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Biomedical subjects

J Adachi

Publications and source records attributed to J Adachi.

At least 73 records · Page 4Linked to original sources
PubMed1996

Comparative allelotype of early and advanced stage non-small cell lung carcinomas.

To identify chromosomal loci of tumor suppressor genes involved in the genesis and progression of non-small cell lung carcinoma (NSCLC), comparative allelotype analysis was performed in 23 stage I primary lung tumors and in 22 metastatic lung tumors to the brain. In total, 84 loci on all 22 autosomal chromosomes were examined for loss of heterozygosity (LOH) by restriction fragment length polymorphism (RFLP) analysis with 40 polymorphic DNA probes and polymerase chain reaction (PCR)-LOH analysis of 44 polymorphic loci. LOH on chromosome arms 3p, 13q, and 17p was detected frequently (> 60%) in both stage I primary lung tumors and brain metastases, whereas the incidence of LOH on chromosome arms 2q, 5q, 9p, 12q, 18q, and 22q was more than 60% only in brain metastases. In particular, the incidence of LOH on chromosome arms 2q, 9p, 18q, and 22q in brain metastases was significantly higher than that in stage I primary lung tumors (P < 0.05). These results indicate that tumor suppressor genes on chromosome arms 3p, 13q, and 17p are involved in the genesis of NSCLC, whereas those on several chromosome arms, especially on 2q, 9p, 18q and 22q, play an important role in the progression of NSCLC.

Brain Neoplasms↗
PubMed1996

Instability of quartet analyses of molecular sequence data by the maximum likelihood method: the Cetacea/Artiodactyla relationships.

By using the maximum likelihood method, we study the reliability of phylogeny based on only four taxa, which have been studied by Philippe and Douzery with the maximum parsimony and neighbor-joining methods. Amino acid sequences of cytochrome b were provided for the analysis to examine the relationships among Ruminantia, Suiformes, and Cetacea with out-group mammals by using one representative species from each group. In accord with Philippe and Douzery's analysis, it was shown that we can find a quartet of species which provides a high bootstrap proportion for each of the three possible trees and that the quartet analyses with only four species can be misleading even with the maximum likelihood. However, if the confidence level of the inferred tree is estimated adequately by the maximum likelihood method and we take a conservative attitude, we can avoid the danger of concluding an erroneous tree by using quartet analysis, although the problem may remain unresolved in many cases. In order to obtain a reliable tree, it is important to carry out analyses based on as many different genes and as many relevant species as possible and to synthesize the results.

Animals↗
PubMed1996

Model of amino acid substitution in proteins encoded by mitochondrial DNA.

Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly, the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method.

Amino Acids↗
PubMed1996

Oxysterols found in opacified cornea of fish.

We describe a new concept implicating oxidized cholesterol derivatives and very long-chain fatty acids as possible factors in the development of corneal opacification after death. Corneal tissues, removed from both fresh and stale fish eyes, were examined for cholesterol derivatives and fatty acids after methanolysis of lipids. Cholesta-3,5-dien-7-one, cholest-4-en-3-one, hexacosenoic acid, and hexacosenoic acid were identified via gas chromatography/mass spectrometry in opacified corneas, but not in significant amounts in fresh ones. The present study confirmed the presence of lipid hydrolysis and a peroxidation process in the opacified cornea.

Animals↗
PubMed1996

Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans.

Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales.

Animals↗
PubMed1996

Phylogenetic position of kinetoplastid protozoa inferred from the protein phylogenies of elongation factors 1alpha and 2.

Partial regions of the mRNA encoding a major part of translation elongation factor 2 (EF-2) from a kinetoplastid protozoan, Trypanosoma cruzi, were amplified by means of polymerase chain reaction and their primary structures were analyzed. The deduced amino acid sequence was aligned with those of other eukaryotic and archaebacterial EF-2s, and the phylogenetic relationships among eukaryotes were inferred by the maximum likelihood (ML) method. ML analyses of EF-2 phylogeny using six different stochastic models of amino acid substitutions consistently suggested that the phylogenetic position of T. cruzi is likely to be closer to higher eukaryotes than that inferred from the phylogeny of small subunit ribosomal RNA (SrRNA). These results are consistent with those for the elongation factor 1alpha (EF-1alpha) phylogeny. When the EF-1alpha and EF-2 phylogenies were totally evaluated, it became much clearer that the divergence of T. cruzi occurred later than that of a mitochondrion-lacking protozoan, Entamoeba histolytica, although this is not conclusive.

Amino Acid Sequence↗
PubMed1996

Tempo and mode of synonymous substitutions in mitochondrial DNA of primates.

