Characterization and Distribution of Agar-degrading Steroidobacter agaridevorans sp. nov., Isolated from Rhizosphere Soils.

The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-BT was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-BT and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-BT. However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95-96% against strain KA5-BT, indicating that they are different species from S. agariperforans KA5-BT. To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a meta-analysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant- and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-BT and YU21-B grew at 15-40°C and pH 6.0-12 and contained C16:0 as the dominant cell fatty acid, whereas KA5-BT showed no growth at 40°C and pH 12 and contained a moderate amount of C16:0. Based on these characteristics, SA29-BT (JCM 333368T=KCTC 72223T) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.

Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique.

PCR clamping by locked nucleic acid (LNA) oligonucleotides is an effective technique for selectively amplifying the community SSU rRNA genes of plant-associated bacteria. However, the original primer set often shows low amplification efficiency. In order to improve this efficiency, new primers were designed at positions to compete with LNA oligonucleotides. Three new sets displayed higher amplification efficiencies than the original; however, efficiency varied among the primer sets. Two new sets appeared to be available in consideration of bacterial profiles by next-generation sequencing. One new set, KU63f and KU1494r, may be applicable to the selective gene amplification of plant-associated bacteria.

Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant-Associated Fungi.

The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant-associated fungi due to the similar homologies of sequences in primer-annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3' end of the primer-binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant-associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant-associated fungi.

Draft Genome Sequences of Streptomyces scabiei S58, Streptomyces turgidiscabies T45, and Streptomyces acidiscabies a10, the Pathogens of Potato Common Scab, Isolated in Japan.

The draft genome sequences of the three pathogens of potato common scab, Streptomyces scabiei S58, Streptomyces turgidiscabies T45, and Streptomyces acidiscabies a10, isolated in Japan, are presented here. The genome size of each strain is >10 Mb, and the three pathogenic strains share genes located in a pathogenicity island previously described in other pathogenic Streptomyces species.

[Effects of manure application on the diversity of corn root endophytic bacterial communities at seedling stage in eroded Mollisols.] / æ–½ç”¨æœ‰æœºè‚¥å¯¹ä¾µèš€é»‘åœŸçŽ‰ç±³è‹—æœŸæ ¹å† ç”Ÿç»†èŒå¤šæ ·æ€§çš„å½±å“.

In order to investigate the change of root endophytic bacterial communities under soil erosion condition, and to evaluate the response of root endophytic bacteria to manure fertilizer, we adopted the LNA-PCR clamping and 454 bar-coded pyrosequencing methods to study the corn root endophytic bacterial communities under 30 cm topsoil erosion and manure fertilization conditions. No topsoil removing (0 cm) and only chemical fertilizer treatment were used as control. A total of 37820 valid sequences of 16S rDNA were obtained, mainly distributed in 4 phyla, 35 classes, 214 genera and 782 OTUs. The dominant phyla were Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, but their proportions varied in different samples. The diversity of corn root endophytic bacteria decreased in soil erosion condition. In the topsoil removing soil and no erosion soil, the diversity of corn root endophytic bacterial communities increased by manure application, and the effect was more obvious in the topsoil removing soil.

Development of LNA oligonucleotide-PCR clamping technique in investigating the community structures of plant-associated bacteria.

Simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is major limitation in investigating the community structures of plant-associated bacteria. Although locked nucleic acid (LNA) oligonucleotides was designed to selectively amplify the bacterial small subunit rRNA genes by applying the PCR clamping technique, those for plastids were applicable only for particular plants, while those for mitochondria were available throughout most plants. To widen the applicable range, new LNA oligonucleotides specific for plastids were designed, and the efficacy was investigated. PCR without LNA oligonucleotides predominantly amplified the organelle genes, while bacterial genes were predominantly observed in having applied the LNA oligonucleotides. Denaturing gradient gel electrophoresis (DGGE) analysis displayed additional bacterial DGGE bands, the amplicons of which were prepared using the LNA oligonucleotides. Thus, new designed LNA oligonucleotides specific for plastids were effective and have widened the scope in investigating the community structures of plant-associated bacteria.

Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost.

A thermophilic, agar-degrading bacterium, strain FAB2(T), was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2(T) belonged to the family Paenibacillaceae within the phylum Firmicutes. However, FAB2(T) was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus, 91.8 % for Paenibacillus barengoltzii, 89.4 % for Cohnella lupini, 90.1 % for Fontibacillus aquaticus, and 89.0 % for Saccharibacillus sacchari. Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50-65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0-8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2(T) ( = NBRC 109510(T) = KCTC 33130(T)) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae, for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.

