Pedobacter luteus sp. nov., isolated from soil.

Two strains of Gram-staining-negative, rod-shaped bacteria that were motile by gliding, N7d-4(T) and B4a-b5, were isolated during a study of culturable bacteria in soil cultivated with potatoes. These isolates grew at 15-37 °C and at pH 6.5-7.0. The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were phosphatidyl-N-methylethanolamine and phosphatidylethanolamine. The strains contained d-18 : 0 and d-19 : 0 sphingosines. The DNA G+C contents of strains N7d-4(T) and B4a-b5 were 48.5 and 46.9 mol% (HPLC), respectively. A phylogenetic analysis based on 16S rRNA gene sequences showed that strains N7d-4(T) and B4a-b5 were affiliated with Pedobacter species in the family Sphingobacteriaceae. Strains N7d-4(T) and B4a-b5 shared 99.9 % sequence similarity, and the most closely related Pedobacter type strains were Pedobacter composti TR6-06(T) (96.5 and 96.7 % sequence similarity, respectively), P. oryzae N7(T) (95.4 and 95.6 %) and P. caeni LMG 22862(T) (94.0 and 94.4 %). Phenotypic data and phylogenetic inference clearly distinguished the two isolates from other Pedobacter species. Based on these data, the isolates are considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter luteus sp. nov. is proposed. The type strain is N7d-4(T) ( = KCTC 22699(T)  = DSM 22385(T)).

Transforming growth factor-beta1 is a molecular target for the peroxisome proliferator-activated receptor delta.

The peroxisome proliferator-activated receptor (PPAR)delta has been implicated in the pathogenesis of atherogenic disorders. However, its physiological roles and functions in vascular smooth muscle cells (VSMCs) remain relatively unclear. In the present study, we show that the gene encoding transforming growth factor (TGF)-beta1 is a PPARdelta target in VSMCs. The PPARdelta activator GW501516 upregulates TGF-beta1 expression in a dose- and time-dependent manner. This induction is attenuated significantly by the presence of small interfering RNA against PPARdelta or GW9662, an inhibitor of PPARdelta. Furthermore, activated PPARdelta induces TGF-beta1 promoter activity by binding to the direct repeat-1 response element TGF-beta1-direct repeat-1. Mutations in the 5' or 3' half-sites of the response element totally abrogate transcriptional activation and PPARdelta binding, which suggests that this site is a novel type of PPARdelta response element. In addition, ligand-activated PPARdelta attenuated the promoter activity and expression of monocyte chemoattractant protein-1 induced by interleukin-1beta. These effects were significantly reduced in the presence of small interfering RNA against PPARdelta, anti-TGF-beta1 antibody, or a TGF-beta type I receptor inhibitor. Decreased monocyte chemoattractant protein-1 expression induced by PPARdelta was mediated by the effector of TGF-beta1, Smad3. Finally, administration of GW501516 to mice upregulated TGF-beta1, whereas the expression of proinflammatory genes including monocyte chemoattractant protein-1 was significantly attenuated in the thoracic aorta. Taken together, these results demonstrate the presence of a novel TGF-beta1-mediated pathway in the antiinflammatory activities of PPARdelta.

Synthesis and antifungal activity of a novel series of 13-(4-isopropylbenzyl)berberine derivatives.

By replacing the methyl group of 13-(4-isopropylbenzyl)berberine 2 with various acyl, alkyl, and benzyl groups via the demethylated intermediate, 13-(4-isopropylbenzyl)berberrubine 4, a novel series of 9-O-alkyl-13-(4-isopropylbenzyl)berberine derivatives was synthesized and examined for antifungal activities against various human pathogenic fungi. The introduction of various alkyl groups led to enhanced antifungal activity but that of acyl groups resulted in decrease of the activity. Among them, 9-O-butyl-13-(4-isopropylbenzyl)berberine 6d exhibited the most potent antifungal activities against Cryptococcus neoformans, Candida species (MIC=0.25-1 µg/ml), and Aspergillus species (MIC=2-4 µg/ml). The compound was found to be relatively safe up to 900 mg/kg in oral administration to mice.

Endoscopic findings and clinical features of esophageal tuberculosis.

