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R Ota

Publications and source records attributed to R Ota.

At least 19 recordsLinked to original sources
PubMed2001

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.

Animals↗
PubMed2000

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.

Biological Evolution↗
PubMed1997

Kinetics of selenium incorporation into tissues of female mallard ducks.

Selenium is essential for both mammalian and avian species, although its metabolism in birds has been less thoroughly studied. Little information has been available on the kinetics of selenium in birds, especially as it relates to the teratogenicity seen in waterfowl consuming excessive amounts. This study describes the pharmacokinetics of small amounts of 75Se as selenious acid injected into female mallard ducks. Labeled selenium was injected into a wing vein of restrained animals and tissues taken at five different time points up to 24 h post-injection. Selenium levels as percent of injected dose were determined in liver, kidney, heart, lung, adrenals, thyroid, spleen, pancreas, ovaries, intestine, muscle and plasma. Estimates of kinetic parameters (uptake and elimination rates, time of maximum concentration and maximum concentration) were obtained with a non-linear kinetics computer program (PCNONLIN, SCI Software, Lexington, KY). Results showed four basic patterns of distribution, uptake and elimination. Visceral tissues exhibited a triphasic pattern with a rapid rise, a decline followed by a distinctive increase in levels between the last two time points. Brain uptake was continuous over the 24 h. Plasma rose rapidly and then declined to a constant level. The ovaries as a tissue of interest relating to the teratogenic effects of selenium showed the greatest relative increase at 24 h, suggesting kinetic mechanisms consistent with a pathway that might lead to accumulation of toxic levels and teratogenic effects during embryo development.

Animals↗
PubMed1995

[Effects of anticoagulant therapy on retinal vein occlusion].

The combined effect of prostaglandin E1, stellate ganglion block, warfarin potassium and photocoagulation on 66 cases (eyes) of retinal vein occlusion was investigated immediately after, and 3 months and 6 months after final treatment. The time between onset and treatment was 2 months or less. Macular hemorrhage and edema were observed in all cases. The effectiveness rate 6 months after treatment was 35% in hemorrhagic central retinal vein occlusion and 63% in branch retinal vein occlusion. Visual acuity increased gradually with time from immediately after to 6 months after treatment. The effectiveness of treatment including warfarin potassium was lower than that of treatment without warfarin potassium in branch retinal vein occlusion, and many cases showed a marked decrease of visual acuity which might be related to the prolonged hemorrhage. These results suggest that combining prostaglandin E1, stellate ganglion block and photocoagulation in retinal vein occlusion produces better effects on visual acuity than ordinary treatment or spontaneous regression.

Aged↗
PubMed1994

MRI changes and deficits of higher brain functions in preterm diplegia.

Forty-one preterm children (29 with spastic diplegia and 12 without motor deficits) who had a normal verbal IQ were studied to clarify the clinical significance of neuroanatomical abnormalities disclosed by T1-weighted and T2-weighted magnetic resonance imaging (MRI). Both types of images clearly showed abnormalities in the frontal corona radiata of the children with spastic diplegia, while there were no abnormalities in the children without motor deficits. We compared the T1-weighted imaging findings with deficits of higher brain functions, evaluated by the performance subtests of the Wechsler Intelligence Scale. Thinning of the parietal and/or occipital white matter was noted in children with visuospatial cognitive deficits. Thus, MRI may be helpful in confirming early clinical suspicions of visuospatial cognitive deficits as well as motor deficits in preterm children, especially those with spastic diplegia.

Brain↗
PubMed1986

Genetic relatedness of disease-associated field isolates of bovid herpesvirus type 4.

Eight field isolates of bovid herpesvirus type 4 (BHV-4) were examined by restriction analysis and Southern blot hybridization with respect to their relatedness to one another and to the BHV-4 prototype strain DN-599. Isolates were obtained from cattle exhibiting a range of disease states including abortion, pneumonia, enteritis, metritis, and vaginal blisters. Initial growth studies of all 9 viruses were performed and revealed that the overall rate of virus growth was slow when compared with that of other herpesviruses. Infection with each virus also resulted in the formation of large fused cells, which in addition to the slow growth rate, indicated that the isolates were of the cytomegalovirus type. Further studies to characterize and compare the various BHV-4 isolates were undertaken by obtaining cell-free virus from infected cell populations. Viral isolates were purified and used as a source of BHV-4 DNA. Purified DNA, representing each of the 8 field isolates and the prototype strain DN-599, were each cleaved with 3 restriction enzymes and were separated by agarose-gel electrophoresis, and the resultant fragment patterns were compared. In general, genomic fragments of the field isolates corresponded to those generated by cleavage of DN-599 DNA, with the exception of the abortion-associated isolate 83-3572. Additional minor differences were also seen between DN-599 DNA and DNA from the other field isolates, but the overall restriction patterns were similar. To confirm that all isolates were members of the BHV-4 type, hybridization studies were performed using DN-599.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1986

Characterization of Tritrichomonas foetus antigens, using bovine antiserum.

Tritrichomonas foetus antigens were identified, using the serum of an Angus heifer that had been repeatedly immunized with suspensions of 1 X 10(8) organisms in Freund's complete adjuvant. Antibody activity against T foetus was determined by dot-blot analysis, using horse-radish peroxidase-conjugated anti-bovine immunoglobulin to detect bound antibody. The antiserum contained antibodies against surface and flagellar components of live or fixed T foetus, as determined by use of immunofluorescence. The antiserum reacted with approximately 38 proteins in a pool of 55 to 60 components resolvable by polyacrylamide-gel electrophoresis of T foetus extracts.

Animals↗