The genus Rhodococcus is a phylogenetically and catabolically diverse group that has been isolated from diverse environments, including polar and alpine regions, for its versatile ability to degrade a wide variety of natural and synthetic organic compounds. Their metabolic capacity and diversity result from their diverse catabolic genes, which are believed to be obtained through frequent recombination events mediated by large catabolic plasmids. Many rhodococci have been used commercially for the biodegradation of environmental pollutants and for the biocatalytic production of high-value chemicals from low-value materials. Recent studies of their physiology, metabolism, and genome have broadened our knowledge regarding the diverse biotechnological applications that exploit their catabolic enzymes and pathways.

Numerous studies suggest that the effects of lactic acid bacteria (LAB) on oxidative stress in vivo are correlated with their antioxidative activities in vitro; however, the relationship is still unclear and contradictory. The antioxidative activities of 27 Lactobacillus plantarum strains isolated from fermented foods were determined in terms of 2,2-diphenyl-1-picrylhydrazyl, hydroxyl radical, and superoxide radical scavenging abilities, reducing activity, resistance to hydrogen peroxide, and ferrous chelating ability in vitro. Two fuzzy synthetic evaluation models, one with an analytic hierarchy process and one using entropy weight, were then used to evaluate the overall antioxidative abilities of these L. plantarum strains. Although there was some difference between the two models, the highest scoring strain (CCFM10), the middle scoring strain (CCFM242), and the lowest scoring strain (RS15-3) were obtained with both models. Examination of the antioxidative abilities of these three strains in $\text\tiny{D}$-galactose-induced oxidative stress mice demonstrated that their overall antioxidative abilities in vitro could reveal the abilities to alleviate oxidative stress in vivo. The current study suggests that assessment of overall antioxidative abilities with fuzzy synthetic models can guide the evaluation of probiotic antioxidants. It might be a more quick and effective method to evaluate the overall antioxidative abilities of LAB.

The anti-melanogenic effects of the extract of Angelica tenuissima (AT) root and the extract of AT root fermented by Aspergillus oryzae (FAT) were investigated. These effects were determined by measuring the inhibitory activity of AT and FAT on melanin production in B16F10 melanocytes and with in vitro tyrosinase activity assays. The AT extract inhibited melanin production at concentrations above $250{\mu}g/ml$, and this inhibitory effect was significantly enhanced by the fermentation process with A. oryzae. HPLC analysis resulted in the isolation of two active compounds from both the AT and FAT extracts. Their chemical structures were identified as decursin and Z-ligustilide through comparison with previously reported NMR data. The decursin and Z-ligustilide contents were increased in the FAT extract and could be responsible for its enhanced inhibitory effects on melanin production and tyrosinase activity compared with that of the AT extract.

DKxanthenes are a class of yellow secondary metabolites produced by myxobacterial genera Myxococcus and Stigmatella. We identified a putative 49.5 kb DKxanthene biosynthetic gene cluster from Myxococcus stipitatus DSM 14675 by genomic sequence and mutational analyses. The cluster consisted of 15 genes (MYSTI_06004-MYSTI_06018) encoding polyketide synthases, non-ribosomal peptide synthases, and proteins with unknown functions. Disruption of the genes by plasmid insertion resulted in defects in the production of yellow pigments. High-performance liquid chromatography and liquid chromatography-tandem mass spectrometry analyses indicated that the yellow pigments produced by M. stipitatus DSM 14675 might be novel DKxanthene derivatives. M. stipitatus did not require DKxanthenes for the formation of heat-resistant viable spores, unlike Myxococcus xanthus. Furthermore, DKxanthenes showed growth inhibitory activity against the fungi Aspergillus niger, Candida albicans, and Rhizopus stolonifer.

