemiological studies have shown that elevated plasma homocysteine (Hcy) levels play an important role in the pathogenesis of Alzheimer’s disease (AD). In spite of the evidence that a C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene elevates plasma Hcy levels, the impact of the C677T polymorphism on the development of AD is controversial. Here, we performed a genetic case-control study in a Japanese population to investigate whether three polymorphisms of the MTHFR gene, C677T (Ala222Val), A1298C (Glu429Ala), and A1793G (Arg594Gln), are associated with the development of late-onset AD (LOAD). In our study, the MTHFR gene had four major regional haplotypes: Haplotype A (677C-1298A-1793G), Haplotype B (677T-1298A-1793G), Haplotype C (677C-1298C-1793G), and Haplotype D (677C-1298C-1793A). The frequency of Haplotype C in LOAD was significantly lower than that in control group. Furthermore, the benefit conferred by the presence of at least one Haplotype C was stronger in LOAD patients who lacked the ApoE &epsiv;4 allele (OR=0.293; 95% CI=0.115–0.744; P=0.010). The results indicate that Haplotype C of the MTHFR gene is protective against the development of LOAD. [Copyright &y& Elsevier]

Sequence polymorphysms of the mitochondrial DNA (mtDNA) control region, hypervariable regions I and II, from 50 unrelated Japanese were determined by PCR amplification and cycle sequencing. [Copyright &y& Elsevier]

Background: Nephronophthisis (NPHP) 4 gene encoding nephrocystin-4, which contributes to end-stage renal disease in children and young adults, is involved in the development of the heart and kidneys. Cardiorenal syndrome (CRS), which consists of bidirectional dysfunction of the heart and kidneys, is a risk factor for cardiovascular events. Single-nucleotide polymorphisms (SNPs) within the NPHP4 gene are reportedly associated with kidney function, even in adults. However, the association of NPHP4 gene variability with CRS and cardiovascular events remains unknown., Methods and Results: This prospective cohort study included 2946 subjects who participated in a community-based health study with a 16-year follow-up period. We genotyped 11 SNPs within the NPHP4 gene whose minor allele frequency was greater than 0.1 in the Japanese population. The SNP rs12058375 was significantly associated with CRS and cardiovascular events. Multivariate logistic analysis demonstrated a significant association between the homozygous A-allele of rs12058375 with the presence of CRS. Haplotype analysis identified the haplotype with the A-allele of rs12058375 as an increased susceptibility factor for CRS. Kaplan-Meier analysis demonstrated that homozygous A-allele carriers of rs12058375 had the greatest risk of developing cardiovascular events among the NPHP4 variants. Multivariate Cox proportional hazard regression analysis revealed that the homozygous A-allele and heterozygous carriers of rs12058375 were associated with cardiovascular events after adjusting for confounding factors. The net reclassification index and integrated discrimination index were significantly improved by the addition of rs12058375 as a cardiovascular risk factor., Conclusion: Genetic variations in the NPHP4 gene were associated with CRS and cardiovascular events in the general population, suggesting that it may facilitate the early identification of high-risk subjects with CRS and cardiovascular events., (© 2021. Springer Japan KK, part of Springer Nature.)

The tufted puffin Fratercula cirrhata (Charadriiformes: Alcidae) is distributed throughout the boreal and low Arctic areas of the North Pacific, from California, USA to Hokkaido, Japan. Few studies have investigated the genetic diversity of this species. Therefore, we analyzed the genetic diversity of two captive populations using nucleotide sequences of two mitochondrial loci (COX1 and D-loop) and one nuclear locus (RHBG). We sequenced these loci for birds from Tokyo Sea Life Park (Kasai Rinkai Suizokuen), originally from Alaska, and birds from Aqua World Oarai, originally from far eastern Russia. We found five COX1 haplotypes and 17 D-loop haplotypes for the mitochondrial loci, and obtained 14 predicted haplotypes for the nuclear RHBG locus. The major haplotypes of all three loci occurred in individuals from both populations. Thus, there were no clear genetic differences between the populations with respect to these three loci. Although the breeding range of the tufted puffin covers the boreal and low Arctic from California to Hokkaido, our results suggest that the species has not genetically diverged within its breeding range.