Nucleotide substitutions of the four-fold degenerate sites and the total third codon positions of mitochondrial DNA from human, common chimpanzee, bonobo, gorilla, and orangutan were examined in detail by three alternative Markov models; (1) Hasegawa, Kishino, and Yano's (1985) model, (2) Tamura and Nei's (1993) model, and (3) the general reversible Markov model. These sites are expected to be relatively free from constraint, and therefore their tempo and mode in evolution should reflect those of mutation. It turned out that, among the alternative models, the general reversible Markov model best approximates the nucleotide substitutions of the four-fold degenerate sites and the total third codon positions, while the maximum likelihood estimates of the numbers of nucleotide substitutions along each branch do not differ significantly among the three models. It was further shown that the transition rate of these sites during evolution, and therefore transitional mutation rate of mtDNA, are higher in humans than in chimpanzees and gorillas probably by about two times. However, transversional mutation rate and amino acid substitution rate do not differ significantly between humans and the African apes. These and additional observations suggest heterogeneity of the mutation rate as well as of the constraint operating on the mtDNA-encoded proteins among different lineages of Hominoidea.

Animals↗
PubMed1996

Phylogenetic position of cetaceans relative to artiodactyls: reanalysis of mitochondrial and nuclear sequences.

By a maximum likelihood analysis of mitochondrial DNA sequences, we examine Graur and Higgins' hypothesis of the Ruminantia/Cetacea clade with Suiformes as an outgroup. Graur and Higgins analyzed these sequences by the neighbor-joining and parsimony methods, as well as by the maximum likelihood method under the assumption that the substitution rate is the same for all sites. The Ruminantia/Suiformes clade assumed by the traditional taxonomy was rejected strongly by this analysis and the Ruminantia/Cetacea clade was supported. Adoption of a more realistic model distinguishing among rates at different codon positions in the maximum likelihood analysis of the same data, however, grossly reduces the significance level on the Graur-Higgins hypothesis. Thus, although the Ruminantia/Suiformes grouping is indeed least likely from Graur and Higgins' data set of mitochondrial DNA, this traditional tree cannot be rejected with statistical significance under the new analysis, and more data are needed to settle the issue. In the same way, we examine Irwin and Arnason's suggestion of the Hippopotamus/Cetacea clade by using cytochrome b and hemoglobins alpha and beta, and it turn out that their suggestion is also fragile. This analysis demonstrates the importance of selecting an appropriate model among the alternatives in the maximum likelihood analysis and of using many different genes from many relevant species in order to make reliable phylogenetic inferences.

Animals↗
PubMed1996

Effect of the cytochrome P-450IIE1 genotype on ethanol elimination rate in alcoholics and control subjects.

We studied an influence of genetic polymorphisms in the cytochrome P-450IIE1 (CYP2E1) gene on ethanol elimination rate in alcoholic patients and healthy subjects. The CYP2E1 genotype was determined by polymerase chain reaction-restriction fragment length polymorphism method for 124 alcoholics and 54 healthy subjects. There was no significant difference in the gene frequency of CYP2E1 between alcoholics and healthy control subjects. Blood ethanol concentrations in the 65 alcoholics on admission ranged from 0.32 to 4.22 mg/ml. In the patients with the c1/c2 genotype, the elimination rate was significantly correlated with blood ethanol concentration. In each of the three genotypes of CYP2E1, the patients were divided into three groups based on ethanol concentrations. The average of the ethanol elimination rate in the patients with c1/c2 having blood ethanol levels of > or = 2.5 mg/ml was significantly higher than the rates in the two other groups of c1/c2. When blood ethanol levels were > or = 2.5 mg/ml, the elimination rate in the patients with c1/c2 was significantly higher than that in those with c1/c1. Regardless of the CYP2E1 genotype, the elimination rate in the alcoholics was higher than that in the control subjects when blood ethanol levels were < 1.0 mg/ml. These results suggest the possibility that the c2 allele of CYP2E1 Influences the rate of ethanol elimination at high ethanol levels. The rate of ethanol elimination was independent of liver disorder judged by serum total bilirubin values.

Adult↗
PubMed1996

Identification of cholesta-3,5-dien-7-one by gas chromatography-mass spectrometry in the erythrocyte membrane of alcoholic patients.

Lipids and oxidized lipids were analyzed by gas chromatography-mass spectrometry in the erythrocyte membranes of alcoholic and control subjects. Cholesta-3,5-dien-7-one and cholesta-trienes were detected in alcoholic samples examined, but not in significant amounts in controls. Levels of polyunsaturated fatty acids (arachidonic acid, 20:4; docosahexaenoic acid, 22:6; and docosatetraenoic acid, 22:4) in alcoholic samples declined significantly, whereas cholesta-3,5-dien-7-one levels increased. A high level of total bilirubin was observed in most patients. A possible mechanism of the accumulation of cholesta-3,5-dien-7-one in the erythrocyte membrane of alcoholics is discussed.

