Biomedical subjects

Yusuke Doi

Publications and source records attributed to Yusuke Doi.

9 recordsLinked to original sources

PubMed2006

The decapping enzyme Dcp1 participates in translation termination through its interaction with the release factor eRF3 in budding yeast.

One of the rate-limiting steps in messenger RNA decay pathway is the 5'-cap cleavage of mRNAs, decapping reaction, which is conducted by the protein complex of Dcp1 and Dcp2. We find here that Dcp1p can interact with the release factor eRF3p (Sup35p) in Saccharomyces cerevisiae. Knockout of DCP1 caused not only the accumulation of nonsense mRNAs possibly due to the impaired decapping activity but also the enhancement of the read-through of nonsense codon. To examine the relationship between the two DCP1-knockout phenotypes, we produced DCP1 point mutants that lack the ability to support the translation termination. Interestingly, decapping activity of Dcp1p was still intact, but its interaction with eRF3p was abolished in the DCP1 mutants, indicating that the two functions originated from different entities of Dcp1p. These results suggest that the decapping enzyme Dcp1p may have an additional role in the translation termination through its interaction with eRF3p.

Codon, Terminator↗

PubMed2006

Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction.

Endonuclease III (Endo III) is a base excision repair enzyme that recognizes oxidized pyrimidine bases including thymine glycol. This enzyme is a glycosylase/lyase and forms a Schiff base-type intermediate with the substrate after the damaged base is removed. To investigate the mechanism of its substrate recognition by X-ray crystallography, we have synthesized oligonucleotides containing 2'-fluorothymidine glycol, expecting that the electron-withdrawing fluorine atom at the 2' position would stabilize the covalent intermediate, as observed for T4 endonuclease V (Endo V) in our previous study. Oxidation of 5'- and 3'-protected 2'-fluorothymidine with OsO4 produced two isomers of thymine glycol. Their configurations were determined by NMR spectroscopy after protection of the hydroxyl functions. The ratio of (5R,6S) and (5S,6R) isomers was 3:1, whereas this ratio was 6:1 in the case of the unmodified sugar. Both of the thymidine glycol isomers were converted to the corresponding phosphoramidite building blocks and were incorporated into oligonucleotides. When the duplexes containing 2'-fluorinated 5R- or 5S-thymidine glycol were treated with Escherichia coli endo III, no stabilized covalent intermediate was observed regardless of the stereochemistry at C5. The 5S isomer was found to form an enzyme-DNA complex, but the incision was inhibited probably by the fluorine-induced stabilization of the glycosidic bond.

Deoxyribonuclease (Pyrimidine Dimer)↗

PubMed2005

Synthesis of oligonucleotides containing 2'-fluorinated thymidine glycol as mechanism-based inhibitors of endonuclease III.

Endonuclease III is a base excision repair enzyme that recognizes oxidized pyrimidine bases including thymine glycol. This enzyme is a glycosylase/AP-lyase and forms a Schiff base-type intermediate with the substrate after the damaged base is removed. To investigate its substrate recognition mechanism by X-ray crystallography, we synthesized oligonucleotides containing 2'-fluorothymidine glycol (1-(2-deoxy-2-fluoro-beta-D-ribofuranosyl)-5,6-dihydro-5,6-dihydroxythymine), expecting that the electron-withdrawing fluorine atom at the 2' position would stabilize the covalent intermediate. Complex formation of the substrate analogs containing each thymine glycol isomer with endonuclease III was analyzed.

Crystallography, X-Ray↗

PubMed2005

A new HLA-DRB1 genotyping method using single nucleotide polymorphism (SNP) analysis with multiplex primer extension reactions and its application to mixed samples.

We have improved on conventional methods for HLA-DRB1 genotyping and devised a new method that is simple, cost-effective, and adequately applicable to routine forensic practice. This method consists of group-specific polymerase chain reaction (PCR) of the exon 2 region of the HLA-DRB1 gene and simultaneous detection of single nucleotide polymorphisms (SNPs) at multiple sites using multiplex primer extension reactions. With this method, we successfully detected HLA-DRB1 genotypes from the following materials: the peripheral blood of 142 donors, 6 aged saliva stains of known DRB1 genotype stored for 5-10 years at room temperature, 10 aged bloodstains of unknown DRB1 genotype stored for 29 years at room temperature, and minimal bloodstains and saliva stains from 3 donors of known DRB1 genotypes. Furthermore, we were able to type DRB1 alleles of the minor component in mixed samples at a proportion of 1/1,000 or 1/10,000. In a criminal case, DRB1 alleles detected from mixed bloodstains on a sword found at the scene enabled us to explain the case. This method is expected to be useful for forensic medicine.

Alleles↗

PubMed2004

A new 39-plex analysis method for SNPs including 15 blood group loci.

