Sulfurimonas aquatica sp. nov., a sulfur-oxidizing bacterium isolated from water of a brackish lake.

A novel chemolithoautotrophic bacterium, strain H1576T, was isolated from water of a brackish lake. Strain H1576T grew aerobically on inorganic sulfur compounds. Hydrogen gas did not support autotrophic growth, and heterotrophic growth was not observed. Cells were rod shaped, motile, 1.5-2.7 µm in length and 0.6-0.7 µm in width. Growth was observed at 3-22 °C with an optimum growth temperature of 13-15 °C. The pH range for growth was 6.0-7.4 with an optimum pH of 6.6-6.8. Major fatty acids were summed feature 3 (C16: 1ω7c and/or C16: 1ω6c). The complete genome of strain H1576T consists of a circular chromosome and a plasmid, with total length of 2.8 Mbp and G+C content of 46.4 mol%. Phylogenetic analyses indicated that strain H1576T belongs to the genus Sulfurimonas but distinct from representatives of existing species. On the basis of genomic and phenotypic characteristics, a new species named Sulfurimonas aquatica sp. nov. is proposed with the type strain of strain H1576T (= BCRC 81254T = JCM 35004T).

Dissulfurispira thermophila gen. nov., sp. nov., a thermophilic chemolithoautotroph growing by sulfur disproportionation, and proposal of novel taxa in the phylum Nitrospirota to reclassify the genus Thermodesulfovibrio.

Recently, presence of sulfur-disproportionating bacterial species belonging to the phylum Nitrospirota was indicated by an enrichment culture-based study. In the present study, a strain representing that species was isolated and characterized. The strain, strain T55JT, was isolated from a microbial mat of a hot spring. The cells were motile, and rods or spiral forms with width of 0.32-0.49 µm. The strain grew autotrophically, only by disproportionation of thiosulfate or elemental sulfur. Growth was observed at a temperature range of 25-60°C, with optimum growth at 53-57°C. The pH range for growth was 5.5-9.0, with optimum pH of 7.0-8.0. The complete genome of strain T55JT is composed of a circular chromosome (2,370,875 bp), with G+C content of 38.7%. Thermodesulfovibrio hydrogeniphilus Hdr5T showed the highest sequence similarity of the 16S rRNA gene to strain T55JT, but it was only 88.2%. On the basis of the phylogenetic and physiologic properties, strain T55JT (= DSM 110365T=NBRC 114245T) is proposed as type strain of a novel species in a new genus, Dissulfurispira thermophila gen. nov., sp. nov. To assign the new genus to family and higher taxa, its taxonomic position was assessed by genome-based phylogeny. As a result, it was shown that the novel genus and Thermodesulfovibrio belong to different families. It was also shown that Thermodesulfovibrio should be reclassified at levels from class to family and creation of some novel taxa is required. Based on these results, Thermodesulfovibrionia class. nov., Thermodesulfovibrionales ord. nov., Thermodesulfovibrionaceae fam. nov., and Dissulfurispiraceae fam. nov. are proposed.

Disproportionation of inorganic sulfur compounds by a novel autotrophic bacterium belonging to Nitrospirota.

The phylum Nitrospirota (previously known as Nitrospirae or Nitrospira) currently encompasses a limited number of bacterial species with validly published names, including sulfate-reducing bacteria (SRB) of the genus Thermodesulfovibrio. Some metagenome-assembled genomes (MAGs) of bacteria occur in this phylum, and genes involved in dissimilatory sulfur metabolism have been identified in them. Currently, however, there is no established way to discriminate SRB and sulfur-disproportionating bacteria (SDB), which obtain energy from the disproportionation of inorganic sulfur compounds. In this study, a thiosulfate-disproportionating enrichment culture was established from a hot spring microbial mat. The culture was dominated by a single species belonging to the phylum Nitrospirota, and growth of the novel bacterium was supported by disproportionation of thiosulfate and elemental sulfur. Its growth was not observed under sulfate-reducing conditions. Therefore, a comparative genomic analysis of SDB and SRB was performed using its draft genome sequence, in order to identify any genetic element that could be used as a marker for SDB. As a result, a characteristic gene cluster was identified as a putative genetic element that characterized the genomes of SDB. The gene cluster was found in some MAGs of the phylum Nitrospirota, and their corresponding bacteria may also be capable of the disproportionation of inorganic sulfur compounds.

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera.

Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family 'Sulfuricellaceae'. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.

Vonoprazan-Based Third-Line Therapy Has a Higher Eradication Rate against Sitafloxacin-Resistant Helicobacter pylori.