OBJECTIVE: Mycobacterial involvement of the esophagus is rare. Similar abnormal lesions of the esophagus may be confused with esophageal cancer and deep fungal infections. We studied the clinical features, endoscopic findings, the role of histopathology, and the outcome of antituberculosis treatment in patients with esophageal tuberculosis. METHODS: A single center based, retrospective study was performed. We reviewed the clinical and pathological records of patients with esophageal tuberculosis that were clinically diagnosed from 1997 to 2006. RESULTS: Esophageal tuberculosis, confirmed by histology, was found in six patients. Five patients presented with local symptoms. The mean number of endoscopic sessions for a diagnosis was 1.8 sessions (range 1-3). For the histopathology, caseous necrosis was found in four patients but positive acid fast bacilli stains and tuberculosis-polymerase chain reaction were not detected. Patients diagnosed with esophageal tuberculosis tolerated medical therapy and responded well. CONCLUSION: Because esophageal tuberculosis presents with various, diverse clinical features, and endoscopic findings, it is difficult to diagnose at one session of endoscopy. However, esophageal tuberculosis should be considered in the differential diagnosis if ulcerative lesions were found in the mid esophagus.

Investigation of possible horizontal gene transfer from transgenic rice to soil microorganisms in paddy rice field.

In order to monitor the possibility of horizontal gene transfer between transgenic rice and microorganisms in paddy rice field, the gene flow from bifunctional fusion (TPSP) rice containing trehalose-6-phosphate synthase and phosphatase to microorganisms in soils was investigated. The soil samples collected every month from the paddy rice field during June, 2004 to March, 2006 were investigated by multiplex PCR, Southern hybridization, and amplified fragment length polymorphism (AFLP). The TPSP gene from soil genomics DNAs was not detected by PCR. Soil genomic DNAs were not shown its homologies on the Southern blotting data, indicating that gene-transfer did not occur during the last two years in paddy rice field. In addition, the AFLP band patterns produced by both soil genomic DNAs extracted from transgenic and non-transgenic rice field appeared similar to each other when analyzed by NTSYSpc program. Thus, these data suggest that transgenic rice does not give a significant impact on the communities of soil microorganisms although long-term observation may be needed.

Monitoring of possible horizontal gene transfer from transgenic potatoes to soil microorganisms in the potato fields and the emergence of variants in Phytophthora infestans.

To examine the possibility of horizontal gene transfer between transgenic potatoes and microorganisms in potato fields, the gene flow from transgenic potatoes containing nucleoside diphosphate kinase 2 (NDPK2) gene to microorganisms in soils was investigated. The soil samples collected from the potato fields from March to October in 2007 were examined by PCR, Southern hybridization, and AFLP fingerprinting. The NDPK2 gene from soil genomic DNAs was not detected by both PCR and Southern hybridization, indicating that gene-transfer did not occur in the potato fields. In addition, no discrepancy was found in pathogenicity and noticeable changes for the appearance of variants of Phytophthora infestans in each generation when serial inoculations and the analysis of genomic DNAs by AFLP was conducted. Thus, these data suggest that transgenic potatoes do not give significant impacts on the communities of soil microorganisms and the emergence of variants although continued research efforts may be necessary to make a decisive conclusion.

Isolation and characterization of a high iturin yielding Bacillus velezensis UV mutant with improved antifungal activity.

To isolate Bacillus velezensis mutants with improved antifungal activity for use in the biological control of phytopathogenic fungi, wild-type Bacillus velezensis KRF-001 producing iturin, surfactin, and fengycin was irradiated by ultraviolet (UV) rays. The in vitro and in vivo antifungal activities of UV mutants and characterization of the cyclic lipopeptides produced by a selected mutant were examined. A mutant strain yielding high levels of iturin showed over 2-fold higher antifungal activity than the wild-type against Fusarium oxysporum. A potent suppressive effect of the mutant was also observed on spore germination of Botrytis cinerea, the causative agent of cucumber gray mold, at different butanol extract concentrations. Further analysis of the mutant by real-time PCR and high-performance liquid chromatography revealed increased expression of iturin and surfactin biosynthesis genes as well as enhanced production of iturin and surfactin metabolites. However, the amounts of fengycin obtained from the mutant strain BSM54 were significantly lesser than those of iturin and surfactin. Particularly, iturin A production by the mutant was 3.5-fold higher than that of the wild-type, suggesting that the higher antifungal activity of the mutant against F. oxysporum resulted from the increased expression of biosynthesis genes associated with iturin production. The commercial greenhouse experiment using soil naturally infested with Sclerotinia sclerotiorum (sclerotinia rot) and F. oxysporum (fusarium wilt) showed that the mutant strain reduced sclerotinia rot and fusarium wilt diseases (P = 0.05) more effectively than the wild-type and commercially available product Cillus® in Korea. These results suggest that the mutant with high iturin yield is a potential candidate for the development of a biological control agent in agriculture.

Novel GH10 xylanase, with a fibronectin type 3 domain, from Cellulosimicrobium sp. strain HY-13, a bacterium in the gut of Eisenia fetida.

