Draft Genome Sequences of Two Antimicrobial Compound-Producing Strains of Bacillus Species, TM-R and SY1-1.

Two antimicrobial compound-producing strains of Bacillus species, namely, TM-R and SY1-1, have been identified previously. In this study, we report the draft genome sequences of these strains and demonstrate the presence of 12 and 14 gene clusters for secondary metabolite biosynthesis in TM-R and SY1-1, respectively.

[A Preliminary Study of Optimal Imaging Acquisition Parameters for Fiducial Markers in Liver Stereotactic Body Radiotherapy].

In liver stereotactic body radiotherapy (SBRT) using fiducial markers, the accuracy of automatic image recognition of fiducial markers is important, and the imaging dose cannot be neglected in image-guided radiotherapy. Optimal imaging parameters of fiducial markers were investigated for automatic image recognition and imaging dose. We investigated automatic recognition with fiducial markers of different shapes and sizes. In addition, the optimum imaging conditions were examined based on the automatic recognition when the presence or absence of a filter, focal spot size, and phantom thickness were altered using the fiducial markers with a high automatic recognition. The results for different shapes and sizes of fiducial markers showed that larger markers were recognized more automatically, whereas shorter markers were recognized in the correct position. By using the filter, we were able to reduce the imaging dose by one third or one half compared to the case without the filter. The results for the focal spot size showed that using a larger size resulted in higher automatic recognition accuracy than using a smaller size. For the relationship between the automatically recognized imaging conditions and the air kerma when the phantom thickness was altered, it was necessary to keep the tube current-time product constant and increase the tube voltage in order to avoid poor recognition accuracy. The parameters we proposed are effective in shortening the treatment time and reducing the imaging dose because they allow us to acquire images with low doses and high accuracy of automatic recognition.

Optimization of injection dose in 18F-FDG PET/CT based on the 2020 national diagnostic reference levels for nuclear medicine in Japan.

OBJECTIVE: Recently, the national diagnostic reference levels (DRLs) in Japan were revised as the DRLs 2020, wherein the body weight-based injection dose optimization in positron emission tomography/computed tomography using 18F-fluoro-2-deoxy-D-glucose (18F-FDG PET/CT) was first proposed. We retrospectively investigated the usefulness of this optimization method in improving image quality and reducing radiation dose. METHODS: A total of 1,231 patients were enrolled in this study. A fixed injection dose of 240 MBq was administered to 624 patients, and a dose adjusted to 3.7 MBq/kg body weight was given to 607 patients. The patients with body weight-based injection doses were further divided according to body weight: group 1 (≤ 49 kg), group 2 (50-59 kg), group 3 (60-69 kg), and group 4 (≥ 70 kg). The effective radiation dose of FDG PET was calculated using the conversion factor of 0.019 mSv/MBq, per the International Commission on Radiological Protection publication 106. Image quality was assessed using noise equivalent count density (NECdensity), which was calculated by excluding the counts of the brain and bladder. The usefulness of the injection dose optimization in terms of radiation dose and image quality was analyzed. RESULTS: The body weight-based injection dose optimization significantly decreased the effective dose by 11%, from 4.54 ± 0.1 mSv to 4.05 ± 0.8 mSv (p < 0.001). Image quality evaluated by NECdensity was also significantly improved by 10%, from 0.39 ± 0.1 to 0.43 ± 0.2 (p < 0.001). In no case did NECdensity deteriorate when the effective dose was decreased. In group 1, the dose decreased by 32%, while there was no significant deterioration in NECdensity (p = 0.054). In group 2, the dose decreased by 17%, and the NECdensity increased significantly (p < 0.01). In group 3, the dose decreased by 3%, and the NECdensity increased significantly (p < 0.01). In group 4, the dose increased by 14%, but there was no significant change in the NECdensity (p = 0.766). CONCLUSION: Body weight-based FDG injection dose optimization contributed to not only the reduction of effective dose but also the improvement of image quality in patients weighing between 50 and 69 kg.

