Takahiko Ishiguro

Intercalation activating fluorescence DNA probe and its application to homogeneous quantification of a target sequence by isothermal sequence amplification in a closed vessel.

We developed a completely homogeneous and isothermal method of detecting RNA sequences and demonstrated ultrarapid and direct quantification of pathogenic gene expression with high sensitivity. The assay is based on performing isothermal RNA sequence amplification in the presence of our novel DNA probe, an intercalation activating fluorescence DNA probe, and measuring the fluorescence intensity of the reaction mixture. When detecting mecA gene expression of methicillin-resistant Staphylococcus aureus, we quantified starting copies ranging from 10 to 10(7) copies within 10min. The primer sequences were designed to bind to secondary structure-free sites of the target RNA, which enabled a totally isothermal protocol to quantify mRNA specifically in a sample of existing genomic DNA. When we applied this to quantifying the expression of marker genes of Vibrio parahaemolyticus and Mycobacterium bovis BCG strain, the results correlated well with the viability of each bacterium. We also demonstrated monitoring Pab gene expression of M. bovis BCG during cultivation with antibiotics. The present method can potentially realize rapid antimicrobial susceptibility testing of slowly growing organisms, such as tuberculosis.

Rapid and Specific Detection of tdh, trh1, and trh2 mRNA of Vibrio parahaemolyticus by Transcription-Reverse Transcription Concerted Reaction with an Automated System

ABSTRACT Vibrio parahaemolyticus strains carrying the thermostable direct hemolysin (TDH) tdh gene, the TDH-related hemolysin (trh) gene, or both genes are considered virulent strains. We previously demonstrated that the transcription-reverse transcription concerted (TRC) method could be used to quantify the amount of mRNA transcribed from the tdh gene by using an automated detection system. In this study, we devised two TRC-based assays to quantify the mRNAs transcribed from the trh1 and trh2 genes, the two representative trh genes. The TRC-based detection assays for the tdh, trh1, and trh2 transcripts could specifically and quantitatively detect 103 to 107 copies of the corresponding calibrator RNAs. We examined by the three TRC assays the total RNA preparations extracted from 103 strains of Vibrio parahaemolyticus carrying the tdh, trh1, or trh2 gene in various combinations. The tdh, trh1, and trh2 mRNAs in the total RNA preparations were specifically quantified, and the time needed for detection ranged from 9 to 19 min, from 14 to 18 min, and from 9 to 12 min, respectively. The results showed that this automated TRC assays could detect the tdh, trh1, and trh2 mRNAs specifically, quantitatively, and rapidly. The relative levels of TDH determined by the immunological method and that of tdh mRNA determined by the TRC assays for most tdh-positive strains correlated. Interestingly, the levels of TDH produced from the strains carrying both tdh and trh genes were lower than those carrying only the tdh gene, whereas the levels of mRNA did not significantly differ between the two groups.

Fluorescence property of oxazole yellow-linked oligonucleotide. Triple helix formation and photocleavage of double-stranded DNA in the presence of spermine

Oxazole yellow is an intercalator that shows enhanced fluorescence upon binding to DNA. We prepared an oxazole yellow-linked oligonucleotide that can form triple helix with interleukin 2 receptor alpha chain promoter. The oxazole yellow-linked oligonucleotide showed linear increase of fluorescence by the triple helix formation with double-stranded DNA and also induced photocleavage of the targeted DNA in the presence of spermine upon visible illumination. Cleavage site of one strand was 7 or 8 bases away from the site of intercalation whereas the other strand was cleaved at the intercalated site.