Abstract: We analyzed 11 Y-STR loci (DYS446, DYS447, DYS449, DYS450, DYS459a/b, DYS463 and DYS464a/b/c/d) in a total of 324 Japanese males from western and southern Japan. Gene diversity ranged from 0.958 at DYS464 in western Japan to 0.259 at DYS450 in southern Japan. A total of 272 different haplotypes were observed, of which 240 were found in single individuals. The overall haplotype diversity and discrimination capacity was 0.9982 and 0.8395, respectively. [Copyright &y& Elsevier]

POPULATION: One hundred and twenty randomly collected Japanese males living in Osaka Prefecture. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19) was announced as an outbreak by the World Health Organization (WHO) in January 2020 and as a pandemic in March 2020. The majority of infected individuals have experienced no or only mild symptoms, ranging from fully asymptomatic cases to mild pneumonic disease. However, a minority of infected individuals develop severe respiratory symptoms. The objective of this study was to identify susceptible HLA alleles and clinical markers that can be used in risk prediction model for the early identification of severe COVID-19 among hospitalized COVID-19 patients. A total of 137 patients with mild COVID-19 (mCOVID-19) and 53 patients with severe COVID-19 (sCOVID-19) were recruited from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan for the period of February-August 2020. High-resolution sequencing-based typing for eight HLA genes was performed using next-generation sequencing. In the HLA association studies, HLA-A*11:01:01:01 [P c = 0.013, OR = 2.26 (1.27-3.91)] and HLA-C*12:02:02:01-HLA-B*52:01:01:02 [P c = 0.020, OR = 2.25 (1.24-3.92)] were found to be significantly associated with the severity of COVID-19. After multivariate analysis controlling for other confounding factors and comorbidities, HLA-A*11:01:01:01 [P = 3.34E-03, OR = 3.41 (1.50-7.73)], age at diagnosis [P = 1.29E-02, OR = 1.04 (1.01-1.07)] and sex at birth [P = 8.88E-03, OR = 2.92 (1.31-6.54)] remained significant. The area under the curve of the risk prediction model utilizing HLA-A*11:01:01:01, age at diagnosis, and sex at birth was 0.772, with sensitivity of 0.715 and specificity of 0.717. To the best of our knowledge, this is the first article that describes associations of HLA alleles with COVID-19 at the 4-field (highest) resolution level. Early identification of potential sCOVID-19 could help clinicians prioritize medical utility and significantly decrease mortality from COVID-19., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Khor, Omae, Nishida, Sugiyama, Kinoshita, Suzuki, Suzuki, Suzuki, Izumi, Hojo, Ohmagari, Mizokami and Tokunaga.)

Locked nucleic acid (LNA) has been widely used for various genetic analyses, and has many benefits, in terms of the specificity or sensitivity of amplification, because LNA-containing primers/probes form more stable duplexes with template DNA than probes lacking LNA. Here, we developed a new method for discriminating HV1 haplotypes from mitochondrial DNA (mtDNA) mixtures by applying PCR clamping using LNA. PCR clamping is based on the selective inhibition of amplification using LNA-containing probes, which can discriminate single-nucleotide differences. Before designing probes, we selected 171 sequences with single-nucleotide variations from the HV1 region, and evaluated the specificity of LNA-containing probes for them by predicting Tm values. The differences of Tm between mismatched and exactly matched probe-template duplexes depended markedly on the type of LNA nucleotides for discriminating single-nucleotide differences, and the cytosine LNA nucleotide at the site of variations in the probes was most effective to discriminate these differences. For mixture analysis, each probe targeted one or two variations (16209C, 16217C, 16257A/16261T, 16297C/16298C, 16304C, 16362C, or 16362T) that are particularly common in the Japanese population, and seven designed probes completely inhibited the amplification of exactly matched templates. We prepared mixed samples by mixing DNA from two individuals at a ratio of 1:9, 1:4, 1:1, 4:1, or 9:1, and then performed Sanger sequencing analysis after PCR clamping with each probe. Our method distinguished each haplotype at lower ratios from two-person mixtures, and enabled sensitive detection at 12 pg of total DNA including 600 copies of mtDNA. Moreover, we analyzed three-person mixtures with representative sequences, and detected the minor haplotype of one individual present at a rate of 10% by adding two selected probes. The ability to discriminate haplotypes in mixed samples by using LNA-mediated PCR clamping indicates the potential value of mtDNA analysis in criminal investigations., (Copyright © 2019 Elsevier B.V. All rights reserved.)

