Jong-Chan Chae

Effect of light on growth, intracellular and extracellular pigment production by five pigment-producing filamentous fungi in synthetic medium

The competence of the living creatures to sense and respond to light is well known. The effect of darkness and different color light quality on biomass, extracellular and intracellular pigment yield of five potent pigment producers Monascus purpureus, Isaria farinosa, Emericella nidulans, Fusarium verticillioides and Penicillium purpurogenum, with different color shades such as red, pink, reddish brown and yellow, were investigated. Incubation in total darkness increased the biomass, extracellular and intracellular pigment production in all the fungi. Extracellular red pigment produced by M. purpureus resulted maximum in darkness 36.75 + or - 2.1 OD and minimum in white unscreened light 5.90 + or - 1.1 OD. Similarly, intracellular red pigment produced by M. purpureus resulted maximum in darkness 18.27 + or - 0.9 OD/g and minimum in yellow light 8.03 + or - 0.6 OD/g of substrate. The maximum biomass production was also noticed in darkness 2.51 g/L and minimum in yellow light 0.5 g/L of dry weight. In contrast, growth of fungi in green and yellow wavelengths resulted in low biomass and pigment yield. It was found that darkness, (red 780-622 nm, blue 492-455 nm) and white light influenced pigment and biomass yield.

Laccase-poly(lactic-co-glycolic acid) (PLGA) nanofiber: Highly stable, reusable, and efficacious for the transformation of diclofenac

Nanobiocatalysis has received growing attention for use in commercial applications. We investigated the efficiency, stability, and reusability of laccase-poly(lactic-co-glycolic acid) (PLGA) nanofiber for diclofenac transformation. NH stretching vibrations (3400-3500 cm(-1) and 1560 cm(-1)) in FT-IR spectra confirmed immobilization of laccase on PLGA nanofibers. The relative activity of immobilized laccase was 82% that of free laccase. Immobilized laccase had better storage, pH, and thermal stability than free laccase. The immobilized laccase produced complete diclofenac transformation in three reuse cycles, which was extended to 6 cycles in the presence of syringaldehyde. Results suggest that laccase-PLGA nanofiber may be useful for removing diclofenac from aqueous sources and has potential for other commercial applications.

Alleviation of salt stress by enterobacter sp. EJ01 in tomato and Arabidopsis is accompanied by up-regulation of conserved salinity responsive factors in plants.

Microbiota in the niches of the rhizosphere zones can affect plant growth and responses to environmental stress conditions via mutualistic interactions with host plants. Specifically, some beneficial bacteria, collectively referred to as Plant Growth Promoting Rhizobacteria (PGPRs), increase plant biomass and innate immunity potential. Here, we report that Enterobacter sp. EJ01, a bacterium isolated from sea china pink (Dianthus japonicus thunb) in reclaimed land of Gyehwa-do in Korea, improved the vegetative growth and alleviated salt stress in tomato and Arabidopsis. EJ01 was capable of producing 1-aminocy-clopropane-1-carboxylate (ACC) deaminase and also exhibited indole-3-acetic acid (IAA) production. The isolate EJ01 conferred increases in fresh weight, dry weight, and plant height of tomato and Arabidopsis under both normal and high salinity conditions. At the molecular level, short-term treatment with EJ01 increased the expression of salt stress responsive genes such as DREB2b, RD29A, RD29B, and RAB18 in Arabidopsis. The expression of proline biosynthetic genes (i.e. P5CS1 and P5CS2) and of genes related to priming processes (i.e. MPK3 and MPK6) were also up-regulated. In addition, reactive oxygen species scavenging activities were enhanced in tomatoes treated with EJ01 in stressed conditions. GFP-tagged EJ01 displayed colonization in the rhizosphere and endosphere in the roots of Arabidopsis. In conclusion, the newly isolated Enterobacter sp. EJ01 is a likely PGPR and alleviates salt stress in host plants through multiple mechanisms, including the rapid up-regulation of conserved plant salt stress responsive signaling pathways.

Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis

DNA stable isotope probing and metagenomic sequencing were used to assess the metabolic potential of iron-reducing bacteria involved in anaerobic aromatic hydrocarbon degradation in oil spill-affected tidal flats. In a microcosm experiment, (13) C-toluene was degraded with the simultaneous reduction of Fe(III)-NTA, which was also verified by quasi-stoichiometric (13) C-CO2 release. The metabolic potential of the dominant member affiliated with the genus Desulfuromonas in the heavy DNA fraction was inferred using assembled scaffolds (designated TF genome, 4.40 Mbp with 58.8 GC mol%), which were obtained by Illumina sequencing. The gene clusters with peripheral pathways for toluene and benzoate conversion possessed the features of strict and facultative anaerobes. In addition to the class II-type benzoyl-CoA reductase (Bam) of strict anaerobes, the class I-type (Bcr) of facultative anaerobes was encoded. Genes related to the utilization of various anaerobic electron acceptors, including iron, nitrate (to ammonia), sulfur and fumarate, were identified. Furthermore, genes encoding terminal oxidases (caa3 , cbb3 and bd) and a diverse array of genes for oxidative stress responses were detected in the TF genome. This metabolic versatility may be an adaptation to the fluctuating availability of electron acceptors and donors in tidal flats.

Isolation, characterization, and abundance of filamentous members of Caldilineae in activated sludge

Chloroflexi are currently believed to serve as backbone forming agents in the activated sludge of wastewater treatment plants (WWTPs). In this study, we isolated and characterized filamentous bacteria in the class Caldilineae of the phylum Chloroflexi in municipal WWTPs. Diversity analysis using Chloroflexi-specific 16S rRNA gene clone libraries showed that 97% of the clones belonged to the subdivision Anaerolineae comprising the two classes Anaerolineae (95%) and Caldilineae (2%). Clones of Caldilineae were related to a thermophilic filament Caldilinea aerophila with 93% 16S rRNA gene sequence similarity. We obtained filamentous isolates classified into the class Caldilineae showing the best match to C. aerophila with 89% 16S rRNA gene sequence similarity. Isolates showed no ability to assimilate glucose or N-acetylglucosamine or to degrade biopolymers which were observed in filamentous Chloroflexi of WWTPs. The assessment of relative abundance based on quantitative PCR of the 16S rRNA gene indicated that members of the class Caldilineae comprised 12–19% of the Chloroflexi in the activated sludge. Additionally, fluorescence in situ hybridization experiments showed that diverse filamentous Caldilineae inhabit the activated sludge of municipal WWTPs. These findings yield insight into the role of filamentous mesophilic Caldilinea in stabilizing flocs of activated sludge in a wide range of WWTPs.

The Effect of Blue-light-emitting Diodes on Antioxidant Properties and Resistance to Botrytis cinerea in Tomato

In higher plants, blue-light is mainly perceived by cryptochromes and phototropins, which subsequently orchestrates phototropism, chloroplast relocation, stomatal opening, rapid inhibition of hypocotyl elongation and leaf expansion. Blue-light signaling is also known to mediate the plant responses to biotic stresses, but relevant mechanisms are largely unknown. Here, we demonstrated that blue LED (Light Emitting Diode)-driven inhibition of gray mold disease was highly correlated with the increases in cellular protectants like proline, antioxidants and ROS (Reactive Oxygen Species) scavenger activities. After twenty one days of exposure to various wavelengths of LED lights, blue-LED treated tomato displayed significant increases in proline accumulation in the leaves and stems, whereas red- and green-LED treated tomato exhibited the lower proline contents. Similarly, the blue-LED treatment increased the amount of polyphenolic compounds in tomatoes, compared to other wavelength of LED lights. The activities of various ROS (Reactive Oxygen Species) scavenging enzymes were also slightly increased under the blue-LED lighted conditions. Finally, blue-LED significantly suppressed symptom development of tomato infected by gray mold. Combined results suggest that blue LED light inhibits the development of gray mold disease, which can be mechanistically explained by the enhanced proline accumulation and antioxidative processes at least in partial.

Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium

Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land. Here we report the 5.05-Mb draft genome sequence of the strain, providing bioinformation about the agronomic benefits of this strain, such as multiple traits relevant to plant root colonization and plant growth promotion.

Selective detection of viable Helicobacter pylori using ethidium monoazide or propidium monoazide in combination with real-time polymerase chain reaction

Because Helicobacter pylori has a role in the pathogenesis of gastric cancer, chronic gastritis and peptic ulcer disease, detection of its viable form is very important. The objective of this study was to optimize a PCR method using ethidium monoazide (EMA) or propidium monoazide (PMA) for selective detection of viable H. pylori cells in mixed samples of viable and dead bacteria. Before conducting the real‐time PCR using SodB primers of H. pylori, EMA or PMA was added to suspensions of viable and/or dead H. pylori cells at concentrations between 1 and 100 μM. PMA at a concentration of 50 μM induced the highest DNA loss in dead cells with little loss of genomic DNA in viable cells. In addition, selective detection of viable cells in the mixtures of viable and dead cells at various ratios was possible with the combined use of PMA and real‐time PCR. In contrast, EMA penetrated the membranes of both viable and dead cells and induced degradation of their genomic DNA. The findings of this study suggest that PMA, but not EMA, can be used effectively to differentiate viable H. pylori from its dead form.

Giardia duodenalis: improved detection of viable cysts by reverse transcription-PCR of heat shock-inducible hsp70 gene.

Giardia duodenalis is a waterborne protozoan parasite that causes the diarrhoeal disease, giardiasis. Its durable and thick cell wall allows the parasite to exhibit resistance to environmental stresses. Because G. duodenalis exists in a water system at low levels, it is necessary to develop a sensitive method to detect its viability in aquatic environments. In the present study, specific primers for the heat shock protein (hsp) 70 gene were designed on the basis of G. duodenalis genome sequence and bioinformatic analysis. Viable G. duodenalis cysts were successfully distinguished by reverse transcription-PCR (RT-PCR) analysis using these primers. The amplicon of hsp70 was obtained from one cyst of G. duodenalis/100 microl, and this detection sensitivity significantly increased by 10(3)-fold when the cysts were given heat shock treatment. These findings prove that viable G. duodenalis cysts were successfully detected with a high degree of sensitivity by RT-PCR analysis targeting the hsp70 gene of G. duodenalis, thereby suggesting its practical potential for detecting viable G. duodenalis in environmental samples.

Characterization of ACC deaminase gene in Pseudomonas entomophila strain PS-PJH isolated from the rhizosphere soil

The enzyme 1‐aminocyclopropane‐1‐carboxylate (ACC) deaminase cleaves the ethylene precursor ACC into α‐ketobutyrate and ammonia. The decreased level of ethylene allows the plant to be more resistant to a wide environmental stress including plant pathogens. In the present study, we characterized the ACC deaminase activity of a Pseudomonas entomophila strain PS‐PJH isolated from the red pepper rhizosphere region of red pepper grown at Jinan, Korea. The isolate produced 23.8 ± 0.4 μmol of α‐ketobutyrate/mg of protein/h during ACC deamination under in vitro conditions. Polymerase chain reaction for acdS gene showed that the isolated P. entomophila strain PS‐PJH carry sequences similar to the known acdS genes. Results of the multiple sequence alignment revealed >99% identity (nucleotide and amino acid) with acdS gene of Pseudomonas putida strains AM15 and UW4. The isolated bacteria promoted 43.3 and 34.1% of growth in Raphanus sativus and Lactuca sativa plants, respectively. Based on the 16S–23S internal transcribed spacer region sequences, the isolate was identified as P. entomophila. To the best of our knowledge this is the first study to report the acdS gene in P. entomophila. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)