Effects of ribosomes on the kinetics of Qβ replication

Bacteriophage Qβ utilizes some host cell translation factors during replication. Previously, we constructed a kinetic model that explains replication of long RNA molecules by Qβ replicase. Here, we expanded the previous kinetic model to include the effects of ribosome concentration on RNA replication. The expanded model quantitatively explained single- and double-strand formation kinetics during replication with various ribosome concentrations for two artificial long RNAs. This expanded model and the knowledge obtained in this study provide useful frameworks to understand the precise replication mechanism of Qβ replicase with ribosomes and to design amplifiable RNA genomes in translation-coupling systems.     

Automated rapid method for microbioassay of amino acids

An automated rapid method for microbioassay of amino acids was investigated by taking advantages of the rapid manual method. The Pye Unicam automatic analytical apparatus was adopted for the automation of assay culture in the rapid microbioassay. The advantages of the present method are that amino acids can be automatically determined on 3.5-hr assay culture, and that an aseptic technique can be omitted. These advantages were confirmed in several amino acid assays. The assay values were the same as those obtained by the conventional method. Application of the automated rapid method to the serine assay showed a linear standard curve without a lag section, leading to more expanded assay range and smaller drift in values.     

Evaluation of intestinal microbiota,short-chain fatty acids,and immunoglobulin a in diversion colitis

It is reported that an increase in aerobic bacteria, a lack of short-chain fatty acids (SCFAs), and immune disorders in the diverted colon are major causes of diversion colitis. However, the precise pathogenesis of this condition remains unclear. The aim of the present study was to examine the microbiota, intestinal SCFAs, and immunoglobulin A (IgA) in the diverted colon. Eight patients underwent operative procedures for colostomies. We assessed the diverted colon using endoscopy and obtained intestinal samples from the diverted colon and oral colon in these patients. We analyzed the microbiota and SCFAs of the intestinal samples. The bacterial communities were investigated using a 16S rRNA gene sequencing method. The microbiota demonstrated a change in the proportion of some species, especially Lactobacillus, which significantly decreased in the diverted colon at the genus level. We also showed that intestinal SCFA values were significantly decreased in the diverted colon. Furthermore, intestinal IgA levels were significantly increased in the diverted colon. This study was the first to show that intestinal SCFAs were significantly decreased and intestinal IgA was significantly increased in the diverted colon. Our data suggest that SCFAs affect the microbiota and may play an immunological role in diversion colitis.     

Thalidomide inhibits lipopolysaccharide-induced nitric oxide production and prevents lipopolysaccharide-mediated lethality in mice

The effect of thalidomide on lipopolysaccharide-induced nitric oxide (NO) production was studied using RAW 264.7 macrophage-like cells. Thalidomide significantly inhibited lipopolysaccharide-induced NO production via reduced expression of an inducible NO synthase. Thalidomide reduced the phosphorylation of the p65 nuclear factor-κB subunit, inhibitory κB (IκB) and IκB kinase in lipopolysaccharide-stimulated cells. However, thalidomide did not affect the expression of interferon-β (IFN-β) and interferon regulatory factor-1 in response to lipopolysaccharide. Further, thalidomide inhibited the MyD88 augmentation in lipopolysaccharide-stimulated cells, whereas it did not alter the expression of TIR domain-containing adaptor-inducing IFN-β in the MyD88-independent pathway. Thalidomide significantly inhibited the NO production in response to Pam₃Cys, CpG DNA and imiquimod as MyD88-dependent Toll-like receptor (TLR) ligands, but not polyI:C as a MyD88-independent TLR ligand. Therefore, thalidomide was suggested to inhibit lipopolysaccharide-induced NO production via downregulation of the MyD88-dependent signal pathway. The anti-inflammatory action of thalidomide might be involved in the prevention of lipopolysaccharide-mediated lethality in mice.     

A new parascylliid species, <Emphasis Type="Italic">Parascyllium sparsimaculatum</Emphasis>, from Western Australia (Elasmobranchii: Orectolobiformes)

Parascyllium sparsimaculatum sp. nov. is described using external and skeletal morphologies on the basis of three female specimens collected from the continental slope off Western Australia. This new species is clearly distinguished from four congeners by having a relatively large head (length greater than 16% of TL); a large eye (horizontal diameter of eye greater than 11% of HL); a large pectoral fin (anterior margin more than 10% of TL); relatively tall, erect dorsal fins with angular apices; 43–49 tooth rows on upper jaw; a yellowish-brown body with large, diffuse-edged, rusty-brown spots; and an extremely faint, collar-like saddle over the gill region. A key to species is provided. Received: November 27, 2000 / Revised: August 27, 2001 / Accepted: September 18, 2001     

Binding of Ribulose 1,5-Bisphosphate to the Non-Catalytic Sites of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase and Its Metabolic Implications

This is the first report showing that ribulose bisphosphatecarboxylase/oxygenase has the non-catalytic sites to bind ribulosebisphosphate (RuBP). A plot of the binding number against theRuBP concentration in the equilibrium binding assay gave a bumpycurve with an intermediate plateau at 0.3 to 0.5 mM RuBP. Thebinding was saturated with 1.5 mM RuBP. The concentrations offree and binding forms of RuBP and the functioning forms ofthe enzyme in chloroplasts could be predicted using the kineticdata of the binding. (Received October 5, 1993; Accepted November 22, 1993)     

Origin and diversification of a metabolic cycle in oligomer world

Based on the oligomer-world hypothesis we propose an abstract model where the molecular recognition among oligomers is described in the shape space. The origin of life in the oligomer world is regarded as the establishment of a metabolic cycle in a primitive cell. The cycle is sustained by the molecular recognition. If an original cell acquires the ability of the replication of oligomers, the relationship among oligomers changes due to the poor fidelity of the replication. This change leads to the diversification of metabolic cycles. The selection among diverse cycles is the basis of the evolution. The evolvability is one of the essential characters of life. We demonstrate the origin and diversification of the metabolic cycle by the computer simulation of our model. Such a simulation is expected to be the simplified demonstration of what actually occurred in the primordial soup. Our model describes an analog era preceding the digital era based on the genetic code.