Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil

Two yellow-coloured bacterial strains, designated JS13-10(T) and JS16-4(T), were isolated from soil from Jeju Island, Republic of Korea. On the basis of 16S rRNA gene sequence analysis, the strains were found to be affiliated with members of the genus Chitinophaga. Phenotypically, the novel strains were identified as being different from each other and from recognized species of the genus Chitinophaga. DNA-DNA hybridization tests between the two novel strains and closely related Chitinophaga reference strains produced DNA relatedness values that were significantly lower (<36 %) than those generally accepted as the highest threshold for the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, these strains represent two novel species of the genus Chitinophaga, for which the names Chitinophaga niabensis sp. nov. (type strain JS13-10(T)=KACC 12952(T)=JCM 15440(T)) and Chitinophaga niastensis sp. nov. (type strain JS16-4(T)=KACC 12954(T)=JCM 15441(T)) are proposed.

Aquitalea denitrificans sp. nov., isolated from a Korean wetland

A novel bacterium, designated strain 5YN1-3(T), was isolated from wetland peat collected from Yongneup, Korea. The bacterium was facultatively anaerobic, Gram-negative, yellow-coloured, rod-shaped, mesophilic and motile with one polar flagellum. The strain grew optimally at 30 degrees C, at pH 6.0-9.0 and with 0-1 % NaCl (w/v). 16S rRNA gene sequence analysis showed the highest similarity to the sequence from Aquitalea magnusonii TRO-001DR8(T), with 98.7 % sequence similarity. However, strain 5YN1-3(T) showed DNA-DNA relatedness of 43 % (40 % in a reciprocal experiment) with A. magnusonii LMG 23054(T). The strain contained summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) and C(16 : 0) as major cellular fatty acids. On the basis of DNA-DNA relatedness and physiological and biochemical characterization, strain 5YN1-3(T) should be assigned to a novel species of the genus Aquitalea, for which the name Aquitalea denitrificans sp. nov. is proposed. The type strain is 5YN1-3(T) (=KACC 12729(T) =DSM 21300(T)).

Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea

A pink-coloured bacterial strain, designated 5715S-9(T), was isolated from an air sample collected in Suwon, Republic of Korea. The cells were strictly aerobic, Gram-negative, non-spore-forming, non-flagellated and short-rod-shaped. On the basis of 16S rRNA gene sequence analysis, the organism was a member of the genus Rubellimicrobium, showing the highest sequence similarities with Rubellimicrobium mesophilum MSL-20(T) (96.2 % sequence similarity) and Rubellimicrobium thermophilum DSM 16684(T) (93.9 %). The major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The major fatty acids (>10 %) were C(18 : 1)omega7c, C(16 : 0) and 11-methyl C(18 : 1)omega7c. The G+C content of the DNA was 69 mol%. On the basis of both phylogenetic and phenotypic evidence, strain 5715S-9(T) represents a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium aerolatum sp. nov. is proposed. The type strain is 5715S-9(T) (=KACC 12504(T)=DSM 19297(T)).

Central lymph node metastases in unilateral papillary thyroid microcarcinoma

BACKGROUND

The indications for and appropriate extent of prophylactic central lymph node (CLN) dissection for clinically node-negative patients with unilateral papillary thyroid microcarcinoma (PTMC) are unknown.

METHODS

The frequency, patterns and predictive factors for CLN metastases in 86 patients with unilateral PTMC and a clinically node-negative neck were analysed with respect to age and sex; metastasis, age, completeness, invasiveness, size (MACIS) score; tumour size; number and location of tumours; presence of ipsilateral CLN metastases; and presence of lymphovascular or capsular invasion. All patients underwent total thyroidectomy and CLN dissection.

RESULTS

Twenty-seven (31 per cent) of 86 patients had metastatic CLNs: 18 ipsilateral and nine bilateral. Univariable analysis suggested male sex and tumour size greater than 0.5 cm to be significant factors in predicting ipsilateral CLN metastases. Only ipsilateral nodal positivity was a significant predictor of contralateral CLN metastases in multivariable analysis (P = 0.007).

CONCLUSION

CLN metastases are relatively common in PTMC.

Sialolithiasis in a stump of Wharton's duct of an aplastic unilateral submandibular gland

Congenital absence of the salivary glands is an uncommon disorder. Isolated aplasia of a unilateral submandibular gland is rare and only 6 cases have been reported. The formation of a sialolith within the remaining Wharton's duct, associated with isolated aplasia of a unilateral submandibular gland, has not been reported previously. The authors report two cases of sialolithiasis within the ipsilateral remaining Wharton's duct in patients with isolated aplasia of a unilateral submandibular gland.

