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In this paper, predictions of creep crack initiation times and growth rates using the NSW-MOD model are compared with experimental data for the parent and weld metals of P91 at 600°C. For the weld metal, creep crack growth rates are found to be bounded by upper and lower bounds of the predictions, but creep crack initiation times are close to the upper bound. For the parent material, creep crack growth rates are bounded by upper and lower bounds of the predictions using the minimum creep rates, but creep crack initiation times are bounded by those using the average creep rates. [ABSTRACT FROM AUTHOR]

BSTRACT [ABSTRACT FROM AUTHOR]

Thermococcus onnurineus NA1 is a hyperthermophilic archaeon that can be used for the screening of thermophilic enzymes. Previously, we characterized the metabolic enzymes of the cytosolic proteome by two-dimensional electrophoresis/tandem mass spectrometry (2-DE/MS-MS). In this study, we identified a subset of hyperthermostable proteins in the cytosolic proteome using enrichment by in vitro heat treatment and protein identification. After heat treatment at 100°C for 2 h, 13 and 149 proteins were identified from the soluble proteome subset by 2-DE/MS-MS and 1-DE/MS-MS analysis, respectively. Representative proteins included intracellular protease I, thioredoxin reductase, triosephosphate isomerase, putative hydroperoxide reductase, proteasome, and translation initiation factors. Intracellular protease, deblocking aminopeptidases, and fructose-1,6-bisphosphatase were overexpressed in Escherichia coli and biological activity above 85°C was confirmed. The folding transition temperature (Tm) of identified proteins was analyzed using the in silico prediction program TargetStar. The proteins enriched with the heat treatment have higher Tm than the homologous proteins from mesophilic strains. These results suggested that the heat-stable protein set of hyperthermophilic T. onnurineus NA1 can be effectively fractionated and enriched by in vitro heat treatment. [ABSTRACT FROM AUTHOR]

This paper presents finite element simulation results of residual stresses in dissimilar metal welds of a PWR pressurizer safety/relief nozzle. The present results are believed to be significant in two aspects. The first one is to consider the effect of the presence of similar metal welds on resulting residual stresses. The second one is the mitigation effect of the overlay welding thickness on residual stresses. After dissimilar metal welding, tensile residual stresses are present both at the inner surface and at the outer surface of dissimilar metal welds. Adjacent similar metal welding, however, decreases residual stresses to compressive ones at the inner surface of dissimilar metal welds, possibly due to the bending mechanism caused radial contraction of the weld. At the outer surface of dissimilar metal welds, similar metal welding increases residual stresses. Overlay welding further decreases residual stresses at the inner surface of dissimilar and similar metal welds, but increases slightly residual stresses at the outer surface. [ABSTRACT FROM AUTHOR]

Although a common reaction in anaerobic environments, the conversion of formate and water to bicarbonate and H2 (with a change in Gibbs free energy of ΔG° = +1.3 kJ mol−1) has not been considered energetic enough to support growth of microorganisms. Recently, experimental evidence for growth on formate was reported for syntrophic communities of Moorella sp. strain AMP and a hydrogen-consuming Methanothermobacter species and of Desulfovibrio sp. strain G11 and Methanobrevibacter arboriphilus strain AZ. The basis of the sustainable growth of the formate-users is explained by H2 consumption by the methanogens, which lowers the H2 partial pressure, thus making the pathway exergonic. However, it has not been shown that a single strain can grow on formate by catalysing its conversion to bicarbonate and H2. Here we report that several hyperthermophilic archaea belonging to the Thermococcus genus are capable of formate-oxidizing, H2-producing growth. The actual ΔG values for the formate metabolism are calculated to range between −8 and −20 kJ mol−1 under the physiological conditions where Thermococcus onnurineus strain NA1 are grown. Furthermore, we detected ATP synthesis in the presence of formate as a sole energy source. Gene expression profiling and disruption identified the gene cluster encoding formate hydrogen lyase, cation/proton antiporter and formate transporter, which were responsible for the growth of T. onnurineus NA1 on formate. This work shows formate-driven growth by a single microorganism with protons as the electron acceptor, and reports the biochemical basis of this ability. [ABSTRACT FROM AUTHOR]