MCT1 (SLC16A1), MCT4 (SLC16A3), and MCT11 (SLC16A11) are members of the monocarboxylate transporter (MCT) family. MCT1 and MCT4 transport pH-related monocarboxylates, such as lactate and pyruvate. MCT11 may also be a proton-coupled monocarboxylate transporter. Although alterations of these substrates are involved in the pathology of cancer and diabetes, little is known about MCT polymorphisms. In this study, genetic variation was evaluated in SLC16A1, SLC16A3, and SLC16A11 in the Japanese population (healthy volunteers, n = 92). Polymorphisms in the coding regions of the SLC16A1, SLC16A3, and SLC16A11 genes were screened by DNA sequencing. A single polymorphism that caused a change in the amino acid sequence was found in SLC16A1 (rs1049434 (T1470A, D490E)) and in SLC16A3 (rs368788465 (C641T, S214F)). Five polymorphisms were detected in the SLC16A11 gene (rs117767867 (G337A, V113I), rs13342692 (A380G, D127G), rs13342232 (T561C, silent), rs75418188 (G1018A, G340S), and rs75493593 (C1327A, P443T)). This information for a healthy population provides a comparison for further studies of patients with various diseases such as cancer and diabetes., (Copyright © 2018. Published by Elsevier Ltd.)

Objective: Recent genome-wide analysis has indicated that the autism susceptibility candidate 2 (AUTS2) gene is involved in the regulation of alcohol consumption. We hypothesised that AUTS2 might be associated with the development of alcohol dependence. Therefore, in this exploratory study, we compared the genotype and allele frequencies of the polymorphisms rs6943555 and rs9886351 in the AUTS2 gene between patients with alcohol dependence and healthy control subjects living in a Japanese provincial prefecture. We also examined whether or not the haplotypes consisting of these polymorphisms are related to alcohol dependence., Methods: The subjects of this study consisted of 64 patients with alcohol dependence and 75 unrelated healthy people. The AUTS2 genotypes were determined by the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method., Results: No significant differences in the genotype and allele frequencies of the polymorphisms AUTS2 rs6943555 and rs9886351 were found between alcohol dependence and control subjects. On the other hand, the frequencies of the AUTS2 haplotypes were significantly different between them, and the rs6943555 and rs9886351 A-A haplotype was associated with alcohol dependence (p=0.0187)., Conclusion: This suggests that the rs6943555 and rs9886351 A-A haplotype might affect the vulnerability to alcohol dependence pathogenesis. Further studies are needed to confirm the reproducibility of the results of this study with increased numbers of subjects.

We describe the cribrimorph cheilostome bryozoan Cribrilina mutabilis n. sp., which we detected as an epibiont on eelgrass (Zostera marina) at Akkeshi, Hokkaido, northern Japan. This species shows three distinct zooid types during summer: the R (rib), I (intermediate), and S (shield) types. Evidence indicates that zooids commit to development as a given type, rather than transform from one type to another with age. Differences in the frontal spinocyst among the types appear to be mediated by a simple developmental mechanism, acceleration or retardation in the production of lateral costal fusions as the costae elongate during ontogeny. Colonies of all three types were identical, or nearly so, in partial nucleotide sequences of the mitochondrial COI gene (555-631 bp), suggesting that they represent a single species. Zooid types varied temporally in overall frequency in the population: colonies contained nearly exclusively R-type zooids in mid-June; predominantly I-type, or both R- and I-type, zooids in mid-July; and I-type, S-type, or both I- and S-type zooids (interspersed or in discrete bands) in mid- to late August. Reproduction occurred throughout the season, but peaked in July, with only R- and I-type zooids reproducing. Reproductive zooids bear a vestigial compound (tripartite) ooecium and brood internally; S-type zooids, first appearing in August, were non-reproductive, which suggests that they may serve as an overwintering stage. As this species is easily accessible, common, and simple in form, it is potentially useful as a model system for studying polyphenism at multiple levels (zooid, colony, and population) in the context of life-history adaptations.