Cell-autonomous signal transduction in the Xenopus egg Wnt/ß-catenin pathway.

Wnt proteins are thought to bind to their receptors on the cell surfaces of neighboring cells. Wnt8 likely substitutes for the dorsal determinants in Xenopus embryos to dorsalize early embryos via the Wnt/ß-catenin pathway. Here, we show that Wnt8 can dorsalize Xenopus embryos working cell autonomously. Wnt8 mRNA was injected into a cleavage-stage blastomere, and the subcellular distribution of Wnt8 protein was analyzed. Wnt8 protein was predominantly found in the endoplasmic reticulum (ER) and resided at the periphery of the cells; however, this protein was restricted to the mRNA-injected cellular region as shown by lineage tracing. A mutant Wnt8 that contained an ER retention signal (Wnt8-KDEL) could dorsalize Xenopus embryos. Finally, Wnt8-induced dorsalization occurred only in cells injected with Wnt8 mRNA. These experiments suggest that the Wnt8 protein acts within the cell, likely in the ER or on the cell surface in an autocrine manner for dorsalization.

Application of Locked Nucleic Acid (LNA) oligonucleotide-PCR clamping technique to selectively PCR amplify the SSU rRNA genes of bacteria in investigating the plant-associated community structures.

The simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is a major limitation in investigating the community structures of bacteria associated with plants because organelle SSU rRNA genes are easily amplified by PCR using primer sets that are specific to bacteria. To inhibit the amplification of organelle genes, the locked nucleic acid (LNA) oligonucleotide-PCR clamping technique was applied to selectively amplify bacterial SSU rRNA genes by PCR. LNA oligonucleotides, the sequences of which were complementary to mitochondria and plastid genes, were designed by overlapping a few bases with the annealing position of the bacterial primer and converting DNA bases into LNA bases specific to mitochondria and plastids at the shifted region from the 3' end of the primer-binding position. PCR with LNA oligonucleotides selectively amplified the bacterial genes while inhibited that of organelle genes. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that conventional amplification without LNA oligonucleotides predominantly generated DGGE bands from mitochondria and plastid genes with few bacterial bands. In contrast, additional bacterial bands were detected in DGGE patterns, the amplicons of which were prepared using LNA oligonucleotides. These results indicated that the detection of bacterial genes had been screened by the excessive amplification of the organelle genes. Sequencing of the bands newly detected by using LNA oligonucleotides revealed that their similarity to the known isolated bacteria was low, suggesting the potential to detect novel bacteria. Thus, application of the LNA oligonucleotide-PCR clamping technique was considered effective for the selective amplification of bacterial genes from extracted DNA containing plant organelle genes.

The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales.

An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5-B(T), belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FS(T), at the species level with 96.5% similarity. Strain KA5-B(T) was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15-37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0-8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso-C15:0, C16:1ω7c, and iso-C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FS(T) was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5-B(T) (JCM 18477(T) = KCTC 32107(T)) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed.

Tuberculosis contact investigation using interferon-gamma release assay with chest x-ray and computed tomography.

Between September 2009 and January 2010, 6 members of the Japanese Eastern Army, who had completed the same training program, were diagnosed with active tuberculosis (TB) on different occasions. The Ministry of Defense conducted a contact investigation of all members who had come into contact with the infected members. The purpose of this study was to verify the efficacy of the TB screening protocol used in this investigation. A total of 884 subjects underwent interferon-gamma release assay (IGRA) and chest X-ray. The 132 subjects who were IGRA positive or with X-ray findings suggestive of TB subsequently underwent chest computer tomography (CT). Chest CT was performed for 132 subjects. Based on CT findings, 24 (2.7%) subjects were classified into the active TB group, 107 (12.1%) into the latent tuberculosis infection (LTBI) group, and 753 (85.2%) into the non-TB group. The first 2 groups underwent anti-TB therapy, and all 3 groups were followed for 2 years after treatment. Although one subject in the active TB group experienced relapse during the follow-up period, no patient in the LTBI or non-TB groups developed TB. IGRA and chest X-ray, followed by chest CT for those IGRA positive or with suspicious X-ray findings, appears to be an effective means of TB contact screening and infection prevention.

A time-varying seasonal autoregressive model-based prediction of respiratory motion for tumor following radiotherapy.