The Thermococcus peptonophilus (Tpe) DNA polymerase gene was expressed under the control of the T7lac promoter on pET-22b(+) in Escherichia coli BL21-CodonPlus(DE3)-RIL in order to fully elucidate its biochemical properties and evaluate its feasibility in polymerase chain reaction (PCR) application. The expressed enzyme was then purified by heat treatment followed by two steps of column chromatography after which optimum pH and temperature of the enzyme were evaluated to be 7.0 and 75 °C, respectively. The optimal buffer for PCR with Tpe DNA polymerase consisted of 50 mM Tris-HCl (pH8.0), 2 mM MgCl2, 80 mM KCl, and 0.02% Triton X-100. Tpe DNA polymerase revealed a 3.6-fold higher fidelity (3.37x10-6) than Taq DNA polymerase (12.13x10-6) and performed significantly more efficiently in PCR amplification than both Taq and Pfu DNA polymerases. Ratios of 31:1 of Taq to Tpe DNA polymerases allowed PCR amplification of targets up to 15 kb in length with a 2.2-fold higher fidelity than Taq DNA polymerase. The results of the PCR experiments indicate that Tpe DNA polymerase may provide a higher fidelity DNA amplification in a shorter reaction time. [ABSTRACT FROM AUTHOR]

The TON_0002 gene, which is in close proximity to the DNA polymerase locus in Thermococcus onnurineus NA1, has been shown to encode an inorganic pyrophosphatase. Its genomic position and function suggest a role for pyrophosphate hydrolysis during DNA polymerization. This is the first report of an inorganic pyrophosphatase belonging to the haloacid dehalogenase superfamily, in which unique residues in motif I and II have been replaced with Trp and Gly, respectively. The optimum pyrophosphatase activity of the recombinant enzyme occurred at pH 6, and it displayed an absolute dependence on divalent metal ions, among which Ni2+ was the most efficient. The site-specific mutation of the Gly residue in motif II to Ala or Ser residue exhibited only a slight change in the enzymatic activity and the Km value. [ABSTRACT FROM AUTHOR]

DNA ligases are divided into two groups according to their cofactor requirement to form ligase-adenylate, ATP-dependent DNA ligases and NAD+-dependent DNA ligases. The conventional view that archaeal DNA ligases only utilize ATP has recently been disputed with discoveries of dual-specificity DNA ligases (ATP/ADP or ATP/NAD+) from the orders Desulfurococcales and Thermococcales. Here, we studied DNA ligase encoded by the hyperthermophilic crenarchaeon Sulfophobococcus zilligii. The ligase exhibited multiple cofactor specificity utilizing ADP and GTP in addition to ATP. The unusual cofactor specificity was confirmed via a DNA ligase nick-closing activity assay using a fluorescein/biotin-labelled oligonucleotide and a radiolabelled oligonucleotide. The exploitation of GTP as a catalytic energy source has not to date been reported in any known DNA ligase. This phenomenon may provide evolutionary evidence of the nucleotide cofactor utilization by DNA ligases. To bolster this hypothesis, we summarize and evaluate previous assertions. We contend that DNA ligase evolution likely started from crenarchaeotal DNA ligases and diverged to eukaryal DNA ligases and euryarchaeotal DNA ligases. Subsequently, the NAD+-utilizing property of some euryarchaeotal DNA ligases may have successfully differentiated to bacterial NAD+-dependent DNA ligases. [ABSTRACT FROM AUTHOR]

The present paper provides experimental J estimation equation based on the load-crack opening displacement (COD) record for testing the circumferential through-wall cracked pipe under combined tension and bending. Based on the limit analysis and the kinematically admissible rigid-body rotation field, the plastic η-factor for the load-COD record is derived and is compared with that for the load-load line displacement record. Comparison with the J results from detailed elastic-plastic finite element analysis shows that the proposed method based on the load-COD record provides reliable J estimates even for shallow cracks (small crack angle), whereas the conventional approach based on the load-load line displacement record gives erroneous results for shallow cracks. Thus, the proposed J estimation method could be recommended for testing the circumferential through-wall cracked pipe, particularly with shallow cracks. [ABSTRACT FROM AUTHOR]