Adult↗
PubMed1996

Rederivation of mice by means of in vitro fertilization and embryo transfer.

In vitro fertilization and embryo transfer were performed for rederivation of four strains of mice harbouring mouse hepatitis virus (MHV) and/or Pasteurella pneumotropica (P. pneumotropica). Superovulated oocytes were fertilized by preincubated cauda epididymis sperm in vitro. Fertilized eggs at 2-cell stage were transferred into the oviducts of specific pathogen free (SPF) recipients. Microbial examination of sperm and/or oocyte donors verified the presence of P. pneumotropica and/or of antibodies to MHV in all strains, but neither in the recipients nor in the offspring antibodies to MHV could they be detected. The results indicate that an in vitro fertilization-embryo transfer (IVF-ET) system is an effective and simple alternative to cesarean operation in infected mice.

Animals↗
PubMed1996

Induction of apoptosis but not G1 arrest by expression of the wild-type p53 gene in small cell lung carcinoma.

Multiple genetic alterations, including inactivation of the p53 and RB genes and loss of heterozygosity on chromosome 3p, occur commonly in small cell lung carcinoma (SCLC). To assess the biological significance of p53 inactivation in the development of SCLC, tetracycline (Tc)-inducible p53 expression plasmids were introduced into a SCLC cell line, N417, in which the p53 gene as well as the RB gene was inactivated. In the absence (induced) of Tc, cells transfected with the wild-type p53 gene formed colonies in 29-58% of those with a mutant p53 gene. However, wild-type p53 genes were expressed in 0 of 43 transfectants, whereas mutant p53 genes were expressed in 75% (36/48) of the transfectants, suggesting that the growth of SCLC cells was suppressed by the expression of the wild-type p53 gene. Thus, wild-type p53-inducible clones were further established by transfection in the presence (repressed) of Tc. The in vitro growth was significantly suppressed by the induction of wild-type p53 expression, and apoptosis but not G1 arrest was observed within 24 h of p53 induction. These results strongly suggest that the restoration of the p53 function is sufficient to suppress the growth of SCLC cells in which other genetic alterations remain uncorrected, and that growth suppression by p53 is due to induction of apoptosis but not due to induction of G1 arrest through the RB pathway.

Apoptosis↗
PubMed1996

Non-rubeotic angle-closure glaucoma associated with ciliary medulloepithelioma.

Non-rubeotic angle-closure glaucoma associated with ciliary medulloepithelioma was reported in a 3-year-old boy. On the first visit, a free-floating white mass was observed in the anterior chamber of his right eye. The mass disappeared spontaneously after 5 months of observation. One year later, angle-closure glaucoma with peripheral anterior synechia occurred in the same eye and intraocular pressure rose to 55 mmHg. After glaucoma surgery, the white mass appeared again in the anterior chamber of his right eye. By cycloscopy, numerous small grayish-white masses could be seen on the ciliary body and in the posterior chamber. Histopathological examination of one mass confirmed medulloepithelioma and the eye was enucleated. Disseminated tumor cells in the anterior chamber had caused the cornea and the peripheral iris to adhere to each other, resulting in the formation of peripheral anterior synechia.

Anterior Chamber↗
PubMed1995

Microsatellite instability in primary and metastatic colorectal cancers.

Microsatellite instability characterizes a sub-set of sporadic colorectal cancers (CRCs) as well as CRCs from patients with hereditary non-polyposis colorectal cancer (HNPCC). In order to clarify when the cells acquire a replication-error phenotype (RER) during colorectal-tumor progression, we examined the incidence of RER in 80 primary tumors and 36 liver metastases at 8 microsatellite loci; 1 mono-, 5 di-, 1 tetra- and 1 pentanucleotide. RER were detected in 20.1% (17/80) of primary tumors, including 5 tumors showing RER at 2 or more loci (RER2), while the incidence of RER in liver metastases (22.2%, 8/36) was almost the same as that in primary tumors, and there was only one RER2 case in metastases. There were 3 cases in which both primary tumors and liver metastases had the same type of RER at the same locus, and there were 2 cases that showed RER in primary tumors but not in liver metastases. In contrast, there was no case in which RER was detected in a metastasis but not in the corresponding primary tumor. The RER phenotype did not show correlation with any clinicopathological parameters of cancer-cell aggressiveness, such as clinical staging, histological grade and survival. These results indicate that a sub-set of CRCs acquire the RER phenotype in the relatively early stages of colorectal carcinogenesis, and that the RER phenotype is not associated with aggressiveness of CRCs.

Adult↗