• 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.

• Journal of Life Science
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• v.33 no.8
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• pp.623-631
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• 2023

This study was conducted to develop microsatellite markers in Parapristipoma trilineatum using next-generation sequencing. A total of 402,244,934 reads were generated on the Illumina Hiseq X Ten System, yielding 60,738,985,034 bp of sequences. The de novo assembly resulted in 1,320,995 contigs. A total of 952,326 contigs (0.016%) including 151 microsatellite loci were derived from the 1,320,995 contigs longer than 640 bp. A total of 34 primer sets were designed from the 151 microsatellite loci. As a result, 15 microsatellite loci were chosen and used for assuming population genetic parameters in the wild and farmed populations. The mean number of effective alleles was 12, ranging from 6 to 25. The observed heterozygosity (H_O) and the expected heterozygosity (H_E) ranged between 0.530 and 0.873, with an average of 0.750, and from 0.647 to 0.895, with an average of 0.793, respectively. According to these results, the developed set of 15 microsatellite markers is expected to be useful for the analysis of genetic characteristics in the population of P. trilineatum in Korea. There are requirements now for further genetic information, fishery resource management, breeding guidelines, support with the selection of breeds and studies on the effects of release, all of which will improve species conservation, and through future research, we aim to offer genetic foundational data with that goal.

• Mycobiology
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• v.51 no.1
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• pp.36-48
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• 2023

Xanthoria elegans is a lichen symbiosis, that inhabits extreme environments and can absorb UV-B. We reported the de novo sequencing and assembly of X. elegans genome. The whole genome was approximately 44.63 Mb, with a GC content of 40.69%. Genome assembly generated 207 scaffolds with an N50 length of 563,100 bp, N90 length of 122,672 bp. The genome comprised 9,581 genes, some encoded enzymes involved in the secondary metabolism such as terpene, polyketides. To further understand the UV-B absorbing and adaptability to extreme environments mechanisms of X. elegans, we searched the secondary metabolites genes and gene-cluster from the genome using genome-mining and bioinformatics analysis. The results revealed that 7 NR-PKSs, 12 HR-PKSs and 2 hybrid PKS-PKSs from X. elegans were isolated, they belong to Type I PKS (T1PKS) according to the domain architecture; phylogenetic analysis and BGCs comparison linked the putative products to two NR-PKSs and three HR-PKSs, the putative products of two NR-PKSs were emodin xanthrone (most likely parietin) and mycophelonic acid, the putative products of three HR-PKSs were soppilines, (+)-asperlin and macrolactone brefeldin A, respectively. 5 PKSs from X. elegans build a correlation between the SMs carbon skeleton and PKS genes based on the domain architecture, phylogenetic and BGC comparison. Although the function of 16 PKSs remains unclear, the findings emphasize that the genes from X. elegans represent an unexploited source of novel polyketide and utilization of lichen gene resources.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.84-84
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• 2003

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. DNA methylation is a highly plastic and critical component of mammalian development The DNA methyltransferases (Dnmts) are responsible for the generation of genomic methylation patterns, which lead to transcriptional silencing. The maintenance DNA methyltransferase enzyme, Dnmt 1, and the de novo methyltransferase, Dnmt3a and Dnmt3b, are indispensable for development because mice homozygous for the targeted disruption of any of these genes are not viable. The occurrence of DNA methylation is not random, and it can result in gene silencing The mechanisms underlying these processes are poorly understood. It is well established that DNA methylation and histone deacetylation operate along a common mechanistic pathway to repress transcription through the action of methyl-binding domain proteins (MBDs), which are components of, or recruit, histone deacetylase (HDAC) complexes to methylated DNA. As a basis for future studies on the role of the DNA-methyl-transferase in porcine development, we have isolated and characterized a partial cDNA coding for the porcine Dnmt1. Total RNA of testis, lung and ovary was isolated with TRlzol according to the manufacture's specifications. 5 ug of total RNA was reverse transcribed with Super Script II in the presence of porcine Dnmt 1 specific primers. Standard PCRs were performed in a total volume of 50 ul with cDNA as template. Two DNA fragmenets in different position were produced about 700bp, 1500bp and were cloned into pCR II-TOPO according to the manufacture's specification. Assembly of all sequences resulted in a cDNA from 158bp of 5'to 4861bp of 3'compare with the known human maintenance methyltransferase. Now, we are cloning the unknown Dnmt 1 region by 5'-RACE method and expression of Dnmt 1 in tissues from adult porcine animals.

