Genetic epidemiology of tooth agenesis in Japan: a population- and family-based study.

Tooth agenesis is one of the most common congenital anomalies in humans. However, the etiology of tooth agenesis remains largely unclear, as well as evidence base useful for genetic counseling. Therefore, we estimated the prevalence and sibling recurrence risk, and investigated agenetic patterns systematically. Tooth agenesis was classified into two subtypes: hypodontia (one to five missing teeth) and oligodontia (six or more missing teeth). The prevalence of these two subtypes were 6.8% [95% confidence interval (CI): 6.1-7.7%] and 0.1% (95% CI: 0.04-0.3%), respectively, and sibling recurrence risk of these were 24.5% (95% CI: 13.8-38.3%) and 43.8% (95% CI: 26.4-62.3%), respectively. This result suggests that the severe phenotype, oligodontia, might be mostly transmitted in a dominant fashion. Using a simple statistical modeling approach, our data were found to be consistent with a bilateral symmetry model, meaning that there was equal probability of missing teeth from the right and left sides.

Complex population history of two Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change rather than human-mediated effects.

Anopheles dirus and Anopheles baimaii are closely related species which feed on primates, particularly humans, and transmit malaria in the tropical forests of mainland Southeast Asia. Here, we report an in-depth phylogeographic picture based on 269 individuals from 21 populations from mainland Southeast Asia. Analysis of 1537 bp of mtDNA sequence revealed that the population history of A. baimaii is far more complex than previously thought. An old expansion (pre-300 kyr BP) was inferred in northern India/Bangladesh with a wave of south-eastwards expansion arriving at the Thai border (ca 135-173 kyr BP) followed by leptokurtic dispersal very recently (ca 16 kyr BP) into peninsular Thailand. The long and complex population history of these anthropophilic species suggests their expansions are not in response to the relatively recent (ca 40 kyr BP) human expansions in mainland Southeast Asia but, rather, fit well with our understanding of Pleistocene climatic change there.

Inheritance of song and stridulatory peg number divergence between Chorthippus brunneus and C. jacobsi, two naturally hybridizing grasshopper species (Orthoptera: Acrididae).

Knowledge of the genetic basis of divergence in mating signal characters that contribute to reproductive isolation is critical to understanding speciation. Here, we describe a semi-automated system for characterizing grasshopper acoustic signals. We used this system to study the genetic basis of divergence in three male calling song components [echeme (EL), syllable (SL) and phrase (PL) lengths] between Chorthippus brunneus and C. jacobsi, two species of grasshoppers that hybridize in northern Spain. We also studied the number of pegs in the stridulatory file. For all characters, additive effects accounted for most of the genetic differentiation between species. However, the three song components also showed small but significant epistatic effects. No sex linkage was detected. Wright-Castle-Lande estimates of the minimum numbers of genetic factors underlying song and peg number divergence were low: peg number (n(e)=5.87+/-5.84), SL (n(e)=2.37+/-4.79) and PL (n(e)=0.87+/-0.86). On the other hand, EL appeared to be controlled by many genes. These results suggest that divergence in SL and PL might be driven by sexual selection whereas EL might not be under selection. This is consistent with experimental results on female song preference in related species. However, the fact that few factors appear to underlie the differences in peg number is surprising. Peg number is not closely related to song characteristics. It often varies between closely related grasshopper species and it has been assumed to be a neutral character. The biometrical approaches used here tend to underestimate the number of factors influencing a trait but provide valuable background for subsequent quantitative trait loci analyses.

Detection of closely linked multiple quantitative trait loci using a genetic algorithm.

The existence of a quantitative trait locus (QTL) is usually tested using the likelihood of the quantitative trait on the basis of phenotypic character data plus the recombination fraction between QTL and flanking markers. When doing this, the likelihood is calculated for all possible locations on the linkage map. When multiple QTL are suspected close by, it is impractical to calculate the likelihood for all possible combinations of numbers and locations of QTL. Here, we propose a genetic algorithm (GA) for the heuristic solution of this problem. GA can globally search the optimum by improving the "genotype" with alterations called "recombination" and "mutation." The "genotype" of our GA is the number and location of QTL. The "fitness" is a function based on the likelihood plus Akaike's information criterion (AIC), which helps avoid false-positive QTL. A simulation study comparing the new method with existing QTL mapping packages shows the advantage of the new GA. The GA reliably distinguishes multiple QTL located in a single marker interval.

Performance of a divergence time estimation method under a probabilistic model of rate evolution.

Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.

A phylogenetic foundation for comparative mammalian genomics.

