• Journal of agriculture & life science
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• v.46 no.6
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• pp.165-171
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• 2012

As a preceding study for investigating the influence of sound wave stimulus on Arabidopsis thaliana metabolomics, the polar secondary metabolomes of the plant were determined using high performance liquid chromatography coupled with tandem mass spectrometry. A total of 10 polar secondary metabolomes were characterized and quantified. Among them, 4 metabolomes, p-coumaroylagmatine isomer (7 and 8), p-coumaroylagmatine isomer (9 and 10) were identified in the plant for the first time. The validation was conducted in terms of linearity, recovery, precision, limit of detection (LOD) and limit of quantification (LOQ). The validated method was applied to the simultaneous quantification of the 10 polar secondary metabolomes.

• Korean Journal of Environmental Agriculture
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• v.38 no.3
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• pp.197-204
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• 2019

BACKGROUND: Living modified microorganisms (LMMs) have been focused in two very different aspects of positive and negative effects on ecology and human health. As a model experiment, wild type and a foreign origin gene-harboring modified E. coli strains were subjected to comparison of their metabolomes and potential effects on soil microbiota in the laboratory sets. This study assumes the unintentional release of LMMs and tries to suggest potential effects on the soil microbiota even at minimal settings. METHODS AND RESULTS: Metabolomes from the wild type and LM E. coli were analyzed by NMR and the profiles were compared. In the laboratory soil experiments, the two types of E. coli were added to the soils and monitored for the bacterial community compositions. Those metabolomic profiles did not show significant differences. The microbial community structures from the time series soil DNAs for both the sets using wild type and LMO also did not indicate significant changes, but minor by the addition of foreign organisms regardless of wild or LMO. CONCLUSION: Even if the recombinant microorganism (LMO) is released into the soil environment, the survival of microorganisms in the environment would be one of the major factors for the transfers of foreign genes to other organisms and diffusion into the soil environment.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2007.11a
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• pp.31-31
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• 2007

• Journal of Ginseng Research
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• v.44 no.6
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• pp.757-769
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• 2020

Background: Panax quinquefolius and Panax notoginseng are widely used and well known for their pharmacological effects. As main pharmacological components, saponins have different distribution patterns in the root tissues of Panax plants. Methods: In this study, the representative ginsenosides were detected and quantified by desorption electrospray ionization mass spectrometry and high-performance liquid chromatography analysis to demonstrate saponin distribution in the root tissues of P. quinquefolius and P. notoginseng, and saponin metabolite profiles were analyzed by metabolomes to obtain the biomarkers of different root tissues. Finally, the transcriptome analysis was performed to demonstrate the molecular mechanisms of saponin distribution by gene profiles. Results: There was saponin distribution in the root tissues differed between P. quinquefolius and P. notoginseng. Eight-eight and 24 potential biomarkers were detected by metabolome analysis, and a total of 340 and 122 transcripts involved in saponin synthesis that were positively correlated with the saponin contents (R > 0.6, P < 0.05) in the root tissues of P. quinquefolius and P. notoginseng, respectively. Among them, GDPS1, CYP51, CYP64, and UGT11 were significantly correlated with the contents of Rg1, Re, Rc, Rb2, and Rd in P. quinquefolius. UGT255 was markedly related to the content of R1; CYP74, CYP89, CYP100, CYP103, CYP109, and UGT190 were markedly correlated with the Rd content in P. notoginseng.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.178-183
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• 2006

Microbes are one of the most important bioresources in bioindustry and provide high economic values. Although there are currently about 6,000 bacterial species with validly published names, microbiologists generally assume that the number may account for less than 1% of the bacterial species present on Earth. To discover the remaining species, studies of metagenomes, metabolomes, and proteomes related to microbes have recently been carried out in various fields. We have constructed an information system that integrates various data on microbial resources and manages bioinformation to support efficient research of microorganisms. We have designated this system 'Bio-Meta Information System (Bio-MIS).' Bio-MIS consists of an integrated microbial resource database, a microbial resource input system, an integrated microbial resource search engine, a microbial resource online distribution system, a portal service, and management via the Internet. In the future, this system is expected to be connected with various public databases. We plan to implement useful bioinformatics software for analyzing microbial genome resources. The Web site is accessible at http://biomis.probionic.com.