Temporal trends in PCB concentrations in mussels collected from areas affected by the Great East Japan Earthquake and Tsunami.

In the Great East Japan Earthquake of 11 March 2011, a magnitude 9.0 earthquake and accompanying tsunami struck the Tohoku region of Japan. The tsunami washed away old equipment containing polychlorinated biphenyls (PCBs) stored in the region's factories, and these PCBs may have leaked out of their casings into the marine environment. In this study, we evaluate marine PCB contamination by comparing mussels collected before (in 2005) and after (June 2011) the tsunami. PCB contamination levels were significantly elevated in mussel samples collected after the tsunami in June 2011 (3 months after the tsunami). This indicates that PCBs (specifically, formulation KC-400) leaked out of old equipment swept away by the tsunami and accumulated in mussels. PCBs were estimated to have an environmental half-life (EHL) in mussels of 4 months. Our results show that an earthquake and subsequent tsunami can cause elevated PCB contamination in the marine environment.

Antifungal spectrum characterization and identification of strong volatile organic compounds produced by Bacillus pumilus TM-R.

To obtain biocontrol agents for suppression of food-deteriorating fungi during storage of agricultural products, bacteria producing volatile organic compounds (VOCs) with strong antifungal activity were screened and isolated from various environmental samples. Among 136 bacterial isolates, strain TM-R showed the strongest and broadest antifungal activity. Based on physiological and genetical characterization, the bacterium was identified as Bacillus pumilus. The effects of VOCs produced by the bacterium, which was grown on four types of agar media (nutrient, Trypto-Soya, Luria-Bertani, and TM Enterprise), were examined against six species of fungi (Alternaria alternata, Aspergillus niger, Cladosporium cladosporioides, Curvularia lunata, Fusarium oxysporum, and Penicillium italicum) in both small- and large-scale tests (plate and 12-L tests, respectively). In the plate test, the bacterium markedly suppressed the mycelial growth of five fungi (Alternaria alternata, Cladosporium cladosporioides, Curvularia lunata, F. oxysporum, and P. italicum) but promoted the growth of Aspergillus niger. In the 12-L test, the degree of growth inhibitiondecreased; however, the bacterium grown on TMEA still exhibited the strongest inhibition, especially against P. italicum (growth inhibition rate of 93%). Surprisingly, the growth of Aspergillus niger was promoted even more strongly (-36%) by the bacterium on TMEA than in the plate test (-9%). Twenty-two of 32 VOCs detected by GC-MS were identified using three databases (NIST 2011, AromaOffice, and AroChemBase). The species and concentration of detected VOCs differed greatly among growth media. To identify causative antifungal VOCs, we estimated the correlation between growth inhibition of P. italicum by the bacterium grown on each of the four media vs. the relative abundance of individual VOCs. As a result, four VOCs (methyl isobutyl ketone, ethanol, 5-methyl-2-heptanone, and S-(-)-2-methylbutylamine) were determined to be the predominant antifungal VOCs. To the best of our knowledge, this study is the first to specify causative antifungal VOCs using such an approach.

Development of a novel scheme for rapid screening for environmental micropollutants in emergency situations (REPE) and its application for comprehensive analysis of tsunami sediments deposited by the great east Japan earthquake.

The tsunami triggered by the Great East Japan Earthquake of March 2011, the strongest quake ever recorded in Japan, deposited tsunami sediments along the coastline of the affected area. Because the sediments contained a wide variety of hazardous chemicals, including organic micropollutants, a method for rapidly evaluating the environmental and human health risks of such chemicals is necessary. For this purpose, we propose a novel three-step scheme designated "rapid screening for environmental micropollutants in emergency situations (REPE)". In the first step, samples are subjected to target screening analysis using an automated identification and quantification system (TSA-AIQS) involving gas chromatography mass spectrometry (GC-MS). In the second step, the chemicals detected by TSA-AIQS analysis are quantified precisely by conventional target analysis. The third step is risk assessment of the target chemicals. TSA-AIQS analysis of the tsunami sediments detected 63 substances, including polycyclic aromatic hydrocarbons (both native and alkylated PAHs) at high concentrations. These PAHs were precisely quantified by target analysis, and the concentrations were used to assess the health risks posed by oral intake, which were found to be negligible. Our results suggest that the REPE scheme will be useful for rapid, comprehensive screening and risk assessment in emergency situations.

