• Journal of Species Research
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• v.13 no.1
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• pp.100-104
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• 2024

The purpose of this study was to isolate and identify wild yeasts from soil samples collected in Daegu and Cheongju city, Republic of Korea. To identify the wild yeast strains, pairwise sequence comparisons of D1/D2 region of the 26S rRNA gene sequence were done using Basic Local Alignment Search Tool (BLAST). The cell morphologies were observed by phase contrast microscope and assimilation test are done using API 20C AUX kit. All strains were assigned to the phylum Basidiomycota. Among 13 strains, 11 strains were previously reported, but two strains were unreported from the Republic of Korea. The two unrecorded yeast strains, GW1-3 and PG1-1-10C, belong to the genus Solicoccozyma (family Piskurozymaceae, order Filobasidiales, class Tremellomycetes). The two strains had oval-shaped and polar budding cells. This research showed the morphological and biochemical properties of the two unreported yeast species that had not officially reported in Korea.

• Journal of Species Research
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• v.13 no.1
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• pp.105-110
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• 2024

The purpose of this study was to isolate and identify wild yeasts from soil samples collected in Seoul and Daejeon, Republic of Korea. To identify wild yeast strains, pairwise sequence comparisons of D1/D2 region of the 26S rRNA gene sequence were done using Basic Local Alignment Search Tool (BLAST). The cell morphologies were observed by phase contrast microscope and carbon source assimilation test were done using API 20C AUX kit. Among the 13 isolated strains, 11 strains were previously reported, but two strains have never been reported from Republic of Korea. The 13 strains were assigned to the phylum Basidiomycota. The two unrecorded yeast strains B2UV-201 and DJ1-5-B-10C belong to the genera Rhodotorula and Rhodosporidiobolus, respectively. The two unrecorded yeast strains are oval shaped and polar budding cells. This research focuses on the morphological and biochemical properties of the two unreported yeast species that have not officially been reported in Korea.

• BMB Reports
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• v.50 no.11
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• pp.590-595
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• 2017

High-mobility group box-1 (HMGB-1) is expressed in almost all cells, and its dysregulated expression correlates with inflammatory diseases, ischemia, and cancer. Some of these conditions accompany HMGB-1-mediated abnormal angiogenesis. Thus far, the mechanism of HMGB-1-induced angiogenesis remains largely unknown. In this study, we performed time-dependent DNA microarray analysis of endothelial cells (ECs) after HMGB-1 or VEGF treatment. The pathway analysis of each gene set upregulated by HMGB-1 or VEGF showed that most HMGB-1-induced angiogenic pathways were also activated by VEGF, although the activation time and gene sets belonging to the pathways differed. In addition, HMGB-1 upregulated some VEGFR signaling-related angiogenic factors including EGR1 and, importantly, novel angiogenic factors, such as ABL2, CEACAM1, KIT, and VIPR1, which are reported to independently promote angiogenesis under physiological and pathological conditions. Our findings suggest that HMGB-1 independently induces angiogenesis by activating HMGB-1-specific angiogenic factors and also functions as an accelerator for VEGF-mediated conventional angiogenesis.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.5
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• pp.393-399
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• 2004

Useful genes can be Screened from various environments by construction of metagenomic DNA libraries. In this study, water samples were collected from several lakes in mid Korea, and analyzed by T-RFLP to examine diversities of the microbial communities. The crude DNAs r were extracted by the SDS-based freezing-thawing method, and then further purified using an $UltraClean^{TM}$ kit (MoBio, USA). The metagenomic libraries were constructed with the DNAs partially digested with EcoR I, BamH I, and Sac II in Escherichia coli DH 10B using the pBACe3.6 vector. About 44.0 Mb of metagenomic libraries were obtained with average inserts 13-15 kb in size. The bphC genes responsible for degradation of aromatic hydrocarbons via mets-cleavage were identified from the metagenomic libraries by colony hybridization using the bphC specific sequence as a probe. The 2,3-dihydroxybiphenyl (2, 3-DHBP) dioxygenase gene (bphC ), capable of degradation of 2,3-DHBP, was cloned and its nucleotide Sequences analyzed. The genes consisted of 966 and 897 base pairs with an ATG initiation codon and a TGA termination codon. The activity of the 2,3-DHBP dioxygenase was highly expressed to 2,3-DHBP and Showed a broad substrate range to 2,3-DHBP, catechol, 3-methylcatechol and 4-methylcatechol. These results in-dicated that the bphC gene identified from the metagenomes derived from lake water might be useful in the development of a potent strain for degradation of aromatic pollutants.