A salt-tolerant cellulase secreted by a marine Bacillus sp. SR22 strain with wide resistance to temperature and pH was purified and characterized. Its approximate mass was 37 kDa. The endoglucanase, named as Bc22Cel, was purified by ammonium sulfate precipitation, gel filtration chromatography, and extraction from the gel after non-reducing sodium dodecyl sufate-polyacrylamide gel electrophoresis. The optimal pH value and temperature of Bc22Cel were 6.5 and $60^{\circ}C$, respectively. The purified Bc22Cel showed a considerable halophilic property, being able to maintain more than 70% of residual activity even when pre-incubated with 1.5 M NaCl for 1 h. Kinetic analysis of the purified enzyme showed the $K_m$ and $V_{max}$ to be 0.704 mg/ml and $29.85{\mu}mol{\cdot}ml^{-1}{\cdot}min^{-1}$, respectively. Taken together, the present data indicate Bc22Cel as a potential and useful candidate for industrial applications, such as the bioconversion of sugarcane bagasse to its derivatives.

Honokiol, a bioactive compound isolated from the cone and bark of Magnolia officinalis, has been shown to have various activities including inhibition of the growth of Candida albicans. We investigated the roles of the Hsp90-calcineurin pathway in the antifungal activity of honokiol. The pharmacologic tool was employed to evaluate the effects of Hsp90 and calcineurin in the antifungal activity of honokiol. We also evaluated the protective effects of the calcineurin inhibitor cyclosporin A (CsA) on honokiol-induced mitochondrial dysfunction by the fluorescence staining method. The Hsp90 inhibitor potentiated the antifungal activity of honokiol. A C. albicans strain with the calcineurin gene deleted displayed enhanced sensitivity to honokiol. However, co-treatment with calcineurin inhibitor CsA attenuated the cytotoxic activity of honokiol due to the protective effect on mitochondria. Our results provide insight into the action mechanism of honokiol.

The peel of astringent persimmon (Diospyros kaki Thunb. cv. Cheongdo-Bansi) is a by-product of dried persimmon (gotgam). We investigated if deastringent peel extracts of persimmon cv. Cheongdo-Bansi had antioxidative and neuroprotective properties. Two different extracts were prepared: thermally and nonthermally treated persimmon peel extracts (TPE and NTPE, respectively). Both TPE and NTPE were fractionated sequentially in n-hexane, chloroform, ethyl acetate, n-butanol, and water. The TPE and NTPE ethyl acetate fractions had the highest total phenolic and flavonoid contents as well as antioxidant capacities among all the fractions. Pretreatment of neuronal PC-12 and SH-SY5Y cells with the TPE and NTPE ethyl acetate fractions increased cell viability after exposure to oxidative stress. The ethyl acetate fraction of TPE attenuated oxidative stress inside both PC-12 and SH-SY5Y cells more effectively than that of NTPE. Furthermore, the TPE and NTPE ethyl acetate fractions inhibited acetylcholinesterase and butyrylcholinesterase. Analysis of ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry results revealed gallic acid, kaempferol, kaempferol-3-O-galactoside, kaempferol-3-O-glucoside, quercetin, quercetin3-O-galactoside, quercetin-3-O-galactoside-2'-O-gallate, and quercetin-3-O-glucoside as the major phenolics of the TPE and NTPE ethyl acetate fractions. Taken together, these results suggest that the ethyl acetate fraction of deastringent persimmon peel is rich in antioxidants and has potential as a functional food to reduce oxidative stress.

The flavin-dependent monooxygenase Sam5 was previously reported to be a bifunctional hydroxylase with coumarate 3-hydroxylase and resveratrol 3'-hydroxylase activities. In this article, we showed the Sam5 enzyme has 3'-hydroxylation activities for methylated resveratrols (pinostilbene and pterostilbene), hydroxylated resveratrol (oxyresveratrol), and glycosylated resveratrol (piceid) as substrates. However, piceid, a glycone-type stilbene used as a substrate for bioconversion experiments with the Sam5 enzyme expressed in Escherichia coli, did not convert to the hydroxylated compound astringin, but it was converted by in vitro enzyme reactions. Finally, we report a novel catalytic activity of Sam5 monooxygenase for the synthesis of piceatannol derivatives, 3'-hydroxylated stilbene compounds. Development of this bioproduction method for the hydroxylation of stilbenes is challenging because of the difficulty in expressing P450-type hydroxylase in E. coli and regiospecific chemical synthesis.