• Korean Journal of Radiology
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• v.24 no.6
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• pp.482-497
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• 2023

Sonazoid, a second-generation ultrasound contrast agent, was introduced for the diagnosis of hepatic nodules. To clarify the issues with Sonazoid contrast-enhanced ultrasonography for the diagnosis of hepatocellular carcinoma (HCC), the Korean Society of Radiology and Korean Society of Abdominal Radiology collaborated on the guidelines. The guidelines are de novo, evidence-based, and selected using an electronic voting system for consensus. These include imaging protocols, diagnostic criteria for HCC, diagnostic value for lesions that are inconclusive on other imaging results, differentiation from non-HCC malignancies, surveillance of HCC, and treatment response after locoregional and systemic treatment for HCC.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.12 no.3
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• pp.178-185
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• 2007

Myrionecta rubra Jankowski 1976(=Mesodinium rubrum Lohmann 1908), a mixotrophic ciliate, is very common and often causes recurrent red tides in diverse marine environments. Since the report on the first laboratory strain of this species in 2000, papers on its novel ecological role and evolutionary importance have been high lighted. This review paper is prepared to promote the de novo recognition M. rubra as a marine mixotrophic species. M. rubra is a ciliate which is able to photosynthesize using plastids originated from cryptophyte (including Teleaulax sp. and Geminigera sp.) prey cells (i.e. kleptoplastidic ciliate). Recently, novel bacterivory of M. rubra was firstly reported. Thus, the nutritional modes of M. rubra include photosynthesis, bacterivory, and algivory. In turn, M. rubra was reported as the prey species of metazoan predators such as calanoid copepods, mysids, larvae of ctenophore and anchovy, and spats of bivalves. In addition, it was reported that dinoflagellate Dinophysis causing diarrhetic shellfish poisoning is one among the predators of M. rubra. Thus, M. rubra, a marine mixotrophic ciliate, may play a pivotal role as a common linking ciliate for the flow of energy and organic material in pelagic food webs.

• Journal of Nutrition and Health
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• v.48 no.4
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• pp.319-326
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• 2015

Purpose: Borage oil (BO) and safflower oil (SO) are efficacious in reversing epidermal hyperproliferation, which is caused by the disruption of epidermal barrier. In this study, we compared the antiproliferative effect of dietary BO and SO. Altered metabolism of ceramide (Cer), the major lipid of epidermal barrier, was further determined by measurement of epidermal levels of individual Cer, glucosylceramide (GlcCer), and sphingomyelin (SM) species, and protein expression of Cer metabolizing enzymes. Methods: Epidermal hyperproliferation was induced in guinea pigs by a hydrogenated coconut diet (HCO) for 8 weeks. Subsequently, animals were fed diets of either BO (group HCO + BO) or SO (group HCO + SO) for 2 weeks. As controls, animals were fed BO (group BO) or HCO (group HCO) diets for 10 weeks. Results: Epidermal hyperproliferation was reversed in groups HCO + BO (67.6% of group HCO) and HCO + SO (84.5% of group HCO). Epidermal levels of Cer1/2, GlcCer-A/B, and ${\beta}$-glucocerebrosidase (GCase), an enzyme of GlcCer hydrolysis for Cer generation, were higher in group HCO + BO than in group HCO, and increased to levels similar to those of group BO. In addition, epidermal levels of SM1, serine palmitoyltransferase (SPT), and acidic sphingomyelinase (aSMase), enzymes of de novo Cer synthesis and SM hydrolysis for Cer generation, but not of Cer3-7, were higher in group HCO + BO than in group HCO. Despite an increase of SPT and aSMase in group HCO + SO to levels higher than in group HCO, epidermal levels of Cer1-7, GlcCer-A/B, and GCase were similar in these two groups. Notably, acidic ceramidase, an enzyme of Cer degradation, was highly expressed in group HCO + SO. Epidermal levels of GlcCer-C/D and SM-2/3 did not differ among groups. Conclusion: Dietary BO was more prominent for reversing epidermal hyperproliferation by enhancing Cer metabolism with increased levels of Cer1/2, GlcCer-A/B, and SM1 species, and of GCase proteins.