The gene encoding a novel modular xylanase from Cellulosimicrobium sp. strain HY-13 was identified and expressed in Escherichia coli, and its truncated gene product was characterized. The enzyme consisted of three distinct functional domains, an N-terminal catalytic GH10 domain, a fibronectin type 3 domain, and C-terminal carbohydrate-binding module 2.

Anti-tumor activity of Gastrodia elata Blume is closely associated with a GTP-Ras-dependent pathway.

Gastrodia elata Blume (GEB) is an important medicinal plant in Korea. In order to confirm the anti-tumor activities of GEB extracts, we carried out various in vitro anti-tumor assays, including a wound assay and an invasion assay using an ethyl ether extract of GEB. The results showed that the GEB extract exhibits potent anti-tumor activity in vitro in a dose-dependent manner. The expression of CD44, cdc42, Timp-2 or RhoA mRNA did not change by GEB treatment, compared to that of the control. GTP-Ras, an active form of a G-coupled protein family, however, is associated with the anti-tumor activity of GEB extracts. We examined various molecular markers related to metastasis by reverse transcriptase-polymerase chain reaction with the extract of GEB-treated B16 cells. There was an increase in GTP-Ras expression by the Gastrodia elata Blume extract. Together, these results suggest that the Gastrodia elata Blume extract could have potential in alleviating tumorigenesis, by a GTP-Ras-dependent pathway; although the precise molecular mechanisms are still being examined.

Ceftezole, a cephem antibiotic, is an alpha-glucosidase inhibitor with in vivo anti-diabetic activity.

Using a high throughput-compatible assay to screen for potential alpha-glucosidase inhibitors, we found that the beta-lactam antibiotic ceftezole exhibited potent alpha-glucosidase inhibitory activity. In in vitro alpha-glucosidase assays, ceftezole was shown to be a reversible, non-competitive inhibitor of yeast alpha-glucosidase with a Ki value of 5.78 x 10(-7) M when the enzyme mixture was pretreated with ceftezole. Using an in vivo streptozotocin-induced mouse model, we confirmed that blood glucose levels decreased by 30% 20 min after ceftezole treatment (10 mg/kg/day). Expression levels of glycogen synthase kinase-3, peroxisome proliferator-activated receptor-gamma, and uncoupling protein-3 mRNA were also slightly decreased compared to controls following ceftezole treatment. Taken together, these in vivo and in vitro results suggest that ceftezole may be a clinically useful anti-diabetic compound.

Inhibitory effect of obovatol from Magnolia obovata on the Salmonella type III secretion system.

In many pathogenic Gram-negative bacteria, such as Salmonella, Escherichia coli, Yersinia and Chlamydia spp., which cause diseases in humans, the type III secretion system (TTSS) is an important virulence factor that translocates effector proteins into the cytosol of host cells. Thus, the TTSS is a good target for antibacterial agents. Here we used a hemolysis assay to search for TTSS inhibitors and found that a compound from Magnolia obovata called obovatol blocks the TTSS of Salmonella. Obovatol showed potent inhibitory activity (IC50=19.8 µM) against the TTSS-related hemolysis of Salmonella, which was not due to a reduction of bacterial growth. Instead, the compound inhibited bacterial motility, TTSS-related mRNA expression and effector protein secretion. These data demonstrate the inhibitory effect of obovatol on the Salmonella TTSS and suggest that it could be useful for the prevention and supplementary treatment of bacterial infections.

Antifungal Activities of Dimeric Sesquiterpenes, Shizukaols C and F, Isolated from Chloranthus japonicus Sieb.

Two dimeric sesquiterpenes were separated from Chloranthus japonicus Sieb. and identified as shizukaols C and F. They exhibited potent antifungal activities (MICs = 4-16 µg/ml) in vitro against various plant pathogenic fungi (Pythium ultimum, Phytophthora infestans, Botrytis cinerea, Colletotrichum lagenarium, Alternaria kikuchiana, and Magnaporthe grisea). Shizukaol C showed 88% and 91% protective activities in the greenhouse against Puccinia recondita (wheat leaf rust) and Phytophthora infestans (tomato late blight), respectively, at 100 µg/ml; shizukaol F exhibited 93% antifungal activity against Puccinia recondita at the same concentration. Therefore, these compounds might serve as interesting candidates for effective antifungal agents.

Organization and characterization of genetic regions in Bacillus subtilis subsp. krictiensis ATCC55079 associated with the biosynthesis of iturin and surfactin compounds.