Jeotgal is a Korean traditional fermented seafood with a high concentration of salt. In this study, we isolated lactic acid bacteria (LAB) from galchi (Trichiurus lepturus, hairtail) and myeolchi (Engraulis japonicas, anchovy) jeotgal on MRS agar and MRS agar containing 5% NaCl (MRS agar+5% NaCl), and identified them by using 16S rRNA gene sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as culture-dependent methods. We also performed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) as a culture-independent method to identify bacterial communities. Five samples of galchi-jeotgal and seven samples of myeolchi-jeotgal were collected from different regions in Korea. A total of 327 and 395 colonies were isolated from the galchi- and myeolchi-jeotgal samples, respectively. 16S rRNA gene sequencing and MALDI-TOF MS revealed that the genus Pediococcus was predominant on MRS agar, and Tetragenococcus halophilus on MRS agar+5% NaCl. PCR-DGGE revealed that T. halophilus, Tetragenococcus muriaticus, and Lactobacillus sakei were predominant in both types of jeotgal. T. halophilus was detected in all samples. Even though the same species were identified by both culture-dependent and -independent methods, many species identified by the culture-dependent methods were not in the bacterial list identified by the culture-independent methods. The distribution of bacteria in galchi-jeotgal was more diverse than in myeolchi-jeotgal. The diverse LAB in galchi- and myeolchi-jeotgals can be further studied as candidates for starter cultures to produce fermented foods.

In this study, we attempted to find new and efficient microbial enzymes for producing rare sugars. A ribose-5-phosphate isomerase B (OsRpiB) was cloned, overexpressed, and preliminarily purified successfully from a newly screened Ochrobactrum sp. CSL1, which could catalyze the isomerization reaction of rare sugars. A study of its substrate specificity showed that the cloned isomerase (OsRpiB) could effectively catalyze the conversion of $\text\tiny{L}$-rhamnose to $\text\tiny{L}$-rhamnulose, which was unconventional for RpiB. The optimal reaction conditions ($50^{\circ}C$, pH 8.0, and 1 mM $Ca^{2+}$) were obtained to maximize the potential of OsRpiB in preparing $\text\tiny{L}$-rhamnulose. The catalytic properties of OsRpiB, including $K_m$, $k_{cat}$, and catalytic efficiency ($k_{cat}/K_m$), were determined as 43.47 mM, $129.4sec^{-1}$, and 2.98 mM/sec. The highest conversion rate of $\text\tiny{L}$-rhamnose under the optimized conditions by OsRpiB could reach 26% after 4.5 h. To the best of our knowledge, this is the first successful attempt of the novel biotransformation of $\text\tiny{L}$-rhamnose to $\text\tiny{L}$-rhamnulose by OsRpiB biocatalysis.

Pseudomonas fluorescens KLR101 was found to be capable of producing polyhydroxyalkanoate (PHA) using various sugars and fatty acids with carbon numbers ranging from 2 to 6. The PHA granules consisted mainly of a poly(3-hydroxybutyrate) homopolymer and/or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer. Genomic DNA of P. fluorescens was fractionated and cloned into a lambda library, in which a 5.8-kb fragment that hybridized to a heterologous phaC probe from Ralstonia eutropha was identified. In vivo expression in Klebsiella aerogenes KC2671 (pUMS), restriction mapping, Southern hybridization experiments, and sequencing data revealed that PHA biosynthesis by P. fluorescens relied upon a polypeptide encoded by a 1,683-bp non-operonal ORF, which was preceded by a possible -24/-12 promoter and highly similar to DNA sequences of a gene encoding PHA synthase in the genus Pseudomonas. In vivo expression of the putative PHA synthase gene ($phaC_{Pf}$) in a recombinant Escherichia coli strain was investigated by using glucose and decanoate as substrates. E. coli (${phaC_{Pf}}^+$, pUMS) grown in medium containing glucose accumulated PHA granules consisting mainly of 3-hydroxybutyrate, whereas only a trace amount of 3-hydroxydecanoate was detected from an E. coli fadR mutant (${phaC_{Pf}}^+$) grown in medium containing decanoate. In vitro enzymatic assessment experiments showed that 3-hydroxybutyryl-CoA was efficiently used as a substrate of purified $PhaC_{Pf}$, suggesting that the putative PHA synthase of P. fluorescens utilizes mainly short-chain-length PHA precursors as a substrate.