Characterization of a gene encoding cellulase from uncultured soil bacteria

To detect cellulases encoded by uncultured microorganisms, we constructed metagenomic libraries from Korean soil DNAs. Screenings of the libraries revealed a clone pCM2 that uses carboxymethyl cellulose (CMC) as a sole carbon source. Further analysis of the insert showed two consecutive ORFs (celM2 and xynM2) encoding proteins of 226 and 662 amino acids, respectively. A multiple sequence analysis with the deduced amino acid sequences of celM2 showed 36% sequence identity with cellulase from the Synechococcus sp., while xynM2 had 59% identity to endo-1,4-beta-xylanase A from Cellulomonas pachnodae. The highest enzymatic CMC hydrolysis was observable at pH 4.0 and 45 degrees C with recombinant CelM2 protein. Although the enzyme CelM2 additionally hydrolyzed avicel and xylan, no substrate hydrolysis was observed on oligosaccharides such as cellobiose, pNP-beta-cellobioside, pNP-beta-glucoside, and pNP-beta-xyloside. These results showed that CelM2 is a novel endo-type cellulase.

Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice

A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20T utilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genus Methylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20T was most closely related to Methylobacterium fujisawaense, Methylobacterium radiotolerans and Methylobacterium mesophilicum; however, DNA-DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20T was 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20T that allows its differentiation from other Methylobacterium species. In addition, strain CBMB20T is the only known member of the genus Methylobacterium to be described from the phyllosphere of rice. Based on the data presented, strain CBMB20T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium oryzae sp. nov. is proposed, with strain CBMB20T (=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.

Aurantimonas ureilytica sp. nov., isolated from an air sample

A novel strain, designated 5715S-12T, was isolated from an air sample collected from Suwon region, Republic of Korea, using R2A medium. The cells were strictly aerobic, Gram-negative, motile, short rods. Comparison of the 16S rRNA gene sequence of strain 5715S-12T showed the highest sequence similarities to Aurantimonas altamirensis S21BT (95.9 %) and Aurantimonas coralicida WP1T (95.4 %). Phylogenetic trees indicated that the strain formed a cluster with members of the family Aurantimonadaceae (A. altamirensis, A. coralicida and Fulvimarina pelagi). The major fatty acid was C18 : 1 ω7c. The predominant isoprenoid quinone was ubiquinone 10 (Q-10). Diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine and four unknown lipids were found as the polar lipid components. The DNA G+C content was 67.0 mol%. On the basis of the phenotypic and phylogenetic features studied, we propose that strain 5715S-12T be assigned to a novel species of the genus Aurantimonas, for which the name Aurantimonas ureilytica sp. nov. (type strain 5715S-12T =KACC 11607T =DSM 18598T) is proposed.

Screening and characterization of an enzyme with beta-glucosidase activity from environmental DNA

A novel beta-glucosidase gene, bglA, was isolated from uncultured soil bacteria and characterized. Using genomic libraries constructed from soil DNA, a gene encoding a protein that hydrolyzes a fluorogenic analog of cellulose, 4-methylumbelliferyl beta-D-cellobioside (MUC), was isolated using a microtiter plate assay. The gene, bglA, was sequenced using a shotgun approach, and expressed in E. coli. The deduced 55-kDa amino acid sequence for bglA showed a 56% identity with the family 1 glycosyl hydrolase Chloroflexus aurantiacus. Bg1A included two conserved family 1 glycosyl hydrolase regions. When using p-nitrophenyl-beta-D-glucoside (pNPG) as the substrate, the maximum activity of the purified beta-glucosidase exhibited at pH 6.5 and 55 degrees C, and was enhanced in the presence of Mn2+. The Km and Vmax values for the purified enzyme with pNPG were 0.16 mM and 19.10 micromol/min, respectively. The purified BglA enzyme hydrolyzed both pNPG and p-nitrophenyl-beta-D-fucoside. The enzyme also exhibited substantial glycosyl hydrolase activities with natural glycosyl substrates, such as sophorose, cellobiose, cellotriose, cellotetraose, and cellopentaose, yet low hydrolytic activities with gentiobiose, salicin, and arbutin. Moreover, Bg1A was able to convert the major ginsenoside Rb1 into the pharmaceutically active minor ginsenoside Rd within 24 h.

