High-sensitivity NH3 gas sensor using pristine graphene doped with CuO nanoparticles.

A highly sensitive and selective NH3 gas sensor was developed based on single-layer pristine graphene doped with copper(II) oxide (CuO) nanoparticles of a specific size. High-quality single-layer graphene was grown using chemical vapor deposition. Approximately 15 nm-sized CuO colloidal nanoparticles were fabricated by a microwave-assisted thermal method using copper acetate as the precursor, and dimethylformamide as the reducing and stabilizing agent. Pristine graphene was doped with an aqueous suspension of CuO nanoparticles at a coating speed of 1500 rpm using a simple spin coater. CuO nanoparticle doping induces changes in the electronic properties of graphene; in particular, p-type doping significantly altered graphene resistivity in the presence of NH3 gas. Upon exposure of the pristine graphene surface to NH3 gas, NH3 reacted with O2-/ O-/ O2- species on the graphene surface and released electrons into graphene. This caused a change in the concentration of charge carriers in the valence channel of graphene and an increase in graphene resistivity, facilitating real-time NH3 monitoring with quick response and rapid recovery at 25 ℃ and ~ 55% relative humidity. Our results indicated that graphene doped with ~ 15 nm-sized CuO nanoparticles can sense NH3 gas selectively with a resistivity response of ~ 83%. Moreover, the sensor exhibited good reusability, fast response (~ 19 s), and rapid recovery (~ 277 s) with a detection limit of 0.041 ppm and a relative standard deviation of 0.76%.

Agathobaculum butyriciproducens Shows Neuroprotective Effects in a 6-OHDA-Induced Mouse Model of Parkinson's Disease.

Parkinson's disease (PD) is the second-most prevalent neurodegenerative disease and is characterized by dopaminergic neuronal death in the midbrain. Recently, the association between alterations in PD pathology and the gut microbiota has been explored. Microbiota-targeted interventions have been suggested as a novel therapeutic approach for PD. Agathobaculum butyriciproducens SR79T (SR79) is an anaerobic bacterium. Previously, we showed that SR79 treatment induced cognitive improvement and reduced Alzheimer's disease pathologies in a mouse model. In this study, we hypothesized that SR79 treatment may have beneficial effects on PD pathology. To investigate the therapeutic effects of SR79 on PD, 6-hydroxydopamine (6-OHDA)-induced mouse models were used. D-Amphetamine sulfate (d-AMPH)-induced behavioral rotations and dopaminergic cell death were analyzed in unilateral 6-OHDA-lesioned mice. Treatment with SR79 significantly decreased ipsilateral rotations induced by d-AMPH. Moreover, SR79 treatment markedly activated the AKT/GSK3ß signaling pathway in the striatum. In addition, SR79 treatment affected the Nrf2/ARE signaling pathway and its downstream target genes in the striatum of 6-OHDA-lesioned mice. Our findings suggest a protective role of SR79 in 6-OHDA-induced toxicity by regulating the AKT/Nrf2/ARE signaling pathway and astrocyte activation. Thus, SR79 may be a potential microbe-based intervention and therapeutic strategy for PD.

Gadd45ß promotes regeneration after injury through TGFß-dependent restitution in experimental colitis.

Dysregulated immune responses and impaired function in intestinal epithelial cells contribute to the pathogenesis of inflammatory bowel disease (IBD). Growth arrest and DNA damage-inducible 45 beta (Gadd45ß) has been implicated in the pathogenesis of various inflammatory symptoms. However, the role of Gadd45ß in IBD is completely unknown. This study aimed to evaluate the role of Gadd45ß in IBD. Gadd45ß-KO mice exhibited drastically greater susceptibility to dextran sulfate sodium (DSS)-induced colitis and mortality than C57BL/6J mice. Bone marrow transplantation experiments revealed that Gadd45ß functions predominantly in the intestinal epithelium and is critical during the recovery phase. Gadd45ß regulates the TGF-ß signaling pathway in colon tissue and epithelial cells by inhibiting Smurf-mediated degradation of TGF-ß receptor type 1 via competitive binding to the N-terminal domain of Smad7. Furthermore, these results indicate that the Gadd45ß-regulated TGF-ß signaling pathway is involved in wound healing by enhancing epithelial restitution. These results expand the current understanding of the function of Gadd45ß and its therapeutic potential in ulcerative colitis.