A major effort is being undertaken to sequence an array of mammalian genomes. Coincidentally, the evolutionary relationships of the 18 presently recognized orders of placental mammals are only just being resolved. In this work we construct and analyse the largest alignments of amino acid sequence data to date. Our findings allow us to set up a series of superordinal groups (clades) to act as prior hypotheses for further testing. Important findings include strong evidence for a clade of Euarchonta+Glires (=Supraprimates) comprised of primates, flying lemurs, tree shrews, lagomorphs and rodents. In addition, there is good evidence for a clade of all placental mammals except Xenarthra and Afrotheria (=Boreotheria) and for the previously recognised clades Laurasiatheria, Scrotifera, Fereuungulata, Ferae, Afrotheria, Euarchonta, Glires, and Eulipotyphla. Accordingly, a revised classification of the placental mammals is put forward. Using this and molecular divergence-time methods, the ages of the superordinal splits are estimated. While results are strongly consistent with the earliest superordinal divergences all being >65 mybp (Cretaceous period), they suffer from greater uncertainty than presently appreciated. The early primate split of tarsiers from the anthropoid lineage at ~55 mybp is seen to be an especially informative fossil calibration point. A statistical framework for testing clades using SINE data is presented and reveals significant support for the tarsier/anthropoid clade, as well as the clades Cetruminantia and Whippomorpha. Results also underline our thesis that while sequence analysis can help set up hypothesised clades, SINEs obtainable from sequencing 1-2 MB regions of placental genomes are essential to testing them. In contrast, derivations suggest that empirical Bayesian methods for sequence data may not be robust estimators of clades. Our findings, including the study of genes such as TP53, make a good case for the tree shrew as a closer relative of primates than rodents, while also showing a slower rate of evolution in key cell cycle genes. Tree shrews are consequently high value experimental animals and a strong candidate for a genome sequencing initiative.

Empirical Bayes procedure for estimating genetic distance between populations and effective population size.

We developed an empirical Bayes procedure to estimate genetic distances between populations using allele frequencies. This procedure makes it possible to describe the skewness of the genetic distance while taking full account of the uncertainty of the sample allele frequencies. Dirichlet priors of the allele frequencies are specified, and the posterior distributions of the various composite parameters are obtained by Monte Carlo simulation. To avoid overdependence on subjective priors, we adopt a hierarchical model and estimate hyperparameters by maximizing the joint marginal-likelihood function. Taking advantage of the empirical Bayesian procedure, we extend the method to estimate the effective population size using temporal changes in allele frequencies. The method is applied to data sets on red sea bream, herring, northern pike, and ayu broodstock. It is shown that overdispersion overestimates the genetic distance and underestimates the effective population size, if it is not taken into account during the analysis. The joint marginal-likelihood function also estimates the rate of gene flow into island populations.

[Characteristics of dropouts and participants in a twelve-year longitudinal research of Japanese elderly].

PURPOSES: The attrition of respondents in panel studies of the elderly can create bias in data analysis. The purposes of this study are two fold; 1) to examine characteristics of dropouts, from a particular panel lost except due to natural attrition (by death) by comparison with continuing participants in that wave, and 2) to assess representativeness of those actually continuing in a particular panel by comparison with those eligible for inclusion in that wave. Only those who died were excluded from the group of respondents at the baseline survey because they constituted natural attrition in this longitudinal survey. METHOD: At baseline (1987), 2,200 individuals age 60+ from 3,288 national representative sample were interviewed. Non-response status to three contacts (1990, 1993, 1996) with the panel was examined in relation to variables included in the baseline interview. A number of characteristics of demographic background, health, life-style, and social relations obtained in the baseline survey (1987) were compared between those re-interviewed in a particular panel and subjects lost through unnatural attrition until that wave. To study the influence of unnatural attrition on variable distributions and each related factors of two health indicators (self-rated health and depressive symptoms), baseline responses were compared between those re-interviewed in a particular panel and all who were eligible to respond in that wave. RESULTS: 1) Dropouts lost to each wave were significantly older and had a lower level of social participation than persons remaining in that wave. Significant differences in health and life-style variables appeared between dropouts lost and continuing participants until third or later waves. 2) Continuing participants in a particular panel were likely to be younger, to be more physically, mentally, or socially healthy than those eligible to respond in the wave. Each related factors of two health indicators were almost same between those re-interviewed in a particular panel and those eligible to respond in that wave. CONCLUSION: Dropouts in longitudinal research were found to appear nonrandomly. While distributions of age and health indicators in those re-interviewed were influenced by respondent attrition, related factors of health indicators may be free of bias that can be created by it.

Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters.

We show how to make appropriate likelihood ratio tests for evolutionary tree models when parameters such as edge (internodes or branches) lengths have nonnegativity constraints. In such cases, under the null model of an edge length being zero, the marginal distribution of this parameter is proven to be a "half-normal", that is, 50% zero values and 50% the positive half of a normal distribution. Other constrained parameters, such as the proportion of invariant sites, give similar results. To make likelihood ratio tests between nested models, e.g., H(0): homogeneous site rates, and H(1): site rates follow a gamma distribution with variance 1/k, then asymptotically as sequence length increases, the distribution under H(0) becomes a mixture of chi distributions, in this case 50% chi(0), and 50% chi(1) (where the subscript denotes degrees of freedom, i.e. , not the usually assumed 100% chi(1); which leads to a conservative test). Such mixtures are sometimes called distributions. Simulations show that even with sequences as short as 125 sites, some parameters, including the proportion of invariant sites, fit asymptotic distributions closely.

Correspondence analysis of genes and tissue types and finding genetic links from microarray data.

In this paper, we propose and use two novel procedures for the analysis of microarray gene expression data. The first is correspondence analysis which visualizes the relationship between genes and tissues as two 2 dimensional graphs, oriented so that distances between genes are preserved, distances between tissues are preserved, and so that genes which primarily distinguish certain types of tissue are spatially close to those tissues. For the inference of genetic links, partial correlations rather than correlations are the key issue. A partial correlation between i and j is the relationship between i and j after the effect of surrounding genes has been subtracted out of their pairwise correlation. This leads to the area of graphical modeling. A limitation of the graphical modeling approach is that the correlation matrix of expression profiles between genes is degenerate whenever the number of genes to be analyzed exceeds the number of distinct expression measurements. This can cause considerable problems, as calculation of partial correlations typically uses the inverse of the correlation matrix. To avoid this limitation, we propose two practical multiple regression procedures with variable selection to measure the net, screened, relationship between pairs of genes. Possible biases arising from the analysis of a subset of genes from the genome are examined in the worked examples. It seems that both these approaches are more natural ways of analyzing gene expression data than the currently popular approach of two way clustering.

Cluster inference methods and graphical models evaluated on NCI60 microarray gene expression data.

At present, there is a lack of a sound methodology to infer causal gene expression relationships on a genome wide basis. We address this first by examining the behaviour of some of the latest and fastest algorithms for tree and cluster analysis, particularly hierarchical methods popular in phylogenetics. Combined with these are two novel distances based on partial, rather than full, correlations. Theoretically, partial correlations should provide better evidence for regulatory genetic links than standard correlations. To compare the clusters obtained by many alternative methods we use tree consensus methods. To compare methods of analysis we used tree partition metrics followed by another level of clustering. These, and a tree fit metric, all suggest that the new distances give quite different trees than those usually obtained. In the second part we consider graphical modeling of the interactions of important genes of the cell cycle. Despite the models seeming to fit well on occasions, and despite the experimental error structure seeming close to multivariate normal, there are considerable problems to overcome. Latent variables, in this case important genes missing from the analysis, are inferred to have a strong effect on the partial correlations. Also, the data show clear evidence of sampling distributions conditional on the status of important cancer related genes, including TP53. Without full information on which genes are wild type the appropriate models cannot be fitted. These findings point to the need to include and distinguish not only all relevant genes but also all splice variants in the design phase of a microarray analysis. Failure to do so will induce problems similar to both latent variables and conditional distributions.

[Comparison of characteristics between respondents and nonrespondents in a national survey of Japanese elderly using six year follow-up study].

PURPOSES: The purpose of this study were twofold: 1) to examine differences between respondents and nonrespondents in sociodemographic or health characteristics, 2) to study nonresponse effects on relationships between variables, using a 6 year follow-up study for both respondents and nonrespondents at the initial survey. METHODS: The data were collected in 1987 through a national survey of Japanese adults aged 60 and over. A total of 2,200 interviews were completed from the list of 3,288 names. In 1993, 1,010 nonrespondents excluding persons who had died, moved, or whose addresses were unknown in the prior interview, were recontacted through a mail questionnaire. A total of 559 persons completed the mail questionnaire. Of the original 2,200 baseline interviewees, some by proxy interviews, 2,260 persons were reinterviewed, at the same time as the mail survey. Sociodemographic and health variables (age and sex), social indicators (educational attainment, marital status, and job status), health status (mortality, existence of diseases, and activities of daily living), subjective well-being (life satisfaction, self-rated health, and economic satisfaction) were compared between respondents and nonrespondents. Relationships between self-rated health and sociodemographic or health variables were examined by multiple regression analysis. RESULTS: 1. Compared to people who participated in the survey, norespondents were likely to be male, in the lower age categories, and with higher educational attainment at the follow-up survey. Also, life satisfaction and self-rated health were lower in nonrespondents than in respondents. Reasons for nonresponse varied but appeared to be somewhat related to characteristics of nonrespondents. 2. No significant relationships between self-rated health and sociodemographic or health variables appeared for the respondent group and also when including the nonrespondent group. CONCLUSION: While differences between respondents and nonrespondents on certain variables were significant, relationships between self-rated health and sociodemographic variables were not observed.

