Design of species-specific oligonucleotide probes for the detection of Bacteroides and Parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal Bacteroides-Parabacteroides microbiota

AIMS

To develop species-specific monitoring techniques for rapid detection of Bacteroides and Parabacteroides inhabiting the mouse intestine by fluorescence in situ hybridization.

METHODS AND RESULTS

The specificity of oligonucleotide probes was evaluated by fluorescence whole-cell hybridization. Oligonucleotide probes specific for each species hybridized only with the target bacteria. Using these probes, caecal Bacteroides-Parabacteroides microbiota of conventional mice and specific pathogen-free (SPF) mice from three different breeders were analysed. It was shown that Bacteroides acidifaciens Group-1, Group-2 and Group-3 were dominant in conventional mice and SPF mice from two out of three breeders. Bacteroides vulgatus and Parabacteroides distasonis were detected in one of these two SPF breeding colonies in addition to Bact. acidifaciens. SPF mice of the remaining breeder harboured characteristic Bacteroides-Parabacteroides microbiota, consisting of Bacteroides sp. ASF519 and Bacteroides caccae.

CONCLUSIONS

Bacteroides acidifaciens is the dominant and most typical species in the mouse Bacteroides-Parabacteroides microbiota. The Group-3 was identified as a novel group and revealed to occupy a major niche together with Bact. acidifaciens Group-1 and Group-2.

SIGNIFICANCE AND IMPACT OF THE STUDY

The species-specific probe set developed in this study was the efficient tool for rapid detection of target bacterial groups inhabiting the mouse intestine. The results of this study provide important new information on the mouse Bacteroides-Parabacteroides community.

Vapor Phase Epitaxy of GaN Using Gallium Tri-Chloride and Ammonia

GaN films with good crystalline quality are grown on sapphire by atmospheric pressure vapor phase epitaxy using gallium tri-chloride (GaCl3) and ammonia (NH3). Epitaxial growth is carried out over temperature and V/III-ratio ranges of 800–1000°C and 100–1000, respectively. Typical growth rate obtained is in the range of 5–20 μm/hr. The films grown below 925°C typically show three dimensional (island) growth, while above that temperature, continuous films are obtained. Films grown at 975°C with a V/III ratio > 300 exhibit a smooth surface. XRD analysis shows that the films are single crystal with hexagonal polytype. Strong band-edge photoluminescence is observed with a FWHM of 60 meV at room temperature and 25 meV at 77K. The results indicate that this simple growth technique is effective for growing high quality bulk GaN, which can be used as a substrate for subsequent epitaxy. In order to further improve the surface morphology, a preliminary experiment on GaN growth on a thin GaN buffer layer prepared by gas source MBE is also presented.

Characterization of microbial consortia that reductively dechlorinate 4-chlorophenol and transform phenol to benzoate enriched from estuarine sediment of Lake Shinji

Monochlorophenols were degraded to benzoate via phenol by the initial dechlorination and the subsequent conversion of phenol to benzoate in anaerobic sediment samples of estuarine Lake Shinji under methanogenic conditions. To characterize bacteria that dechlorinate 4-chlorophenol and transform phenol to benzoate, we analyzed the microbial community structure of the enrichment culture with each 4-chlorophenol and phenol by the limiting dilution method with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene. After serial dilution of the culture, the 4-chlorophenol-dechlorinating culture consisted of two dominant bacteria, one of which was most homologous with Dehalobacter sp. In the enriched culture with phenol, minor band homologous with Cryptanaerobacter phenolicass corresponded to the transformation activity.

Observation of quasi-two-dimensional nonlinear interactions in a drift-wave streamer

A streamer, which is a bunching of drift-wave fluctuations, and its mediator, which generates the streamer by coupling with other fluctuations, have been observed in a cylindrical magnetized plasma. Their radial structures were investigated in detail by using the biphase analysis. Their quasi-two-dimensional structures were revealed to be equivalent with a pair of fast and slow modes predicted by a nonlinear Schrödinger equation based on the Hasegawa-Mima model.

