Complete genome sequence of NA05 (=NBRC 116153), a phosphate-solubilizing bacterium isolated from crop field soil.

We report the complete genome sequence of the phosphate-solubilizing bacterium NA05 (=NBRC 116153), consisting of a circular chromosome of ~3.8 M bp and two circular plasmids. The data presented here provide further insight into the genetic and functional potential of and the mechanism of phosphate solubilization.

Bacterial and fungal community composition and community-level physiological profiles in forest soils.

We characterized the potential functioning and composition of the bacterial and fungal communities in the O and A horizons of forest soils using community-level physiological profile (CLPP) based on BIOLOG analysis, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S and 18S rDNA fragments, respectively. In addition, relationships between the potential functioning and the community composition in each horizon, and between the O and A horizons, were assessed using Procrustes analysis. For the bacterial and fungal communities, the CLPP and DGGE profile were clearly separated between the O and A horizons in a principal coordinate analysis except for the fungal CLPP.

Prokaryotic Community Structure of Long-Term Fertilization Field Andisols in Central Japan.

Long-term fertilization experiments are a useful way to elucidate the impacts of fertilization on soil ecosystems. Here, we report the prokaryotic community structure in experimental field soil after 80 years of successive fertilization. Our 16S rRNA gene sequencing detected 20,996 amplicon sequence variants, including major phyla such as Proteobacteria, Acidobacteria, and Actinobacteria.

Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.

Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols.

Nitrogen supply rate regulates microbial resource allocation for synthesis of nitrogen-acquiring enzymes.

Although microorganisms will preferentially allocate resources to synthesis of nitrogen (N)-acquiring enzymes when soil N availability is low according to the resource allocation model for extracellular enzyme synthesis, a robust link between microbial N-acquiring enzyme activity and soil N concentration has not been reported. To verify this link, we measured several indices of soil N availability and enzyme activity of four N-acquiring enzymes [N-acetyl-β-glucosaminidase (NAG), protease (PR), urease (UR), and L-asparaginase (LA)] and a carbon (C)-acquiring enzyme [β-D-glucosidase (BG)] in arable and forest soils. Although the ratios of NAG/BG and PR/BG were not significantly related with indices of soil N availability, ratios of LA/BG and UR/BG were strongly and negatively related with potentially mineralizable N estimated by aerobic incubation but not with pools of labile inorganic N and organic N.

Hepatitis C virus-induced innate immune responses in human iPS cell-derived hepatocyte-like cells.

Hepatitis C virus (HCV) infection is a major cause of liver-related morbidity and mortality. In order to develop effective remedies for hepatitis C, it is important to understand the HCV infection profile and host-HCV interaction. HCV-induced innate immune responses play a crucial role in spontaneous HCV clearance; however, HCV-induced innate immune responses have not been fully evaluated in hepatocytes, partly because there are few in vitro models of HCV-induced innate immunity.

Evaluating the Effects of Metals on Microorganisms in Flooded Paddy Soils Using the SEM/AVS-Based Approach and Measurements of Exchangeable Metal Concentrations.

We examined possible adverse effects of heavy metals on microbial activity, biomass, and community composition using the simultaneously extracted metals (SEM)/acid-volatile sulfide (AVS)-based approach and measurements of exchangeable metal concentrations in three paddy soils (wastewater-contaminated soil, mine-contaminated soil, and noncontaminated soil) incubated for 60 days under flooded conditions. Incubation under flooding increased pH and decreased Eh in all samples. AVS increased when Eh decreased to approximately -200 mV for the mine-contaminated and noncontaminated soils, while the wastewater-contaminated soil originally had a high concentration of AVS despite its air-dried condition.

Spatial and temporal trends of alternative flame retardants and polybrominated diphenyl ethers in ringed seals (Phoca hispida) across the Canadian Arctic.

Concentrations of alternative flame retardants and polybrominated diphenyl ethers (PBDEs) were analyzed in ringed seal (Phoca hispida) blubber collected across the Canadian Arctic during subsistence hunts between 1998 and 2013. More than 80% of sampled animals were females and juvenile males. The highest mean ΣPBDE concentrations (sum of 13 congeners) were found in seals from Nain (Nunatsiavut) as well as Inukjuaq and Arviat (Hudson Bay) and the lowest mean levels were found in seals from Lancaster Sound.