Photo-induced semimetallic states realised in electron-hole coupled insulators.

Using light to manipulate materials into desired states is one of the goals in condensed matter physics, since light control can provide ultrafast and environmentally friendly photonics devices. However, it is generally difficult to realise a photo-induced phase which is not merely a higher entropy phase corresponding to a high-temperature phase at equilibrium. Here, we report realisation of photo-induced insulator-to-metal transitions in Ta2Ni(Se1-xSx)5 including the excitonic insulator phase using time- and angle-resolved photoemission spectroscopy. From the dynamic properties of the system, we determine that screening of excitonic correlations plays a key role in the timescale of the transition to the metallic phase, which supports the existence of an excitonic insulator phase at equilibrium. The non-equilibrium metallic state observed unexpectedly in the direct-gap excitonic insulator opens up a new avenue to optical band engineering in electron-hole coupled systems.

Enhancement of CO2 adsorption on oxygen-functionalized epitaxial graphene surface under near-ambient conditions.

The functionalization of graphene is important in practical applications of graphene, such as in catalysts. However, the experimental study of the interactions of adsorbed molecules with functionalized graphene is difficult under ambient conditions at which catalysts are operated. Here, the adsorption of CO2 on an oxygen-functionalized epitaxial graphene surface was studied under near-ambient conditions using ambient-pressure X-ray photoelectron spectroscopy (AP-XPS). The oxygen-functionalization of graphene is achieved in situ by the photo-induced dissociation of CO2 with X-rays on graphene in a CO2 gas atmosphere. The oxygen species on the graphene surface is identified as the epoxy group by XPS binding energies and thermal stability. Under near-ambient conditions of 1.6 mbar CO2 gas pressure and 175 K sample temperature, CO2 molecules are not adsorbed on the pristine graphene, but are adsorbed on the oxygen-functionalized graphene surface. The increase in the adsorption energy of CO2 on the oxygen-functionalized graphene surface is supported by first-principles calculations with the van der Waals density functional (vdW-DF) method. The adsorption of CO2 on the oxygen-functionalized graphene surface is enhanced by both the electrostatic interactions between the CO2 and the epoxy group and the vdW interactions between the CO2 and graphene. The detailed understanding of the interaction between CO2 and the oxygen-functionalized graphene surface obtained in this study may assist in developing guidelines for designing novel graphene-based catalysts.

Variability and reliability of POP concentrations in multiple breast milk samples collected from the same mothers.

Risk assessment of infant using a realistic persistent organic pollutant (POP) exposure through breast milk is essential to devise future regulation of POPs. However, recent investigations have demonstrated that POP levels in breast milk collected from the same mother showed a wide range of variation daily and monthly. To estimate the appropriate sample size of breast milk from the same mother to obtain reliable POP concentrations, breast milk samples were collected from five mothers living in Japan from 2006 to 2012. Milk samples from each mother were collected 3 to 6 times a day through 3 to 7 days consecutively. Food samples as the duplicated method were collected from two mothers during the period of breast milk sample collection. Those were employed for POP (PCBs, DDTs, chlordanes, and HCB) analysis. PCB concentrations detected in breast milk samples showed a wide range of variation which was maximum 63 and 60% of relative standard deviation (RSD) in lipid and wet weight basis, respectively. The time course trend of those variations among the mothers did not show any typical pattern. A larger amount of PCB intake through food seemed to affect 10 h after those concentrations in breast milk in lipid weight basis. Intraclass correlation coefficient (ICC) analyses indicated that the appropriate sample size for good reproducibility of POP concentrations in breast milk required at least two samples for lipid and wet weight basis.

Femtosecond to picosecond transient effects in WSe 2 observed by pump-probe angle-resolved photoemission spectroscopy.

