Multiplication of a restriction-modification gene complex

Previous works have suggested that some gene complexes encoding a restriction (R) enzyme and a cognate modification (M) enzyme may behave as selfish mobile genetic elements. RM gene complexes, which destroy 'non-self' elements marked by the absence of proper methylation, are often associated with mobile genetic elements and are involved in various genome rearrangements. Here, we found amplification of a restriction-modification gene complex. BamHI gene complex inserted into the Bacillus chromosome showed resistance to replacement by a homologous stretch of DNA. Some cells became transformed with the donor without losing BamHI. In most of these transformants, multiple copies of BamHI and the donor allele were arranged as tandem repeats. When a clone carrying one copy of each allele was propagated, extensive amplification of BamHI and the donor unit was observed in a manner dependent on restriction enzyme gene. This suggests that restriction cutting of the genome participates in the amplification. Visualization by fluorescent in situ hybridization revealed that the amplification occurred in single cells in a burst-like fashion that is reminiscent of induction of provirus replication. The multiplication ability in a bacterium with natural capacity for DNA release, uptake and transformation will be discussed in relation to spreading of RM gene -complexes.     

Selective detection of L-glutamate using a microfluidic device integrated with an enzyme-modified pre-reactor and an electrochemical detector

A microfluidic device integrated with a nanoliter volume enzyme pre-reactor and an enzyme-modified electrode was developed for the highly selective continuous measurement of glutamate (Glu). The device consists mainly of two glass plates. One plate incorporates an electrochemical cell that consists of working electrode (WE), reference electrode (RE) and counter electrode (CE). The WE is modified with a bilayer film of Os-polyvinylpyrridine-based mediator containing horseradish peroxidase (Os-gel-HRP). The WE was operated at -50 mV versus Ag. The other plate has a thin layer flow channel integrated with a pre-reactor. The reactor has a number of micropillars (20 microm in diameter, 20 microm high and separated from each other by a 20 microm gap) modified with ascorbate oxidase (AAOx) to eliminate L-ascorbic acid (AA). The enzymatic oxidation of AA is superior to that obtained with our previously reported pre-electrolysis type micro-reactor since electrochemically reversible transmitters such as catecholamines do not provide a cathodic current at the WE. In addition, the high operation potential of the pre-reactor causes unknown electroactive species, which also cause interference at the detection electrode. As a result, we were able to detect 1 microM Glu continuously at a low flow rate even when AA concentration was 100 microM.     

Solution structure of ADO1, a toxin extracted from the saliva of the assassin bug, Agriosphodrus dohrni

ADO1 is a toxin purified from the saliva of the assassin bug, Agriosphodrus dohrni. Because of its similarity in sequence to Ptu1 from another assassin bug, we did not assess its pharmacologic target. Here, we demonstrate by electrophysiologic means that ADO1 targets the P/Q-type voltage-sensitive calcium channel. We also determine the solution structure of ADO1 using two-dimensional NMR techniques, followed by distance geometry and molecular dynamics. The structure of ADO1 belongs to the inhibitory cystine knot (ICK) structural family (i.e., a compact disulfide-bonded core from which four loops emerge). ADO1 contains a two-stranded, antiparallel beta-sheet structure. We compare the structure of ADO1 with other voltage-sensitive calcium-channel blockers, analyze the topologic juxtaposition of key functional residues, and conclude that the recognition of voltage-sensitive calcium channels by toxins belonging to the ICK structural family requires residues located on two distinct areas of the molecular surface of the toxins.     

Absorption and metabolism of delphinidin 3-O-beta-D-glucopyranoside in rats

The absorption and metabolism of delphinidin 3-O-beta-d-glucopyranoside (Dp3G), which is the most potent antioxidant among the blueberry anthocyanins, were studied in rats. Dp3G rapidly appeared in the blood plasma within 15 min of oral administration (100 mg/kg body wt). The plasma level of absorbed Dp3G showed two peaks at 15 and 60 min after ingestion and then decreased time-dependently. However, the plasma level was maintained at approximately 30 nmol/l even after 4 h. Besides the Dp3G peak, a single major metabolite peak was detected by HPLC in the blood plasma obtained at 15 min. MS and NMR spectroscopy clarified that the chemical structure of the metabolite was 4'-O-methyl delphinidin 3-O-beta-d-glucopyranoside (methylation of the 4'-OH on the delphinidin B-ring). The present finding of this unique metabolite in anthocyanin metabolism strongly suggests that methylation of the 4'-OH on the flavonoid B-ring is a common metabolic pathway for flavonoids that carry the pyrogallol structure on the B-ring, as the same type of metabolite has been reported for other flavonoids such as epigallocatechin, but not for flavonoids carrying the catechol structure.     