Eradication of Helicobacter pylori (H. pylori) is an effective strategy for preventing various gastrointestinal diseases such as gastric cancer and mucosa-associated lymphoid tissue (MALT) lymphoma. However, the eradication success rate is decreasing because of a recent increase in drug-resistant strains of H. pylori. Here, we evaluated the success rate of eradication therapy with vonoprazan (VPZ), a new potassium-competitive acid blocker, against drug-resistant H. pylori. In total, 793 patients who received H. pylori eradication therapy were investigated retrospectively. All underwent esomeprazole (EPZ)-based triple therapy (n = 386) or VPZ-based triple therapy (n = 407) for first-, second- and third-line H. pylori eradication for 7 days. The overall success rates of first- and third-line H. pylori eradication were significantly higher for VPZ-based triple therapy (88.4% and 93.0%, respectively, per protocol (PP)) than for EPZ-based triple therapy (69.5% and 56.5%, respectively, PP). Moreover, the success rates of first- and third-line eradication of clarithromycin (CLR)- and sitafloxacin (STFX)-resistant H. pylori were significantly higher for VPZ-based triple therapy (72.0% and 91.7%, PP) than for EPZ-based triple therapy (38.5% and 20.0%, PP). In addition, patient age did not affect the eradication rate of VPZ-based first-line therapy, whereas the success rate of EPZ-based therapy was lower in patients under 65 years of age. Our results clearly demonstrated that VPZ-based therapy achieved a higher eradication rate even against CLR- and STFX-resistant H. pylori, and that patient age did not affect the eradication rate of VPZ-based therapy. These findings suggest that dual therapy using VPZ and amoxicillin may be sufficient for standard H. pylori eradication, and may thus also be beneficial for avoiding antibiotic misuse.

Deficiency of the Stroma-Lamellar Protein LIL8/PSB33 Affects Energy Transfer Around PSI in Arabidopsis.

Light-harvesting-like (LIL) proteins are a group of proteins that share a consensus amino acid sequence with light-harvesting Chl-binding (LHC) proteins. We hypothesized that they might be involved in photosynthesis-related processes. In order to gain a better understanding of a potential role in photosynthesis-related processes, we examined the most recently identified LIL protein, LIL8/PSB33. Recently, it was suggested that this protein is an auxiliary PSII core protein which is involved in organization of the PSII supercomplex. However, we found that the majority of LIL8/PSB33 was localized in stroma lamellae, where PSI is predominant. Moreover, the PSI antenna sizes measured under visible light were slightly increased in the lil8 mutants which lack LIL8/PSB33 protein. Analysis of fluorescence decay kinetics and fluorescence decay-associated spectra indicated that energy transfer to quenching sites within PSI was partially hampered in these mutants. On the other hand, analysis of the steady-state fluorescence spectra in these mutants indicates that a population of LHCII is energetically disconnected from PSII. Taken together, we suggest that LIL8/PSB33 is involved in the fine-tuning of light harvesting and/or energy transfer around both photosystems.

The SUFBC2 D complex is required for the biogenesis of all major classes of plastid Fe-S proteins.

Iron-sulfur (Fe-S) proteins play crucial roles in plastids, participating in photosynthesis and other metabolic pathways. Fe-S clusters are thought to be assembled on a scaffold complex composed of SUFB, SUFC and SUFD proteins. However, several additional proteins provide putative scaffold functions in plastids, and, therefore, the contribution of SUFB, C and D proteins to overall Fe-S assembly still remains unclear. In order to gain insights regarding Fe-S cluster biosynthesis in plastids, we analyzed the complex composed of SUFB, C and D in Arabidopsis by blue native-polyacrylamide gel electrophoresis. Using this approach, a major complex of 170 kDa containing all subunits was detected, indicating that these proteins constitute a SUFBC2 D complex similar to their well characterized bacterial counterparts. The functional effects of SUFB, SUFC or SUFD depletion were analyzed using an inducible RNAi silencing system to specifically target the aforementioned components; resulting in a decrease of various plastidic Fe-S proteins including the PsaA/B and PsaC subunits of photosystem I, ferredoxin and glutamine oxoglutarate aminotransferase. In contrast, the knockout of potential Fe-S scaffold proteins, NFU2 and HCF101, resulted in a specific decrease in the PsaA/B and PsaC levels. These results indicate that the functions of SUFB, SUFC and SUFD for Fe-S cluster biosynthesis cannot be replaced by other scaffold proteins and that SUFBC2 D, NFU2 and HCF101 are involved in the same pathway for the biogenesis of PSI. Taken together, our results provide in vivo evidence supporting the hypothesis that SUFBC2 D is the major, and possibly sole scaffold in plastids.