Time-dependent responses of materials to an ultrashort optical pulse carry valuable information about the electronic and lattice dynamics; this research area has been widely studied on novel two-dimensional materials such as graphene, transition metal dichalcogenides (TMDs) and topological insulators (TIs). We report herein a time-resolved and angle-resolved photoemission spectroscopy (TRARPES) study of WSe2, a layered semiconductor of interest for valley electronics. The results for below-gap optical pumping reveal energy-gain and -loss Floquet replica valence bands that appear instantaneously in concert with the pump pulse. Energy shift, broadening, and complex intensity variation and oscillation at twice the phonon frequency for the valence bands are observed at time scales ranging from the femtosecond to the picosecond and beyond. The underlying physics is rich, including ponderomotive interaction, dressing of the electronic states, creation of coherent phonon pairs, and diffusion of charge carriers - effects operating at vastly different time domains.

Optically detecting the edge-state of a three-dimensional topological insulator under ambient conditions by ultrafast infrared photoluminescence spectroscopy.

Ultrafast infrared photoluminescence spectroscopy was applied to a three-dimensional topological insulator TlBiSe2 under ambient conditions. The dynamics of the luminescence exhibited bulk-insulating and gapless characteristics bounded by the bulk band gap energy. The existence of the topologically protected surface state and the picosecond-order relaxation time of the surface carriers, which was distinguishable from the bulk response, were observed. Our results provide a practical method applicable to topological insulators under ambient conditions for device applications.

Exposure assessment of organophosphorus and organobromine flame retardants via indoor dust from elementary schools and domestic houses.

To assess the exposure of flame retardants (FRs) for school-children, organophosphorus flame retardants and plasticizers (PFRs) and organobromine flame retardants (BFRs) were determined in the indoor dust samples collected from elementary schools and domestic houses in Japan in 2009 and 2010. PFRs were detected in all the dust samples analyzed and the highest concentration of total PFRs was thousand-fold higher than that of BFRs. Among the PFRs, tris(butoxyethyl)phosphate (TBOEP) showed the highest concentration with a median (med.) of 270,000 ng g(-1) dry weight (3700-5,500,000 ng g(-1) dry weight), followed by tris(methylphenyl)phosphate (TMPPs)>triphenyl phosphate (TPHP)=tris(1,3-dichloro-2-propyl)phosphate (TDCIPP)=tris(2-chloroisopropyl)phosphate (TCIPP)=tris(2chloroethyl)phosphate (TCEP)>ethylhexyl diphenyl phosphate (EHDPP). Significantly higher concentrations of TBOEP, tri-n-butyl phosphate (TNBP), TPHP, TMPPs, and total-PFRs were found in dust samples from elementary schools than from domestic houses. It might be due to that higher concentrations of TBOEP (as leveling agent) were detected from the floor polisher/wax products collected in those elementary schools. On the other hand, significantly higher concentrations of TCEP, TCIPPs, and total chloroalkyl-PFRs were found in domestic houses than in elementary schools. Exposure assessments of PFRs via indoor dust from elementary schools and domestic houses were conducted by calculating the hazard quotient (HQ). Among PFRs, HQs for TBOEP exceeded 1 (higher than reference dose: RfD) and its highest value was 1.9. To reduce the intake of TBOEP by school-children, it is recommended that the use of floor polisher/wax containing TBOEP be reduced in schools.

Double-color fluorescence in situ hybridization (FISH) for the detection of Bacillus anthracis spores in environmental samples with a novel permeabilization protocol.