The present paper provides plastic limit load solutions for axial and circumferential through-wall cracked pipes based on detailed three-dimensional (3D) finite element (FE) limit analysis using elastic-perfectly plastic behavior. As a loading condition, axial tension, global bending moment, internal pressure, combined tension and bending, and combined internal pressure and bending are considered for circumferential through-wall cracked pipes, while only internal pressure is considered for axial through-wall cracked pipes. In particular more emphasis is given for through-wall cracked pipes subject to combined loading. Comparisons with existing solutions show a large discrepancy in short through-wall crack (both axial and circumferential) for internal pressure. In the case of combined loading, the FE limit analyses results show the thickness effect on limit load solutions. Furthermore, the plastic limit load solution for circumferential through-wall cracked pipes under bending is applied to derive plastic η and γ factor of testing circumferential through-wall cracked pipes to estimate fracture toughness. Being based on detailed 3D FE limit analysis, the present solutions are believed to be meaningful for structural integrity assessment of through-wall cracked pipes. [ABSTRACT FROM AUTHOR]

This paper provides plastic limit and TES (twice-elastic-slope) plastic load solutions for 90° pipe bends under combined pressure and out-of-plane bending, via three-dimensional non-linear FE analyses using elastic-perfectly plastic materials. Without internal pressure, a closed-form approximation is given. For combined pressure and out-of-plane bending, tabulated data are given, from which TES plastic loads can be interpolated. It is found that TES plastic loads for pipe bends under out-of-plane bending are lower than those under in-plane opening bending, but are higher than those under in-plane closing bending. It suggests that the in-plane closing bending mode is the most critical loading mode for 90° pipe bends, which is fully consistent to existing findings. [ABSTRACT FROM AUTHOR]

The present work provides mismatch limit loads and approximate J estimates for tensile plates with constant-depth, part-through surface cracks in the center of the weld metal. Based on systematic three-dimensional FE limit analyses, effects of strength mismatch related variables on limit loads are firstly quantified by the strength mismatch ratio and one geometry-related parameter. Mismatch limit loads for part-through surface cracks are then correlated to those for two-dimensional, through-wall crack problems. Based on the proposed limit load solutions, the applicability of the reference stress based J estimates is also investigated. When the reference stress is defined by the mismatch limit load, predicted J values agree overall well with FE results. [ABSTRACT FROM AUTHOR]

The present paper provides plastic limit load solutions for axial and circumferential through-wall cracked pipes based on detailed three-dimensional (3D) finite element (FE) limit analysis using elastic-perfectly plastic behavior. As a loading condition, axial tension, global bending moment, internal pressure, combined tension and bending, and combined internal pressure and bending are considered for circumferential through-wall cracked pipes, while only internal pressure is considered for axial through-wall cracked pipes. In particular, more emphasis is given for through-wall cracked pipes subject to combined loading. Comparisons with existing solutions show a large discrepancy in short through-wall crack (both axial and circumferential) for internal pressure. In the case of combined loading, the FE limit analyses results show the thickness effect on limit load solutions. Furthermore, the plastic limit load solution for circumferential through-wall cracked pipes under bending is applied to derive plastic η and γ factor of testing circumferential through-wall cracked pipes to estimate fracture toughness. Being based on detailed 3D FE limit analysis, the present solutions are believed to be meaningful for structural integrity assessment of through-wall cracked pipes. [ABSTRACT FROM AUTHOR]

This paper investigates the effect of the Ramberg–Osgood (R-O) fitting procedures on plastic displacement rate estimates in creep crack growth testing, via detailed two-dimensional and three-dimensional finite-element analyses of the standard compact tension specimen. Four different R-O fitting procedures are considered: (i) fitting the entire true stress–strain data up to the ultimate tensile strength, (ii) fitting the true stress–strain data from 0.1% strain to 0.8 of the true ultimate strain, (iii) fitting the true stress–strain data only up to 5% strain and (iv) fitting the engineering stress–strain data. It is found that the first two fitting procedures can produce significant errors in plastic displacement rate estimates. The last two procedures, on the other hand, provide reasonably accurate plastic displacement rates and thus should be recommended in creep crack growth testing. Several advantages of fitting the engineering stress–strain data over fitting the true stress–strain data only up to 5% strain are discussed. [ABSTRACT FROM AUTHOR]