Production of polyselenodipenicillamines, unique selenium compounds

Selenite (H(2)SeO(3)) reacts with thiol compounds (RSH) under acidic conditions to form selenotrisulfides (RSSeSR, i.e. monoselenodithiols). The stoichiometry of the reaction is proposed as 4RSH+H(2)SeO(3)-->RSSeSR+RSSR+3H(2)O. Surprisingly, we found novel polynuclear selenium-containing compounds, i.e. polyselenodipenicillamines (PenSSe(2-4)SPen), in the reaction of D-penicillamine (PenSH) with H(2)SeO(3). The selenium-centered features of PenSSe(2-4)SPen were determined by (1)H-NMR and LC-MS/MS analyses, showing that the selenium isotope abundance patterns of the compounds were in good agreement with the theoretically-calculated ones. In order to better understand the mechanisms for PenSSe(2-4)SPen production, various molar ratio of H(2)SeO(3) (1/8 to 4 times of PenSH) was reacted with PenSH, and the concentration of the products was calculated from integral values of dimethyl proton signals for PenSSe(1-2)SPen as compared with methyl proton signals for acetic acid (an internal standard). Total PenSSe(1-2)SPen concentration was increased with increasing of H(2)SeO(3), in which concomitant decrease of PenSSPen (disulfide form of PenSH) was observed. Based on these results, we proposed the PenSSe(2-4)SPen production mechanisms being involved in penicillamine selenopersulfides (PenSSe(1-2)H).

Diffusion of GM primer and dentin adhesive into EDTA-conditioned dentin

The aim of this study was to investigate the diffusion of red-stained experimental GM primer and blue-stained dentin bonding agent into EDTA-conditioned dentin and the effect of GM priming on contraction gap formation. After GM priming at 0, 35, 70, or 100 vol%, marginal adaptation was evaluated by measuring the wall-to-wall contraction gap width of a light-activated resin composite (Palfique Estelite, Tokuyama Dental, Japan) mediated with a commercial dentin bonding agent (Clearfil Photo Bond, Kuraray Medical, Japan). Contraction gap formation was completely prevented when treated with 35 vol% GM primer. Moreover, after treatment with 35 vol% GM, the red and blue dyes of stained GM primer and dentin bonding agent diffused up to a depth of 40 µm into the dentin surface. The diffusion of primer and bonding agent into EDTA-conditioned dentin was essential for bonding efficacy although SEM observation revealed an absence of hybrid layer formation.

Ultralow-repetition-rate, high-energy, polarization-maintaining, Er-doped, ultrashort-pulse fiber laser using single-wall-carbon-nanotube saturable absorber

An ultralow-repetition-rate, all-polarization-maintaining (PM), Er-doped, ultrashort-pulse fiber laser was demonstrated using a single-wall-carbon-nanotube polyimide film. Using a ring cavity configuration, output pulses with pulse energy of 0.7-2.6 nJ were obtained at an ultralow repetition rate of 943-154 kHz for a fiber length of 0.1-1.3 km. A novel θ (theta) cavity configuration was proposed, which enabled us to reduce the required fiber length by half. A repetition rate of 132 kHz was achieved using this configuration with 909 m of PM fiber.

The locus coeruleus projects to the mesencephalic trigeminal nucleus in rats

The ganglion-cells in the mesencephalic trigeminal nucleus (Me5) process proprioceptive signals from the masticatory muscles and the periodontal ligaments, and are considered to regulate the rhythm of biting and bite strength. The locus coeruleus (LC) is the major source of noradrenergic projections in the brain and plays an important role in stressful situations and aggressive behavior. The two nuclei are adjacently located to each other in the lateral part of the periaqueductal gray matter of the fourth ventricle. In the present study, a small number of neurons were labeled in the LC with a neuronal tracer biotinylated dextran amine. The labeled single axons were traced from the labeled LC neuronal somata to the ipsilateral Me5 region where they produced terminal-like swellings. Some of the swellings appeared to make contact with the ganglion-cells of the Me5. These results suggest that the LC regulates the bite strength by modifying the ganglion-cell activity in the Me5. Additionally, these findings shed light on the enigma of why the main part of the Me5 at the level of pons is located at the lateral end of the gray matter ventral to the fourth ventricle, instead of at the trigeminal ganglion.

