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Biomedical subjects

K Sumiyama

Publications and source records attributed to K Sumiyama.

14 recordsLinked to original sources
PubMed2001

An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships.

The discovery of cis-element control motifs in noncoding DNA poses a difficult problem in genome analysis. Functional analysis by means of reporter constructs expressed in transgenic organisms is the most reliable method, but is by itself time-consuming and expensive. Searching noncoding DNA for known control motifs by sequence analysis is problematic, since protein binding motifs are short, in the range of 8-10 bp, and occur frequently by chance. Heretofore, the most reliable sequence analysis method has been the comparison of homologous sequence domains in related but moderately evolutionarily divergent species such as, for example, mouse and human. In such pairwise combinations, control regions are conserved because they serve a vital function and can be identified by their similar sequences. Single pairwise comparisons, however, allow the discovery of conserved sequence strings only at low resolution and without specific identity. We have investigated the possibility of using multiple sequence comparisons to correct these shortcomings. We applied this method to the Hoxc8 early enhancer region that has been previously analyzed in depth by functional methods and through its application successfully identified known protein binding cis-element motifs. Candidate protein binding sites could also be identified. This method, based on evolutionarily related sequence comparisons, should be quite useful as a prescreening step prior to functional analysis with corresponding savings in time and resources.

Animals↗
PubMed2001

Hemodynamic analysis of esophageal varices using color Doppler endoscopic ultrasonography to predict recurrence after endoscopic treatment.

BACKGROUND AND STUDY AIMS: The time to recurrence of esophageal varices may vary greatly between patients even after the same endoscopic therapy. To clarify the factors which contribute to recurrence after endoscopic treatment, the hemodynamics and morphology of the left gastric vein (LGV) were investigated using color Doppler endoscopic ultrasonography (EUS). PATIENTS AND METHODS: A total of 31 patients with high-risk esophageal varices underwent color Doppler-EUS before receiving endoscopic variceal ligation and endoscopic injection sclerotherapy combined therapy. Endoscopic examination was performed every 3 months after the treatment to evaluate recurrence of varices. RESULTS: A total of 18 patients responded to the therapy, while 13 patients did not respond, and had recurrence within 12 months. The hepatofugal flow velocity in the LGV trunk was significantly lower in the responders (9.9 vs. 13.9 cm/sec; P = 0.02). The branch pattern of the LGV was categorized into three groups: anterior branch dominant, posterior branch dominant, and no-dominant type. The incidence of the anterior branch dominant type was significantly less in responders (17 vs. 70 %; P = 0.01). There was no significant difference in the LGV trunk diameter and the size of the paraesophageal vein between the two groups. CONCLUSION: Risk factors for recurrence can be analyzed in detail using color Doppler-EUS. Further investigation using color Doppler-EUS may enable us to select the optimal way to treat esophageal varices to prevent recurrence.

Adult↗
PubMed2001

Low power diode laser treatment using indocyanine green for eradication of esophageal varices.

BACKGROUND AND STUDY AIMS: Endoscopic variceal ligation (EVL) is an alternative to sclerotherapy for the treatment of esophageal varices, but is associated with higher rates of recurrence and subsequent bleeding than sclerotherapy. To prevent recurrence of varices after EVL, we have developed a low-dose diode laser therapy combined with the injection of indocyanine green, which allows enhanced tissue absorption of the laser beam selectively around varices. In this study we investigated the efficacy and safety of this technique. PATIENTS AND METHODS: Eight patients with F2 or F3 esophageal varices were enrolled. At 1 week after EVL, indocyanine green solution (1 mg/ml) was injected submucosally around the remaining varices. A diode laser (power 10 watts) was applied to the surface from the esophagogastric junction to 5 cm above it. The spot size was kept to 5 mm in diameter. RESULTS: Laser irradiation was performed safely, without bleeding from the varices, or perforation. There were no major complications. Endoscopy 1 month later showed F0 forms in seven patients, F1 in one patient, and no red color sign in any patient. No recurrence of varices has been observed in any of the patients during the follow-up period of at least 12 months. CONCLUSION: This technique may provide a simple, safe and effective procedure, as an additional treatment to EVL, for the prevention of recurrence of esophageal varices.