2'-Fucosyllactose (2'-FL) is one of the most important human milk oligosaccharides and has several health benefits for infants. The levels of 2'-FL in breast milk or samples from other sources can be quantified by high-performance liquid chromatography. However, this method cannot be used for simultaneous detection of the target compound in numerous samples. Here, we developed a simple method for quantifying 2'-FL in a microplate format. The method involves two steps: (i) release of $\text\tiny{L}$-fucose from 2'-FL by ${\alpha}$-(1-2,3,4,6)-$\text\tiny{L}$-fucosidase and (ii) measurement of NADPH formed during the oxidation of $\text\tiny{L}$-fucose by $\text\tiny{L}$-fucose dehydrogenase. This method enables measurement of up to 5 g/l 2'-FL in 50 min using a 96-well microplate. The efficiency and simplicity of the proposed method make it suitable for the analyses of a large number of samples simultaneously.

The degradation efficiency and catabolism pathways of the different methylxanthines (MXs) in isolated caffeine-tolerant strain Pseudomonas putida CT25 were comprehensively studied. The results showed that the degradation efficiency of various MXs varied with the number and position of the methyl groups on the molecule (i.e., xanthine > 7-methylxanthine ${\approx}$ theobromine > caffeine > theophylline > 1-methylxanthine). Multiple MX catabolism pathways coexisted in strain CT25, and a different pathway would be triggered by various MXs. Demethylation dominated in the degradation of N-7-methylated MXs (such as 7-methylxanthine, theobromine, and caffeine), where C-8 oxidation was the major pathway in the catabolism of 1-methylxanthine, whereas demethylation and C-8 oxidation are likely both involved in the degradation of theophylline. Enzymes responsible for MX degradation were located inside the cell. Both cell culture and cell-free enzyme assays revealed that N-1 demethylation might be a rate-limiting step for the catabolism of the MXs. Surprisingly, accumulation of uric acid was observed in a cell-free reaction system, which might be attributed to the lack of activity of uricase, a cytochrome c-coupled membrane integral enzyme.

The aim of this study was to isolate and characterize lead (Pb)-solubilizing bacteria from heavy metal-contaminated mine soils and to evaluate their inoculation effects on the growth and Pb absorption of Brassica juncea. The isolates were also evaluated for their plant growth-promoting characteristics as well as heavy metal and salt tolerance. A total of 171 Pb-tolerant isolates were identified, of which only 15 bacterial strains were able to produce clear haloes in solid medium containing PbO or $PbCO_3$, indicating Pb solubilization. All of these 15 strains were also able to dissolve the Pb minerals in a liquid medium, which was accompanied by significant decreases in pH values of the medium. Based on 16S rRNA gene sequence analysis, the Pb-solubilizing strains belonged to genera Bacillus, Paenibacillus, Brevibacterium, and Staphylococcus. A majority of the Pb-solubilizing strains were able to produce indole acetic acid and siderophores to different extents. Two of the Pb-solubilizing isolates were able to solubilize inorganic phosphate as well. Some of the strains displayed tolerance to different heavy metals and to salt stress and were able to grow in a wide pH range. Inoculation with two selected Pb-solubilizing and plant growth-promoting strains, (i.e., Brevibacterium frigoritolerans YSP40 and Bacillus paralicheniformis YSP151) and their consortium enhanced the growth and Pb uptake of B. juncea plants grown in a metal-contaminated soil. The bacterial strains isolated in this study are promising candidates to develop novel microbe-assisted phytoremediation strategies for metal-contaminated soils.