Wide-angle display-type retarding field analyzer with high energy and angular resolutions.

Deployments of spherical grids to obtain high energy and angular resolutions for retarding field analyzers (RFAs) having acceptance angles as large as or larger than ±45° were explored under the condition of using commercially available microchannel plates with effective diameters of approximately 100 mm. As a result of electron trajectory simulations, a deployment of three spherical grids with significantly different grid separations instead of conventional equidistant separations showed an energy resolving power (E/ΔE) of 3200 and an angular resolution of 0.6°. The mesh number of the wire mesh retarding grid used for the simulation was 250. An RFA constructed with the simulated design experimentally showed an E/ΔE of 1100 and an angular resolution of 1°. Using the RFA and synchrotron radiation of 900 eV, photoelectron diffraction (PED) measurements were performed for single-crystal graphite. A clear C 1s PED pattern was observed even when the differential energy of the RFA was set at 0.5 eV. Further improvement of the energy resolution was theoretically examined under the assumption of utilizing a retarding grid fabricated by making a large number of radially directed cylindrical holes through a partial spherical shell instead of using a wire mesh retarding grid. An E/ΔE of 14 500 was predicted for a hole design with a diameter of 60 µm and a depth of 100 µm. A retarding grid with this hole design and a holed area corresponding to an acceptance angle of ±7° was fabricated. An RFA constructed with this retarding grid experimentally showed an E/ΔE of 1800. Possible reasons for the experimental E/ΔE lower than the theoretical values are discussed.

First-line eradication for Helicobacter pylori-positive gastritis by esomeprazole-based triple therapy is influenced by CYP2C19 genotype.

AIM: To evaluate the effect of first line esomeprazole (EPZ)-based triple therapy on Helicobacter pylori (H. pylori) eradication. METHODS: A total of 80 Japanese patients with gastritis who were diagnosed as positive for H. pylori infection by endoscopic biopsy-based or (13)C-urea breath tests were included in this study. The average age of the patients was 57.2 years (male/female, 42/38). These patients were treated by first-line eradication therapy with EPZ 40 mg/d, amoxicillin 1500 mg/d, and clarithromycin 400 mg/d for 7 d. All drugs were given twice per day. Correlations between H. pylori eradication, CYP2C19 genotype, and serum pepsinogen (PG) level were analyzed. This study was registered with the UMIN Clinical Trials Registry (UMIN000009642). RESULTS: The H. pylori eradication rates by EPZ-based triple therapy evaluated by intention-to-treat and per protocol were 67.5% and 68.4%, respectively, which were similar to triple therapies with other first-generation proton pump inhibitors (PPIs). The eradication rates in three different CYP2C19 genotypes, described as extensive metabolizer (EM), intermediate metabolizer, and poor metabolizer, were 52.2%, 72.1%, and 84.6%, respectively. The H. pylori eradication rate was significantly lower in EM than non-EM (P < 0.05). The serum PG I level and PG I/II ratio were significantly increased after eradication of H. pylori (P < 0.01), suggesting that gastric atrophy was improved by H. pylori eradication. Thus, first-line eradication by EPZ-based triple therapy for patients with H. pylori-positive gastritis was influenced by CYP2C19 genotype, and the eradication rate was on the same level with other first-generation PPIs in the Japanese population. CONCLUSION: The results from this study suggest that there is no advantage to EPZ-based triple therapy on H. pylori eradication compared to other first-generation PPIs.

[A case of small intestine type steroid-naïve Crohn disease in which osteomalacia was diagnosed by fractures on the transcervical bone].

We present a 35-year-old Japanese man with Crohn disease. He underwent ileocolectomy for ileum perforation when he was 28 years old, Crohn ileitis was diagnosed and medical treatment was commenced. When he was 35 years old, he complained of severe pain of the right upper torso and the left leg with no apparent trigger. A full check-up revealed that he had multiple fractures including a transcervical fracture of the left femur, ribs on both sides, and fracture of the sacroiliac joint. He had no history of prior use of steroids, and the fractures were thought to have been caused by vitamin D deficiency. This case suggests that clinicians should be aware of the possibility of osteomalacia caused by malabsorption of fat-soluble vitamin D when examining patients with ileocolic Crohn disease.

Te concentration dependent photoemission and inverse-photoemission study of FeSe1-xTex.