Ureaplasma Urealyticum Infection Contributes to the Development of Pelvic Endometriosis Through Toll-Like Receptor 2.

Endometriosis is a chronic gynecological disorder, characterized by the presence of ectopic endometrial tissue outside the uterine cavity. Among several hypotheses, Sampson's theory of retrograde menstruation is still applicable. Recent studies have reported the importance of inflammation among endometrial tissue, the peritoneum, and immune cells. However, less is known regarding the role of bacterial infection in the pathophysiology of endometriosis. We hypothesized that Ureaplasma urealyticum infection might contribute to the development of endometriosis by inducing the production of inflammatory mediators by peritoneal mesothelial cells (PMCs), possibly through TLR2. Hence, our objective was to reveal whether PMC infection by U. urealyticum is associated with endometriosis. Moreover, we aimed to demonstrate the molecular mechanism involved in this relationship. We developed a new infection-induced mouse model of endometriosis with wild type and Tlr2-deficient mice. Based on the in vivo mouse model, U. urealyticum-infected mice showed significantly increased numbers and sizes of ectopic endometriotic lesions. U. urealyticum upregulated not only the production of IL-6, CXCL1, and CCL2, but also the expression of ICAM-1, VCAM-1, and MMP2 in murine PMCs. Similarly, endometrial stromal cells dose-dependently produced IL-6, CXCL1, and CCL2 in response to U. urealyticum infection. The series of inflammatory responses in PMCs was mediated mainly through TLR2. The phosphorylation of ERK and JNK was observed when U. urealyticum was added to PMCs and knock out of Tlr2 inhibited these MAPKs phosphorylation. Based on our co-culture study, U. urealyticum-infected PMCs exhibited significantly increased attachment to ESCs compared with uninfected PMCs. Collectively, U. urealyticum infection promotes the development of endometriosis by increasing inflammatory mediators, adhesion molecules, and MMP-2 expression in PMCs through TLR2 signaling. Through our results, we present a theory that infection-induced pelvic inflammation contributes to the initiation and progression of endometriosis. Appropriate treatment of reproductive tract infection may decrease the prevalence of endometriosis.

Rapid-Response and Highly Sensitive Boronate Derivative-Based Fluorescence Probe for Detecting H2O2 in Living Cells.

Intracellular H2O2 monitoring is important and has driven researchers to pursue advancements for the rapid identification of H2O2, since H2O2 is short-lived in cell lines. An arylboronate derivative has been investigated as a chemospecific fluorescence recognition agent for H2O2. Triphenylimidazoleoxadiazolephenyl (TPIOP) boronate was contrived as a novel candidate for the rapid and sensitive recognition of H2O2. The probe was conjugated using the TPIOP functional group acting as an excellent fluorescent enhancer. The TPIOP group stimulated the polarization of C-B bond due to its extended π-conjugation, which included heteroatoms, and induced the production of rapid signal because of the highly polar C-B bond along with the corresponding boronate unit. While H2O2 reacts with TPIOP boronate, its nucleophilic addition to the boron generates a charged tetrahedral boronate complex, and then the C-B bond migrates toward one of the electrophilic peroxide oxygen atoms. The resulting boronate ester is then hydrolyzed by water into a phenol, which significantly enhances fluorescence through aggregation-induced emission. The TPIOP boronate probe responded to H2O2 rapidly, within 2 min, and exhibited high sensitivity with a limit of detection of 8 nM and a 1000-fold selectivity in the presence of other reactive oxygen species. Therefore, the developed TPIOP boronate chemodosimeter was successfully utilized to visualize and quantify intracellular H2O2 from human breast cancer (MCF-7) cells, as well as gaseous and aqueous H2O2 from environmental samples using Whatman paper strips coated with TPIOP boronate.

Pseudomonas kribbensis sp. nov., isolated from garden soils in Daejeon, Korea.