This paper investigates interfacial crack tip stress fields and the J-integral for bi-materials with plastic hardening mismatch via detailed elastic-plastic finite element analyses. For small scale yielding, the modified boundary layer formulation with the elastic T-stress is employed. For fully plastic yielding, plane strain single-edge- cracked specimens under pure bending are considered. Interfacial crack tip stress fields are explained by modified Prandtl slip-line fields. It is found that, for bi-materials consisting of two elastic-plastic materials, increasing plastic hardening mismatch increases both crack-tip stress constraint in the lower hardening material and the J-contribution there. The implication of asymmetric J-integral in bi-materials is also discussed. [ABSTRACT FROM AUTHOR]

The present paper proposes ductile failure criteria in terms of true fracture strain (the equivalent strain to fracture) as a function of the stress triaxiality (defined by the ratio of the hydrostatic stress to the equivalent stress) for the API X65 steel. To determine the stress-modified fracture strain, smooth and notched tensile bars with four different notch radii are tested, from which true fracture strains are determined as a function of the notch radius. Then detailed elastic–plastic, large strain finite element analyses are performed to estimate variations of stress triaxiality in the tensile bars, which leads to true fracture strains as a function of the stress triaxiality, by combining them with experimental results. Two different failure criteria are proposed, one based on local stress and strain information at the site where failure initiation is likely to take place, and the other based on averaged stress and strain information over the ligament where ductile fracture is expected. As a case study, ligament failures of API X65 pipes with a gouge are predicted and compared with experimental data. [ABSTRACT FROM AUTHOR]

The article presents a study that describes the cloning of the gene and characterization of the recombinant enzyme with regard to its enzymatic properties. Escherichia coli was used for plasmid propagation and nucleotide sequencing. The carboxypeptidase gene was cloned and overexpressed in Escherichia coli.

Genomic analysis of a hyperthermophilic archaeon, Thermococcus sp. NA1, revealed an ORF of 1689 bases encoding 562 amino acids that showed a high similarity to DNA ligases from other hyperthermophilic archaea. The ligase, which was designated TNA1_lig ( Thermococcus sp. NA1 ligase), was cloned and expressed in Escherichia coli. The recombinant TNA1_lig was purified by metal affinity chromatography. The optimum ligase activity of the recombinant TNA1_lig occurred at 80 °C and pH 7.5. The enzyme was activated by MgCl2 and ZnCl2 but was inhibited by MnCl2 and NiCl2. Additionally, the enzyme was activated by either ATP or NAD+. [ABSTRACT FROM AUTHOR]

Genomic analysis of a hyperthermophilic archaeon, Thermococcus sp. strain NA1, revealed the presence of a 1,068-hp open reading frame encoding a protein consisting of 356 amino acids with a calculated molecular mass of 39,714 Da (GenBank accession no. DQ144132). Sequence analysis showed that it was similar to the putative aminopeptidase P (APP) of Thermococcus kodakaraensis KOD1. Amino acid residues important for catalytic activity and the metal binding ligands conserved in bacterial, nematode, insect, and mammalian APPs were also conserved in the Thermococcus sp. strain NA1 APP. The archaeal APP, designated TNA1--APP (Thermococcus sp. strain NA1 APP), was cloned and expressed in Escherichia coli. The recombinant enzyme hydrolyzed the amino-terminal Xaa-Pro bond of Lys(Nϵ-Abz)-Pro-Pro-pNA and the dipeptide Met-Pro (Km 0.96 mM), revealing its functional identity. Further enzyme characterization showed the enzyme to be a Co2+-, Mn2+-, or Zn2+-dependent metallopeptidase. Optimal APP activity with Met-Pro as the substrate occurred at pH 5 and a temperature of 100°C. The APP was thermostable, with a half-life of >100 mm at 80°C. This study represents the first characterization of a hyperthermophilic archaeon APP. [ABSTRACT FROM AUTHOR]

