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Biomedical subjects

K Takai

Publications and source records attributed to K Takai.

At least 55 records · Page 3Linked to original sources

Self-cleavage of p2Sp1 RNA with Mg2+ and non-ionic detergent (Brij 58).

The precursor of an RNA molecule from T4-infected E. coli cells (p2Sp1 RNA) has the capacity to cleave itself at specific positions [(UpA (139-140) and CpA (170-171)], within a putative loop and stem structure. This sequence-specific cleavage requires at least a monovalent cation and non-ionic detergents. We studied the self-cleavage reaction of an RNA fragment (GUUUCGUACAAAC) (R1) with the sequence corresponding to the p2Sp1 RNA in the presence of Mg2+ and non-ionic detergents. It requires Mg2+ and is aided by a non-ionic detergent, Brij 58. The cleavage reaction is time, temperature, and pH-dependent. The cleavage occurs at the phosphodiester bond between UpA and CpA on the RNA fragment (GUUUCGUACAAAC) (R1). Furthermore, the maximum of cleavage of R1 occurs at a very low Mg2+ concentration (< or = 5 mM).

Cetomacrogol↗

Specific inactivation of Escherichia coli tRNA(Phe) by antisense DNA-treatment under Mg2+-deficient conditions.

The preparation of an Escherichia coli tRNA mixture lacking several specific species may be useful for applications ranging from cell-free protein preparation to protein engineering. We have already demonstrated that tRNA(Asp) can be inactivated, or 'knocked out', with practical specificity by an antisense strategy. In the present study, we synthesized five tRNA(Phe)-targeted antisense oligonucleotides and tested if this tRNA can also be inactivated specifically. The salt conditions used previously for the tRNA(Asp) inactivation were not applicable to tRNA(Phe). Instead, Mg2+-deficient conditions were found to be useful for the inactivation of tRNAPhe by the antisense oligonucleotides. These conditions were also applicable to the inactivation of tRNA(Asp). The susceptibility to the antisense DNAs can change drastically, depending on the concentration of Mg2+.

Base Sequence↗

Effects of anticodon 2'-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation.

The methylation of 2'-hydroxyl groups is one of the most common posttranscriptional modifications of naturally occurring stable RNA molecules. Some tRNA species have a 2'-O-methyl nucleoside at the first position of the anticodon, and it was suggested that this modification stabilizes the codon-anticodon duplex. However, no tRNA species have been found to have the modification at the second or third position of the anticodon. In the present study, we measured the effects of anticodon 2'-O-methylation on the codon-reading efficiencies of the anticodon variants of the unmodified forms of Escherichia coli tRNA1(Ser), using a cell-free protein synthesis assay. The modification of C in the first position of the anticodon into 2'-O-methylcytidine increased the efficiency of reading the G-ending codon. On the other hand, the modifications of the second and/or third positions were detrimental to the codon-reading activity. Thus, 2'-hydroxyl groups at the second and third positions of the anticodon may have some role in the translation reaction, and this may be the reason why 2'-O-methyl nucleosides are not found in these positions within natural tRNA species.

Amino Acid Sequence↗

Cystic renal cell carcinoma diagnosed by cystofiberscopy.

A 64-year-old man suffered from hypertensive syncope and was admitted to Branch Hospital, Faculty of Medicine, The University of Tokyo. On admission he had no symptoms; however, two renal cysts of about 5 cm in diameter were found in his left kidney. Cystofiberscopy with a thin optical fiberscope was performed in addition to puncture and cystography. Cytology revealed class I, but the wall surface of the lower cyst was uneven, fluid-filled, colloid-like and white-gray compared with that seen in the upper cyst. It was diagnosed as renal cell carcinoma (RCC) and left nephrectomy was performed (5 cm in diameter, RCC, papillary tubular, common, clear cell subtype, G2>G1, INF beta, pT2, pMx, pV0, ew(-)).

Carcinoma, Renal Cell↗

Inhibition of human telomerase activity by antisense phosphorothioate oligonucleotides encapsulated with the transfection reagent, FuGENE6, in HeLa cells.