[Relationship between Arsenic (+3 Oxidation State) Methyltransferase Genetic Polymorphisms and Methylation Capacity of Inorganic Arsenic].

Arsenic metabolism affects the susceptibility of humans to arsenic toxicity; therefore, clarification of the factors associated with individual variations in arsenic metabolism is an important task. Genetic polymorphisms such as single nucleotide polymorphisms (SNPs) in arsenic (+3 oxidation state) methyltransferase (AS3MT), which can methylate arsenic compounds using S-adenosyl-l-methionine (AdoMet), have been reported to modify arsenic methylation. In this review, we summarize studies conducted by us in Vietnam and by others on the association of AS3MT genetic polymorphisms with arsenic metabolism as well as human health effects.

Haptoglobin genotyping of Vietnamese: global distribution of HP del, complete deletion allele of the HP gene.

The haptoglobin (HP) gene deletion allele (HP(del)) is responsible for anhaptoglobinemia and a genetic risk factor for anaphylaxis reaction after transfusion due to production of the anti-HP antibody. The distribution of this allele has been explored by several groups including ours. Here, we studied the frequency of HP(del) in addition to the distribution of common HP genotypes in 293 Vietnamese.

Individual variations in arsenic metabolism in Vietnamese: the association with arsenic exposure and GSTP1 genetic polymorphism.

We investigated the association of As exposure and genetic polymorphism in glutathione S-transferase π1 (GSTP1) with As metabolism in 190 local residents from the As contaminated groundwater areas in the Red River Delta, Vietnam. Total As concentrations in groundwater ranged from <0.1 to 502 μg l(-1).

Polymorphic trial in oxidative damage of arsenic exposed Vietnamese.

Arsenic causes DNA damage and changes the cellular capacity for DNA repair. Genes in the base excision repair (BER) pathway influence the generation and repair of oxidative lesions. Single nucleotide polymorphisms (SNPs) in human 8-oxoguanine DNA glycosylase (hOGG1) Ser326Cys; apurinic/apyrimidinic endonuclease (APE1) Asp148Glu; X-ray and repair and cross-complementing group 1 (XRCC1) Arg280His and Arg399Gln in the BER genes were analyzed, and the relationship between these 4 SNPs and the urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG) concentrations of 100 Vietnamese population exposed to arsenic was investigated.

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.

The presence of mercury selenide in various tissues of the striped dolphin: evidence from μ-XRF-XRD and XAFS analyses.

Marine mammals accumulate mercury in their tissues at high concentration and detoxify by forming mercury selenide (HgSe, tiemannite) mainly in the liver. We investigated the possibility of formation of HgSe in various tissues (liver, kidney, lung, spleen, pancreas, muscle and brain) other than the liver of the striped dolphin (Stenella coeruleoalba). We applied a combination method of micro-X-ray fluorescence (μ-XRF) imaging and micro-X-ray diffraction (μ-XRD) using a synchrotron radiation X-ray microbeam to analyze the tissue samples directly with minimal sample preparation.

Accumulation of trace elements in harp seals (Phoca groenlandica) from Pangnirtung in the Baffin Island, Canada.

Nineteen trace elements were determined in liver, muscle, kidney, gonads, and hair of 18 harp seals (Phoca groenlandica) from Pangnirtung in the Baffin Island, Canada. Concentrations of V, Mn, Fe, Cu, Mo, Ag, and Hg in the liver, Co, Cd, and Tl in the kidney, and Ba and Pb in the hair were significantly higher than those in other tissues. Significant positive correlations between Hg concentrations in the hair, and liver, kidney and testis imply usefulness of the hair sample for non-destructive monitoring of Hg in the harp seals.

Exposure, metabolism, and health effects of arsenic in residents from arsenic-contaminated groundwater areas of Vietnam and Cambodia: a review.

In this review, we summarize the current knowledge on exposure, metabolism, and health effects of arsenic (As) in residents from As-contaminated groundwater areas of Vietnam and Cambodia based on our findings from 2000 and other studies. The health effects of As in humans include severe gastrointestinal disorders, hepatic and renal failure, cardiovascular disturbances, skin pigmentation, hyperkeratosis, and cancers in the lung, bladder, liver, kidney, and skin. Arsenic contamination in groundwater is widely present at Vietnam and Cambodia and the highest As levels are frequently found in groundwater from Cambodia.