Precise identification of diatom species is fundamental to correctly interpreting their roles in the marine ecosystems; the documentation of species records with illustrations is therefore essential to guarantee ecological works and the continuous use of compositional data in future works. We document the diatom flora in the Kuroshio Extension (KE) area of the northwestern Pacific. Samples were collected by sediment trap deployment from November 2017 to August 2018 and identified using light microscopy and scanning electron microscopy. Eighty-two taxa belonging to 17 families and 38 genera were documented with representative references, morphological dimensions, brief diagnosis, distribution, and short taxonomic comments. All of the taxa were divided into three distribution patterns (cold, warm, and eurythermal taxa) based on the previous distribution records; each group may be transported by the Oyashio and Kuroshio Currents, respectively. The mixed occurrence of cold- and warm-water species indicates that the KE area is a crossroads for them. A preliminary checklist was compiled from previous studies, incorporating our records, and 206 diatom taxa occurred in the northeastern path of the Kuroshio Current. The diatom flora in the KE area will be used to understand the hydrology of the Kuroshio Current in future work.

Offshore wind turbines are supported by various foundations, each with its considerations in design and construction. Gravity, monopile, and suction bucket foundations encounter geotechnical issues, while jacket and tripod foundations face fatigue problems. Considering this, a gravity foundation based on a steel skirt was developed, and a monopile foundation was analyzed for Pile-Soil Interaction using the p–y curve and 3D finite element method (3D FEM). In addition, for suction bucket foundations, the effects of lateral and vertical loads were analyzed using 3D FEM and centrifuge tests. Fatigue analysis for jacket and tripod foundations was conducted using a hotspot stress approach. Some hybrid foundations and shape optimization techniques that change the shape to complement the problems of each foundation described above were assessed. Hybrid foundations could increase lateral resistance compared to existing foundations because of the combined appendages, and optimization techniques could reduce costs by maximizing the efficiency of the structure or by reducing costs and weight. This paper presents the characteristics and research directions of the foundation through various studies on the foundation. In addition, the optimal design method is presented by explaining the problems of the foundation and suggesting ways to supplement them.

Acetogenic bacteria can utilize C1 compounds, such as carbon monoxide (CO), formate, and methanol, via the Wood-Ljungdahl pathway (WLP) to produce biofuels and biochemicals. Two novel acetogenic bacteria of the family Eubacteriaceae ES2 and ES3 were isolated from Eulsukdo, a delta island in South Korea. We conducted whole genome sequencing of the ES strains and comparative genome analysis on the core clusters of WLP with Acetobacterium woodii DSM1030T and Eubacterium limosum ATCC8486T. The methyl-branch cluster included a formate transporter and duplicates or triplicates copies of the fhs gene, which encodes formyl-tetrahydrofolate synthetase. The formate dehydrogenase cluster did not include the hydrogenase gene, which might be replaced by a functional complex with a separate electron bifurcating hydrogenase (HytABCDE). Additionally, duplicated copies of the acsB gene, encoding acetyl-CoA synthase, are located within or close to the carbonyl-branch cluster. The serum bottle culture showed that ES strains can utilize a diverse range of C1 compounds, including CO, formate, and methanol, as well as CO2. Notably, ES2 exhibited remarkable resistance to high concentrations of C1 substrates, such as 100% CO (200 kPa), 700 mM formate, and 500 mM methanol. Moreover, ES2 demonstrated remarkable growth rates under 50% CO (0.45 h−1) and 200 mM formate (0.34 h−1). These growth rates are comparable to or surpassing those previously reported in other acetogenic bacteria. Our study introduces novel acetogenic ES strains and describes their genetic and physiological characteristics, which can be utilized in C1-based biomanufacturing.

Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in Thermococcus onnurineus NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in T. onnurineus NA1 and "Pyrococcus abyssi". [ABSTRACT FROM AUTHOR]

Synthetic carbon monoxide:formate oxidoreductase is designed for direct electron transfer between non-interacting CO dehydrogenase and formate dehydrogenase using an electron-transferring Fe-S fusion protein in T. onnurineus.

