• Nutrition Research and Practice
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• v.17 no.4
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• pp.682-697
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• 2023

BACKGROUND/OBJECTIVES: Tibetan tea is a kind of dark tea, due to the inherent complexity of natural products, the chemical composition and beneficial effects of Tibetan tea are not fully understood. The objective of this study was to unravel the composition of Tibetan tea using knowledge-guided multilayer network (KGMN) techniques and explore its potential antioxidant and hypolipidemic mechanisms in mice. MATERIALS/METHODS: The C57BL/6J mice were continuously gavaged with Tibetan tea extract (T group), green tea extract (G group) and ddH2O (H group) for 15 days. The activity of total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) in mice was detected. Transcriptome sequencing technology was used to investigate the molecular mechanisms underlying the antioxidant and lipid-lowering effects of Tibetan tea in mice. Furthermore, the expression levels of liver antioxidant and lipid metabolism related genes in various groups were detected by the real-time quantitative polymerase chain reaction (qPCR) method. RESULTS: The results showed that a total of 42 flavonoids are provisionally annotated in Tibetan tea using KGMN strategies. Tibetan tea significantly reduced body weight gain and increased T-AOC and SOD activities in mice compared with the H group. Based on the results of transcriptome and qPCR, it was confirmed that Tibetan tea could play a key role in antioxidant and lipid lowering by regulating oxidative stress and lipid metabolism related pathways such as insulin resistance, P53 signaling pathway, insulin signaling pathway, fatty acid elongation and fatty acid metabolism. CONCLUSIONS: This study was the first to use computational tools to deeply explore the composition of Tibetan tea and revealed its potential antioxidant and hypolipidemic mechanisms, and it provides new insights into the composition and bioactivity of Tibetan tea.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.4
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• pp.235-243
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• 2023

As next-generation sequencing has been developed and used widely, RNA-sequencing (RNA-seq) has rapidly emerged as the first choice of tools to validate global transcriptome profiling. With the significant advances in RNA-seq, various types of RNA-seq have evolved in conjunction with the progress in bioinformatic tools. On the other hand, it is difficult to interpret the complex data underlying the biological meaning without a general understanding of the types of RNA-seq and bioinformatic approaches. In this regard, this paper discusses the two main sections of RNA-seq. First, two major variants of RNA-seq are described and compared with the standard RNA-seq. This provides insights into which RNA-seq method is most appropriate for their research. Second, the most widely used RNA-seq data analyses are discussed: (1) exploratory data analysis and (2) pathway enrichment analysis. This paper introduces the most widely used exploratory data analysis for RNA-seq, such as principal component analysis, heatmap, and volcano plot, which can provide the overall trends in the dataset. The pathway enrichment analysis section introduces three generations of pathway enrichment analysis and how they generate enriched pathways with the RNA-seq dataset.

• Applied Biological Chemistry
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• v.48 no.1
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• pp.1-15
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• 2005

Pathogens, insects and weeds have significantly reduced agricultural productivity. Thus, to increase the productivity, synthetic agricultural chemicals have been overused. However, these synthetic compounds that are different from natural products cannot be broken down easily in natural systems, causing the destruction of soil quality and agricultural environments and the gradually difficulty in continuous agriculture. Now agriculture is faced with the various problems of minimizing the damage in agricultural environments, securing the safety of human health, while simultaneously increasing agricultural productivity. Meanwhile, plants produce secondary metabolites to protect themselves from external invaders and to secure their region for survival. Plants infected with pathogens produce antibiotics phytoalexin; monocotyledonous plants produce flavonoids and diterpenoids phytoalexins, and dicotylodoneous plant, despite of infected pathogens, produce family-specific phytoalexin such as flavonoids in Leguminosae, indole derivatives in Cruciferae, sesquitepenoids in Solanaceae, coumarins in Umbelliferae, making the plant resistant to specific pathogen. Growth inhibitor or antifeedant substances to insects are terpenoids pyrethrin, azadirachtin, limonin, cedrelanoid, toosendanin and fraxinellone/dictamnine, and terpenoid-alkaloid mixed compounds sesquiterpene pyridine and norditerpenoids, and azepine-, amide-, loline-, stemofoline-, pyrrolizidine-alkaloids and so on. Also plants produces the substances to inhibit other plant growths to secure the regions for plant itself, which is including terpenoids essential oil and sesquiterpene lactone, and additionally, benzoxazinoids, glucosinolate, quassinoid, cyanogenic glycoside, saponin, sorgolennone, juglone and lots of other different of secondary metabolites. Hence, phytoalexin, an antibiotic compound produced by plants infected with pathogens, can be employed for pathogen control. Terpenoids and alkaloids inhibiting insect growth can be utilized for insect control. Allelochemicals, a compound released from a certain plant to hinder the growth of other plants for their survival, can be also used directly as a herbicides for weed control as well. Therefore, the use of the natural secondary metabolites for pest control might be one of the alternatives for environmentally friendly agriculture. However, the natural substances are destroyed easily causing low the pest-control efficacy, and also there is the limitation to producing the substances using plant cell. In the future, effects should be made to try to find the secondary metabolites with good pest-control effect and no harmful to human health. Also the biosynthetic pathways of secondary metabolites have to be elucidated continuously, and the metabolic engineering should be applied to improve transgenics having the resistance to specific pest.