Telomerase, a ribonucleoprotein, synthesizes telomeric repeats (TTAGGG) onto the ends of chromosomes to maintain the constant length of the telomere DNA, and its activity is detectable in approximately 85%-90% of primary human cancers. Thus, it is postulated that human telomerase might be associated with malignant tumor development and could be a highly selective target for antitumor drug design. Antisense phosphorothioate oligonucleotides (S-ODN) were investigated for their abilities to inhibit telomerase activity in the HeLa cell line. The S-ODN were designed to be complementary to nucleotides within the RNA active site of telomerase. As a transfection reagent, FuGENE6 (Boehringer Mannheim, Mannheim, Germany) was used to enhance the cellular uptake of the oligonucleotides in cell cultures. The S-ODN encapsulated with FuGENE6 clearly inhibited telomerase activity in HeLa cells and showed sequence-specific inhibition. The encapsulated S-ODN-3 with a 19-nucleotide, (nt) chain length had inhibitory effects similar to those of the 21-mer and 23-mer S-ODN sequences (S-ODN-4 and 5), but the 15-mer and 17-mer S-ODN sequences (S-ODN-1 and 2) failed to satisfactorily prevent telomerase activity. However, apoptotic HeLa cell death was not associated with telomerase inhibition. Furthermore, the encapsulated S-ODN did not appear to be cytotoxic in terms of the cell growth rate. The oligonucleotides encapsulated with the transfection reagent had enhanced cellular uptake, and cytoplasmic and nuclear localizations were observed. However, weak fluorescent signals were observed within the cytoplasms of HeLa cells treated with the free S-ODN-3. Thus, the activities of the S-ODN were effectively enhanced by using the transfection reagent. The transfection reagent, FuGENE6, may thus be a potentially useful delivery vehicle for oligonucleotide-based therapeutics and transgenes and is appropriate for use in vitro and in vivo.

Capsules↗

Properties of quadruplex oligonucleotides with anti-HIV-1 activity.

A phosphorothioate oligonucleotide composed of deoxyguanosine and thymidine was identified as an inhibitor of HIV-1 infection at an early stage of the HIV-1 replication cycle in vitro. The phosphodiester and phosphorothioate chimeric oligonucleotides were found to be potent inhibitors of several steps of HIV-1 infection: the interaction with CD4 and the chemokine receptor, the reverse transcriptase activity, and the integrase activity. To elucidate the mechanism of the anti-HIV-1 function of these oligonucleotides in terms of their structure, we focussed on their G-serial sequences and investigated the characteristics of their solution structures. These oligonucleotides were proved to be able to adopt G-quadruplex structures by UV and CD measurements. We presume that the anti-HIV-1 activities of these oligonucleotides are consequently attributable to G-quadruplex formation.

Anti-HIV Agents↗

Effective suppression of HIV-1 gene expression by a mammalian tRNA 3' processing endoribonuclease and external guide sequence oligozymes.

We examined the suppression of virus expression by cleavage of the HIV-1 RNA gene using a mammalian tRNA 3' processing endoribonuclease and an External Guide Sequence Oligozyme (EGS) in vivo. We constructed an EGS expression vector that used the tRNA(met) promoter as an expression cassette for EGS. The EGS expression vector was targeted to the upstream region of gag, region. The EGS expression vector was co-transfected into COS cells with the HIV-1 gene plasmid vector. As compared with the EGS non-expressing cells and the EGS expressing cells, the EGS expressing cells with the targeted gag start codon had a clearly decreased amount of the HIV-1 gag p24 protein. The EGS expressing cells with the targeted gag start codon showed effective suppression of HIV-1 gene expression. Thus, these studies describe novel gene targeting agents for the inhibition of gene expression and antiviral activity.

Animals↗

Inhibition of influenza virus RNA (PB2 mRNA) expression by a modified DNA enzyme.

DNA enzymes are RNA-cleaving single stranded DNA molecules. The structure and the catalytic domain of a DNA enzyme were determined by Santro et al. in 1997. In this study, we have designed several types of DNA enzymes (PB2Dz) targeted to the PB2 mRNA translation initiation region of influenza A virus, and examined their cleavage kinetics, nuclease resistance, and a luciferase gene reporter assay. Using a synthetic substrate, these DNA enzymes were shown to have cleavage activity that is dependent on the length of the substrate recognition domain. To confer serum nuclease resistance to the DNA enzymes, we designed a new type of DNA enzyme that has the N3'-P5' phosphoramidate modification (PB2Dz-N) at each terminal. We examined the activity of this DNA enzyme in vivo. The DNA enzymes used in this study inhibited the expression of the PB2-luciferase gene in COS cells. These results suggest that DNA enzymes are potentially useful as gene inactivating agents of influenza A virus.

