• Journal of Ginseng Research
• /
• v.43 no.4
• /
• pp.654-665
• /
• 2019

Background: Panax ginseng Meyer has widely been used as a traditional herbal medicine because of its diverse health benefits. Amounts of ginseng compounds, mainly ginsenosides, vary according to seasons, varieties, geographical regions, and age of ginseng plants. However, no study has comprehensively determined perturbations of various metabolites in ginseng plants including roots and leaves as they grow. Methods: Nuclear magnetic resonance ($^1H$ NMR)-based metabolomics was applied to better understand the metabolic physiology of ginseng plants and their association with climate through global profiling of ginseng metabolites in roots and leaves during whole growing periods. Results: The results revealed that all metabolites including carbohydrates, amino acids, organic acids, and ginsenosides in ginseng roots and leaves were clearly dependent on growing seasons from March to October. In particular, ginsenosides, arginine, sterols, fatty acids, and uracil diphosphate glucose-sugars were markedly synthesized from March until May, together with accelerated sucrose catabolism, possibly associated with climatic changes such as sun exposure time and rainfall. Conclusion: This study highlights the intrinsic metabolic characteristics of ginseng plants and their associations with climate changes during their growth. It provides important information not only for better understanding of the metabolic phenotype of ginseng but also for quality improvement of ginseng through modification of cultivation.

• Nutrition Research and Practice
• /
• v.17 no.6
• /
• pp.1238-1254
• /
• 2023

BACKGROUND/OBJECTIVES: Weight loss via a mobile application (App) or a paper-based diary (Paper) may confer favorable metabolic and anthropometric changes. SUBJECTS/METHODS: A randomized parallel trial was conducted among 57 adults whose body mass indices (BMIs) were 25 kg/m² or greater. Participants randomly assigned to either the App group (n = 30) or the Paper group (n = 27) were advised to record their foods and supplements through App or Paper during the 12-week intervention period. Relative changes of anthropometries and biomarker levels were compared between the 2 intervention groups. Untargeted metabolic profiling was identified to discriminate metabolic profiles. RESULTS: Out of the 57 participants, 54 participants completed the trial. Changes in body weight and BMI were not significantly different between the 2 groups (P = 0.11). However, body fat and low-density lipoprotein (LDL)-cholesterol levels increased in the App group but decreased in the Paper group, and the difference was statistically significant (P = 0.03 for body fat and 0.02 for LDL-cholesterol). In the metabolomics analysis, decreases in methylglyoxal and (S)-malate in pyruvate metabolism and phosphatidylcholine (lecithin) in linoleic acid metabolism from pre- to post-intervention were observed in the Paper group. CONCLUSIONS: In the 12-week randomized parallel trial of weight loss through a App or a Paper, we found no significant difference in change in BMI or weight between the App and Paper groups, but improvement in body fatness and LDL-cholesterol levels only in the Paper group under the circumstances with minimal contact by dietitians or health care providers.

• Journal of Ginseng Research
• /
• v.38 no.4
• /
• pp.278-288
• /
• 2014

Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

• Journal of Plant Biotechnology
• /
• v.37 no.1
• /
• pp.12-24
• /
• 2010

Plant metabolomics is a research field for identifying all of the metabolites found in a certain plant cell, tissue, organ, or whole plant in a given time and conditions and for studying changes in metabolic profiling as time goes or conditions change. Metabolomics is one of the most recently developed omics for holistic approach to biology and is a kind of systems biology. Metabolomics or metabolite fingerprinting techniques usually involves collecting spectra of crude solvent extracts without purification and separation of pure compounds or not in standardized conditions. Therefore, that requires a high degree of reproducibility, which can be achieved by using a standardized method for sample preparation and data acquisition and analysis. In plant biology, metabolomics is applied for various research fields including rapid discrimination between plant species, cultivar and GM plants, metabolic evaluation of commercial food stocks and medicinal herbs, understanding various physiological, stress responses, and determination of gene functions. Recently, plant metabolomics is applied for characterization of gene function often in combination with transcriptomics by analyzing tagged mutants of the model plants of Arabidopsis and rice. The use of plant metabolomics combined by transcriptomics in functional genomics will be the challenge for the coming year. This review paper attempted to introduce current status and prospects of plant metabolomics research.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.2
• /
• pp.379-383
• /
• 2010

Metabolites of colorectal cancer tissues from 12 patients were analyzed and compared with those of the normal tissues by two-dimensional NMR spectroscopy. NMR data were analyzed with the help of the metabolome database and the statistics software. Cancerous tissues showed significantly altered metabolic profiles as compared to the normal tissues. Among such metabolites, the concentrations of taurine, glutamate, choline were notably increased in the cancerous tissues of most patients, and those of glucose, malate, and glycerol were decreased. Changes in individual metabolites varied significantly from patient to patient, but the combination of such changes could be used to distinguish cancerous tissues from normal ones, which could be done by PCA analysis. The traditional chemometric analysis was also performed using AMIX software. By comparing those two results, the analysis via $^1H-^{13}C$ HSQC spectra proved to be more robust and effective in assessing and classifying global metabolic profiles of the colorectal tissues.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.6
• /
• pp.1150-1156
• /
• 2017

Understanding phosphorus metabolism in photosynthetic organisms is important as it is closely associated with enhanced crop productivity and pollution management for natural ecosystems (e.g., algal blooming). Accordingly, we exploited highly time-resolved metabolic responses to different levels of phosphate deprivation in Chlamydomonas reinhardtii, a photosynthetic model organism. We conducted non-targeted primary metabolite profiling using gas-chromatography time-of-flight mass spectrometric analysis. Primarily, we systematically identified main contributors to degree-wise responses corresponding to the levels of phosphate deprivation. Additionally, we systematically characterized the metabolite sets specific to different phosphate conditions and their interactions with culture time. Among them were various types of fatty acids that were most dynamically modulated by the phosphate availability and culture time in addition to phosphorylated compounds.