Two bacterial strains, 46-1 and 46-2T, were isolated from garden soil. These strains were observed to be aerobic, Gram-stain negative, rod-shaped, non-spore-forming, motile and catalase and oxidase positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains shared 100 % sequence similarity with each other and belong to the genus Pseudomonas in the class Gammaproteobacteria. The concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences further confirmed that the isolates belong to the Pseudomonas koreensis subgroup (SG), with P. koreensis Ps 9-14T, Pseudomonas moraviensis 1B4T and Pseudomonas granadensis F-278,770T as their close relatives (>96 % pairwise similarity). DNA-DNA hybridization with the closely related type strain P. koreensis SG revealed a low level of relatedness (<50 %). A cladogram constructed using whole-cell matrix-assisted laser desorption/ionization time-of-flight (WC-MALDI-TOF) MS analysis showed the isolates formed a completely separate monophyletic group. The isolates were negative for utilization of glycogen, D-psicose, α-keto butyric acid, α-keto valeric acid, succinamic acid and D, L-α-glycerol phosphate. In contrast, all these reactions were positive in P. koreensis JCM 14769T and P. moraviensis DSM 16007T. The fatty acid C17:0 cyclo was detected as one of the major cellular fatty acids (>15 %) in the isolates but it was a minor component (<4 %) in both reference type strains. In contrast, the fatty acid, C12:0 was not observed in the isolates but was present in both reference strains. Based on differences such as phylogenetic position, low-level DNA-DNA hybridization, WC-MALDI-TOF MS analysis, fluorescence pigmentation, fatty acid profiles, and substrate utilization, we propose that the isolates 46-1 and 46-2T represent a novel species of the genus Pseudomonas, for which the name Pseudomonas kribbensis sp. nov. is proposed; the type strain is 46-2T (=KCTC 32541T = DSM 100278T).

Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.

A novel bacterial strain, SR79T, was isolated from a Korean faecal sample and characterized using a polyphasic approach. SR79T was found to be a strictly anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase- and oxidase-negative short rod with no flagella. SR79T grew optimally at 37 °C in the presence of 0.5 % (w/v) NaCl at pH 7. The NaCl range for growth was 0-1 % (w/v). The isolate produced butyric acid (>18 mM) as a major end product. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the most closely related type strains were Eubacteriumdesmolans ATCC 43058T and Butyricicoccus pullicaecorum 25-3T (96.4 and 96.0 % similarity, respectively). The DNA G+C content was determined to be 52.9 mol%. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1cis-9, C19 : 1 cyc 9,10 and C14 : 0. Meso-diaminopimelic acid was present in the cell wall peptidoglycan and the cell wall hydrolysates contained ribose, glucose and galactose. The 16S rRNA gene sequence similarity, phylogenetic analysis, chemotaxonomic and phenotypic characteristics allowed differentiation of SR79T, which represents a novel species of a new genus within the family Ruminococcaceae, for which the name Agathobaculum butyriciproducens gen. nov. sp. nov. is proposed. The type strain is SR79T (=KCTC 15532T=DSM 100391T). Based on the results of this study, it is also proposed to transfer Eubacteriumdesmolans to this new genus, as Agathobaculum desmolans comb. nov. The type strain of Agathobaculum desmolans is ATCC 43058T (=CCUG 27818T).

Dermabacter vaginalis sp. nov., isolated from human vaginal fluid.

A novel actinobacterial strain, AD1-86T, was isolated from the vaginal fluid of a Korean female and was characterized by a polyphasic approach. The strain was a facultatively anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase-positive and oxidase-negative short rod. Colonies were creamy white, of low convexity and 1-2 mm in diameter after growth on DSM 92 agar plates at 37 °C for 2 days. The most closely related strains were Dermabacter hominis DSM 7083T and Helcobacillus massiliensis 6401990T (98.3 and 96.3 % 16S rRNA gene sequence similarity, respectively). The isolate grew optimally at 37 °C and pH 7 in the presence of 0.5% (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the cell-wall hydrolysates contained ribose, galactose and glucose. The DNA G+C content was 62.6 mol% and the mean DNA-DNA relatedness value of the isolate to D. hominis DSM 7083T was 31.1±3.0% (reciprocal: 48.2±5.3%). The major cellular fatty acids (>10%) were anteiso-C17:0, anteiso-C15:0 and iso-C16:0, and the menaquinones were MK-9, MK-8 and MK-7. The polar lipid profile of strain AD1-86T consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids and a glycolipid. Data from this polyphasic study indicate that strain AD1-86T represents a novel species of the genus Dermabacter, for which the name Dermabacter vaginalis sp. nov. is proposed; the type strain is AD1-86T (=KCTC 39585T=DSM 100050T).