Generation of a specific marker to discriminate Gacillus anthracis from other bacteria of the Bacillus cereus group

Bacillus anthracis is a soil pathogen capable of causing anthrax that is closely related to several environmental species, including B. cereus, B. mycoides, and B. thuringiensis. DNA homology studies showed that B. anthracis, B. cereus, B. mycoides, and B. thuringiensis are closely related, with a high sequence homology. To establish a method to specifically detect B. anthracis in situations such as environmental contamination, we initially performed RAPD-PCR with a 10-mer random primer and confirmed the presence of specific PCR bands only in B. anthracis species. One region specific for B. anthracis was cloned and sequenced, and an internal primer set was designed to amplify a 241-bp DNA fragment within the sequenced region. The PCR system involving these specific primer sets has practical applications. Using lyses methods to prepare the samples for PCR, it was possible to quickly amplify the 241-bp DNA segment from samples containing only a few bacteria. Thus, the PCR detection method developed in this study is expected to facilitate the monitoring of environmental B. anthracis contamination.

Idiomarina homiensis sp. nov., isolated from seashore sand in Korea

A halophilic, aerobic bacterium, designated PO-M2(T), was isolated from seashore sand, from Pohang, Korea and characterized on the basis of physiological and biochemical features. Phylogenetic analysis of 16S rRNA gene sequences revealed a clear affiliation of the novel strain with members of the genus Idiomarina. Sequence similarities between strain PO-M2(T) and the type strains of species belonging to the genus Idiomarina ranged from 94.3 to 95.5 %. Cells of strain PO-M2(T) were straight or slightly curved rods and formed light-yellow colonies on marine agar medium. The major isoprenoid quinone was ubiquinone (Q-8) and the predominant cellular fatty acids were C(15 : 0) iso (19.3 %), C(17 : 1)omega9c iso (11.9 %), C(17 : 0) iso (10.9 %), C(18 : 1)omega7c (10.4 %), C(16 : 0) (9.0 %) and C(16 : 1)omega7c and/or C(15 : 0) iso 2-OH (7.2 %). The G+C content of the DNA was 45.1 mol%. Based on physiological, biochemical and chemotaxonomic traits and comparative 16S rRNA gene sequence analysis, it is demonstrated that the isolate represents a novel species of the genus Idiomarina, for which the name Idiomarina homiensis sp. nov. is proposed. The type strain is PO-M2(T) (=KACC 11514(T)=DSM 17923(T)).

Development of high-throughput assay of lethal factor using native substrate

The design of inhibitors for anthrax lethal factor (LF) is currently of interest as an approach for the treatment of anthrax because LF plays a major role in the cytotoxicity of target cells. LF is a zinc-dependent metalloprotease that specifically cleaves the mitogen-activated protein kinase kinase (MKK) family. Current assay systems for the screening of LF inhibitor use the optimized synthetic peptide coupled with various kinds of fluorophores, enabling fast, sensitive, and robust assays suited to high-throughput screening. However, evidence suggests that the regions beside the cleavage site are also involved in specificity and proteolytic activity of LF. In the current study, we tried to develop a high-throughput assay for LF activity based on native substrate, mitogen-activated ERK kinase 1 (MEK1). The assay system relies on the enhanced chemiluminescence signal resulting from a specific antibody against the C-terminal region of native substrate. A glutathione-coated multiwell plate was used as a solid support to immobilize the native substrate by its N-terminal glutathione-S-transferase moiety. Immobilized substrate increases the specificity and sensitivity of LF-catalyzed substrate hydrolysis compared with the solution phase assay. This assay system might be used to discover a wide spectrum of anthrax inhibitors.

The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice

The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.

Targeting of Bacillus anthracis interaction factors for human macrophages using two-dimensional gel electrophoresis

Bacillus anthracis, a gram-positive, endospore-forming, aerobic rod-shaped bacterium, interacts with macrophages at various stages of the disease. Spore germination and the outgrowth of vegetative bacilli are crucial steps enabling the bacteria to proliferate actively and to synthesize the virulence factors leading to a massive septicemia. In this study, we performed a proteomic analysis and MALDI-TOF/MS were carried out to identify proteins using human macrophages infected with the spores of B. anthracis live-Sterne or inactivated-Sterne. We identified 21 proteins which are related to the infection of B. anthracis spores on human macrophages at the early stage events. These proteins function in processes such as cytoskeleton regulation, apoptosis, cell division, and protein degradation. Proteins such as PAK 2 revealed a relationship to apoptosis in human macrophages. These proteins play an important role in the macrophage survival and death on human macrophages with infected B. anthracis spores.