We have characterized the electronic structure of FeSe1-x Te x for various x values using soft x-ray photoemission spectroscopy (SXPES), high-resolution photoemission spectroscopy (HRPES) and inverse photoemission spectroscopy (IPES). The SXPES valence band spectral shape shows that the 2 eV feature in FeSe, which was ascribed to the lower Hubbard band in previous theoretical studies, becomes less prominent with increasing x. HRPES exhibits systematic x dependence of the structure near the Fermi level (EF): its splitting near EF and filling of the pseudogap in FeSe. IPES shows two features, near EF and approximately 6 eV above EF; the former may be related to the Fe 3d states hybridized with chalcogenide p states, while the latter may consist of plane-wave-like and Se d components. In the incident electron energy dependence of IPES, the density of states near EF for FeSe and FeTe has the Fano lineshape characteristic of resonant behavior. These compounds exhibit different resonance profiles, which may reflect the differences in their electronic structures. By combining the PES and IPES data the on-site Coulomb energy was estimated at 3.5 eV for FeSe.

Development of a soft X-ray angle-resolved photoemission system applicable to 100†µm crystals.

A system for angle-resolved photoemission spectroscopy (ARPES) of small single crystals with sizes down to 100 µm has been developed. Soft X-ray synchrotron radiation with a spot size of ∼40 µm × 65 µm at the sample position is used for the excitation. Using this system an ARPES measurement has been performed on a Si crystal of size 120 µm × 100 µm × 80 µm. The crystal was properly oriented on a sample stage by measuring the Laue spots. The crystal was cleaved in situ with a microcleaver at 100 K. The cleaved surface was adjusted to the beam spot using an optical microscope. Consequently, clear band dispersions along the Γ-X direction reflecting the bulk electronic states were observed with a photon energy of 879 eV.

[A case of pneumatosis cystoides intestinalis induced by steroid pulse therapy for severe acute hepatitis B].

A 26-year-old Japanese woman was admitted to the hospital because of fever and general fatigue. A diagnosis of acute hepatitis B was given because of high levels of transaminase and positivity for HBs-Ag, HBe-Ag and HBc-IgM. On the 2nd day progression to fulminant hepatitis was suspected, and steroid pulse therapy, cyclosporin, entecavir, and interferon-ß were started. Her laboratory data improved until transaminase showed an increase on 18th day, and steroid was once again administered. Abdominal CT scan and plain abdominal X-ray showed pneumatosis cystoides intestinalis (PCI) mainly along the ascending colon without any symptoms. After discontinuation of steroid therapy, abnormal gas gradually disappeared. This is a very rare case of PCI, which may have been caused by short-term steroid pulse therapy.

Ultrahigh-vacuum cleaving system for sub-100-microm crystals.

An ultrahigh-vacuum cleaver has been developed for cleaving small crystals with sizes of less than 100 microm. The cleaver is fully driven by stepping motors in order to control its position on the micrometer scale. A pair of blades with sharp edges is used to nip and cleave crystals. To position the edges of the blades relative to a small crystal, they are observed using an optical microscope with a long working distance. A silicon crystal with a size of approximately 80 microm has been cleaved by using the developed system, and the cleanliness of the obtained surface has been verified by photoemission spectroscopy.

In situ positioning of a few hundred micrometer-sized cleaved surfaces for soft-x-ray angle-resolved photoemission spectroscopy by use of an optical microscope.

A method to position samples with small cleaved regions has been developed to be applied to the angle-resolved photoemission spectroscopy (ARPES) which uses soft-x-ray synchrotron radiation focused down to 160 x 180 microm(2). A long-working-distance optical microscope is used for the sample observation. A selected region on a sample can be optimally set at the position of measurements, which is realized by the spatial resolution of the photoelectron analyzer. Using this method, electronic band dispersions of bulk silicon have been measured by ARPES for a partially cleaved region with a size of approximately 200 x 500 microm(2).

A video camera system for coaxial observation of a sample with an incident soft X-ray beam.

A video camera system for observing a sample from the direction of an incident soft X-ray beam has been developed. The sample is seen via two reflecting mirrors. The first mirror, which has a hole to allow the soft X-ray beam to pass through, is set on the beam axis in a vacuum. The second mirror is used to cancel out the mirror inversion of the image. This camera system is used for efficient positioning of samples in a soft X-ray beam.

Atomic-layer resolved magnetic and electronic structure analysis of ni thin film on a Cu(001) surface by diffraction spectroscopy.

Up until now there has been no direct method for detecting the electronic and magnetic structure of each atomic layer at the surface, which is an essential analysis technique for nanotechnology. For this purpose, we have developed a new method, diffraction spectroscopy, based on the photon energy dependence of the angular distribution of Auger electron emission. We have applied this method to analyze the magnetic structure of a Ni ultrathin film on a Cu(001) surface around the spin reorientation transition. Atomic-layer resolved x-ray absorption and magnetic circular dichroism spectra were obtained. Surface and interior core-level shifts and magnetic moments are determined for each atomic layer individually.