Animals↗

An easy cell-free protein synthesis system dependent on the addition of crude Escherichia coli tRNA.

The protein-synthesizing S30 extract of Escherichia coli contains tRNA, which limits its applications in cell-free protein synthesis. Here, we show that at least Arg- and Ser-acceptor activities can be removed from a standard S30 extract by treatment with an immobilized RNase A resin. This RNase-treated extract exhibits no protein synthesis activity, but regains it when supplied with crude E. coli tRNA and a small amount of human placental RNase inhibitor. The protein synthesis is dependent on the addition of tRNA in the presence of the RNase inhibitor. Chloramphenicol acetyltransferase was synthesized with this system and found to be active.

Bacterial Proteins↗

Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney.

A novel barophilic, hyperthermophilic archaeon was isolated from a deep-sea hydrothermal vent chimney at the Myojin Knoll in the Ogasawara-Bonin Arc, Japan. The cells were found to be irregular cocci and motile with multiple polar flagella. Growth was observed between 60 and 88 degrees C (opt. 83 degrees C; 30 min doubling time), pH 4.0 and 8.0 (opt. pH 6.0), 20 and 73 g sea salts l-1 (opt. 47 g l-1) and 0.1 and 60 MPa (opt. 30 MPa). The isolate was a strictly anaerobic chemoorganotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein in the presence of elemental sulfur or ferrous iron. The G + C content of the genomic DNA was 53.5 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was a member of an ancient lineage of the Thermococcales that diverged prior to the formation of the two genera Thermococcus and Pyrococcus. On the basis of the physiological and molecular properties of the new isolate, the name Palaeococcus ferrophilus gen. nov., sp. nov. is proposed. The type strain is strain DMJT (= JCM 10417) [corrected].

Anti-Bacterial Agents↗

[The bacteriocidal effect of the electrolysed functioning water against Helicobacter pylori].

The bacteriocidal effect of electrolysed functioning water against Helicobacter pylori was examined by both the culture method (viable count on agar plate) and the bacterial ATP content analysis (biolumminescence assay). The culture method revealed the water's reduced bacteriocidal effect on organic substances such as horse serum and bovine serum albumin. The bacterial ATP content determined by the treatment with lysis solution correlated with the bacterial cell count. The ATP of bacteria treated with electrolysed functioning water, benzalkonium chloride, and chlorhexidine gluconate was still present after contact with these solutions for 30 minutes, while the bacterial growth was completely inhibited by the culture method. Therefore, it was suggested that the bacterial ATP was derived from the coccoid form which was observed morphologically due to the action of these solutions. These results demonstrate that these solutions are not effective bacteriocidally against the coccoid form. Consequently, when we utilize functioning water in the field, we should keep in mind its nonbacteriocidal effect against the coccoid form, as well as its reduced effect under the condition of the contamination by organic substances.

Adenosine Triphosphate↗

[Emphysematous cystitis and neuropathy; a report of the case with diabetes mellitus].

A study was made of a 55 years old male, who suffered from emphysematous cystitis with diabetes mellitus. He had multiple complications due to diabetic neuropathy such as foot ulceration, oculomotor nerve palsy, peroneal nerve palsy and a neurogenic bladder. Klebsiella pneumoniae and Pseudomonous aeruginosa were cultured from urine specimens. There have been only 19 reported cases of emphysematous cystitis since 1962. Fourteen of these cases had diabetes mellitus.

Cystitis↗

Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes.

We describe a rapid, reproducible, and sensitive method for detection and quantification of archaea in naturally occurring microbial communities. A domain-specific PCR primer set and a domain-specific fluorogenic probe having strong and weak selectivity, respectively, for archaeal rRNA genes (rDNAs) were designed. A universal PCR primer set and a universal fluorogenic probe for both bacterial and archaeal rDNAs were also designed. Using these primers and probes, we demonstrated that detection and quantification of archaeal rDNAs in controlled microbial rDNA assemblages can be successfully achieved. The system which we designed was also able to detect and quantify archaeal rDNAs in DNA samples obtained not only from environments in which thermophilic archaea are abundant but also from environments in which methanogenic archaea are abundant. Our findings indicate that this method is applicable to culture-independent molecular analysis of microbial communities in various environments.

Archaea↗

A case of rectal Dieulafoy's ulcer and successful endoscopic sclerotherapy.