• Journal of the Korean Magnetic Resonance Society
• /
• v.21 no.3
• /
• pp.102-108
• /
• 2017

Escherichia coli responds to ever-changing external and internal stresses by rapidly adjusting its physiology for better survival. This adjustment occurs at all levels including metabolites as well as mRNAs and proteins. Although there has been many reports describing E. coli's adaptation to various stresses regarding transcriptomics or proteomics, only a few investigations have been reported regarding this adaptation viewed from metabolites' perspective. We applied four different types of stresses at four different doses as imposed by NaCl, sorbitol, ethanol, and pH to investigate the similarities or differences among the stresses, and which stress causes the largest perturbation of the metabolite composition. We profiled the metabolites under such external stresses by using two-dimensional NMR spectroscopy and identified 39 metabolites including amino acids, sugars, organic acids, and nucleic acids. According to our statistical analysis, the osmotic stress caused by sorbitol differentiated itself from others, while NaCl showed the largest dose dependent metabolic perturbations. We hope this work will form a foundation on which an approach to a successful protein production is systematically provided by a favorable metabolic environment by imposing proper external stresses.

• Journal of Microbiology and Biotechnology
• /
• v.23 no.6
• /
• pp.750-758
• /
• 2013

Anthrax is a bacterial disease caused by the aerobic spore-forming bacterium Bacillus anthracis, which is an important pathogen owing to its ability to be used as a terror agent. B. anthracis spores can escape phagocytosis and initiate the germination process even in antimicrobial conditions, such as oxidative stress. To analyze the oxidative stress response in B. anthracis and thereby learn how to prevent antimicrobial resistance, we performed protein expression profiling of B. anthracis strain HY1 treated with 0.3 mM hydrogen peroxide using a comparative proteomics-based approach. The results showed a total of 60 differentially expressed proteins; among them, 17 showed differences in expression over time. We observed time-dependent changes in the production of metabolic and repair/protection signaling proteins. These results will be useful for uncovering the metabolic pathways and protection mechanisms of the oxidative response in B. anthracis.

• Journal of Applied Biological Chemistry
• /
• v.65 no.1
• /
• pp.63-74
• /
• 2022

Microbial dysbiosis in the gut is associated with human diseases, and variations in mucus alter gut microbiota. Therefore, we explored the effects of mucin on the gut microbiota using a community of 19 synthetic gut microbial species. Cultivation of these species in modified Gifu anaerobic medium (GAM) supplemented with mucin before synthetic community assembly facilitated substantial growth of the Bacteroides, Akkermansia, and Clostridium genera. The results of 16S rRNA microbial relative abundance profiling revealed more of the beneficial microbes Collinsella, Bifidobacterium, Ruminococcus, and Lactobacillus. This increased acetate levels in the community cultivated with, rather than without (control), mucin. We identified differences in predicted cell function and metabolism between microbes cultivated in GAM with and without mucin. Mucin not only changed the composition of the gut microbial community, but also modulated metabolic functions, indicating that it could help to modulate microbial changes associated with human diseases.

• Toxicological Research
• /
• v.33 no.1
• /
• pp.63-69
• /
• 2017

Transmembrane protein 39A (TMEM39A) belongs to the TMEM39 family. TMEM39A gene is a susceptibility locus for multiple sclerosis. In addition, TMEM39A seems to be implicated in systemic lupus erythematosus. However, any possible involvement of TMEM39A in cancer remains largely unknown. In the present report, we provide evidence that TMEM39A may play a role in brain tumors. Western blotting using an anti-TMEM39A antibody indicated that TMEM39A was overexpressed in glioblastoma cell lines, including U87-MG and U251-MG. Deep-sequencing transcriptomic profiling of U87-MG and U251-MG cells revealed that TMEM39A transcripts were upregulated in such cells compared with those of the cerebral cortex. Confocal microscopic analysis of U251-MG cells stained with anti-TMEM39A antibody showed that TMEM39A was located in dot-like structures lying close to the nucleus. TMEM39A probably located to mitochondria or to endosomes. Immunohistochemical analysis of glioma tissue specimens indicated that TMEM39A was markedly upregulated in such samples. Bioinformatic analysis of the Rembrandt knowledge base also supported upregulation of TMEM39A mRNA levels in glioma patients. Together, the results afford strong evidence that TMEM39A is upregulated in glioma cell lines and glioma tissue specimens. Therefore, TMEM39A may serve as a novel diagnostic marker of, and a therapeutic target for, gliomas and other cancers.