Genetic variants associated with arsenic metabolism within human arsenic (+3 oxidation state) methyltransferase show wide variation across multiple populations.

Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene in Mexican and German populations. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was assessed on healthy individuals: 38 Mestizo, 69 Nahuas, 50 Huicholes, and 32 Germans.

Global analysis of genetic variation in human arsenic (+3 oxidation state) methyltransferase (AS3MT).

Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene at the global level. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was performed in 827 individuals from 10 populations (Japanese, Korean, Chinese, Mongolian, Tibetans, Sri Lankan Tamils, Sri Lankan Sinhalese, Nepal Tamangs, Ovambo, and Ghanaian).

Genetic polymorphisms in glutathione S-transferase (GST) superfamily and arsenic metabolism in residents of the Red River Delta, Vietnam.

To elucidate the role of genetic factors in arsenic metabolism, we investigated associations of genetic polymorphisms in the members of glutathione S-transferase (GST) superfamily with the arsenic concentrations in hair and urine, and urinary arsenic profile in residents in the Red River Delta, Vietnam. Genotyping was conducted for GST omega1 (GSTO1) Ala140Asp, Glu155del, Glu208Lys, Thr217Asn, and Ala236Val, GST omega2 (GSTO2) Asn142Asp, GST pi1 (GSTP1) Ile105Val, GST mu1 (GSTM1) wild/null, and GST theta1 (GSTT1) wild/null. There were no mutation alleles for GSTO1 Glu208Lys, Thr217Asn, and Ala236Val in this population.

Genetic polymorphisms in AS3MT and arsenic metabolism in residents of the Red River Delta, Vietnam.

To elucidate the role of genetic factors in arsenic (As) metabolism, we studied associations of single nucleotide polymorphisms (SNPs) in As (+3 oxidation state) methyltransferase (AS3MT) with the As concentrations in hair and urine, and urinary As profile in residents in the Red River Delta, Vietnam. Concentrations of total As in groundwater were 0.7-502 mug/l.

Effects of plant litter type and additions of nitrogen and phosphorus on bacterial community-level physiological profiles in a brown forest soil.

Effects of plant litter type (larch needle-leaves, mixed broad-leaves, and sasa green leaves) and nutrient addition (nitrogen and phosphorus) on bacterial community-level physiological profiles (CLPPs) of a forest soil were examined using BIOLOG EcoPlates(TM). Both the litter and nutrient additions significantly increased color development in most of the wells in the BIOLOG microplates, with the effect of the latter being especially great for soils amended with plant leaves low in nutrients. Nitrogen addition to soils decreased the color development of some nitrogenous substrates.

Two N-linked glycosylation sites (Asn18 and Asn106) are both required for full enzymatic activity, thermal stability, and resistance to proteolysis in mammalian deoxyribonuclease I.

Deoxyribonuclease I (DNase I) is known to be a glycoprotein, and two potential N-linked glycosylation sites (N18 and N106) are known for mammalian enzymes. In the present study, N18 and N106 were mutated in order to investigate the biological role of N-linked glycosylation in three mammalian (human, bovine, and equine) DNases I. The enzyme activities of N18Q and N106Q were lower than that of the wild type, and that of the double mutant (N18Q/N106Q) was lower than those of the single mutants, in accord with the sugar moiety contents in the three mammals.

Relationship of urinary arsenic metabolites to intake estimates in residents of the Red River Delta, Vietnam.

This study investigated the status of arsenic (As) exposure from groundwater and rice, and its methylation capacity in residents from the Red River Delta, Vietnam. Arsenic levels in groundwater ranged from <1.8 to 486 microg/L.

Multivariate characterization of elements accumulated in King Bolete Boletus edulis mushroom at lowland and high mountain regions.

Based on ICP-MS, ICP-OES, HG-AAS, CV-AAS and elementary instrumental analysis of King Bolete collected from four sites of different soil bedrock geochemistry considered could be as mushroom abundant in certain elements. King's Bolete fruiting bodies are very rich in K (> 20 mg/g dry weight), rich in Ca, Mg, Na, Rb and Zn (> 100 microg/g dw), and relatively also rich in Ag, Cd, Cs, Cu, Fe, Mn and Se (> 10 microg/g dw). The caps of King Bolete when compared to stipes around two-to three-fold more abundant are in Ag, Cd, Cs, Cu, Hg, K, Mg, Mo, N, Rb, Se and Zn.