Rapid detection of tdh and trh mRNAs of Vibrio parahaemolyticus by the transcription-reverse transcription concerted (TRC) method

We developed a novel method named the transcription-reverse transcription concerted (TRC) method and an instrument that allowed rapid and completely homogeneous real-time monitoring of RNA isothermal sequence amplification without any post-amplification analysis in our previous study [Ishiguro et al., Anal. Biochem., 314, 77-86 (2003)]. In this study, we newly established rapid and sensitive TRC systems for the detection of the mRNAs transcribed from two major virulence genes of Vibrio parahaemolyticus: the tdh gene encoding the thermostable direct hemolysin (tdh) and the trh gene encoding the thermostable direct hemolysin-related hemolysin. Examination of the standard RNAs prepared in vitro showed that a positive result, increase in the fluorescence intensity to the cut-off value within 25 min, was obtained for as few as 100 copies of RNA. The TRC method specific to the trh mRNA detected the mRNAs transcribed from the trh1 and trh2 genes, two representative trh variants sharing 84% sequence identity. The detection time gave a linear relationship to the logarithm of starting RNA copies ranging from 10(3) to 10(7) copies, showing that quantitative analysis is possible. The detection time for 10(3) copies of the standard RNAs ranged from 11 to 15 min. Examination of the total RNAs extracted from the standard strains of V. parahaemolyticus demonstrated that the new TRC systems are sufficiently sensitive to detect as few as 100 CFUs of the strains carrying the target genes. Total RNA preparations extracted from 24 strains of V. parahaemolyticus, 52 strains belonging to 31 other species of the genus Vibrio and 11 strains belonging to 8 species of non-Vibrio genera were examined. The results of the detection of tdh- and trh-specific mRNAs by the two TRC systems and those of the respective genes by the DNA colony hybridization method agreed. We conclude that the new TRC systems are rapid, highly sensitive, easy to manipulate, and are suitable for routine examination of virulent strains of V. parahaemolyticus in microbiological laboratories.

Isothermal RNA Sequence Amplification Method for Rapid Antituberculosis Drug Susceptibility Testing of Mycobacterium tuberculosis

ABSTRACT RNA transcript quantification by an isothermal sequence amplification reaction was evaluated for susceptibility testing of 15 Mycobacterium tuberculosis strains. Agreement with the proportion method on Ogawa egg medium and the BACTEC MGIT 960 system was 100 and 87% for rifampin, 93 and 100% for isoniazid, 60 and 53% for ethambutol, and 80 and 80% for streptomycin, respectively.

Fusion protein of interleukin-6 and interleukin-6 receptor without a polypeptide linker

FP6, a novel recombinant fusion protein of interleukin-6 (IL-6) and IL-6 receptor (IL-6R), was prepared in the methylotrophic yeast Pichia pastoris. This protein was a potent activator of a cell surface transducing glycoprotein, gp130 and is a potential therapeutical reagent in the hemopoietic field. A linker is generally thought to be required for two fused molecules to retain their proper structures although it should preferably be removed to reduce possible antigenicity. It was found that the C-terminal residue of IL-6R could be directly linked to the N-terminal residue of IL-6 without decreasing the ability of IL-6 to bind gp130 and send the IL-6 signal. It was also found that the peptide bond between Lys-37 and Asp-38 of IL-6 was prone to proteolytic cleavage and that the immunoglobulin (Ig)-like region of IL-6R underwent extensive and heterogeneous glycosylation when expressed in P. pastoris. Based on these findings, we designed FP6 without the Ig-like region, in which the C-terminal residue of Ala-333 of IL-6R was directly linked to Asp-38 of IL-6 by a peptide bond. Purified FP6 had both an in vitro effect on hemopoietic progenitors to generate various colonies and an in vivo effect on megakaryocyte progenitors to increase platelet counts. Four purified FP6s were obtained, which had the same molecular mass and different isoelectric points without any detectable modification in the course of purification. The difference in isoelectric points was shown to be due to microheterogeneity of the carbohydrate chains. Each FP6 had the same specific activity in the cell growth assay with or without endoglycosidase digestion. Homogeneous FP6 with respect to isoelectric point as well as molecular mass merits more detailed characterization and evaluation for possible clinical application.

PCR-Coupled Activation of Intercalating Dyes

An easy and simple method of the quantification of a target nucleotide sequence has been required in clinical diagnostics, or molecular pathology as well as for the elucidation of various biochemical processes. In particular, therapy of virus infected diseases such as chronic hepatitis caused by HCV comes to require monitoring the virus population itself in serum in the planning of the therapy.