For anti-bioterrorism measures against the use of Bacillus anthracis, a double-color fluorescence in situ hybridization (FISH) is proposed, for the rapid and specific detection of B. anthracis. The probes were designed based on the differences in 16S and 23S rRNA genes of B. cereus group. A new permeabilization protocol was developed to enhance the permeability of FISH probes into B. anthracis spores. The highest detection rate (90.8 ± 0.69) of B. anthracis spores by FISH was obtained with successive incubation steps with 50% ethanol at 80 °C, a mixture of SDS/DTT solution (10mg/ml SDS, 50mM DTT) at 65 °C and finally in a lysozyme solution (20mg/ml) at 37 °C for 30 min each. This protocol was evaluated for the detection of B. anthracis spores in soil and air samples after adding formalin-fixed spores at different densities. The results have proven the success of double-color FISH in detecting B. anthracis spores in air samples in the range of 10(3) spores/m(3) and above. Conversely, for detecting B. anthracis spores in a soil sample, the lowest detection limit was found to be 10(7) spores/g dry soils. These results confirm the applicability of the developed permeabilization protocol, combined with the double-color FISH technique in specific detection of B. anthracis in soil and air samples.

Visualization and direct counting of individual denitrifying bacterial cells in soil by nirK-targeted direct in situ PCR.

The abundance of denitrifying bacteria in soil has been determined primarily by the conventional most probable number (MPN) method. We have developed a single-cell identification technique that is culture-independent, direct in situ PCR, to enumerate denitrifying bacteria in soils. The specificity of this method was evaluated with six species of denitrifying bacteria using nirK as the target gene; Escherichia coli was used as a negative control. Almost all (97.3%-100%) of the nirK-type denitrifying bacteria (Agromonas oligotrophica, Alcaligenes faecalis, Achromobacter denitrificans, Bradyrhizobium japonicum, and Pseudomonas chlororaphis) were detected by direct in situ PCR, whereas no E. coli cells and only a few cells (2.4%) of nirS-type denitrifying bacteria (Pseudomonas aeruginosa) were detected. Numbers of denitrifying bacteria in upland and paddy soil samples quantified by this method were 3.3 × 10(8) to 2.6 × 10(9) cells g(-1) dry soil. These values are approximately 1,000 to 300,000 times higher than those estimated by the MPN method. These results suggest that direct in situ PCR is a better tool for quantifying denitrifying bacteria in soil than the conventional MPN method.

CIELAB color variables as indicators of compost stability.

The composting process of different organic wastes both in laboratory and on a large-scale was characterized using CIELAB color variables to evaluate compost stability for the better application in agriculture. The time courses of the CIELAB variables of composting materials were determined directly from the bottom of a glass petri dish filled with dried and ground samples using a Minolta Color Reader (CR-13) calibrated with clean empty petri dishes placed on a white tile. To compare the proposed method with conventional methods, the same materials were also evaluated using commonly used compost stability evaluation indices. Most of the CIELAB variables of a compost made from a mixture of green tea waste and rice bran reached a plateau after 84 days of composting and showed strong relationships with the commonly used compost stability evaluation indices. The time needed for CIELAB variables, especially the L*and b* values, to stabilize at large-scale composting plants of cattle litter, farmyard manure, kitchen garbage and bark compost, were more or less similar to the times of maturation evaluated by the respective compost producers. The CIELAB color variable offers a new, simple, rapid and inexpensive means of evaluating compost stability and its quality prior to agricultural use.

Direct viable count combined with fluorescence in situ hybridization (DVC-FISH) for specific enumeration of viable escherichia coli in cow manure.

A direct viable count procedure combined with fluorescence in situ hybridization (DVC-FISH) was developed for the specific detection and enumeration of viable Escherichia coli in cow manure. The DVC method was performed by trapping bacterial cells, extracted from cow manure samples, onto Nucleopore filters followed by incubation on a DVC medium containing yeast extract and four gyrase inhibitors. E. coli cells were identified by using the probe ES445. The DVC method efficiently promoted the elongation of E. coli cells and allowed for the recognition of individual cell division events, by observing microcolonies. Cell recovery by DVC-FISH together with bacterial extraction, was 53% with an inoculum of 10(7) to 10(10) cells g(-1) dry weight, when the manure samples were inoculated with a fresh culture of E. coli and determinations were made immediately. An examination of the survival of E. coli in a cow manure microcosm showed that an increasing fraction of E. coli became non-culturable but were still detectable by DVC-FISH. All these results suggest that DVC-FISH is useful for enumerating viable, even non-culturable, E. coli in cow manure.