The aim of this study was to investigate the microbial community of three tannery wastewater treatment plants (WWTPs) involved in nitrification by Illumina MiSeq sequencing. The results showed that highly diverse communities were present in tannery wastewater. A total of six phyla, including Proteobacteria (37-41%), Bacteroidetes (6.04-16.80), Planctomycetes (3.65-16.55), Chloroflexi (2.51-11.48), Actinobacteria (1.91-9.21), and Acidobacteria (3.04-6.20), were identified as the main phyla, and Proteobacteria dominated in all the samples. Within Proteobacteria, Beta-proteobacteria was the most abundant class, with the sequence percentages ranging from 9.66% to 17.44%. Analysis of the community at the genus level suggested that Thauera, Gp4, Ignavibacterium, Phycisphaera, and Arenimonas were the core genera shared by at least two tannery WWTPs. A detailed analysis of the abundance of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) indicated that Nitrosospira, Nitrosomonas, and Nitrospira were the main AOB and NOB in tannery wastewater, respectively, which exhibited relatively high abundance in all samples. In addition, real-time quantitative PCR was conducted to validate the results by quantifying the abundance of the AOB and total bacteria, and similar results were obtained. Overall, the results presented in this study may provide new insights into our understanding of key microorganisms and the entire community of tannery wastewater and contribute to improving the nitrogen removal efficiency.

The spread of antibiotic-resistant Enterobacteriaceae in the community is one of the main challenges for antibiotic treatment of community-onset infections. We evaluated the microbiological and molecular characteristics of stool samples from adults with comprehensive health examinations. Of 109 fecal samples, bacterial growth was observed in 86 samples and 61 gram-negative bacterial isolates were identified, of which 45 were Escherichia coli isolates (73.8%). Two isolates of Raoultella showed imipenem resistance, and both E. coli and Citrobacter freundii showed intermediate resistance to imipenem. Colistin resistance was identified in isolates of Klebsiella variicola and Salmonella subterranean, but no isolates carried mcr-1. As for E. coli genotypes, 35 sequence types were identified. $bla_{TEM-1}$, $bla_{TEM-30}$, and $bla_{CTX-M}$ were identified in 15, 1, and 4 E. coli isolates, respectively. In addition, all four Klebsiella pneumoniae isolates carried $bla_{SHV}$. Many genotypes that have been identified in isolates causing human infections were found in isolates in this study. There is a need to control the rise and spread of antibiotic-resistant pathogens by fecal carriage.

The nucleosomal organization of chromatin using histone proteins is a fundamental and ubiquitous feature of eukaryotic nuclei, with the major exception of dinoflagellates. Although a number of recent genomic and transcriptomic analyses have detected numerous histone genes in dinoflagellates, little is known about their expression. Here in, we aimed to investigate the expression pattern of histone genes under nutritional stress, and an attempt was made to detect histone expression at the protein level in Alexandrium pacificum. The presence of histones at the mRNA level was confirmed in this study by the amplification, cloning, and sequencing of 10 different genes. Relative expression profiling of these genes under different growth conditions was determined with real-time PCR and revealed considerable levels of histone transcription in nutritionally stressed cells. We were unable to detect the expression of histones at the protein level even after immunodetection and analysis using mass spectrometry, although a histone-like protein was detected as a major nuclear component. A. pacificum expresses multiple variants of histone, and protein sequences revealed both conservation and divergence with respect to other eukaryotes. We concluded that A. pacificum maintained an active transcription of histone genes within the cell, and enhanced expression of histone genes in nutritional stress strongly suggest that histones have functional significance in dinoflagellates, although expression at the protein level was below our current detection limits, which suggests a limited role of histones in DNA packaging. Finally, the plausible regulation of histone expression at the gene and protein levels in A. pacificum is discussed.