The Seoul Metropolitan Preschool Vision Screening Programme: results from South Korea

AIM

To report on a new model of preschool vision screening that was performed in metropolitan Seoul and to investigate the distribution of various ocular disorders in this metropolitan preschool population.

METHODS

Vision screening was conducted on 36 973 kindergarten children aged 3-5 years in a stepwise manner. The first step was home screening using a set of five picture cards and a questionnaire. The children who did not pass the first step (VA <0.5 in at least one eye or any abnormal responses on the questionnaire) were retested with regular vision charts at the regional public healthcare centres. After this retest, some children were referred to ophthalmologists. The referral criteria for visual acuity were <0.5 at 3 years and <0.63 at 4 or 5 years in at least one eye.

RESULTS

Of those screened, 7116 (19.2%) children did not pass the home screening tests and 2058 (28.9%) out of the 7116 were referred. The results of the ophthalmological examination in eye clinics were only available for 894 children (43.4%) of those who were referred. The rest of the children did not visit ophthalmologists because they had been checked at an eye clinic, were currently under treatment, or for personal reasons. Refractive errors were found in 608 (1.6%) children. Astigmatism was associated in 78.2% of ametropes. Amblyopia was discovered in 149 (0.4%) children and refractive error was the major aetiology with a predominant rate (82.5%). Manifest strabismus was detected in 52 children. The positive predictive value of vision screening for any ophthalmological disorder was 0.77, and 0.49 for significant disorders requiring treatment.

CONCLUSIONS

This preschool vision screening model was highly accessible to the children and their parents, easy to administer, and effective to detect a variety of ocular disorders. However, the participation rate of the referred children in the examinations by ophthalmologists was quite low. The performance and efficiency of this screening programme need to be optimised with further revision.

Production and proteolytic assay of lethal factor from Bacillus anthracis

Bacillus anthracis is the causative agent of anthrax. The major virulence factors are a poly-D-glutamic acid capsule and three-protein component exotoxin, protective antigen (PA, 83 kDa), lethal factor (LF, 90 kDa), and edema factor (EF, 89 kDa), respectively. These three proteins individually have no known toxic activities, but in combination with PA form two toxins (lethal toxin or edema toxin), causing different pathogenic responses in animals and cultured cells. In this study, we constructed and produced rLF as a form of GST fusion protein in Escherichia coli. rLF was rapidly purified through a single affinity purification step to near homogeneity. Furthermore, we developed an in vitro immobilized proteolytic assay of LF under the condition containing full-length native substrate, MEK1, rather than short synthetic peptide. The availability of full-length substrate and of an immobilized LF assay could facilitate not only the in-depth investigation of structure-function relationship of the enzyme toward its substrate but also wide spectrum screening of inhibitor collections based on the 96-well plate system.

The thin latissimus dorsi perforator-based free flap for resurfacing

The authors present their experience with "thin" latissimus dorsi perforator-based free flaps for resurfacing defects. Perforator-based free flaps have been used for various kinds of reconstruction by presenting important donor structures. The thin latissimus dorsi perforatorbased free flap included only the skin and superficial adipose layer to reduce its bulkiness by dissection through the superficial fascial plane. This flap was used in 12 clinical cases, without flap necrosis or other serious postoperative complications. All of the patients were examined by preoperative power Doppler ultrasound in the spectral Doppler mode to search for the most reliable perforator. This noninvasive ultrasound technique determines the exact location and course of and ensures the reliable flow of the perforators; therefore, it greatly assists microsurgeons in saving operation time and in selecting the most suitable design for perforator flap reconstruction. We used perforators that were identified several centimeters from the lateral border of the latissimus dorsi muscle. The thin flap dimensions could be safely designed for flaps measuring up to 20 cm in length and 8 cm in width for primary closure of the donor site. Generally, a long pedicle is not required for resurfacing reconstructions, where small recipient arteries in the bed are acceptable for anastomosis with pedicles. However, pedicle dissection to the proximal vessels through the latissimus dorsi muscle was required when it was necessary to match the recipient vein for anastomosis. The authors conclude that this thin latissimus dorsi perforator-based free flap has great potential for resurfacing because of its constant thickness, easy elevation with the help of power Doppler ultrasound information, and proper flap size for moderate defects caused by scar contracture release, superficial tumor ablation, and so on.

