Quick two-step RNA ligation employing periodate oxidation

The introduction of modified or labeled nucleotides into RNA is a powerful RNA engineering tool as it enables us to investigate how native RNA modifications affect RNA function and structure. It also helps in the structural analysis of RNA. A modified nucleotide can be introduced into a specific position of RNA by the method of two-step enzymatic ligation of RNA fragments. However, this method requires a complicated purification step between the two ligation steps that results in low yields of the ligation product. Here we have developed a new ligation technique employing periodate oxide that eliminates this purification step. This increases the total yield of the ligation product and makes it a faster procedure.     

Effect of pH on the Steady State Kinetics of Bovine Heart NADH: Coenzyme Q Oxidoreductase

Complete initial steady state kinetics of NADH-decylubiquinone (DQ) oxidoreductase reaction between pH 6.5 and 9.0 show an ordered sequential mechanism in which the order of substrate bindings and product releases is NADH-DQ–DQH₂-NAD⁺. NADH binding to the free enzyme is accelerated by protonation of an amino acid (possibly a histidine) residue. The NADH release is negligibly slow under the turnover conditions. The rate of DQ binding to the NADH-bound enzyme and the maximal rate at the saturating concentrations of the two substrates, which is determined by the rates of DQH₂ formation in the active site and releases of DQH₂ and NAD⁺ from the enzyme, are insensitive to pH, in contrast to clear pH dependencies of the maximal rates of cytochrome c oxidase and cytochrome bc ₁ complex. Physiological significances of these results are discussed.     

Augmentation of NO-mediated vasodilation in metabolic acidosis

Reduction of perivascular pH in acidemia produces hyporesponsiveness of vascular bed to vasoconstrictors. In the present study, we examined the effects of modest acidification on dilatory responses of isolated rat thoracic aorta. Acetylcholine produced endothelium-dependent relaxation in phenylephrine-precontracted aorta, which was markedly enhanced by acidification of Krebs-Henseleit solution from pH 7.4 to 7.0. A similar augmentation was observed in the relaxing responses to NO donors (SNP, SIN-1, SNAP), 8-Br-cGMP and NS-1619 (a putative K(Ca) channel opener and/or Ca channel inhibitor) in endothelium-denuded, phenylephrine-contracted aorta. However, papaverine-induced relaxation was not affected by the change in pH. At pH 7.4, the relaxing responses to acetylcholine and SNP were partially inhibited by charybdotoxin (K(Ca) channel inhibitor) but not glibenclamide (K(ATP) channel inhibitor), while at pH 7.0 the relaxation induced by either drug was not affected by K(+) channel inhibitors. Relaxation induced by 8-Br-cGMP or NS-1619 was not inhibited by charybdotoxin or glibenclamide. Acidification to pH 7.0 increased the cGMP production in response to acetylcholine in endothelium-intact aorta and to SNP in endothelium-denuded aorta. These results show that modest acidification augments NO-mediated relaxation in rat aorta, probably due to an enhancement of cGMP-dependent but K(+) channel-unrelated relaxation mechanisms.     

Persistent parapoxvirus infection in cattle

The possibility of persistent parapoxvirus (PPV) infection was investigated by serologically and genetically using cattle infected with the virus experimentally and naturally. Three cattle were inoculated with the virus subcutaneously at several spots in the lips and abdominal regions. Small papules developed in the inoculated regions, and antibodies to the virus developed and continued persistently. One animal, from which one PPV had been previously isolated, was also subjected to serological and viral detection tests as a naturally infected case. Two of these four cattle were injected with dexamethasone (DM), and one was injected with interferon-gamma (IFN-gamma). The viral genome was rarely detected from the peripheral blood leukocytes in the ordinary condition, but frequently when the animals were injected with IFN-gamma. The viral genome was also detected from the lymph nodes as these PPV infected animals were euthanized. These results indicated that cattle were infected with PPV subclinically and persistently, and the virus was activated in stressed or immunosuppressed animals. The virus would be harbored in the lymphotic tissues of the animals when they show no clinical symptoms.     

Viral load in Epstein-Barr virus-associated hemophagocytic syndrome

The viral load in peripheral blood from patients with Epstein-Barr virus (EBV)-associated hemophagocytic syndrome was measured by real-time quantitative PCR and compared with that in infectious mononucleosis. Patients with EBV-associated hemophagocytic syndrome generally had larger viral burdens, although it was difficult to differentiate EBV-associated hemophagocytic syndrome from infectious mononucleosis simply by viral load. The difference in viral load seemed to be clearer in peripheral blood mononuclear cells than in plasma.     