• Journal of Life Science
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• v.20 no.9
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• pp.1324-1331
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• 2010

Mifepristone (MIF) and Tamoxifen (TAM) have been used in the treatment of prostate cancer and breast cancer for more than a decade. MIF can induce apoptosis in both AR-positive and negative prostate cancer cells. Because of its pleiotropic ligand-receptor properties, TAM exerts cytotoxic activity in estrogen (ER)-positive and various ER.negative cancer cells. However, the molecular mechanisms of these two substances are not yet clear. In the present work, we report that the cytotoxic effects of MIF and TAM are due to the modulation of intracellular $Ca^{2+}$ level in DU-145, androgen-insensitive cells. When the cells were treated with micromolar concentrations of either MIF or TAM, the growth and viability were significantly decreased in a dose- and time-dependent manner. The apoptosis induced by MIF or TAM was further proved and analyzed by confocal laser scanning microscopy (CLSM) and fluorescence-activated cell sorting (FACS). In the cells cultivated in a normal 1.5 mM $Ca^{2+}$ medium, both MIF and TAM also induced an increase of the intracellular $Ca^{2+}$ level in a dose-dependent fashion. Since a change in calcium level could not be found in cells of the $Ca^{2+}$-free medium, the increase of intracellular $Ca^{2+}$ level might be due to an increase in extracellular calcium uptake. Our results show that the apoptotic effect was more prominent in TAM treatment compared to MIF treatment in DU-145 cells. The above findings might be due to the difference in the uppermost pathways of apoptosis induced by either MIF or TAM. When we checked the level of procaspase-8 activation, TAM showed minor level of activation, as opposed to MIF, which exerted strong activation. In both treatments, the levels of anti-apoptotic protein Bcl-2 decreased, and pro-apoptotic protein Bax level increased more than 2-fold. The activation of caspase-3, a key protease enzyme in the downstream pathway of apoptosis, was much higher in the cells treated with TAM, compared to the MIF treatment. The overall apoptotic activity shown in the present work was closely related to intracellular $Ca^{2+}$ concentration levels. Therefore, the cytotoxic activity induced by MIF and TAM might have been due to intracellular calcium modulation.

• Korean Journal of Environmental Biology
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• v.41 no.3
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• pp.325-334
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• 2023

The invasive red swamp crayfish, Procambarus clarkii, is native to south-central United States and northeastern Mexico. Recently, it has been being spreading in the wild in South Korea. However, its primary sources, introduction routes, establishment, and expansion in South Korea remain unclear. Here, we analyzed genetic diversity and population genetic structures of its domestic natural populations during early invasion, commercial stock from local aquaria (a suspected introduction source), and original United States population using mitochondrial COI gene sequences for 267 individuals and eight microsatellite markers for 158 individuals. Natural and commercial populations of P. clarkii showed reduced genetic diversity (e.g., haplotype diversity and allelic richness). The highest genetic diversity was observed in one original source population based on both genetic markers. Despite a large number of individuals in commercial aquaria, we detected remarkably low genetic diversity and only three haplotypes among 226 individuals, suggesting an inbred population likely originating from a small founder group. Additionally, the low genetic diversity in the natural population indicates a small effective population size during early establishment of P. clarkii in South Korea. Interestingly, genetic differentiation between natural populations and the United States population was lower than that between natural populations and aquarium populations. This suggests that various genetic types from the United States likely have entered different domestic aquariums, leading to distinct natural populations through separate pathways. Results of our study will provide an insight on the level of genetic divergence and population differentiation during the initial stage of invasion of non-indigenous species into new environments.

