Takehiko Shimizu

Nuclear factor I-B (Nfib) deficient mice have severe lung hypoplasia

Binding sites for transcription factor nuclear factor one (NFI) proteins, encoded by four genes in the mouse, have been characterized from many tissue-specific genes. NFI genes are expressed in unique but overlapping patterns in embryonic and in adult tissues. Nfib is highly expressed in the embryonic lung. Here we show that Nfib null mutants die early postnatally and display severe lung hypoplasia. Heterozygotes do survive, but exhibit delayed pulmonary differentiation. Expression of transforming growth factor beta 1 (TGF-beta1) and sonic hedgehog (Shh) is not down-regulated in mutant lung epithelium at late stages of morphogenesis, which may result in incomplete lung maturation. Our study demonstrates that Nfib is essential for normal lung development, and suggests that it could be involved in the pathogenesis of respiratory distress syndromes in humans.

Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)

The genetic differences between mungbean and its presumed wild ancestor were analyzed for domestication related traits by QTL mapping. A genetic linkage map of mungbean was constructed using 430 SSR and EST-SSR markers from mungbean and its related species, and all these markers were mapped onto 11 linkage groups spanning a total of 727.6 cM. The present mungbean map is the first map where the number of linkage groups coincided with the haploid chromosome number of mungbean. In total 105 QTLs and genes for 38 domestication related traits were identified. Compared with the situation in other Vigna crops, many linkage groups have played an important role in the domestication of mungbean. In particular the QTLs with high contribution were distributed on seven out of 11 linkage groups. In addition, a large number of QTLs with small contribution were found. The accumulation of many mutations with large and/or small contribution has contributed to the differentiation between wild and cultivated mungbean. The useful QTLs for seed size, pod dehiscence and pod maturity that have not been found in other Asian Vigna species were identified in mungbean, and these QTLs may play the important role as new gene resources for other Asian Vigna species. The results provide the foundation that will be useful for improvement of mungbean and related legumes.

Enamel Formation Genes Influence Enamel Microhardness Before and After Cariogenic Challenge

There is evidence for a genetic component in caries susceptibility, and studies in humans have suggested that variation in enamel formation genes may contribute to caries. For the present study, we used DNA samples collected from 1,831 individuals from various population data sets. Single nucleotide polymorphism markers were genotyped in selected genes (ameloblastin, amelogenin, enamelin, tuftelin, and tuftelin interacting protein 11) that influence enamel formation. Allele and genotype frequencies were compared between groups with distinct caries experience. Associations with caries experience can be detected but they are not necessarily replicated in all population groups and the most expressive results was for a marker in AMELX (p = 0.0007). To help interpret these results, we evaluated if enamel microhardness changes under simulated cariogenic challenges are associated with genetic variations in these same genes. After creating an artificial caries lesion, associations could be seen between genetic variation in TUFT1 (p = 0.006) and TUIP11 (p = 0.0006) with enamel microhardness. Our results suggest that the influence of genetic variation of enamel formation genes may influence the dynamic interactions between the enamel surface and the oral cavity.

Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement.

Craniofacial and dental characteristics of Kabuki syndrome

We describe oral manifestations in six patients (three females and three males aged 6 to 24 years) with Kabuki syndrome (KS), based on their physical, orthopantomographic, and cephalometric findings. All six patients had a high-arched palate, malocclusion, most commonly unilateral posterior cross-bite (5/6), severe maxillary recession and mid-facial hypoplasia. Other frequently observed oral manifestations included small dental arch and hypodontia. Three patients lacked permanent teeth, mostly the central/lateral incisors. Both tooth size (in primary and permanent teeth) and dental arch (in length and width) tended to be small. We would like to stress that oral care and management is a must for the well-being of KS patients.

Identification of a new fragrance allele in soybean and development of its functional marker

We have previously reported an association between a single nucleotide polymorphism (SNP) in exon 10 of GmBADH2 gene and fragrance in vegetable soybean [Glycine max (L.) Merr.] cultivar Kaori. The SNP causes amino acid substitution in a highly conserved motif of GmBADH2 protein, which is necessary for functional activity of the protein. In this study, we sequenced GmBADH2 in another fragrant soybean cultivar Chamame and discovered a new fragrance allele, which has a 2-bp (TT) deletion in exon 10. The deletion causes a reading frame shift and introduces a premature stop codon, which could abolish protein function and result in fragrance. The old and new fragrance-promoting alleles were designated Gmbadh2-1 and Gmbadh2-2, respectively. A simple and co-dominant functional marker was developed for genotyping Gmbadh2-2. The marker can discriminate between fragrant and non-fragrant soybeans and distinguish the two different fragrant soybeans, and thus is useful for routine genotyping for the fragrance trait in breeding programs. Quantitative trait locus (QTL) mapping in an F2 population using Chamame as the fragrance donor revealed that the location of the fragrance QTL nearly coincided with that of the functional marker, confirming the association between GmBADH2 and fragrance in Chamame.