Bacillus subtilis subsp. krictiensis ATCC55079 produces the cyclic lipopeptide antibiotics iturin A-F as well as several surfactins. Here, we analyzed and characterized the biosynthetic genes associated with iturin and surfactin production in this strain. We aligned the sequences of each iturin and surfactin synthetase ORF obtained from a genomic library screen and next generation sequencing. The resulting 37,249-bp and 37,645-bp sequences associated with iturin and surfactin production, respectively, contained several ORFs that are predicted to encode proteins involved in iturin and surfactin biosynthesis. These ORFs showed higher sequence homologies with the respective iturin and surfactin synthetase genes of B. methylotrophicus CAU B946 than with those of B. subtilis RB14 and B. subtilis ATCC6633. Moreover, comparative analysis of the secondary metabolites produced by the wild-type and surfactin-less mutant (with a spectinomycin resistance cassette inserted into the srfAB gene within the putative surfactin gene region) strains demonstrated that the mutant strain showed significantly higher antifungal activity against Fusarium oxysporum than the wild-type strain. In addition, the wild-type strain-specific surfactin high performance liquid chromatography (HPLC) peaks were not observed in the surfactin-less mutant strain. In contrast, the iturin A peak detected by HPLC and liquid chromatography-mass spectrometry (LC/MS) in the surfactin-less mutant strain was 30% greater than that in the wild-type strain. These results suggested that the gene cluster we identified is involved in surfactin biosynthesis, and the biosynthetic pathways for iturin and surfactin in Bacillus strains producing both iturin and surfactin may utilize a common pathway.

Inhibition of the Calcineurin Pathway by Two Flavonoids Isolated from Miliusa sinensis Finet & Gagnep.

In order to discover plant-derived signaling pathway inhibitors with antifungal properties, a two-component screening system utilizing the calcineurin and Hog1 mitogen-activated protein kinase pathways responsible for the virulence networks of Cryptococcus neoformans was employed, owing to the counter-regulatory actions of these pathways. Of the 1,000 plant extracts tested, two bioactive compounds from Miliusa sinensis were found to act specifically on the calcineurin pathway of C. neoformans. These compounds, identified as pashanone and 5-hydroxy-6,7-dimethoxyflavanone, exhibited potent antifungal activities against various human pathogenic fungi with minimum inhibitory concentration values ranging from 4.0 to >128 µg/ml.

Association of vascular endothelial growth factor gene polymorphisms with behcet disease in a Korean population.

Vascular endothelial growth factor (VEGF) is important for angiogenesis and inflammation, both of which are codependent and contribute to the pathophysiology of Behcet disease (BD). The increased expressions of VEGF have been observed in the active stage and in the ocular inflammation of BD. Polymorphisms of the VEGF gene have been associated with chronic inflammatory disease including rheumatoid arthritis. We sought to investigate whether polymorphisms on the regulatory region of the VEGF gene are associated with susceptibility of Korean patients with BD. One hundred one native Korean patients with BD and 138 healthy unrelated controls were recruited. Genotype and allele frequencies of the four selected polymorphisms (-2578, -1154, -634, and 936) were not different between the BD group and controls. Among the BD patients, the frequency of the -634 CC genotype decreased in patients with uveitis (2.6% vs. 20.6%, adjusted OR = 0.100, 95% CI 0.011-0.875, p = 0.037), although it became insignificant after correction for multiple comparisons. These results indicate that the VEGF gene polymorphisms are not associated with BD in the Korean population, but they may be involved in the development of the ocular inflammation of BD.

BRD-glucan exhibits potent immunochemotherapeutic activity in vitro and in vivo.

We carried out in vitro and in vivo assays to investigate the immunomodulatory and immunochemotherapeutic action mechanism of BRD-glucan, a high molecular weight ( approximately 3,500 kDa) polysaccharide isolated from Aureobasidium sp, and assessed the efficacy of BRD-glucan/adriamycin co-treatment of animal cancer models. RT-PCR and suspension hemolytic, plaque forming, wounding, invasion and cell proliferation assays were utilized to investigate the in vitro immunochemotherapeutic effects of BRD-glucan. In vivo, the effects of BRD-glucan and BRD-glucan/adriamycin co-treatment were tested in a B16 melanoma initiation model and in C57BL/6 mice. In vitro, BRD-glucan did not affect the cellular wounding response or invasion activity; treatment with BRD-glucan led to increase proliferation of B cells, natural killer cells and macrophages, but not T cells. In addition, we found that the BRD-glucan activation of B cells and macrophages was dependent on Toll-like receptor2 (TLR2) and TLR4, which play important roles in innate and adaptive immunity. In vivo, BRD-glucan/adriamycin co-treatment effectively reduced the number and size of metastatic colonies. Based on the results of our in vitro and in vivo toxicity, safety and immunochemotherapy assays, we propose that BRD-glucan is a promising immunochemotherapeutic anti-tumor agent.