• Journal of Life Science
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• v.34 no.7
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• pp.465-475
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• 2024

Lactiplantibacillus plantarum K9 is a probiotic strain that can be utilized from various bioactive substances isolated from Protaetia brevitarsis seulensis larvae. In this study, a genetic analysis of L. plantarum K9 revealed the existence of a bacterial chromosome and three plasmids. The glycolysis pathway and pentose phosphate pathway were examined for their normal functioning via an analysis of the core metabolic pathways of L. plantarum K9. Since the key enzymes, fluctose-1,6-bisphospatase (EC: 3.1.3.11) and 6-phosphogluconate dehydratase (EC: 4.2.1.12)/2-keto-deoxy-6-phosphogluconate (KDPG) aldolase (EC: 4.2.1.55), of gluconeogenesis and the ED pathway were not identified from the L. plantarum K9 genome, we suggest that gluconeogenesis and the ED pathway are not performed in L. plantarum K9. Additionally, while some enzymes, related to fumarate and malate biosyntheses, involved in the TCA cycle were identified from L. plantarum K9, the enzymes associated with the remaining TCA cycle were absent, indicating that the TCA cycle cannot proceed. Meanwhile, based on our findings, we propose that the oxidative electron transport system performs class IIB-type (bd-type) electron transfer. In summary, we assert that L. plantarum K9 performs homolactic fermentation, executes gluconeogenesis and the pentose phosphate pathway, and carries out energy metabolism through the class IIB-type oxidative electron transport system. Therefore, we suggest that L. plantarum K9 has relatively high lactic acid production, and that it has excellent antibacterial activity, as a result, compared to other lactic acid bacterial strains. Moreover, we speculate that L. plantarum K9 has an oxidative electron transport capability, indicating that it is highly resistant to oxygen and suggesting that it has fine cultivation characteristics, which collectively make it highly suitable for use as a probiotic.

• Journal of Life Science
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• v.22 no.6
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• pp.713-722
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• 2012

When proteins extracted from longissimus dorsi muscles of Landrace and Berkshire at the finishing stage were compared by 2-DE, the Landrace demonstrated a quantitative increase in proteins related to slow skeletal muscle function, such as serum albumin precursor, troponin T (slow skeletal muscle; sTnT) and myoglobin. In contrast, the Berkshire exhibited comparatively elevated enzymes involved in metabolic pathways, fast skeletal muscle function, and energy production, such as heat shock 27-kDa protein (HSP27)-1, TnT (fast skeletal muscle; fTnT), muscle creatine kinase, phosphoglucomutase 1 (PGM1), triosephosphate isomerase (Tpi1) and adenylate kinase isoenzyme 1 (AK1). When compared to growing Berkshire, finishing Berkshire showed increased levels of aldehyde dehydrogenase 1 family, member L1 (ALDHL1), and muscle creatine kinase. In contrast, the growing Berkshire muscle had elevated levels of HSP27-1, sTnT, fTnT, serum albumin precursor, PGM1, AK1, and Tpi 1 as compared to the finishing Berkshire. The Landrace longissimus dorsi muscle may be composed of slower skeletal muscle, whereas Berkshire is composed of a faster skeletal muscle. The uniquely elevated quantities of proteins involved in skeletal muscle function, energy metabolism, and cytoskeleton function in the growing Berkshire indicate that these factors support growth and maintenance during the growing stage when compared with the finishing Berkshire.