Adult↗
PubMed2001

Collaborated surgical works (surgical planning) in virtual space with tactile sensation between Japan and Germany.

Surgeons in Japan and Germany applied tele-virtual surgery and a force feedback device during a hepatectomy simulation. Using this system, surgeons in each country were able to perform various surgical maneuvers upon the same patient. They palpated abdominal skin, made electrical scalpel incisions and widened the incision line by using surgical tools in virtual space. While surgeons performed a virtual operation, the force feedback device conveyed tactile sensations. In each location, the force feedback devices and two graphic workstations of equal capability were employed. As each workstation communicated only event signals through an ISDN (64 Kb) line, it was possible to obtain real time tele-virtual surgery without a large capacity communication infrastructure.

Computer Graphics↗
PubMed2000

Gene diversity of chimpanzee ABO blood group genes elucidated from exon 7 sequences.

Human and non-human primate ABO blood group genes show relatively large numbers of nucleotide differences. In this study, we determined exon 7 sequences for 10 individuals of common chimpanzee and for four individuals of bonobo to estimate nucleotide diversities among them. Sequence data showed the existence of chimpanzee specific 9-base deletion in the beginning of the exon 7 coding region. From a phylogenetic network of exon 7 sequences of ABO blood group genes for human, common chimpanzee, bonobo and gorilla, effects of parallel substitutions and/or some kinds of convergent events are inferred in the chimpanzee lineage. We also estimated nucleotide diversities for common chimpanzee and bonobo ABO blood group genes, and these values were 0.4% and 0.2%, respectively. These values are higher than that of most human genes.

ABO Blood-Group System↗
PubMed1998

Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene.

We have sequenced the complete coding region of the Rh blood group gene for mouse and rat and that of Rh-related 50 kD glycoprotein (Rh50) for mouse, rat, and crab-eating macaque. Phylogenetic analyses of Rh and Rh50 amino acid sequences indicate that the Rh50 gene has been evolving about two times more slowly than the Rh blood group gene in both primates and rodents. This conservative nature of the Rh50 gene suggests its relative importance to the Rh blood group gene. The time of gene duplication that produced the Rh and Rh50 genes was estimated to be about 240-310 million years ago. We also conducted window analyses of synonymous and nonsynonymous nucleotide substitutions for those two genes. Some peaks where nonsynonymous substitutions are higher than synonymous ones were located on outer membrane regions. This suggests the existence of positive Darwinian selection on Rh and Rh50 genes through host-parasite interactions.

Animals↗
PubMed1997

Nucleotide compositional constraints on genomes generate alanine-, glycine-, and proline-rich structures in transcription factors.

Correlation between amino acid composition and nucleotide composition is examined. Class III POU transcription factors having higher third GC contents showed higher contents of alanine, glycine, and proline residues encoded by GC-rich nucleotides, and vice versa. This correlation was observed even among various types of transcription factors from vertebrates and invertebrates regardless of functional and structural constraints inherent to each protein. Furthermore, reptile class III POU sequences revealed no evolutionary directionality increasing the GC contents from cold- to warm-blooded vertebrates.

Alanine↗
PubMed1996

Class III POU genes: generation of homopolymeric amino acid repeats under GC pressure in mammals.