• Tuberculosis and Respiratory Diseases
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• v.58 no.3
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• pp.267-276
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• 2005

Background : The transforming growth $factor-{\beta}1$ ($TGF-{\beta}1$) plays a key role in lung fibrosis. However, the molecular mechanisms involved in $TGF-{\beta}1$-induced lung fibrosis are unclear. $TGF-{\beta}1$ is the key inducer of myofibroblast transdifferentiation via de novo synthesis of ${\alpha}-smooth$ muscle actin (${\alpha}-SMA$). Since $TGF-{\beta}1$ signals through reactive oxygen species (ROS) and ROS have been shown to induce accumulation of extracellular matrix (ECM) in various tissues, this study examined if ROS play a role in $TGF-{\beta}1$-induced fibronectin secretion and ${\alpha}-SMA$ expression in human lung fibroblasts, MRC-5 cells. Methods : Growth arrested and synchronized MRC-5 cells were stimulated with $TGF-{\beta}1$ (0.2-10 ng/ml) in the presence or absence of N-acetylcysteine (NAC) or diphenyleneiodonium (DPI) for up to 96 hours. Dichlorofluorescein (DCF)-sensitive cellular ROS were measured by FACScan and secreted fibronectin and cellular ${\alpha}-SMA$ by Western blot analysis. Results : $TGF-{\beta}1$ increased the level of fibronectin secretion and ${\alpha}-SMA$ expression in MRC-5 cells in a dosedependent manner. Both NAC (20 and 30 mM) and DPI (1 and $5{\mu}M$) significantly inhibited $TGF-{\beta}1$-induced fibronectin and ${\alpha}-SMA$ upregulation. The $TGF-{\beta}1$-induced cellular ROS level was also significantly reduced by NAC and DPI. Conclusions : The results suggest that NADPH oxidase-dependent ROS play an important role in $TGF-{\beta}1$-induced fibronectin secretion and ${\alpha}-SMA$ expression in MRC-5 cells, which leads to myofibroblast transdifferentiation and progressive lung fibrosis.

• Journal of the Korean Society of Food Science and Nutrition
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• v.33 no.10
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• pp.1626-1633
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• 2004

In recent, the roles of oleic acid, most abundant fatty acid in myelin, were investigated in relation to the brain functions. This study examined the effects of diets either with desirable ratios of $\omega$6/ $\omega$9 and P/M/S (mixed oil-fed group: MO) or with defficient in $\omega$3 series fatty acids (safflower oil-fed group: SO) on the oleic acid composition in RBC and brain synaptosomal, mitochondrial & microsomal phospholipids. The desirable fatty acid composition was computer-searched with different fats and oils to meet right ratios of both $\omega$6/ $\omega$3 and P/M/S. Diets were fed 3 weeks before conception and new-born pups were fed maternal milk from the same mothers and same diets until 9 wks of age. At 3 wks of age, the compositions of oleic acid in brain subcellular fractions and red blood cells were constantly remained whatever the composition of dietary fatty acids. But at 9 wks of age, the composition of oleic acid in synaptosome and mitochondria were significantly higher in MO group than SO group. The composition of oleic acid in milk was significantly higher in MO group than SO group, but in case of SO group, that of oleic acid was increased by 48%, in comparison with dietary fatty acid compositions. -9 desaturase index (18:0\longrightarrow8:1) of brain synaptosome was significantly higher in MO group than SO group at 3 and 9 weeks of ages, but that of brain microsome was higher in SO group than MO group at 9 wks of age. Taken together, the presences of oleic acid in the diet was important to maintain brain functions. The origins of oleic acid in brain may suggests two hypotheses; first, the central nervous system has priority for the uptake of oleic acid, and second the nervous system can synthesize all the oleic acid it needs, independently of its presence in the diet.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.1
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• pp.537-545
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• 2018

In this study, transcriptome analysis was conducted to collect various information from Fagopyrum esculentum and Fagopyrum tataricum during the early germination stage. Total RNA was extracted from the seeds and at 12, 24, and 36 hrs after germination of Jeju native Fagopyrum esculentum and Fagopyrum tataricum and sequenced using the Illumina Hiseq 2000 platform. Raw data analysis was conducted using the Dynamic Trim and Lengths ORT programs in the SolexaQA package, and assembly and annotation were performed. Based on RNA-seq raw data, we obtained 16.5 Gb and 16.2 Gb of transcriptome data corresponding to about 84.2% and 81.5% of raw data, respectively. De novo assembly and annotation revealed 43,494 representative transcripts corresponding to 47.5Mb. Among them, 23,165 sequences were shown to have similar sequences with annotation DB. Moreover, Gene Ontology (GO) analysis of buckwheat representative transcripts confirmed that the gene is involved in metabolic processes (49.49%) of biological processes, as well as cell function (46.12%) in metabolic process, and catalytic activity (80.43%) in molecular function In the case of gibberellin receptor GID1C, which is related to germination of seeds, the expression levels increased with time after germination in both F. esculentum and F. tataricum. The expression levels of gibberellin 20-oxidase 1 were increased within 12 hrs of gemination in F. esculentum but continuously until 36 hrs in F. tataricum. This buckwheat transcriptome profile analysis of the early germination stage will help to identify the mechanism causing functional and morphological differences between species.