To achieve a better therapeutic effect and suppress side effects for lung cancer treatments, latency involved in current radiotherapy devices is aimed to be compensated for improving accuracy of continuous (not gating) irradiation to a respiratory moving tumor. A novel prediction method of lung tumor motion is developed for compensating the latency. An essential core of the method is to extract information valuable for the prediction, that is, the periodic nature inherent in respiratory motion. A seasonal autoregressive model useful to represent periodic motion has been extended to take into account the fluctuation of periodic nature in respiratory motion. The extended model estimates the fluctuation by using a correlation-based analysis for adaptation. The prediction performance of the proposed method was evaluated by using data sets of actual tumor motion and compared with those of the state-of-the-art methods. The proposed method demonstrated a high performance within submillimeter accuracy. That is, the average error of 1.0 s ahead predictions was 0.931 ± 0.055 mm. The accuracy achieved by the proposed method was the best among those by the others. The results suggest that the method can compensate the latency with sufficient accuracy for clinical use and contribute to improve the irradiation accuracy to the moving tumor.

Application of peptide nucleic acid (PNA)-PCR clamping technique to investigate the community structures of rhizobacteria associated with plant roots.

The contamination of plant organelle (mitochondria and plastid) genes in the DNA extraction step becomes a major drawback in investigating the community structures of bacteria associated with plant samples. This is because organelle small subunit ribosomal RNA (SSU rRNA) genes are easily amplified by polymerase chain reaction (PCR) with a set of universal primers for bacteria. To suppress the PCR amplification of the organelle SSU rRNA genes, a peptide nucleic acid (PNA)-PCR clamping technique was applied for selective amplification of bacterial SSU rRNA genes. The PNA oligomers, which had sequences that were complementary to mitochondria and plastid SSU rRNA genes, were designed to overlap the region in the 1492r primer-binding site. PCR with the PNA oligomers significantly suppressed the amplification of the organelle SSU rRNA genes from spinach and cucumber roots. Terminal restriction fragment length polymorphism (T-RFLP) analysis showed that the conventional amplification without PNA oligomers generated the predominant T-RFLP fragments derived from mitochondria and plastids, whereas there was little detection of the rhizobacterial fragments. In contrast, several other T-RFLP fragments derived from rhizobacteria were detected in the products amplified with PNA oligomers, thereby enabling us to differentiate the community structures in spinach and cucumber roots. Thus, application of PNA-PCR clamping was considered to be effective and is a useful technique to amplify the rhizobacterial SSU rRNA genes from selectively extracted DNA containing plant mitochondria and plastid genes.

Markerless Lung Tumor Motion Tracking by Dynamic Decomposition of X-Ray Image Intensity.

We propose a new markerless tracking technique of lung tumor motion by using an X-ray fluoroscopic image sequence for real-time image-guided radiation therapy (IGRT). A core innovation of the new technique is to extract a moving tumor intensity component from the fluoroscopic image intensity. The fluoroscopic intensity is the superimposition of intensity components of all the structures passed through by the X-ray. The tumor can then be extracted by decomposing the fluoroscopic intensity into the tumor intensity component and the others. The decomposition problem for more than two structures is ill posed, but it can be transformed into a well-posed one by temporally accumulating constraints that must be satisfied by the decomposed moving tumor component and the rest of the intensity components. The extracted tumor image can then be used to achieve accurate tumor motion tracking without implanted markers that are widely used in the current tracking techniques. The performance evaluation showed that the extraction error was sufficiently small and the extracted tumor tracking achieved a high and sufficient accuracy less than 1 mm for clinical datasets. These results clearly demonstrate the usefulness of the proposed method for markerless tumor motion tracking.

High cell-autonomy of the anterior endomesoderm viewed in blastomere fate shift during regulative development in the isolated right halves of four-cell stage Xenopus embryos.

The isolated right half (RH) or left half (LH) of Xenopus embryos can undergo regulation so as to form well-proportioned larvae. To assess how the combined actions of maternal determinants and cell-cell interactions contribute to form the well-proportioned larvae, we quantitatively compared four-cell stage blastomere fate between normal larvae and regulated larvae from RH embryos. In normal larvae, the clones of the right dorsal blastomere (RD) and right ventral blastomere (RV) were located unilaterally. In contrast, in regulated larvae: (i) the RD clone exclusively occupied the anterior endomesoderm (AE) derivatives, coinciding no RV progeny in those derivatives of normal larvae. The clone bilaterally populated tissues along the dorsal midline, which characteristically included the medial regions of both somites adjoining the notochord, with higher percentages on the right and anterior sides. (ii) The RV clone extensively compensated for the missing left side at the expense of its right side contribution, and bilaterally occupied the ventroposterior and also dorsal regions excluding the AE derivatives. This clone considerably populated, with altered orientations, the derivatives of the left half gastrocoel roof plate (GRP), the left half GRP being essential for laterality determination. These results show that the high cell-autonomy in the AE constitutes a mechanism common to both normal and regulative development. In regulated larvae, cell-cell interactions shifted the midlines on the dorsal side slightly and the ventral side to a greater extent. The cell lineage difference in the left half GRP could result in a different utilization of maternal determinants in that area.