Osteoarthritis is a disease that affects the articular cartilage and osseous tissue, and can be worsened by aging, overweight status, and post-traumatic arthritis. The present study aimed to evaluate the effect of ID-CBT5101 (tyndallized Clostridium butyricum) on bone metabolism and the inflammatory response in a monosodium iodoacetate-induced rat model of osteoarthritis. ID-CBT5101 was administered orally at doses of $10^8$ or $10^{10}CFU/day$ for 2 weeks before direct injection of monosodium iodoacetate ($3mg/50{\mu}l$ of 0.9% saline) into the intra-articular space of the rats' right knees. The rats subsequently received the same doses of oral ID-CBT5101 for another 4 weeks. We evaluated the treatment effects based on serum biomarkers, mRNA expression, morphological and histopathological analyses of the knee joints, and weight-bearing distribution analysis. Compared with those in control rats, the ID-CBT5101 treatments significantly reduced the serum concentration of inflammation and bone metabolism markers (i.e., COX-2, IL-6, $LTB_4$, and COMP), and significantly increased the concentration of $IFN-{\gamma}$ and glycosaminoglycans. In addition, the ID-CBT5101 treatments inhibited the mRNA expression of matrix metalloproteinases and tissue inhibitors of metalloproteinases (i.e., MMP-2, MMP-3, MMP-9, MMP-13, TIMP-1, and TIMP-2). Furthermore, the ID-CBT5101 treatments effectively preserved the knee cartilage and synovial membrane, and significantly decreased the amount of fibrous tissue. Moreover, compared with that of the negative control group, the ID-CBT5101 treatments increased the weight-bearing distribution by ${\geq}20%$. The results indicate that ID-CBT5101 prevented and alleviated osteoarthritis symptoms. Thus, ID-CBT5101 may be a novel therapeutic option for the management of osteoarthritis.

This study aimed to evaluate the antimicrobial activity of 2-phenylethynyl-butyltellurium (PEBT) in Escherichia coli and the relation to its pro-oxidant effect. For this, we carried out the disk diffusion test, minimum inhibitory concentration (MIC) assay, and survival curve analysis. We also measured the level of extracellular reactive oxygen species (ROS), activity of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT), and level of non-protein thiols (NPSH). PEBT at 1.28 and 0.128 mg/disk exhibited antimicrobial capability in the disk diffusion test, with an MIC value of 1.92 mg/ml, whereas PEBT at 0.96, 1.92, and 3.84 mg/ml inhibited bacterial growth after a 9-h exposure. PEBT at 3.84, 1.92, and 0.96 mg/ml increased extracellular ROS production, decreased the intracellular NPSH level, and reduced the SOD and CAT activities. Glutathione or ascorbic acid in the medium protected the bacterial cells from the antimicrobial effect of PEBT. In conclusion, PEBT exhibited antimicrobial activity against E. coli, involving the generation of ROS, oxidation of NPSH, and reduction of the antioxidant defenses in the bacterial cells.

Seaweeds produce antioxidants to counteract environmental stresses, and these antioxidant genes are regarded as important defense strategies for marine algae. In this study, the expression of Pyropia yezoensis (Bangiales, Rhodophyta) ascorbate peroxidase (PyAPX) and manganese-superoxide dismutase (PyMnSOD) was examined by qRT-PCR in P. yezoensis blades under abiotic stress conditions. Furthermore, the functional relevance of these genes was explored by overexpressing them in Chlamydomonas. A comparison of the different expression levels of PyAPX and PyMnSOD after exposure to each stress revealed that both genes were induced by high salt and UVB exposure, being increased approximately 3-fold after 12 h. The expression of the PyAPX and PyMnSOD genes also increased following exposure to $H_2O_2$. When these two genes were overexpressed in Chlamydomonas, the cells had a higher growth rate than control cells under conditions of hydrogen peroxide-induced oxidative stress, increased salinity, and UV exposure. These data suggest that Chlamydomonas is a suitable model for studying the function of stress genes, and that PyAPX and PyMnSOD genes are involved in the adaptation and defense against stresses that alter metabolism.