• Journal of Ginseng Research
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• v.44 no.3
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• pp.413-423
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• 2020

Background: Ginseng berries (GBs) show temporal metabolic variations among different maturation stages, determining their organoleptic and functional properties. Methods: We analyzed metabolic variations concomitant to five different maturation stages of GBs including immature green (IG), mature green (MG), partially red (PR), fully red (FR), and overmature red (OR) using mass spectrometry (MS)-based metabolomic profiling and multivariate analyses. Results: The partial least squares discriminant analysis score plot based on gas chromatography-MS datasets highlighted metabolic disparity between preharvest (IG and MG) and harvest/postharvest (PR, FR, and OR) GB extracts along PLS1 (34.9%) with MG distinctly segregated across PLS2 (18.2%). Forty-three significantly discriminant primary metabolites were identified encompassing five developmental stages (variable importance in projection > 1.0, p < 0.05). Among them, most amino acids, organic acids, 5-C sugars, ethanolamines, purines, and palmitic acid were detected in preharvest GB extracts, whereas 6-C sugars, phenolic acid, and oleamide levels were distinctly higher during later maturation stages. Similarly, the partial least squares discriminant analysis based on liquid chromatography-MS datasets displayed preharvest and harvest/postharvest stages clustered across PLS1 (11.1 %); however, MG and PR were separated from IG, FR, and OR along PLS2 (5.6 %). Overall, 24 secondary metabolites were observed significantly discriminant (variable importance in projection > 1.0, p < 0.05), with most displaying higher relative abundance during preharvest stages excluding ginsenosides Rg1 and Re. Furthermore, we observed strong positive correlations between total flavonoid and phenolic metabolite contents in GB extracts and antioxidant activity. Conclusion: Comprehending the dynamic metabolic variations associated with GB maturation stages rationalize their optimal harvest time per se the related agroeconomic traits.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1260-1269
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• 2018

Production of good Koji primarily depends upon the selection of substrate materials and fermentative microflora, which together influence the characteristic flavor and aroma. Herein, we performed comparative metabolomic analyses of volatile organic compounds (VOCs) and primary metabolites for Koji samples fermented individually with Bacillus amyloliquefaciens and Aspergillus oryzae. The VOCs and primary metabolites were analyzed using headspace solid phase microextraction (HS-SPME) followed by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). In particular, alcohols, ketones, and furans were mainly detected in Bacillus-fermented Koji (Bacillus Koji, BK), potentially due to the increased levels of lipid oxidation. A cheesy and rancid flavor was characteristic of Bacillus Koji, which is attributable to high content of typical 'off-flavor' compounds. Furthermore, the umami taste engendered by 2-methoxyphenol, (E,E)-2,4-decadienal, and glutamic acid was primarily detected in Bacillus Koji. Alternatively, malty flavor compounds (2-methylpropanal, 2-methylbutanal, 3-methylbutanal) and sweet flavor compounds (monosaccharides and maltol) were relatively abundant in Aspergillus-fermented Koji (Aspergillus Koji, AK). Hence, we argue that the VOC profile of Koji is largely determined by the rational choice of inocula, which modifies the primary metabolomes in Koji substrates, potentially shaping its volatolome as well as the aroma characteristics.