Abstract Interstitial lung disease associated with primary Sjögren’s syndrome (SJS-ILD) has a variable clinical course. We aimed to investigate the role of blood biomarkers in predicting prognosis for SJS-ILD. Clinical data of 46 SJS-ILD patients were retrospectively reviewed. Plasma biomarker levels, including Krebs von den Lungen-6 (KL-6), CC chemokine ligand 18 (CCL18), chitinase-3-like-1 (YKL-40), interleukin-4 receptor alpha (IL-4Ra), and matrix metalloproteinase-7 (MMP-7) were measured using the multiplex Luminex assays (R&D Systems, Minneapolis, USA). The median follow-up period was 69.0 months. The mean age of the patients was 59.4 years; 17.4% were men. The KL-6 level was significantly higher in non-survivors (n = 12; 119.6 vs. 59.5 pg/mL, P = 0.037) than survivors (n = 34), while the levels of the other biomarkers did not differ. Receiver operating characteristic analysis indicated that KL-6 shows the best performance for predicting survival (area under the curve = 0.705, P = 0.037; best cut-off value = 53.5 pg/mL). Multivariable Cox analysis that was adjusted by age and diffusing capacity for carbon monoxide suggested a high KL-6 level (> 53.5 pg/mL) as an independent prognostic factor for survival (hazard ratio = 5.939, 95% confidence interval 1.312–26.881, P = 0.021). Our results suggest that blood KL-6 might be a useful in predicting the prognosis for patients with SJS-ILD.

Abstract Interstitial lung disease (ILD) is the most common lung manifestation in patients with Sjögren syndrome (SJS) and is associated with poor outcomes. This study aimed to investigate the long-term clinical course and prognostic factors in patients with SJS-ILD. Clinical data and high-resolution computed tomography (HRCT) images of 62 patients with primary SJS-ILD were retrospectively analyzed (biopsy-proven cases, n = 16). The mean patient age was 59.8 years; 83.9% of the patients were females, and 38.7% showed a usual interstitial pneumonia (UIP) pattern on HRCT. The median follow-up period was 61.5 months. During follow-up, 15 patients (24.2%) died, 7 (11.3%) experienced acute exacerbation (AE), and 27 (43.5%) progressed. The 1-, 3- and 5-year survival rates were 93.5%, 85.8%, and 81.1%, respectively. Age (hazard ratio [HR]: 1.158, P = 0.003), C-reactive protein (CRP) level (HR: 1.212, P = 0.045), FVC (HR: 0.902, P = 0.005), and a UIP pattern on HRCT (HR: 4.580, P = 0.029) were significant prognostic factors in multivariable Cox analysis. In conclusion, death, AE, and ILD progression occurred in 25%, 10%, and 50% of the patients with SJS-ILD, respectively. Older age, higher CRP level, lower FVC, and a UIP pattern on HRCT indicated poor prognosis.

Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.

Little is known about the community structure and metabolic potential of microbial communities in hydrothermal fields in the Central Indian Ridge (CIR). In this study, a metagenomic sequencing approach was conducted to explore the microbial diversity in three sediment samples collected during the 2019 expedition from two recently discovered hydrothermal vent fields; Invent E and Onnuri Vent Field (OVF). Analysis of unassembled metagenomic reads using the Metagenomic analysis server (MG-RAST) revealed that microbial communities of the two sampling sites were very similar, showing the dominance of Bacteria over Archaea. Proteobacteria, Firmicutes, Bacteroidetes, as well as Euryarchaeota were dominant in all samples. Functional annotation based on KEGG categories shows that the microbial populations in these vent fields possess metabolic capabilities for aerobic respiration, carbon fixation through the Calvin–Bassham–Benson (CBB) cycle, the reverse tricarboxylic acid (rTCA) cycle, and reductive acetyl-CoA pathway as well as sulfur and nitrogen metabolisms. Comparative metagenome analysis with different datasets obtained from different ocean ridges showed that microbial communities at low activity or hydrothermally influenced area differ from highly active hydrothermal communities. This study provides insights into the genetic diversity and functional capability of the microbial communities of slow to intermediate spreading hydrothermal systems.