Similar to wild mammals on the continents, mange caused by the mange mite, Sarcoptes scabiei (Acari: Sarcoptidae) is spreading in wild mammals in most of Japan. We collected crusted or alopetic skin from 120 raccoon dogs (Nyctereutes procyonoides viverrinus), three raccoons (Procyon lotor), six Japanese badgers (Meles anakuma), one Japanese marten (Martes melampus), one stray dog (Canis lupus familiaris), four wild boars (Sus scrofa leucomystax), and one Japanese serow (Capricornis crispus), mainly in an area where mangy wild animals have been increasingly noted in the past 4 yr. The second internal transcribed spacer (ITS2) region of the ribosomal RNA gene and the partial 16S and cytochrome c oxidase subunit I (cox-1) genes of mitochondrial DNA (mtDNA) were characterized in these skin samples. The ITS2 sequencing (404 base pairs [bp]) identified the causative mite for mangy skin lesions of 128 animals as S. scabiei, regardless of host origin. The cat mite (Notoedres cati) was the cause in one raccoon dog and one raccoon. Most mites had almost identical ITS2 nucleotide sequences to those recorded in a variety of mammals worldwide. Partial 16S and cox-1 fragments of mtDNA amplified and sequenced successfully (331 bp and 410 bp, respectively) showed an identical nucleotide sequence except for one site (C vs. T) for the former and four sites (G, C, C, C vs. A, T, T, T, respectively) for the latter fragment. These substitutions were always synchronized, with the two mitochondrial DNA haplotypes (i.e., C/GCCC and T/ATTT) appearing to separately colonize in geographic units. The T/ATTT haplotype fell into a clade where animal-derived mites worldwide dominated, whereas the C/GCCC haplotype formed a geographic branch unique to Japanese isolates. These results suggest that heterologous populations of monospecific S. scabiei are expanding their populations and distributions regardless of host species in an apparently local mange epizootic of wild mammals in Japan.

Objective: Previous studies have indicated that type-1 and type-2 interleukin-1 (IL-1) receptors (IL-1R1 and IL-1R2) play important roles in periodontitis progression. We investigated the association between periodontitis and polymorphisms in the IL-1R1 and IL-1R2 genes (IL1R1 and IL1R2)., Design: We searched for genetic variants in IL1R1 and IL1R2 in 24 Japanese patients with aggressive periodontitis (AgP) and 24 periodontally healthy controls. Thirty-eight single nucleotide polymorphisms (SNPs) were identified within genomic regions containing all exons and relevant exon-intron boundaries in IL1R1 and IL1R2. Possible associations of each gene locus with AgP were investigated in 119 AgP patients and 102 periodontally healthy controls using allelotypes, genotypes, and haplotypes., Results: Significant differences were noted in the frequencies of 3 SNPs in IL1R2 (rs3819370, rs3218974 and rs3218977) for AgPs and controls (p=0.012, p=0.008, and p=0.038, respectively), after adjustment for gender and smoking status in the additive model (p=0.016, p=0.007, and p=0.027, respectively) and 2 haplotypes (p=0.010 and p=0.011, respectively) constructed from 2 SNPs (rs3819370 and rs3218974) that showed the lowest p-values after adjustment of covariates in additive models., Conclusion: A genetic susceptibility locus for AgP may lie within or close to the IL1R2 locus. Further studies in other populations are necessary to confirm these results., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

This study aimed to identify single nucleotide polymorphism (SNP) alleles at multiple loci associated with racial differences in skin color using SNP genotyping. A total of 122 Caucasians in Toledo, Ohio and 100 Mongoloids in Japan were genotyped for 20 SNPs in 7 candidate genes, encoding the Agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), tyrosinase (TYR), melanocortin 1 receptor (MC1R), oculocutaneous albinism II (OCA2), microphthalmia-associated transcription factor (MITF), and myosin VA (MYO5A). Data were used to analyze associations between the 20 SNP alleles using linkage disequilibrium (LD). Combinations of SNP alleles were jointly tested under LD for associations with racial groups by performing a chi(2) test for independence. Results showed that SNP alleles at multiple loci can be considered the haplotype that contributes to significant differences between the two population groups and suggest a high probability of LD. Confirmation of these findings requires further study with other ethnic groups to analyze the associations between SNP alleles at multiple loci and skin color variation among races.