Sphingomonas parvus sp. nov. isolated from a ginseng-cultivated soil.

Strain GP20-2(T) was isolated from a soil cultivated with ginseng in Korea. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Sphingomonas daechungensis CH15-11(T) (96.7%) and Sphingomonas sediminicola Dae 20(T) (96.2%) among the type strains. The strain GP20-2(T) was a strictly aerobic, Gram-negative, non-motile, rod-shaped bacterium that formed very tiny colonies, less than 0.3 mm in diameter after 10 days on R2A agar. The strain grew at 10-35-C (optimum, 35-C), at a pH of 5.0-8.0 (optimum, pH 6.0), and in the absence of NaCl. The DNA G+C content of strain GP20-2(T) was 67.2 mol%. It contained ubiquinone Q-10 as the major isoprenoid quinone, and summed feature 8 (C18:1ω6c and/or C18:1ω7c, 49.8%) and C16:0 (17.0%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain GP20-2(T) should be classified as a novel species of the genus Sphingomonas, for which the name Sphingomonas parvus sp. nov. is proposed. The type strain is GP20-2(T) (=KACC 12865(T) =DSM 100456(T)).

Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse.

A novel strictly anaerobic strain, ALO17(T), was isolated from mouse faeces and found to produce lactic acid as a major metabolic end product. The isolate was observed to be Gram-stain positive, non-motile, non-spore forming small rods, oxidase and catalase negative, and to form cream-coloured colonies on DSM 104 agar plates. The NaCl range for growth was determined to be 0-2 % (w/v). The isolate was found to grow optimally at 37 °C, with 0.5 % (w/v) NaCl and at pH 7. The cell wall hydrolysates were found to contain ribose as a major sugar. The genomic DNA G+C content was determined to be 52.3 mol%. A phylogenetic analysis of the 16S rRNA gene sequence revealed that Holdemanella biformis DSM 3989(T), Faecalicoccus pleomorphus ATCC 29734(T), Faecalitalea cylindroides ATCC 27803(T), and Allobaculum stercoricanis DSM 13633(T) are closely related to the isolate (87.4, 87.3, 86.9 and 86.9 % sequence similarity), respectively. The major cellular fatty acids (>10 %) of the isolate were identified as C18:1 cis 9 FAME (36.9 %), C16:0 FAME (33.7 %) and C18:0 FAME (13.2 %). In contrast to the tested reference strains, C20:0 FAME (4.0 %) was detected only in strain ALO17(T) whilst C16:0 DMA was absent. The isolate also differed in its substrate oxidation profiles from the reference strains by being positive for D-melibiose and stachyose but negative for N-acetyl-D-galactosamine and 3-methyl-D-glucose. On the basis of polyphasic taxonomic evidence from this study, the isolate is concluded to belong to a novel genus within the family Erysipelothricaceae. We propose the name Faecalibaculum rodentium gen. nov., sp. nov. to accommodate strain ALO17(T) (=KCTC 15484(T) = JCM 30274(T)) as the type strain.

Mucilaginibacter ginsengisoli sp. nov., isolated from a ginseng-cultivated soil.

A dark-pink-coloured bacterial strain, B4Y-8T, was isolated from a soil cultivated with ginseng. The 16S rRNA gene sequence of this strain showed highest similarity with Mucilaginibacter litoreus BR-18T (96.8 %), Mucilaginibacter lutimaris BR-3T (96.6 %) and Mucilaginibacter defluvii A5T (96.2 %) among the type strains of species of the genus Mucilaginibacter. Strain B4Y-8T was a strictly aerobic, Gram-stain-negative, non-motile, short-rod-shaped bacterium producing a large amount of extracellular polymeric substance. The strain grew at 10-35 °C (optimum, 25 °C), at pH 3.0-11.0 (optimum, pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum, 0 %). The DNA G+C content of strain B4Y-8T was 49.0 mol%. It contained menaquinone 7 (MK-7) as the major isoprenoid quinone, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0 as the major fatty acids. On the basis of evidence from the present polyphasic taxonomic study, strain B4Y-8T should be classified as representing a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ginsengisoli sp. nov. is proposed. The type strain is B4Y-8T ( = KACC 18152T = JCM 30759T).

Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae).