Genetic Analysis of Crown Size in the First Molars Using SMXA Recombinant Inbred Mouse Strains

Tooth crown size may be determined by both genetic and environmental factors. The aim of this study was to identify quantitative trait loci (QTLs) affecting dental crown size and determine whether there is genetic independence between upper and lower teeth, using SMXA recombinant inbred strains of mice. Mesiodistal and buccolingual crown diameters (MD and BL, respectively) of the upper and lower first molars (M1 and M1, respectively) were measured. For each trait, mean values of substrains showed a continuous spectrum of distribution. Genome-wide scan detected QTLs exceeding suggestive threshold levels for MD of M1 (chromosomes 7, 13, and 17), BL of M1 (chromosomes 8 and 13), MD of M1 (chromosomes 7 and 13), and BL of M1 (chromosomes 3 and 15). These findings suggest that tooth crown size is controlled by multiple genes, and that there is some independence of genetic control between M1 and M1.

Fine-Mapping of 5q12.1-13.3 Unveils New Genetic Contributors to Caries

Caries is a multifactorial disease and little is still known about the host genetic factors influencing susceptibility. Our previous genome-wide linkage scan has identified the interval 5q12.1–5q13.3 as linked to low caries susceptibility in Filipino families. Here we fine-mapped this region in order to identify genetic contributors to caries susceptibility. Four hundred and seventy-seven subjects from 72 pedigrees with similar cultural and behavioral habits and limited access to dental care living in the Philippines were studied. DMFT scores and genotype data of 75 single-nucleotide polymorphisms were evaluated in the Filipino families with the Family-Based Association Test. For replication purposes, a total 1,467 independent subjects from five different populations were analyzed in a case-control format. In the Filipino cohort, statistically significant and borderline associations were found between low caries experience and four genes spanning 13 million base pairs (PART1, ZSWIM6, CCNB1, and BTF3). We were able to replicate these results in some of the populations studied. We detected PART1 and BTF3 expression in whole saliva, and the expression of BTF3 was associated with caries experience. Our results suggest BTF3 may have a functional role in protecting against caries.

Carcinoembryonic Antigen-Related Cell Adhesion Molecule 10 Expressed Specifically Early in Pregnancy in the Decidua is Dispensable for Normal Murine Development

ABSTRACT The carcinoembryonic antigen (CEA) family consists of a large group of evolutionarily and structurally divergent glycoproteins. The murine CEACAM9 and CEACAM11-related proteins as well as the pregnancy-specific glycoproteins (PSG) are secreted members of the CEA family which are differentially expressed in fetal trophoblast cell populations during placental development. PSG are essential for a successful pregnancy, possibly by protecting the semiallotypic fetus from the maternal immune system. In contrast, Ceacam10 mRNA, coding for a protein identical in structure with CEACAM11-related proteins, is expressed in the maternal decidua surrounding the implantation site of the conceptus only during early stages of gestation between day 6.5 and day 10.5 postcoitum. To determine its role during murine development, we inactivated Ceacam10. Ceacam10−/− mice developed, like the previously established Ceacam9−/− mice, indistinguishably from wild-type littermates with respect to sex ratio, weight gain, and fertility. However, a small but significant reduction of the litter size by 23% was observed in Ceacam10−/− matings. Furthermore, combining the Ceacam9 and Ceacam10 null alleles, both located on chromosome 7, by meiotic recombination and subsequent mating of heterozygotes carrying both knockout alleles on one chromosome yielded wild-type and double knockout offspring at the expected Mendelian ratio. Taken together, both Ceacam10 and Ceacam9, alone or in combination, are not essential for either murine placental and embryonic development or for adult life.

Role of TRAV locus in low caries experience

Caries is the most common chronic, multifactorial disease in the world today; and little is still known about the genetic factors influencing susceptibility. Our previous genome-wide linkage scan has identified five loci related to caries susceptibility: 5q13.3, 13q31.1, 14q11.2, 14q 24.3, and Xq27. In the present study, we fine mapped the 14q11.2 locus to identify genetic contributors to caries susceptibility. Four hundred seventy-seven subjects from 72 pedigrees with similar cultural and behavioral habits and limited access to dental care living in the Philippines were studied. An additional 387 DNA samples from unrelated individuals were used to determine allele frequencies. For replication purposes, a total of 1,446 independent subjects from four different populations were analyzed based on their caries experience (low versus high). Forty-eight markers in 14q11.2 were genotyped using TaqMan chemistry. Transmission disequilibrium test was used to detect over transmission of alleles in the Filipino families, and Chi-square, Fisher’s exact and logistic regression were used to test for association between low caries experience and variant alleles in the replication data sets. We finally assessed the mRNA expression of TRAV4 in the saliva of 143 study subjects. In the Filipino families, statistically significant associations were found between low caries experience and markers in TRAV4. We were able to replicate these results in the populations studied that were characteristically from underserved areas. Direct sequencing of 22 subjects carrying the associated alleles detects one missense mutation (Y30R) that is predicted to be probably damaging. Finally, we observed higher expression in children and teenagers with low caries experience, correlating with specific alleles in TRAV4. Our results suggest that TRAV4 may have a role in protecting against caries.