An observation of the initial stage towards a symbiotic relationship

Two well-characterized and phylogeneticaly different species, Escherichia coli and Dictyostelium discoideum, were used as the model organisms. When the two species were mixed and allowed to grow on minimal agar plates at 22 degrees C, remarkably, the two species achieved a state of coexistence at an average of 2-4 weeks. In addition, the emerged colonies housing the coexisting species had a mucoidal nature that was not observed from its origin. Moreover, the state of coexistence was confirmed to be stable, and so was the mucoidal nature of the emerged colonies. Comparing with the pure E. coli origin, the mucoidal colony showed a significant increase in higher molecular weight extracellular components, with polysaccharides as the major constituent. Qualitative analysis of the monosaccharide contents in the extracellular components of the mucoidal colony revealed not only a significant increase in the glucose content, but also significant amount of additional xylose and galactose. The system permits the initial stages of the development of relationship between two species be captured within a short period of time. This feature, together with being simple and reproducible in laboratory conditions, provides a new model system for the study of symbiosis, especially when initial stages are concerned.     

Novel surrogate end-point biomarker to evaluate agents for use in the chemoprevention of reactive oxygen species-associated cancer

Cancer chemoprevention is the use of chemical agents to inhibit, delay or reverse carcinogenesis. We established a novel method to evaluate agents for use in the chemoprevention of reactive oxygen species (ROS)-associated cancer. Induction of renal cell carcinoma in rats by ferric nitrilotriacetate (Fe-NTA) is an established model of ROS-associated cancer. We recently identified the p16INK4A tumor suppressor gene as one of the major target genes in this model, and showed by the use of in situ hybridization that allelic loss of p16IK4A occurs in the increased fraction of renal tubular cells within a few weeks. In the present study, we tested whether diets including green tea powder or a processed grain food are effective chemopreventive agents in this animal model. Consumption of these modified diets led to a significant decrease in the fraction of aneuploid cells after 1 week of repeated Fe-NTA administration. A decrease in renal lipid peroxidation after a single administration of Fe-NTA was also observed. Therefore, intake of green tea or processed grain foods stabilizes p16INK4A in the genome, at least in this model, and might be helpful for the prevention of ROS-associated cancer. This novel method is versatile, and may work as a surrogate end-point biomarker for screening the usefulness of agents for cancer chemoprevention.     

Iron and carcinogenesis: from Fenton reaction to target genes

Reactive oxygen species (ROS) have been shown to be associated with a wide variety of pathological phenomena such as carcinogenesis, inflammation, radiation and reperfusion injury. Iron, the most abundant transition metal ion in our body, may work as a catalyst for the generation of ROS in pathological conditions. In the past few years, there have been great advances in the understanding of iron metabolism. These include the discoveries of iron transporters and the gene responsible for hereditary hemochromatosis. Iron overload has been shown to be associated with carcinogenesis. We recently identified the major target genes (p16(INK4A) and p15(INK4B) tumor suppressor genes, which encode cyclin-dependent kinase inhibitors) in a ferric nitrilotriacetate-induced rat renal carcinogenesis model, in which the Fenton reaction is induced in the renal proximal tubules. Allelic loss of the p16 gene occurs early in carcinogenesis and specifically at the p16 loci as compared with other tumor suppressor genes. This led to the novel concept of 'genomic sites vulnerable to the Fenton reaction'. Here, recent new findings on iron metabolism are reviewed and the concept of the vulnerable sites explored. More effort to link iron metabolism with human carcinogenesis is anticipated.     

Inhibition of BMP activity by the FGF signal promotes posterior neural development in zebrafish

The expression patterns of region-specific neuroectodermal genes and fate-map analyses in zebrafish gastrulae suggest that posterior neural development is initiated by nonaxial signals, distinct from organizer-derived secreted bone morphogenetic protein (BMP) antagonists. This notion is further supported by the misexpression of a constitutively active form of zebrafish BMP type IA receptor (CA-BRIA) in the zebrafish embryos. It effectively suppressed the anterior neural marker, otx2, but not the posterior marker, hoxb1b. Furthermore, we demonstrated that the cells in the presumptive posterior neural region lose their neural fate only when CA-BRIA and Xenopus dominant-negative fibroblast growth factor (FGF) receptors (XFD) are coexpressed. The indications are that FGF signaling is involved in the formation of the posterior neural region, counteracting the BMP signaling pathway within the target cells. We then examined the functions of Fgf3 in posterior neural development. Zebrafish fgf3 is expressed in the correct place (dorsolateral margin) and at the correct time (late blastula to early gastrula stages), the same point that the most precocious posterior neural marker, hoxb1b, is first activated. Unlike other members of the FGF family, Fgf3 had little mesoderm-inducing activity. When ectopically expressed, Fgf3 expands the neural region with suppression of anterior neural fate. However, this effect was mediated by Chordino (zebrafish Chordin), because Fgf3 induces chordino expression in the epiblast and Fgf3-induced neural expansion was substantially suppressed in dino mutants with mutated chordino genes. The results obtained in the present study reveal multiple actions of the FGF signal on neural development: it antagonizes BMP signaling within posterior neural cells, induces the expression of secreted BMP antagonists, and suppresses anterior neural fate.