A 54-year-old woman presented a massive hematochezia 7 days after sigmoidectomy. Repeated colonoscopy and angiography failed to locate the site of bleeding and Hartman's operation was performed. Rebleeding from the rectum on the day of operation occurred and pulsate arterial bleeding with minimal surrounding ulcer 1 cm above the pectinate line was observed. Screlotherapy with ethanol and electro coagulation was successfully performed to achieve permanent hemostasis. The importance of detailed rectal examination and an awareness of this clinical entity in life-threatening lower intestinal bleeding is discussed.

Electrocoagulation↗

Endoscopic submucosal tumor biopsy using Stiegmann-Goff endoscopic ligator.

Endoscopic biopsy is an important tool for histological diagnosis of lesions residing in gastrointestinal tracts. However, it is less useful in submucosal lesions due to the existence of normal overlying mucosa. We developed a new and safe technique for the diagnosis of submucosal tumor using Stiegmann-Goff endoscopic ligator. After removing surface mucosa to expose submucosal tissue by this method, conventional secured histological diagnosis could be performed. To determine definitive histological diagnosis, this technique is useful as well as Endoscopic Ultrasound (EUS) with fine needle aspiration biopsy and other modalities.

Biopsy↗

[Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms].

Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that the deep-sea hydrothermal vents are the windows to a deep subsurface biosphere. A vast array of chemoautotrophic deep-sea animal communities have been found to exist in cold seep environments, and most of these animals are common with those found in hydrothermal vent environments. Thus, it is possible to consider that the cold seeps are also one of slit windows to a deep subsurface biosphere. We conclude that the deep-sea extremophiles are very closely related into the unseen majority in subsurface biosphere, and the subsurface biosphere probably concerns to consider the "exobiology".

Archaea↗

A transparent sheath for endoscopic surgery and its application in surgical evacuation of spontaneous intracerebral hematomas. Technical note.

The authors advocate the use of a transparent sheath for guiding an endoscope, a simple and unique tool for endoscopic surgery, and describe preliminary results of its application in the evacuation of hypertensive intracerebral hematomas. This sheath is a 10-cm-long tube made of clear acrylic plastic, which greatly improves visualization of the surgical field through a 2.7-mm nonangled endoscope inserted within. Between April 1997 and December 1998, the authors performed endoscopic evacuation of intracerebral hematomas by using this sheath inserted into the patients' heads through a burr hole. In nine consecutive cases in which the hematoma was larger than 40 ml in volume, nearly complete evacuation (86-100%) of the lesion was achieved without complication. Excellent visualization of the border between the brain parenchyma and the hematoma facilitated accurate intraoperative orientation, and also allowed easy identification of the bleeding point. Thus, this combination of sheath and endoscope achieves both minimal invasiveness and the maximum extent of hematoma removal with secure hemostasis. This tool will reduce the inherent disadvantage of endoscopic procedures and may expand their application in other areas of neurosurgical management.

Aged↗

Anti-human immunodeficiency virus type 1 of a two-strand-system targeted to the polypurine tract.

The polypurine tract (PPT) is highly conserved among the known human immunodeficiency virus (HIV)-1 strains, and is a possible target for triplex formation. We show the effects of triple-helix formation by assays of primer extension inhibition in vitro, using a two-strand-system (FTFOs) targeted to the PPT of HIV-1. The two-stranded composition of a triple-helix is thermodynamically and kinetically superior to the three-strand-system. The FTFOs inhibited the RT activity in a sequence-specific manner, i.e., the triplex actually formed at the PPT and blocked the RT. The FTFOs containing the phosphorothioate groups at the antisense sequences showed greater 3'-exonuclease resistance. In the observation of the FITC-DsDGloopT5-37 with MOLT-4 cells by a confocal laser scanning microscope, diffuse fluorescence was apparently observed in the cytoplasm and nucleus. However, weak fluorescence was observed within the cytoplasm and nucleus of MOLT-4 cells treated with the antisense phosphorothioate oligonucleotides (S-ODN-gag-AUG). In HIV-1 infected MOLT-4 cells, the FTFOs containing the phosphorothioate groups at the antisense sequence sites and guanosine rich parts within the third Hoogsteen base pairing sequence inhibit the replication of HIV-1 more effectively than the antisense oligonucleotides, indicating sequence-specific inhibition of HIV-1 replication.

Amino Acid Sequence↗