[Analysis of items missing in responses to a series of follow-up surveys in Japanese elderly].

PURPOSES: We examined whether the percentage of items missing and the factors related to item missing differ across follow-up surveys, Variables targeted to examine missing items included health indicators (activities of daily living, cognitive function, self-rated health, Center for Epidemiologic Studies--Depression, and PGC Morale Scale), health habits (cigarette smoking, alcohol consumption, physical exercise, and relative weight), and socioeconomic indicators (educational attainment, income, and social networks). METHODS: Longitudinal data were collected at intervals of three years since 1987 through a national survey of Japanese adults aged 60 and over, At the baseline survey, a total of 2,200 interviews were completed from the list of 3,288 names. At the following three follow-up surveys, 1,671, 1,369, and 1,068 persons were reinterviewed respectively. Possible factors related to appearance of a missing item consisted of five aspects; 1) demographic variables (age and sex), 2) social status (educational attainment, existence of a spouse, and job status), 3) health status (activities of daily living and cognitive function), 4) cooperative attitude toward a survey, and 5) whether an item had been missing at the previous survey (s). Those factors were analyzed for each variable respectively. If a group with scaled or collective items had one or more missing items, we classified that group as a missing item group. RESULTS: 1. The percentage of cases with items missing was 5 percent or more for four variables; CES-D, PGC Morale Scale, income, and health habits. Those percentages were almost constant over the four surveys. 2. Factors related to appearance of items missing differed by psychological variables such as, CES-D and PGC Morale Scale, income, or health habits. Those factors had constant impact on appearance of items missing over follow-up surveys. 3. Regarding CES-D, PGC Morale Scale, income, or health habits, persons with an item missing at a previous survey, or who did not have a cooperative attitude toward the survey had a significant impact on an increase in the percentage of missing items. CONCLUSION: Characteristics of persons with items missing differs among the variables, and those characteristics may contribute to the incidence of items missing in subsequent surveys.

Estimating the rate of evolution of the rate of molecular evolution.

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.

Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae: Teleostei): inconsistent implications from morphology, nuclear and mitochondrial genomes.

In order to infer phylogenetic relationships between tuna species of the genus Thunnus, partial sequences of the mitochondrial cytochrome b and ATPase genes were determined in all eight species. Supplemental restriction analysis on the nuclear rRNA gene was also carried out. Pacific northern bluefin tuna (Thunnus thynnus orientalis) was found to have mtDNA distinct from that of the Atlantic subspecies (T. t. thynnus) but very similar to that from the species albacore (T. alaluga). In contrast, no differentiation in nuclear genome was observed between the Atlantic and Pacific northern bluefin tunas. The Atlantic northern bluefin and southern bluefin tunas possessed mtDNA sequences very similar to species of yellowfin tuna group and not so similar to albacore and bigeye tunas which were morphologically assigned to the bluefin tuna group. The molecular data indicate that (1) mtDNA from albacore has been incorporated into the Pacific population of northern bluefin tuna and has extensively displaced the original mtDNA, and (2) albacore is the earliest offshoot, followed by bigeye tuna in this genus, which is inconsistent with the phylogenetic relationships between these tuna species inferred from morphology.

Characteristics of specific 125I-omega-conotoxin GVIA binding in rat whole brain.

Characteristics of specific 125I-omega-conotoxin (omega-CgTX) binding were systematically investigated in crude membranes from rat whole brain. Kd and Bmax Values for the binding were 49.7 pM and 181.5 fmol/mg of protein, respectively. The effects of various types of Ca channel antagonists on the binding were investigated. Dynorphin A (1-13), in particular, specifically inhibited 125I-omega-CgTX binding, but not that of [3H](+)PN200-110. Spider venom from Plectreurys tristes did not specifically inhibit specific binding of 125I-omega-CgTX, because the venom also inhibited the binding of [3H](+)PN200-110 to a similar degree. The amount of specific binding of 125I-omega-CgTX was less in the cerebellum than that in any other area of whole brain. The cross-linker disuccinimidyl suberate did not label with 125I-omega-CgTX and its binding sites in rat whole brain, although it did in chick whole brain, which was used as a positive control. These findings suggested that dynorphine A (1-13) was a selective blocker of omega-CgTX-sensitive Ca channels in crude membranes from rat whole brain and that omega-CgTX-sensitive Ca channels were mainly present a rat brain except cerebellum.