Abstract Background Gas-fermenting acetogens have received a great deal of attention for their ability to grow on various syngas and waste gas containing carbon monoxide (CO), producing acetate as the primary metabolite. Among them, some Clostridium species, such as C. ljungdahlii and C. autoethanogenum, are of particular interest as they produce fuel alcohols as well. Despite recent efforts, alcohol production by these species is still unsatisfactory due to their low productivity and acetate accumulation, necessitating the isolation of strains with better phenotypes. Results In this study, a novel alcohol-producing acetogen (Clostridium sp. AWRP) was isolated, and its complete genome was sequenced. This bacterium belongs the same phylogenetic group as C. ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii based on 16S rRNA homology; however, the levels of genome-wide average nucleotide identity (gANI) for strain AWRP compared with these strains range between 95 and 96%, suggesting that this strain can be classified as a novel species. In addition, strain AWRP produced a substantial amount of ethanol (70–90 mM) from syngas in batch serum bottle cultures, which was comparable to or even exceeded the typical values obtained using its close relatives cultivated under similar conditions. In a batch bioreactor, strain AWRP produced 119 and 12 mM of ethanol and 2,3-butanediol, respectively, while yielding only 1.4 mM of residual acetate. Interestingly, the alcohologenesis of this strain was strongly affected by oxidoreduction potential (ORP), which has not been reported with other gas-fermenting clostridia. Conclusion Considering its ethanol production under low oxidoreduction potential (ORP) conditions, Clostridium sp. AWRP will be an interesting host for biochemical studies to understand the physiology of alcohol-producing acetogens, which will contribute to metabolic engineering of those strains for the production of alcohols and other value-added compounds from syngas.

Kidney disease: stem cells to the rescue Stem cells can halt the progression of kidney damage owing to diabetes by reducing inflammation and improving energy production in kidney cells. Eun Hee Koh at the University of Ulsan College of Medicine in Seoul, South Korea, and colleagues found that adult stem cells, known as mesenchymal stem cells (MSCs), derived from human umbilical cord blood had a protective effect on the kidneys of diabetic mice. Repeated administration of MSCs prevented the recruitment of pro-inflammatory cells into the kidney and increased the levels of arginase-1, a marker of cells with anti-inflammatory activity. Experiments in cells showed that MSCs stimulated the production of arginase-1 in that, in turn, were able to increase the production and activity of mitochondria in kidney cells. This study confirms an important role for MSCs in organ repair.

Renal allograft biopsy is the gold standard procedure for diagnosis of kidney rejection via specific pathological changes. To provide a better assessment of immunologic events in acute T-cell-mediated rejection (acute TCMR) and BK virus-associated nephropathy (BKVAN) cases, we used multiplex immunofluorescence staining to identify infiltrating mononuclear cell subsets in the cortex area of transplanted kidneys. Antibodies to CD4, CD8, CD20, CD68, Foxp3, and cytokeratin were used. In cortical interstitium, CD8+ cells were significantly more prevalent in acute TCMR than BKVAN cases (34% vs. 22.8%, p = 0.034). In medulla, CD20+ cells were significantly more prevalent in BKVAN than acute TCMR cases (51.9% vs. 11.3%, p = 0.028).

This study investigated the loading rate effect on the fracture resistance under cyclic loading conditions to understand clearly the fracture behavior of piping materials under seismic conditions. J–R fracture toughness tests were conducted under monotonic and cyclic loading conditions at various displacement rates at room temperature and the operating temperature of nuclear power plants (i.e., 316°C). SA508 Gr.1a low-alloy steel and SA312 TP316 stainless steel piping materials were used for the tests. The fracture resistance under a reversible cyclic load was considerably lower than that under monotonic load regardless of test temperature, material, and loading rate. Under both cyclic and monotonic loading conditions, the fracture behavior of SA312 TP316 stainless steel was independent of the loading rate at both room temperature and 316°C. For SA508 Gr.1a low-alloy steel, the loading rate effect on the fracture behavior was appreciable at 316°C under cyclic and monotonic loading conditions. However, the loading rate effect diminished when the cyclic load ratio of the load (R) was −1. Thus, it was recognized that the fracture behavior of piping materials, including seismic loading characteristics, can be evaluated when tested under a cyclic load of R = −1 at a quasistatic loading rate.

Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus. [ABSTRACT FROM AUTHOR]