A novel, Gram-stain positive, facultative anaerobic, non-motile and straight to curve rod shaped bacterium, strain LV19(T) was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus, which was collected from Yeong-dong, Chuncheongbuk-do, South Korea. The colonies of the new isolate were convex, circular, cream white in color and 1-2 mm in diameter after 3 days incubation on Tryptic Soy Agar at 37 °C. Based on the 16S rRNA gene sequence similarity, the new isolate was most closely related to Erysipelothrix inopinata MF-EP02(T), E. rhusiopathiae ATCC 19414 (T) and E. tonsillarum T-305(T) (94.8, 93.8 and 93.7 % similarity, respectively). Strain LV19(T) grew optimally at 37 °C, at pH 8.0 and in the presence of 0.5 % (w/v) NaCl. Oxidase activity and catalase activity were negative. The major cellular fatty acids (>10 %) were C18:2 cis-9,12 (28.9 %), C18:1 cis-9 (22.3 %), C16:0 (22.2 %) and C18:0 (18.5 %). The cell-wall hydrolysates contained ribose as a major sugar. Major polar lipids were phosphatidylglycerol and three unidentified glycolipids. No quinone was detected. The G+C content of the genomic DNA was 36.3 mol%. The levels of DNA-DNA relatedness between strain LV19(T) and all the reference strains were less than 20 %. On the basis of polyphasic evidence from this study, the isolate is considered to represent a novel species of the genus Erysipelothrix, for which the name Erysipelothrix larvae sp. nov. is proposed; the type strain is LV19(T) (=KCTC 33523(T) = DSM 28480(T)).

Paenibacillus cucumis sp. nov. isolated from greenhouse soil.

Strain CO 4-7(T) was isolated from greenhouse soil used for cultivation of cucumbers in Korea. The 16S rRNA gene sequence of strain CO 4-7(T) showed the highest sequence similarity with Paenibacillus contaminans CKOBP-6(T) (94.2%) among the type strains. Strain CO 4-7(T) was a strictly aerobic, Gram-staining-positive, endospore-forming, and motile rodshaped bacterium. Strain CO 4-7(T) grew at 10-45°C (optimum, 30°C), at pH 6.0-7.5 (optimum, pH 6.5) and in the presence of 0-5% NaCl (optimum, 0.5%). The DNA G+C content of strain CO 4-7(T) was 48.5 mol%. It contained MK-7 as the major isoprenoid quinone and anteiso-C15:0 (51.8%), C16:0 (12.7%), and iso-C16:0 (8.6%) as the major fatty acids. The cell wall contained meso-diaminopimelic acid. Based on evidence from our polyphasic taxonomic study, it was concluded that strain CO 4-7T should be classified as a novel species of the genus Paenibacillus, for which, the name Paenibacillus cucumis sp. nov. is proposed. The type strain is CO 4-7(T) (=KACC 17444(T)=JCM 19515(T)).

Bacillus solimangrovi sp. nov., isolated from mangrove soil.

Two novel bacterial strains, GH2-4T and GH2-5, were isolated from mangrove soil near the seashore of Weno island in Chuuk state, Micronesia, and were characterized by a polyphasic approach. The two strains were strictly aerobic, Gram-staining-positive, motile, endospore-forming rods that were catalase- and oxidase-positive. Colonies were circular, convex, stringy and transparent yellowish (GH2-4T) or opaque whitish (GH2-5). The 16S rRNA gene sequences of the two isolates were identical. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus kochii WCC 4582T, B. horneckiae DSM 23495T, B. azotoformans LMG 9581T, B. cohnii DSM 6307T and B. halmapalus DSM 8723T (95.6, 95.4, 95.4, 95.2 and 95.2% similarity, respectively). The partial groEL sequence of strain GH2-4T was identical to that of strain GH2-5 and showed <85% similarity to those of the most closely related strains. The isolates grew at pH 5-12 (optimal growth at pH 9), at 10-40 °C (optimum 30-35 °C) and at 0-9% (w/v) NaCl (optimum 1-3% NaCl). The cell-wall peptidoglycan of strains GH2-4T and GH2-5 contained meso-diaminopimelic acid and cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 36 mol%, and DNA-DNA relatedness between the isolates and five related reference strains was 20-24%. Strain GH2-4T exhibited 81% DNA-DNA relatedness with strain GH2-5. The major cellular fatty acids of both strains were iso-C15:0, iso-C16:0, iso-C14:0 and anteiso-C15:0 and the predominant menaquinone was MK-7. On the basis of the evidence from this polyphasic study, strains GH2-4T and GH2-5 (=KCTC 33143=JCM 18995=DSM 27084) represent a novel species of the genus Bacillus, for which the name Bacillus solimangrovi sp. nov. is proposed; the type strain is GH2-4T (=KCTC 33142T=JCM 18994T=DSM 27083T).