The class III POU transcription factor genes play an important role in the nervous system. Comparison of their entire amino acid sequences disclosed a remarkable feature of particular mammalian class III POU genes. Alanine, glycine, and proline repeats were present in the mammalian Brain-1 gene, whereas most of these repeats were absent in the nonmammalian homologue. The mammalian Brain-2 gene had alanine, glycine, proline, and glutamine repeats, which were missing in the nonmammalian homologue. The mammalian Scip gene had alanine, glycine, proline, and histidine repeats, but the nonmammalian homologue completely lacked these repeats. In contrast, the mammalian Brain-4 gene had no amino acid repeats like its nonmammalian homologue. The mammalian genes containing the characteristic amino acid repeats had another feature, higher GC content. We found a positive correlation between the GC content and the amino acid repeat ratio. Those amino acids were encoded by triplet codons with relatively high GC content. These results suggest that the GC pressure has facilitated generation of the homopolymeric amino acid repeats.

Alanine↗
PubMed1993

Increased level/dose ratio of amphotericin-B in premature infants with renal failure.

We introduced continuous intravenous infusion of amphotericin-B (AMPH-B) to extremely low birthweight (ELBW) infants (< 1000 g) with or without renal failure as a single agent for treating definite or probable systemic candidiasis. The species of Candida isolated from blood or tracheal aspirate or urine were C. albicans in seven infants, C glabrata in two, C. tropicalis in one and C. parapsilosis in one. The minimal inhibitory concentrations (MIC) of AMPH-B required against these isolates were less than 0.2 micrograms/mL except for that against one strain of C. albicans (0.78 microgram/mL). Serum AMPH-B levels were 0.31-0.78 (0.51 +/- 0.14) micrograms/mL when doses of 0.2-0.55 (0.32 +/- 0.11) mg/kg per day were being administered. The serum level was higher than the MIC of each isolate in all but one infant who died of disseminated intravascular coagulation and Candida pneumonia. Another infant died of congenital heart disease. The other nine infants survived. The serum level showed no correlation with the daily dose. The ratio of the serum level to the daily dose (L/D ratio) showed a significant correlation to serum creatinine (r = 0.787) and the linear regression curve followed the equation: L/D ratio = 0.223 x serum creatinine + 1.11 (P < 0.01). Few adverse effects due to AMPH-B were noted. Our data may give a simple reference to serum AMPH-B levels during continuous intravenous infusion from the dose and the serum creatinine level.

Acute Kidney Injury↗
PubMed1991

Combination therapy with transfer factor and high dose stronger neo-minophagen C in chronic hepatitis B in children (HBe Ag positive).

This study mainly describes the efficacy of the combination therapy with Transfer Factor (TF) and high dose Stronger Neo-Minophagen C (SNMC) for HBV carrier children with HBe Ag positive chronic hepatitis. There were 12 patients, 10 males and 2 females aged from 7 months to 14 years 8 months. Liver biopsy was done in 11 patients, and the histopathological findings of the liver were chronic active hepatitis (8 cases) and chronic inactive hepatitis (3 cases). In 6 of 8 patients, HBe-Ag became negative (75%) within 18 weeks (mean 8 weeks) after the initiation of the combination therapy with TF and SNMC (HBe-seronegative), and 4 of these 8 patients (50%) became anti-HBe positive within 29 weeks (mean 15 weeks) (HBe-seroconversion). These results suggest that combination therapy with TF and high dose SNMC may be beneficial in the treatment of chronic hepatitis B in children.

Adolescent↗
PubMedDate not supplied

Gene diversity of chimpanzee ABO blood group genes elucidated from intron 6 sequences.

The human and nonhuman primate ABO blood group gene shows relatively large numbers of nucleotide differences around the exon 7 region. In this study we determined intron 6 sequences for 9 alleles of common chimpanzee and for 3 alleles of bonobo to estimate nucleotide diversities among them. Sequence length polymorphisms are observed in this region as a repeat appears one to five times. From a phylogenetic network of intron 6 sequences of ABO blood group genes for humans, common chimpanzee, and bonobo, parallel substitutions and/or some kinds of convergent events are predicted in the chimpanzee lineage. We also estimated nucleotide diversities for common chimpanzee and bonobo ABO blood group genes; these values were 0.219% and 0.208%, respectively.

ABO Blood-Group System↗