Biomedical subjects

Toshihide Kitakado

Publications and source records attributed to Toshihide Kitakado.

4 recordsLinked to original sources

PubMed2006

An integrated-likelihood method for estimating genetic differentiation between populations.

The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood (PL) methods that use sample counts of alleles may cause severe underestimations of FST, which means overestimations of theta=4Nm, when the number of sampling localities is small. To reduce such bias in the estimation of genetic differentiation, we propose an IL method in which the mean allele frequencies over populations are regarded as nuisance parameters and are eliminated by integration. To maximize the IL function, we have developed two algorithms, a Monte Carlo EM algorithm and a Laplace approximation. Our simulation studies show that the method proposed here outperforms the conventional ML and PL methods in terms of unbiasedness and precision. The IL method was applied to real data for Pacific herring and African elephants.

Algorithms↗

PubMed2006

Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan.

In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a composite population are expressed as a mixture of the allele frequencies in the natural and released populations. The estimation of mixing rates is possible, under successive sampling from the composite population, on the basis of temporal changes in allele frequencies. The allele frequencies in the natural population may be estimated from those of the composite population in the preceding year. However, it should be noted that these frequencies can vary between generations due to genetic drift. In this article, we develop a new method for simultaneous estimation of mixing rates and genetic drift in a stock enhancement program. Numerical simulation shows that our procedure estimates the mixing rate with little bias. Although the genetic drift is underestimated when the amount of information is small, reduction of the bias is possible by analyzing multiple unlinked loci. The method was applied to real data on mud crab stocking, and the result showed a yearly variation in the mixing rate.

Animals↗

PubMed2003

Abundance estimation of diving animals by the double-platform line transect method.

In conventional line transect theory, it is assumed that all animals on the line are detected. This article introduces an extended and generalized hazard probability model without the need for such an assumption. The proposed method needs a survey design with independent observers having the same visual region and assumes an explicit distinction of simultaneous and delayed duplicates. It can take account of random heterogeneity caused by surfacing behavior as well as systematic heterogeneity by covariate effects. Furthermore, it can be easily extended to cases in which data from incompletely independent observers are available. The abundance estimate is based on the Horvitz-Thompson estimator in unequal detectability sampling scheme. Simulation studies suggest that the proposed method has good performance. The method is applied to a real data set on Antarctic minke whales in the illustration.

Animals↗

PubMed2003

Isolation and characterization of halophilic lactic acid bacteria isolated from "terasi" shrimp paste: a traditional fermented seafood product in Indonesia.

Lactic acid bacteria from "terasi" shrimp paste, a highly popular fermented seafood in Indonesia were isolated and characterized. Viable cell counts were 10(4) to 10(6) cfu/g on MRS medium. All the isolates were catalase-negative, gram-positive cocci and were able to grow at 15% NaCl. Numerical phenotypic analysis showed that the isolates clustered into one group. However, they could be classified into two types: the Tetragenococcus halophilus group and the T. muriaticus group as revealed by a restriction fragment length polymorphism (RFLP) analysis and sequencing of the 16S rRNA gene. This study is the first to show that both species of Tetragenococcus are distributed in Indonesian fermented foods.

Colony Count, Microbial↗