Rumen microbes and fermentation of wild sika deer on the Shiretoko peninsula of Hokkaido Island,Japan

A total of 32 wild Hokkaido sika deer (Cervus nippon yesoensis) were shot (13 in summer, nine in autumn and 10 in winter) in the Syari district, Shiretoko Peninsula of Hokkaido Island, Japan. The ingested foods, rumen fermentation parameters and microbes were determined to evaluate digestive strategy and food availability in each season. Ingested foods and ruminal characteristics greatly varied by season. Rumen digesta mainly comprised of graminoids in summer, graminoids and agricultural products in autumn, and bark and twigs in winter. Rumen pH showed seasonal differences (P<0.05) and was lowest in summer, highest in winter, and intermediate in autumn, reflecting the seasonal differences in ruminal concentration of total volatile fatty acids which were significantly lower (P<0.05) in winter than in summer and autumn. Acetate proportions were significantly higher in winter than in other seasons (P<0.05), while the opposite trend was seen in proportions of propionate and butyrate. Rumen ammonia levels showed significant seasonal differences (P<0.05), decreasing from summer to autumn to winter. Rumen protozoa levels in autumn and winter decreased to 28 and 10% of the levels observed in summer, respectively (P<0.05 for both). The rumen bacteria level in winter was lower (P<0.05) than that in autumn, but no difference was seen for the other seasonal comparisons. Gram negative cocci were present in significantly higher proportions in winter than in other seasons (P<0.05), while Gram negative curved rods were less frequently observed in winter (P<0.05). Based on these results, wild sika deer in this area are shown to survive with rumen microbial populations altered with the dietary conditions that vary greatly by season.     

Identification of radiation-sensitive mutants in the Medaka, Oryzias latipes

We screened populations of N-ethyl-N-nitrosourea (ENU)-mutagenized Medaka, (Oryzias latipes) for radiation-sensitive mutants to investigate the mechanism of genome stability induced by ionizing radiation in developing embryos. F3 embryos derived from male founders that were homozygous for induced the mutations were irradiated with gamma-rays at the organogenesis stage (48hpf) at a dose that did not cause malformation in wild-type embryos. We screened 2130 F2 pairs and identified three types of mutants with high incidence of radiation-induced curly tailed (ric) malformations using a low dose of irradiation. The homozygous strain from one of these mutants, ric1, which is highly fertile and easy to breed, was established and characterized related to gamma-irradiation response. The ric1 strain also showed higher incidence of malformation and lower hatchability compared to the wild-type CAB strain after gamma-irradiation at the morula and pre-early gastrula stages. We found that the decrease in hatching success after gamma-irradiation, depends on the maternal genotype at the ric1 locus. Terminal deoxynucleotidyl transferase-mediated deoxy-UTP nick end-labeling assays showed a high frequency of apoptosis in the ric1 embryos immediately after gamma-irradiation at the pre-early gastrula stage but apoptotic cells were not observed before midblastula transition (MBT). The neutral comet assay revealed that the ric1 mutant has a defect in the rapid repair of DNA double-strand breaks induced by gamma-rays. These results suggest that RIC1 is involved in the DNA double strand break repair in embryos from morula to organogenesis stages, and unrepaired DNA double strand breaks in ric1 trigger apoptosis after MBT. These results support the use of the ric1 strain for investigating various biological consequences of DNA double strand breaks in vivo and for sensitive monitoring of genotoxicity related to low dose radiation.     

Inhibitory Effects of Extracellular Matrix Modulator(s) on Lipopolysaccharide (LPS)- and Acidosis-Damaged Glia Containing Cerebellar Granule Cell Cultures

The inhibitory effects of a novel chondroitin sulfate compound on lipopolysaccharide (LPS)- and acidosis-induced neuronal dysfunctions were examined. Cell viabilities in cultured neurons and/or astrocyte-rich cerebellar granule cells were measured by the calcein-AM method. Ten and 20 microg, as a final dosage, of LPS damaged less than 20% cells during a-2 h incubation. More than 5000 ng/ml of chondroitin sulphate-dipalmitoylphosphatidylethanolamine (CS-PE), but not chondroitin sulfate (CS) treatment, significantly inhibited such damage. Twenty microg of LPS damaged more than 40% cells during 24 h incubation, and these cell damages were significantly inhibited by less than 1000 ng/ml of CS-PE. Moreover, treatments with between 5 and 500 ng/ml CS-PE, but not CS, significantly reduced the number of acidosis-damaged cells in a dose-dependent manner. The current results indicate that modulator(s) of ECM and its derivative containing covalently linked dipalmitoylphosphatidylethanolamine show neuroprotective effects under conditions of brain inflammation.     

Extraordinary Changes in Excitatory Amino Acid Levels in Cerebrospinal Fluid of Influenza-Associated Encephalopathy of Children

The correlation between the glutamate-glutamine cycle and nitric oxide (NO) production in the central nervous system (CNS) of a new type of influenza-associated encephalopathy in children is discussed. When measurements of several amino acids and NOx (nitrite/nitrate) levels in the cerebrospinal fluid (CSF) using HPLC-fluorescence and -UV methods, respectively, were made. the CSF glutamate levels of patients with the new type of encephalitis were significantly lower, and both glutamine and NOx levels were significantly higher than those of the control group and the patients of the meningitis group. Results indicate that the turnover rate of glutamate in CNS, particularly in the brain, increases in the influenza-associated encephalopathy. The high mortality in the disease may correlate with the hyperactivity of supra-spinal glutamate neurons and the subsequent high activity levels of NOx in CNS.     

Novel evidence suggesting Clostridium difficile is present in human gut microbiota more frequently than previously suspected

Prevalence rate of Clostridium difficile in healthy human adults is believed to be very low. Our RT-PCR system using glass powder, which can eliminate PCR inhibitors, detected C. difficile toxin B mRNA in 16 of 30 fecal samples (53.3%) from healthy human adults. In contrast, we failed to detect toxin B in the same fecal samples by PCR using DNA templates extracted with phenol-chloroform. Our results suggest that PCR inhibitors in feces carried through phenol-chloroform extraction procedure might suppress the sensitivity of PCR and that C. difficile is actually present in human gut microbiota more frequently than previously suspected.