• Journal of Life Science
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• v.27 no.1
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• pp.100-121
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• 2017

The sexual reproduction of the unicellular green alga Chlamydomonas is reviewed for a comprehensive understanding of the complex processes. The sexual life cycle of C. reinhardtii is distinguished into five main stages: gametogenesis, gamete activation, cell fusion, zygote maturation, and meiosis and germination. Gametogenesis is induced by nitrogen starvation in the environment. C. reinhardtii has two mating types: mating type plus ($mt^+$) and mating type minus ($mt^-$), controlled by a single complex mating type locus ($MT^+$ or $MT^-$) on linkage group VI. In the early gametogenesis agglutinins are synthesized. The $mt^+$ and $mt^-$ agglutinins are encoded by the autosomal genes SAG1 (Sexual AGglutination1) and SAD1 (Sexual ADhesion1), respectively. The agglutinins are responsible for the flagellar adhesion of the two mating type of gametes. The flagellar adhesion initiates a cAMP mediated signal transduction pathways and activates the flagellar tips. In response to the cAMP signal, mating structures between two flagella are activated. The $mt^+$ and $mt^-$ gamete-specific fusion proteins, Fus1 and Hap2/Gcs1, are present on the plasma membrane of the two mating structures. Contact of the two mating structures leads to develop a fertilization tubule forming a cytoplasmic bridge between the two gametes. Upon fusion of nuclei and chloroplasts of $mt^+$ and $mt^-$ cells, the zygotes become zygospores. It is notable that the young zygote shows uniparental inheritance of chloroplast DNA from the $mt^+$ parent and mitochondrial DNA from the $mt^-$ parent. Under the favorable conditions, the zygospores divide meiotically and germinate and then new haploid progenies, vegetative cells, are released.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3395-3402
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• 2015

Background: Preoperative 5-fluorouracil (5-FU)-based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, CRC cells often develop chemoradiation resistance (CRR). Recent studies have shown that long non-coding RNA (lncRNA) plays critical roles in a myriad of biological processes and human diseases, as well as chemotherapy resistance. Since the roles of lncRNAs in 5-FU-based CRR in human CRC cells remain unknown, they were investigated in this study. Materials and Methods: A 5-FU-based concurrent CRR cell model was established using human CRC cell line HCT116. Microarray expression profiling of lncRNAs and mRNAs was undertaken in parental HCT116 and 5-FU-based CRR cell lines. Results: In total, 2,662 differentially expressed lncRNAs and 2,398 mRNAs were identified in 5-FU-based CRR HCT116 cells when compared with those in parental HCT116. Moreover, 6 lncRNAs and 6 mRNAs found to be differentially expressed were validated by quantitative real time PCR (qRT-PCR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for the differentially expressed mRNAs indicated involvement of many, such as Jak-STAT, PI3K-Akt and NF-kappa B signaling pathways. To better understand the molecular basis of 5-FU-based CRR in CRC cells, correlated expression networks were constructed based on 8 intergenic lncRNAs and their nearby coding genes. Conclusions: Changes in lncRNA expression are involved in 5-FU-based CRR in CRC cells. These findings may provide novel insight for the prognosis and prediction of response to therapy in CRC patients.

• Journal of Life Science
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• v.15 no.2 s.69
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• pp.169-175
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• 2005

Resveratrol (3,4',5-trihydroxy-trans-stilbene), a phytoalexin found in grape skins, peanuts, and red wine, has been reported to have a wide range of biological and pharmacological properties. $Amyloid-\beta$ deposition and senile plaque-associated astrocytes are common neuropathological features of Alzheimer's disease. In this study, we have explored the effects of resveratrol on $amyloid-\beta-peptide-mediated$ cytotoxicity in vitro and modulation of cell growth-regulatory gene products in astroglioma C6 cells to elucidate its possible mechanism for anti-cytotoxicity. Exposure of C6 cells to $Amyloid-\beta$ resulted in dose-dependent growth inhibition and morphological changes of C6 cells, which were recovered by pre-treatment with resveratrol. The anti-proliferative effect of $amyloid-\beta$ was associated with the induction of tumor suppressor p53 and cyclin-dependent kinase (Cdk) inhibitor p21 (WAF1/CIP1) expression assessed by RT-PCR and Western blot analysis in time-dependent manner in C6 cells. In addition, the pro-apoptotic Bax expression was also up-regulated in $amyloid-\beta-treated$ C6 cells without alteration of anti-apoptotic Bcl-2 and $Bcl-X_L$ expression. However, pre-treatment of resveratrol significantly inhibited $amyloid-\beta-induced$ p53, p21 and Bax levels, suggesting that the modulation of p53, p21 and Bax levels could be one of the possible pathways by which resveratrol functions as anti-cytotoxic agent. Our results demonstrate that resveratrol may enhance the protection against $amyloid-\beta-induced$ cytotoxicity by promoting the survival of glial cells.