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle.

Three strictly anaerobic, methanogenic strains JH1(T), JH4 and JH8 were isolated from rumen of the Korean native cattle (HanWoo; Bos taurus coreanae) in South Korea. The colonies were circular, opaque, and slightly yellowish. Phylogenetic analyses of 16S rRNA gene and mcrA (encoding α subunit of methyl-coenzyme M reductase) sequences confirmed the affiliation of the novel strains with the Methanobacteriales, and Methanobrevibacter wolinii SH(T) was the most closely related species. The 16S rRNA gene and mcrA sequence similarities between strains JH1(T), JH4 and JH8 and M. wolinii SH(T) were 96.2 and 89.0 % respectively, and DNA-DNA hybridization of the isolates and M. wolinii DSM 11976(T) showed a 20 % reassociation. Strain JH1(T) exhibited 92 % DNA-DNA relatedness with strains JH4 and JH8, and their 16S rRNA gene and mcrA sequences were identical. Cells stained Gram-positive and were non-motile rods, 1.5-1.8 µm long and 0.6 µm wide. The strains were able to use H2/CO2 and formate. The optimum temperature and pH ranges for growth were 37-40 °C and pH 6.5-7.0. The DNA G+C content of strain JH1(T) was 28 mol%. Based on data from this study using a polyphasic approach, the three strains represent a novel species of genus Methanobrevibacter, for which the name Methanobrevibacter boviskoreani sp. nov. is proposed. The type strain is JH1(T) ( = KCTC 4102(T) = JCM 18376(T)).

Sunxiuqinia dokdonensis sp. nov., isolated from deep sub-seafloor sediment.

A novel facultatively anaerobic strain DH1(T) was isolated from deep sub-seafloor sediment at a depth of 900 m below the seafloor off Seo-do (the west part of Dokdo Island) in the East Sea of the Republic of Korea. The new strain was characterized using polyphasic approaches. The isolate was Gram-stain-negative, motile by gliding, non-spore-forming rods, oxidase-negative, and catalase-positive; and formed colonies of orange-red color. The NaCl range for growth was 0.5-7.0% (w/v) and no growth was observed in the absence of NaCl. The isolate grew optimally at 30°C, with 2% (w/v) NaCl and at pH 7. The cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 40.8 mol%. The closest related strains are Sunxiuqinia faeciviva JAM-BA0302(T) and Sunxiuqinia elliptica DQHS-4(T) (97.9 and 96.3% sequence similarity, respectively). The level of DNA-DNA relatedness between strain DH1(T) and S. faeciviva JAM-BA0302(T) was around 41% (but only 6% between DH1T and S. elliptica DQHS-4(T)). The major cellular fatty acids of the isolate were contained iso-C15:0 (25.9%), anteiso-C15:0 (16.7%), and summed feature 9 (comprising C16:0 3-OH and/or unknown fatty acid of dimethylacetal ECL 17.157; 13.2%). The predominant menaquinone was MK-7. On the basis of polyphasic evidence from this study, the isolate was considered to represent a novel species of the genus Sunxiuqinia, for which the name Sunxiuqinia dokdonensis sp. nov. is proposed; the type strain is DH1(T) (=KCTC 32503(T) =CGMCC 1.12676(T) =JCM 19380(T)).

Construction and characterization of Japanese medaka (Oryzias latipes) hepatic cDNA library and its implementation to biomarker screening in aquatic toxicology.