A novel 39-plex typing system for single nucleotide polymorphisms (SNPs) has been developed. This multiplex approach has the advantage of being able to type 38 autosomal SNPs and one sex-discriminating base exchange site on the X and Y chromosomes rapidly and simultaneously. The SNP loci on the autosomes, which we examined, contain 15 loci distributed on blood type genes: three on RhCE, two each on Km and Gc, and one each on Duffy, AcP1, Tf, MN, GPT, EsD, PI, and Kidd genes. Thirty-seven genomic DNA fragments containing a total of 38 SNPs and one sex-discriminating site were amplified in one multiplex PCR reaction. Following the reaction, single nucleotide primer extension reaction was performed by dividing these SNP loci into five groups. The SNP type of each of the 39 loci was determined at one time by capillary electrophoresis using the newly designed multi-injection method. The combined PD (power of discrimination) of this typing system was (1-1.1) x 10(-14), and the MEC (mean exclusion chance) was 0.9990. We applied this system to forensic cases, including 16 paternity testing cases (13 non-exclusion and three exclusion cases) and one personal identification case. For the paternity testing cases, the highest Essen-Möller's W-value was 0.9999995. The pM (matching probability) of the personal identification case was 2.22 x 10(-17). These data showed that this system was an excellent tool for use in forensic cases of paternity testing and personal identification.

Blood Group Antigens↗

PubMed2004

A new method for ABO genotyping using a multiplex single-base primer extension reaction and its application to forensic casework samples.

We developed a new method for ABO genotyping using a multiplex single-base primer extension reaction. The method allows for the simultaneous detection of six SNP sites in the ABO gene (nt 261, 297, 681, 703, 802, and 803) and the determination of ABO genotypes from their combinations. It enabled ABO genotyping of all samples of peripheral blood DNA extracted from 103 Japanese individuals, and had a highly satisfactory detection sensitivity being capable of genotyping 0.1 ng of genomic DNA. Using this method, we were able to determine ABO genotypes of minute stain samples, heated bloodstains, aged bloodstains and mixed samples. Experiments with samples from 26 animal species and bacterial samples to test the species-specificity of the method showed that genotyping was possible in the chimpanzee and gorilla, but their genotypes were extremely rare in humans. In addition, we applied this method to casework samples, and successfully determined ABO genotypes of bones, teeth, muscles, organs, nails, and semen-contaminated vaginal fluid in which ABO grouping by conventional serological techniques was not possible. This new method enables the sensitive, simultaneous detection of six SNP sites in the ABO gene by two specific reactions, i.e. PCR and a primer extension reaction. Therefore, it holds promise as an effective method of ABO genotyping particularly for forensic samples.

ABO Blood-Group System↗

PubMed2003

Energy exchange in collisions of intrinsic localized modes.

Energy transfer process is examined numerically for the binary collision of intrinsic localized modes (ILMs) in the Fermi-Pasta-Ulam beta lattice. Unlike "solitons" in the integrable systems, ILMs exchange their energy in collision due to the discreteness effect. The mechanism of this energy exchange is examined in detail, and it is shown that the phase difference is the most dominant factor in the energy exchange process and, generally speaking, the ILM with advanced phase absorbs energy from the other. Heuristic model equations which describe the energy transfer of ILMs are proposed by considering the ILMs as interacting "particles." The results due to these equations agree qualitatively very well with those of the numerical simulations. In some cases, the relation between the phase difference of the ILMs and the transferred energy becomes singular, which may be regarded as one of the major mechanisms responsible for the generation of "chaotic breathers."

Journal Article↗

PubMed2002

Typing of Y chromosome single nucleotide polymorphisms in a Japanese population by a multiplexed single nucleotide primer extension reaction.

We have developed a new method for typing single nucleotide polymorphisms (SNPs) on the human Y chromosome based on a multiplexed single nucleotide primer extension. This method has the advantage that several SNPs are typed rapidly and simultaneously. We examined 15 different SNP loci on Y chromosome, M9, M105, M122, M125, M128, M130, SRY465, IMS-JST006241, IMS-JST006841, IMS-JST002611, IMS-JST003305, IMS-JST008425, IMS-JST021354, IMS-JST021355 and IMS-JST055457, in 159 Japanese males. From the typing results of these 15 loci, we found 13 haplotypes. Gene diversity for each locus ranged from 0.025 to 0.486 and the haplotype diversity was estimated to be 0.838. This method could be readily applied for personal identification and paternity testing.

Journal Article↗

PubMed2002

Evaluation of a method for typing the microsatellite D12S391 locus using a new primer pair and capillary electrophoresis.

We describe a modified method for typing a polymorphic microsatellite D12S391 locus by PCR using a newly designed primer pair. This primer pair produces shorter D12S391 amplified fragments (104-156 bp) than the primer pair originally described by Lareu et al. (209-261 bp). The detection system for the D12S391 locus using the new primer pair and capillary electrophoresis (CE) analysis was evaluated using various forensic samples. The typing results from 70 DNA samples using the new primer pair and the original primer pair were completely identical. One hundred twenty-five amplified fragments from D12S391 alleles were sized correctly within +/- 0.25 bp of the D12S391 allelic ladder. A rare allele, 19.3, previously found only in Caucasians, was found for the first time in a Japanese subject, and it was clearly distinguished from allele 20 by the CE analysis. This detection system was sensitive and could detect D12S391 types from 16 pg of genomic DNA, and from a minor component at a ratio of 1:10 in mixed samples. This system was more useful for the analysis of degraded DNA than was the method using the original primer pair, and could detect D12S391 types from bloodstains that had been stored for 26 years. In addition, the specificity of the method was demonstrated using nonhuman DNA.

Alleles↗