Respiratory motion prediction for tumor following radiotherapy by using time-variant seasonal autoregressive techniques.

We develop a new prediction method of respiratory motion for accurate dynamic radiotherapy, called tumor following radiotherapy. The method is based on a time-variant seasonal autoregressive (TVSAR) model and extended to further capture time-variant and complex nature of various respiratory patterns. The extended TVSAR can represent not only the conventional quasi-periodical nature, but also the residual components, which cannot be expressed by the quasi-periodical model. Then, the residuals are adaptively predicted by using another autoregressive model. The proposed method was tested on 105 clinical data sets of tumor motion. The average errors were 1.28 ± 0.87 mm and 1.75 ± 1.13 mm for 0.5 s and 1.0 s ahead prediction, respectively. The results demonstrate that the proposed method can outperform the state-of-the-art prediction methods.

Effect of Tris-HCl buffer on DNA adsorption by a variety of soil constituents.

We investigated the effect of tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl) buffer (pH 7.0) as a bulk solution on the adsorption of DNA by gibbsite, goethite, montmorillonite, kaolinite, synthetic and natural allophanes, two humic acids and two andosols. The natural allophane, gibbsite, kaolinite and an andosol adsorbed significantly more DNA in a 0.1 M Tris-HCl buffer than in a 0.1 M NaCl solution (t-test, P<0.005). In contrast, montmorillonite adsorbed significantly less DNA in the Tris-HCl than NaCl solution (P<0.05). Care should be taken when using Tris-HCl in studies on the adsorption of extracellular DNA molecules by soil particles.

Mobile and accurate detection system for infection by the 2009 pandemic influenza A (H1N1) virus with a pocket-warmer reverse-transcriptase loop-mediated isothermal amplification.

The 2009 pandemic H1N1 influenza A virus spread quickly worldwide in 2009. Since most of the fatal cases were reported in developing countries, rapid and accurate diagnosis methods that are usable in poorly equipped laboratories are necessary. In this study, a mobile detection system for the 2009 H1N1 influenza A virus was developed using a reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) kit with a disposable pocket-warmer as a heating device (designated as pwRT-LAMP). The pwRT-LAMP can detect as few as 100 copies of the virus--which is nearly as sensitive as real-time reverse-transcription polymerase chain reaction (RT-PCR)--and does not cross-react with RNA of seasonal influenza viruses. To evaluate the usefulness of the pwRT-LAMP system, nasal swab samples were collected from 56 patients with flu-like symptoms and were tested. Real-time RT-PCR confirmed that the 2009 H1N1 influenza A virus was present in 27 of the 56 samples. Of these 27 positive samples, QuickVue Influenza A+B immunochromatography detected the virus in only 11 samples (11/27; 40.7%), whereas the pwRT-LAMP system detected the virus in 26 of the 56 samples (26/27 of the positive samples; 96.3%). These findings indicate that the mobile pwRT-LAMP system is an accurate diagnostic system for the 2009 H1N1 influenza A virus, and has great potential utility in diagnosing future influenza pandemics.

Ventricular fibrillation diagnosed during electrophysiological study for non-sustained tachycardia.

Ventricular fibrillation diagnoses such as Brugada syndrome pose a risk of sudden incapacitation or death in aircrew. This case report presents a 44-yr-old male fighter pilot who unexpectedly developed ventricular fibrillation (VF) during an electrophysiological study (EPS) prior to therapy for non-sustained ventricular tachycardia (nsVT). The initial aeromedical disposition for this case was "qualified for flying duties". with the restriction that he must fly with another pilot due to repeatedly observed nsVT. This pilot wanted to return to flight duty in single-seat aircraft without any restrictions. Therefore, this patient decided to undergo catheter therapy for nsVT. Unexpectedly, not VT but VF was induced by catheter manipulation during EPS. Pilsicainide-induced coved-type ST wave elevation consistent with Brugada syndrome was noted in this patient's electrocardiogram. He was ultimately disqualified due to the diagnosis of VF. This report suggests EPS on rare occasions may uncover another severe disease similar to this case report.