To strengthen the toxicogenomic study, we constructed a library of hepatic cDNA from Japanese medaka under influence of specific chemical mediated stress responses. Gene expression profile analysis of the cDNA microarrays followed by real time RT-PCR assay were conducted to screen particular biomarkers for 17-beta estradiol (E2), nonylphenol (NP) and 2-chlorophenol (2CP). Information of 1509 high-quality ESTs including 260 new ESTs was added onto GenBank and dbEST. The ESTs were clustered and assembled into 159 contigs and 372 singletons. Among them, 128 contigs and 163 singletons (54.8%) were functionally characterized and 13 UniESTs (2.5%) were hypothetical proteins. Ontology analysis resulting in 282 UniESTs which involved with 2102 GOs and 93 sequences associated with 116 enzyme codes. For each test chemical, two specific biomarkers were selected from the gene expression profiling of microarrays. The expression patterns of the marker genes in real time PCR analysis were consistent with the regulated gene expression patterns in microarrays. The tentative biomarkers showed unique gene expression patterns depending on chemical concentration(s) and exposure duration in real time RT-PCR analysis. The analysis accomplished of the hepatic cDNA library and its information added to genetic and genomic resources could be sufficiently valuable specifically for aquatic toxicity studies.

Cloning, expression and characterization of xylose isomerase, XylA, from Caldanaerobacter subterraneus subsp. yonseiensis.

The xylA gene, coding for xylose isomerase, from the extreme thermophile, Caldanaerobacter subterraneus subsp. yonseiensis was cloned, sequenced, and expressed in Escherichia coli. The nucleotide sequence of the xylA gene encoded a polypeptide of 438 residues with a calculated molecular weight of 50,170 Da. The purified XylA showed high sequence homology (92% identity) with that of Thermoanaerobacter thermohydrosulfuricus. The recombinant enzyme expressed in Escherichia coli was purified by heat treatment and gel chromatography. The purified enzyme was thermostable with optimal activity at 95 degrees C. The enzyme required divalent cations including Zn(2+) for its maximal activity and thermostability.

Native-feather degradation by Fervidobacterium islandicum AW-1, a newly isolated keratinase-producing thermophilic anaerobe.

A native-feather-degrading thermophilic anaerobe was isolated from a geothermal hot stream in Indonesia. Isolate AW-1, identified as a member of the species Fervidobacterium islandicum, was shown to degrade native feathers (0.8%, w/v) completely at 70 degrees C and pH 7 with a maximum specific growth rate (0.14 h(-1)) in Thermotoga- Fervidobacterium(TF) medium. After 24 h of culture, feather degradation led to an increase in free amino acids such as histidine, cysteine and lysine. Moreover, nutritionally essential amino acids such as tryptophan and methionine, which are rare in feather keratin, were also produced as microbial metabolites. A homomultimeric membrane-bound keratinolytic protease (>200 kDa; 97 kDa subunits) was purified from a cell extract of F. islandicum AW-1. The enzyme exhibited activity toward casein and soluble keratin optimally at 100 degrees C and pH 9, and had a half-life of 90 min at 100 degrees C. The enzyme showed higher specific activity for the keratinous substrates than other proteases and catalyzed the cleavage of peptide bonds more rapidly following the reduction of disulfide bridges in feather keratin by 10 mM dithiothreitol. Therefore, the enzyme from F. islandicum AW-1 is a novel, thermostable keratinolytic serine protease.

Cloning, expression and characterization of L-arabinose isomerase from Thermotoga neapolitana: bioconversion of D-galactose to D-tagatose using the enzyme.

Gene araA encoding an L-arabinose isomerase (AraA) from the hyperthermophile, Thermotoga neapolitana 5068 was cloned, sequenced, and expressed in Escherichia coli. The gene encoded a polypeptide of 496 residues with a calculated molecular mass of 56677 Da. The deduced amino acid sequence has 94.8% identical amino acids compared with the residues in a putative L-arabinose isomerase of Thermotoga maritima. The recombinant enzyme expressed in E. coli was purified to homogeneity by heat treatment, ion exchange chromatography and gel filtration. The thermophilic enzyme had a maximum activity of L-arabinose isomerization and D-galactose isomerization at 85 degrees C, and required divalent cations such as Co(2+) and Mn(2+) for its activity and thermostability. The apparent K(m) values of the enzyme for L-arabinose and D-galactose were 116 mM (v(max), 119 micromol min(-1) mg(-1)) and 250 mM (v(max), 14.3 micromol min(-1) mg(-1)), respectively, that were determined in the presence of both 1 mM Co(2+) and 1 mM Mn(2+). A 68% conversion of D-galactose to D-tagatose was obtained using the recombinant enzyme at the isomerization temperature of 80 degrees C.