Wisteria floribunda gall extract inhibits cell migration in mouse B16F1 melanoma cells by regulating CD44 expression and GTP-RhoA activity.

Extracts from galls grown on Wisteria floribunda are used as an anti-tumoral preparation in oriental traditional medicine. Here, we investigated the molecular mechanism of this anti-tumoral effect by first examining whether the extract inhibited cell migration in a B16 cell-based wound healing assay. The gall extract delayed wound healing in a dose- and time-dependent manner, indicating that one or more components of the fraction inhibited cell migration. Examination of two molecules known to be involved in metastasis, CD44, and RhoA-GTP, revealed that the gall extract decreased CD44 expression in a concentration-dependent manner, and also increased RhoA-GTP activity in comparison to untreated controls. Taken together, these results suggest that the Wisteria gall extract may inhibit cancer cell migration via inhibition of CD44 mRNA expression and activation of the GTP-RhoA protein.

A Phenylpropanoid Glycoside as a Calcineurin Inhibitor Isolated from Magnolia obovata Thunb.

To identify plant-derived cell signaling inhibitors with antifungal properties, a twocomponent screening system using both wild-type Cryptococcus neoformans and a calcineurin mutant was employed owing to their counter-regulatory actions on the Hog1 mitogenactivated protein kinase and calcineurin pathways. Of the 2,000 plant extracts evaluated, a single bioactive compound from M. obovata Thunb. was found to act specifically on the calcineurin pathway of C. neoformans. This compound was identified as magnoloside A, and had potent antifungal activities against various Cryptococcus strains with minimum inhibitory concentration values ranging from 1.0 to 4.0 µg/ml.

Plant virus cDNA chip hybridization for detection and differentiation of four cucurbit-infecting Tobamoviruses.

A plant virus cDNA chip was developed by using viral cDNA clones and microarray technology. The cDNA chip was designed for detection and differentiation of the four species of selected cucurbit-infecting tobamoviruses [target viruses: Cucumber green mottle mosaic virus (CGMMV); Cucumber fruit mottle mosaic virus (CFMMV); Kyuri green mottle mosaic virus (KGMMV); and Zucchini green mottle mosaic virus (ZGMMV)]. The chip consisted of cDNA clones of the four cucurbit-infecting tobamoviruses, two target-related tobamoviruses, and another three unrelated plant viruses. Polymerase chain reaction products were amplified from the selected cDNA clones and arrayed onto slide glass. The cDNA chip, which was called cucurbit-virus chip, detected successfully specific target viruses. When applied to probes made from ZGMMV-infected samples, ZGMMV reacted strongly with its homologous cDNA and moderately reacted with KGMMV and CFMMV, while it did not react with CGMMV on the same chip. CGMMV probe gave strong signal intensity to its homologous cDNA spot and weakly reacted with ZGMMV, KGMMV, and CFMMV. The signal intensity of all combinations of probe and target was correlated significantly with nucleotide sequence identities between the probes and target viruses based on scatter diagrams. The signals could be made as image files for specific virus detection, and this could be useful for virus identification and differentiation. This is the first report of plant virus detection by using cDNA chip technology.

9-O-butyl-13-(4-isopropylbenzyl)berberine, KR-72, is a potent antifungal agent that inhibits the growth of Cryptococcus neoformans by regulating gene expression.

In this study we explored the mode of action of KR-72, a 9-O-butyl-13-(4-isopropylbenzyl)berberine derivative previously shown to exhibit potent antifungal activity against a variety of human fungal pathogens. The DNA microarray data revealed that KR-72 treatment significantly changed the transcription profiles of C. neoformans, affecting the expression of more than 2,000 genes. Genes involved in translation and transcription were mostly upregulated, whereas those involved in the cytoskeleton, intracellular trafficking, and lipid metabolism were downregulated. KR-72 also exhibited a strong synergistic effect with the antifungal agent FK506. KR-72 treatment regulated the expression of several essential genes, including ECM16, NOP14, HSP10 and MGE1, which are required for C. neoformans growth. The KR-72-mediated induction of MGE1 also likely reduced the viability of C. neoformans by impairing cell cycle or the DNA repair system. In conclusion, KR-72 showed antifungal activity by modulating diverse biological processes through a mode of action distinct from those of clinically available antifungal drugs such as polyene and azole drugs.