Measurement of shear bond strength to intact dentin

Previously, we reported that the integrity of a resin composite restoration deteriorated when the dentin cavity wall was decalcified by conditioning. In this study, to evaluate the bonding between dentin adhesive and non-decalcified dentin surface, we experimented with a novel method of using a high-pressure water spray device to prepare smear layer-free dentin surfaces. When the smear layer was removed, shear bond strength significantly increased regardless of the removal method employed. Further, with glyceryl monomethacrylate (GM) priming, no significant differences in bond strength were observed among these smear layer removal methods: ethylenediamine tetraacetic acid (EDTA) conditioning, phosphoric acid conditioning, and removal by water spray. It was also found that GM priming was key to achieving marginal integrity, whereas contraction gap width increased with phosphoric acid conditioning. It was thus concluded that the efficacy of a dentin adhesive should be evaluated by consistently observing the contraction gap in three-dimensional cavities rather than by mere measurement of bond strength to a flat dentin surface.

Wideband spectral compression of wavelength-tunable ultrashort soliton pulse using comb-profile fiber

We demonstrated spectral compression of ultrashort soliton pulses in a wide wavelength region based on an adiabatic soliton spectral compression technique using a comb-profile fiber. The comb-profile fiber was carefully designed using numerical analysis and fabricated using a conventional single-mode fiber and a dispersion-shifted fiber. The spectral width of a 200 fs soliton pulse was compressed from 12 to 15 nm to 0.54-0.71 nm in the wavelength region 1620-1850 nm, giving a spectral compression factor of up to 19.8-25.9. Owing to the soliton effect, the side lobe level was suppressed to -19.2 to -9.7 dB.

Effects of herbicides on Lemna gibba and recovery from damage after prolonged exposure

To determine the potential impact of contaminants on the aquatic vascular plants Lemna sp., toxicity tests are usually conducted for a 4- to 14-day exposure, and the toxicity is usually expressed as EC50. However, the effects of longer exposure and the recovery potential after exposure to chemicals are other important factors which should be considered. We present the relative risks of a variety of exposure scenarios and recovery potentials from damage, using herbicides with different modes of action. Toxicity was assessed on the basis of both EC50 and relative growth rate (RGR) compared with untreated controls in exposure and recovery. The EC50 of atrazine was found to be 89 ppb, and its phytostatic concentrations were 1600 and 800 ppb for exposure periods of 14 and 28 days, respectively, and no phytocidal effects were observed up to 3200 ppb for a 28-day exposure. The RGR in recovery was not affected by the RGR in exposure, and regrowth was possible even after complete inhibition of growth for 28 days at the highest concentration tested. Alachlor, with an EC50 of 31 ppb, was phytostatic at 400 ppb for a 14-day exposure and phytocidal at 200 ppb for 21- and 28-day exposures. Paraquat, with an EC50 of 31 ppb, showed phytocidal rather than phytostatic effects. All phytostatic fronds could not grow in the recovery period, and the phytocidal concentration decreased with exposure period, from 80 ppb for a 7-day exposure to 20 ppb for 21- and 28-day exposures. The RGR of alachlor and paraquat in recovery was dependent on the RGR in exposure. In the case of cyclosulfamuron, phytostatic concentrations were 100 and 50 ppb for 7- and 14-day exposures, respectively. In the case of exposures longer than 21 days, however, it exhibited phytocidal activity at 10 ppb. The results of this study suggest that it is important to examine the effects of chemicals over a longer exposure period as well as the recovery potential from damage for reliable ecological risk assessment.

Objective skill analysis and assessment in neurosurgery by using an ultra-miniaturized inertial measurement unit WB-3--pilot tests

In recent years there has been an ever increasing amount of research and development of technologies and methods to improve the quality and the performance of advanced surgery. In several fields, such as laparoscopy, various training methods and metrics have been proposed, both to improve the surgeon's abilities and also to assess her/his skills. For neurosurgery, however, the extremely small movements and target operating space involved have prevented until now the development of similar methodologies and systems. In this paper we present the development of an ultra-miniaturized Inertial Measurement Unit (IMU) and its application for neurosurgery skill assessment in a simple pick and place scenario. This analysis is a preliminary yet fundamental step to realize a better training/evaluation system for neurosurgeons, and to objectively evaluate and understand how the neurosurgery is performed.