Hepatic involvement in hypereosinophilia: sonographic findings

Hypereosinophilic syndrome may cause eosinophil-related tissue damage to various organs. The purpose of this paper is to describe sonographic findings in 13 patients with hypereosinophilia in whom the liver was involved. The diagnosis in these 13 patients was based on liver biopsy in seven patients with bone marrow biopsy in six patients. Eight patients had hypereosinophilic syndrome and five patients had clonorchiasis. All 13 patients had mild to marked hepatomegaly. Seven of 13 patients showed multiple round or oval hypoechoic (n = 6) or variably echogenic (n = 1) lesions measuring 1 to 2 cm with poorly defined margins in both lobes of the liver. Four patients had one or two hypoechoic lesions 3 to 4 cm in size, with geographic pattern and poorly defined margins. Two patients showed diffuse hepatomegaly with increased parenchymal echogenicity. The number of lesions and the extent of diffuse lesions seem to be proportional to the degree of eosinophilia. Hypereosinophilia may produce multiple small focal hepatic lesions or diffuse segmental or lobar echogenic lesions simulating primary or metastatic tumor of the liver.

Change of plasma lipoproteins by heparin-released lipoprotein lipase

Lipoprotein lipase (LPL) is known to be attached to the luminal surface of vascular endothelial cells in a complex with membrane-bound heparan sulfate, and released into blood stream by heparin. LPL that catalyzes hydrolysis of triglyceride (TGL) on chylomicron and VLDL into two fatty acids and monoacylglycerol, is also implicated to participate in an enhancement of cholesterol uptake by arterial endothelial cells in vitro. But little is known about the LPL-mediated cholesterol uptake in physiological state. In this study, changes in blood lipid composition and levels of lipoproteins were determined after the injection of heparin in human. The level of LPL in plasma was increased from 0 to 11 mU/ml within 30-40 min post-heparin administration and decreased to the basal level within 2 h. The level of TGL in plasma decreased from 70 mg/dl to 20 mg/dl within 1 h and gradually increased to 80 mg/dl within 4 h. However the level of total cholesterol in plasma remained at 140 mg/dl during an experimental period of 4 h. Analysis of Lipoproteins in plasma by NaBr density gradient ultracentrifugation showed that the level of VLDL decreased from 50 mg/dl to 10 mg/dl within 1-2 h and returned to normal plasm level at 4 h. However there were no significant changes in the level of LDL and HDL. These results suggest that, at least, in normo-lipidemic subjects, increased free plasm LPL acts primarily on VLDL and failed to show any significant uptake of cholesterol-rich lipoproteins in human.

Genetic variations at four tetrameric tandem repeat loci in Korean population

Allele and genotype frequencies for four tetrameric short tandem repeat (STR) loci, HumFES/FPS, HumFOLP23, HumGABRB15, and HumCYAR04, have been determined by polymerase chain reaction (PCR) amplification and subsequent polyacrylamide gel electrophoresis from approximately 200 genetically unrelated Koreans. This method allows a single base pair resolution and rapid typing with silver staining. The allele and genotype distributions satisfy Hardy-Weinberg expectation. Also, these STR loci have proven to be useful for forensic analyses and paternity tests in which the variable number of tandem repeat (VNTR) loci have some limitations.

Efficacy of ciprofloxacin and dexamethasone in experimental pseudomonas endophthalmitis

To determine injection time and effective dose of ciprofloxacin in endophthalmitis and to evaluate the effectiveness of dexamethasone. In rabbits, Pseudomonas aeruginosa (2 x 10(4) CFU/0.1 ml) was inoculated intravitreally. At 6, 12, 18, 24 hours postinoculation, single intravitreal doses of ciprofloxacin (300 micrograms/0.15 ml or 100 micrograms/0.05 ml) alone or with dexamethasone (400 micrograms) were given. Electrophysiological and histologic measures were utilized to rate drug effectiveness. 300 micrograms ciprofloxacin was effective in killing P. aeruginosa at 6 and 12 hours postinoculation, but one hundred ug ciprofloxacin was not effective. 300 ug ciprofloxacin had no significant effect in killing P. aeruginosa at 18 hrs and 24 hrs postinoculation. Eyes treated with dexamethasone (400 micrograms) and ciprofloxacin (300 micrograms) at 6 hours postinoculation did not differ from eyes treated with ciprofloxacin alone. Cultures from eyes treated with dexamethasone and ciprofloxacin at 12 hours postinoculation were positive. Cultures from eyes treated with ciprofloxacin alone were negative. The failure of treatment at 18 hrs and 24 hrs postinoculation may be due to either an increased rate of clearance of drugs from the eyes or a reduced bactericidal effect of ciprofloxacin which could be altered by acidic pH, degree of hypoxia or bacterial counts. Dexamethasone had no beneficial effect in the treatment of P. aeruginosa endophthalmitis in the early phase.