[Aortic regurgitation developed seven years after mediastinal radiation therapy: report of a case].

We report on radiation-induced valvular dysfunction in a 41-year-old woman who developed aortic regurgitation with clinical symptoms, requiring aortic valve replacement seven years after mediastinal radiation therapy for carcinoma of the breast. She was treated with cobalt radiation therapy of 4000 rads to her left mediastinum. The excised three-cuspid aortic valve was edematous and densely fibrotic without commissural fusion. Histological examination strongly suggested that the aortic valve with diffuse fibrosis, destruction of elastic fibers and bizarre nucleus in fibroblasts had been induced by mediastinal radiation therapy. To our knowledge, symptomatic radiation-induced valvular dysfunction in the aortic position has been reported infrequently, with only eleven reported cases. In this case, symptomatic aortic regurgitation was diagnosed seven years after mediastinal radiation therapy. It is emphasized that long-term follow-up is important for patients receiving mediastinal radiation therapy.

Characteristics of 45Ca uptake stimulated by high KCl of differentiated and undifferentiated NG108-15 and PC12h cells.

The characteristics of KCl-stimulated 45Ca uptake by neuroblastoma X glioma hybrid NG108-15 cells induced to differentiate with dibutyryl cAMP (Bt2cAMP) and of PC12h pheochromocytoma cells induced to differentiate with nerve growth factor (NGF) were studied. The extent and rate of KCl-stimulated 45Ca uptake by differentiated NG108-15 cells induced with Bt2cAMP were significantly higher than those of the undifferentiated cells. However, differentiation of PC12h cells induced with NGF did not enhance their extent or rate of KCl-stimulated 45Ca uptake. The effects of Ca agonist and antagonists indicated that the characteristics of KCl-stimulated 45Ca uptake by Bt2cAMP-treated NG108-15 cells and NGF-treated PC12h cells mainly reflected those of peripheral L-type voltage-sensitive calcium channels activated by high KCl. These results suggest that differentiated neural cells did not all show an enhanced capacity for KCl-stimulated 45Ca uptake, although the characteristic patterns of differentiation (extension of neurite-like processes, etc.) and that of effect by Ca agonist or antagonists on NG108-15 cells and PC12h cells were similar.

Specific bindings of [3H](+)PN200-110 and [125I]omega-conotoxin to crude membranes from differentiated NG108-15 cells.

The characteristics of the specific bindings of [3H](+)PN200-110 (PN: L-type Ca channel antagonist) and [125I]omega-conotoxin G VI A (omega-CgTX: neuronal L- or N-type Ca channel antagonist) to crude membranes from undifferentiated neuroblastoma X glioma hybrid NG108-15 (NG108-15) cells and differentiated cells induced with dibutyryl cAMP (Bt2cAMP) were examined, because we have already observed that the magnitude and rate of KCl-stimulated 45Ca uptake by NG108-15 cells increased progressively during differentiation of the cells induced with Bt2-cAMP (unpublished results). The specific binding of [3H](+)PN to these crude membranes was saturable at various concentrations of 2.5-5.0 nM [3H](+)PN. Scatchard analysis showed that the specific binding of [3H](+)PN at equilibrium was significantly increased after differentiation of the NG108-15 cells with Bt2cAMP, but that the apparent Kd value for the specific binding of [3H](+)PN was not influenced by treatment with Bt2cAMP. The specific binding of [3H](+)PN to crude membranes from Bt2cAMP-treated NG108-15 cells was inhibited by a calcium agonist and antagonists, the order of their inhibitory potencies being (+)PN > nitrendipine > (-)PN > or = Bay K 8644 > > diltiazem = verapamil. Thus, PNs showed significant stereoselective inhibition of the specific binding of [3H](+)PN. On the other hand, [125I]omega-CgTX at concentrations of 0.075-0.6 nM showed scarcely any specific binding to these crude membranes, although at 0.6 nM it showed specific binding to crude membranes from rat brain in the same experimental conditions.(ABSTRACT TRUNCATED AT 250 WORDS)