• Journal of Microbiology and Biotechnology
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• v.28 no.2
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• pp.199-209
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• 2018

Volatile organic compounds (VOCs) are increasingly been recognized as the chemical mediators of mold interactions, shaping their community dynamics, growth, and metabolism. Herein, we selectively examined the time-correlated (0 D-11 D, where D = incubation days) effects of intraspecies VOC-mediated interactions (VMI) on Aspergillus oryzae KCCM 60345 (S1), following co-cultivation with partner strain A. oryzae KACC 44967 (S2), in a specially designed twin plate assembly. The comparative evaluation of $S1_{VMI}$ (S1 subjected to VMI with S2) and its control ($S1_{Con}$) showed a notable disparity in their radial growth ($S1_{VMI}$ < $S1_{Con}$) at 5 D, protease activity ($S1_{VMI}$ > $S1_{Con}$) at 3-5 D, amylase activity ($S1_{VMI}$ < $S1_{Con}$) at 3-5 D, and antioxidant levels ($S1_{VMI}$ > $S1_{Con}$) at 3 D. Furthermore, we observed a distinct clustering pattern for gas chromatography-time of flight-mass spectrometry datasets from 5 D extracts of $S1_{VMI}$ and $S1_{Con}$ in principle component analysis (PC1: 30.85%; PC2: 10.31%) and partial least squares discriminant analysis (PLS-DA) (PLS1: 30.77; PLS2: 10.15%). Overall, 43 significantly discriminant metabolites were determined for engendering the metabolic variance based on the PLS-DA model (VIP > 0.7, p < 0.05). In general, a marked disparity in the relative abundance of amino acids ($S1_{VMI}$ > $S1_{Con}$) at 5 D, organic acids ($S1_{VMI}$ > $S1_{Con}$) at 5 D, and kojic acid ($S1_{VMI}$ < $S1_{Con}$) at 5-7 D were observed. Examining the headspace VOCs shared between S1 and S2 in the twin plate for 5 D incubated samples, we observed the relatively higher abundance of C-8 VOCs (1-octen-3-ol, (5Z)-octa-1,5-dien-3-ol, 3-octanone, 1-octen-3-ol acetate) having known semiochemical functions. The present study potentially illuminates the effects of VMI on commercially important A. oryzae's growth and biochemical phenotypes with subtle details of altered metabolomes.

• Journal of Ginseng Research
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• v.41 no.1
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• pp.60-68
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• 2017

Background: Various Panax ginseng cultivars exhibit a range of diversity for morphological and physiological traits. However, there are few studies on diversity of metabolic profiles and genetic background to understand the complex metabolic pathway in ginseng. Methods: To understand the complex metabolic pathway and related genes in ginseng, we tried to conduct integrated analysis of primary metabolite profiles and related gene expression using five ginseng cultivars showing different morphology. We investigated primary metabolite profiles via gas chromatography-mass spectrometry (GC-MS) and analyzed transcriptomes by Illumina sequencing using adventitious roots grown under the same conditions to elucidate the differences in metabolism underlying such genetic diversity. Results: GC-MS analysis revealed that primary metabolite profiling allowed us to classify the five cultivars into three independent groups and the grouping was also explained by eight major primary metabolites as biomarkers. We selected three cultivars (Chunpoong, Cheongsun, and Sunhyang) to represent each group and analyzed their transcriptomes. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways. Conclusion: Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.

• Journal of Ginseng Research
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• v.47 no.1
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• pp.44-53
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• 2023

Background: The genus Panax in the Araliaceae family has been used as traditional medicinal plants worldwide and is known to biosynthesize ginsenosides and phytosterols. However, genetic variation between Panax species has influenced their biosynthetic pathways is not fully understood. Methods: Simultaneous analysis of transcriptomes and metabolomes obtained from adventitious roots of two tetraploid species (Panax ginseng and P. quinquefolius) and two diploid species (P. notoginseng and P. vietnamensis) revealed the diversity of their metabolites and related gene expression profiles. Results: The transcriptome analysis showed that 2,3-OXIDOSQUALENE CYCLASEs (OSCs) involved in phytosterol biosynthesis are upregulated in the diploid species, while the expression of OSCs contributing to ginsenoside biosynthesis is higher in the tetraploid species. In agreement with these results, the contents of dammarenediol-type ginsenosides were higher in the tetraploid species relative to the diploid species. Conclusion: These results suggest that a whole-genome duplication event has influenced the triterpene biosynthesis pathway in tetraploid Panax species during their evolution or ecological adaptation. This study provides a basis for further efforts to explore the genetic variation of the Panax genus.