Is Histoplasma capsulatum a native inhabitant of Japan?

Histoplasmosis is an infectious disease caused by inhaling spores of the fungal pathogen H. capsulatum and in Japan is considered an imported mycosis. However, some patients in Japan with histoplasmosis have no history of traveling overseas nor of risk of occupational exposure to Histoplasma. To investigate the possibility of native distribution of Histoplasma in Japan, 187 bat guano samples from 67 bat-inhabited caves in 17 prefectures were collected. These were examined for H. capsulatum by culture and Histoplasma-specific PCR in three independent laboratories. No H. capsulatum was detected by either method, therefore H. capsulatum is unlikely to be present in bat guano in Japanese caves.

Inhibitory effect of branched-chain amino acid granules on progression of compensated liver cirrhosis due to hepatitis C virus.

BACKGROUND: A phase II randomized controlled trial was conducted in patients with compensated liver cirrhosis to investigate the inhibitory effect of branched-chain amino acid (BCAA) granules for oral use (TK-98) on disease progression. METHODS: Patients who had compensated liver cirrhosis due to hepatitis C virus with baseline serum albumin levels between 3.6 and 4.5 g/dl were assigned to the TK-98 group, which was treated with BCAA granules (TK-98) for 168 weeks, or to a control group (no treatment). RESULTS: No symptoms indicating decompensated cirrhosis, including ascites, edema, and hepatic encephalopathy were reported in either the TK-98 or control group during the study observation period. Hepatocellular carcinoma (HCC) was noted in eight of the 39 patients studied, and of these three received TK-98 (15.8%) and five were untreated (25.0%). A time-to-event analysis for the effect of BCAA therapy on development of HCC revealed no statistically significant differences between the two groups. However, an additional analysis of data from a subgroup with a baseline serum albumin level of <4.0 g/dl showed that the incidence of HCC was likely to be lower in BCAA-treated patients. CONCLUSIONS: BCAA may inhibit hepatic carcinogenesis in patients with compensated cirrhosis with a serum albumin level of <4.0 g/dl.

Rapid and automated enumeration of viable bacteria in compost using a micro-colony auto counting system.

The micro-colony method was used to enumerate viable bacteria in composts. Cells were vacuum-filtered onto polycarbonate filters and incubated for 18 h on LB medium at 37 degrees C. Bacteria on the filters were stained with SYBR Green II, and enumerated using a newly developed micro-colony auto counting system which can automatically count micro-colonies on half the area of the filter within 90 s. A large number of bacteria in samples retained physiological activity and formed micro-colonies within 18 h, whereas most could not form large colonies on conventional media within 1 week. The results showed that this convenient technique can enumerate viable bacteria in compost rapidly for its efficient quality control.

Factors associated with the virological response of lamivudine-resistant hepatitis B virus during combination therapy with adefovir dipivoxil plus lamivudine.

BACKGROUND: The aim of this study was to investigate the factors associated with the response of lamivudine-resistant hepatitis B virus (HBV) during combination therapy with adefovir dipivoxil plus lamivudine. METHODS: Sixty-three patients with breakthrough hepatitis received a 10-mg once-daily dose of oral adefovir dipivoxil. RESULTS: The rates of undetectable serum HBV-DNA were 49.2% after 24 weeks, 61.9% after 48 weeks, and 67.2% after 72 weeks. The cumulative hepatitis B e antigen (HBeAg) loss rates in patients with alanine aminotransferase (ALT) levels of more than twice the upper limit of normal (ULN) were significantly higher than in patients with ALT less than twice the ULN (P = 0.0145). Multivariate analysis revealed that baseline ALT level (P = 0.003) and HBeAg status (P = 0.049) were associated with early virological response. CONCLUSIONS: Baseline ALT level was associated with HBeAg loss and seroconversion, and baseline ALT level and HBeAg status were associated with the virological response of lamivudine-resistant HBV during combination therapy with adefovir dipivoxil plus lamivudine.