• Journal of Physiology & Pathology in Korean Medicine
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• v.17 no.3
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• pp.780-786
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• 2003

This study was carried out to know the immunity responses of the Spatholubus suberectus Dunn(hereinafter referred to STSD) to the synovial cells isolated from patients with rheumatoid arthritis. Various experiments were performed in vitro to analyse the immunity effects of STSD. Gene expression and production of pro-inflammatory cytokines such as IL-1β, IL-6, TNF-α, iNOS and COX-2 were determined by RT-PCR and ELISA kit. And also the binding activity of NF-kB and AP-1 were measured by Electromobility shift assay (EMSA) and the production of ROS was measured by flow cytometry. The results were obtained as follows 1. The gene expression and production of pro-inflammatory cytokines IL-1β, IL-6, TNF-α were reduced significantly. 2. The gene expression of iNOS and COX-2 were reduced. 3. The binding activity of NF-kB and AP-1 were inhibited. 4. The production of ROS in human synovial cells was reduced significantly. Comparison of the results for this study showed that STSD had immunomodulatory effects of suppressing or enhancing. So we expect that STSD should be used as a effective drugs for not only rheumatoid arthritis but also another auto-immune disease. Therefore we have to survey continuously in looking for the effective substance and mechanism in the future.

• Journal of Life Science
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• v.20 no.6
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• pp.929-933
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• 2010

We tried to identify differentially expressed genes (DEGs) from a silkworm, Bombyx mori, involved in fungal (Aspergillus niger) infection. A total RNA purified from fungal-induced and normal B. mori ($5^{th}$ instar larvae) was used for the cDNA synthesis. Differentially expressed genes were screened by annealing control primer (ACP)-based PCR technique. Comparing the gene expression profiles between fungal infection and control silkworm, we detected 10 genes that were differentially expressed in fungal induction and performed molecular cloning and nucleotide sequencing of the 10 genes. We confirmed the expression patterns of 3 DEGs by RT-PCR. The 3 DEGs over-expressed in fungal infection were identified as lysozyme, enbocin and an unknown gene. They were first identified to be genes induced by fungal infection. Although the detailed functions of 3 genes and their products remain to be determined, the genes will provide insight into the molecular mechanisms of insect-immune systems induced by fungal infection.

• The Korean Journal of Food And Nutrition
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• v.20 no.3
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• pp.245-252
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• 2007

This study investigated the effects of conjugated linoleic acid(CLA) on the fat deposition, triglyceride levels and the expression of stearoyl-CoA desaturase 1(SCD1) in the livers of male ICR mice that were fed with either soybean oil or beef tallow supplemented with CLA. Mice weighing $25{\sim}30$ g were divided into four groups; soybean oil(SBO), and SBO supplemented with 1% CLA(SBOC), beef tallow(BT) and BT supplemented with 1% CLA(BTC). Each group consisted of 10 mice that were fed the experimental diets for 4 weeks. The experimental diets consisted of 64% carbohydrate, 20% protein, and 16% fat in terms of their contributions to total calories. All other nutrients were identical in the diets. Triglyceride measurements were completed using a kit. Fatty acid compositions were analyzed in the liver using gas chromatography. The levels of SCD1 expression were analyzed by RT-PCR in the liver. No significant differences were found for food intake level, body weight and food efficiency among the experimental groups. However, the weights of epididymal fat pads and plasma triglyceride levels were significantly lower in SBOC and BTC(p<0.05) compared to the SBO and BT groups. These effects were similar in the CLA supplemented groups. The expression level of SCD1 gene and ${\Delta}9$ desaturase index were not significantly different, regardless of the fat used for CLA supplementation. Based on these results, addition of CLA showed decreasing effects on the fat depots weight and the concentration of triglyceride regardless of the fat sources. The SCD1 gene expression and ${\Delta}9$ desaturase index were not influenced by the types of fats with respect to the CLA effects.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1331-1342
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• 2021

In this study, we evaluated the mechanism of long non-coding RNA MIR22 host gene (LncRNA MIR22HG) in osteosarcoma cells. Forty-eight paired osteosarcoma and adjacent tissues samples were collected and the bioinformatic analyses were performed. Target genes and potential binding sites of MIR22HG, microRNA (miR)-629-5p and tet methylcytosine dioxygenase 3 (TET3) were predicted by Starbase and TargetScan V7.2 and confirmed by dual-luciferase reporter assay. Cell Counting Kit-8, colony formation and flow cytometry assays were utilized to determine the viability, proliferation and apoptosis of transfected osteosarcoma cells. Pearson's analysis was introduced for the correlation analysis between MIR22HG and miR-629-5p in osteosarcoma tissue. Relative expressions of MIR22HG, miR-629-5p and TET3 were measured by quantitative real-time polymerase chain reaction or Western blot. MiR-629-5p could competitively bind with and was negatively correlated with MIR22HG, the latter of which was evidenced by the high expression of miR-629-5p and low expression of MIR22HG in osteosarcoma tissues. Overexpressed MIR22HG repressed the viability and proliferation but enhanced apoptosis of osteosarcoma cells, which was reversed by miR-629-5p upregulation. TET3 was the target gene of miR-629-5p, and the promotive effects of upregulated miR-629-5p on the viability and proliferation as well as its repressive effect on apoptosis were abrogated via overexpressed TET3. To sum up, overexpressed MIR22HG inhibits the viability and proliferation of osteosarcoma cells, which was achieved via regulation of the miR-629-5p/TET3 axis.

• Animal Bioscience
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• v.37 no.8
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• pp.1317-1332
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• 2024

Objective: Rare study of the non-coding and regulatory regions of the genome limits our ability to decode the mechanisms of fatty liver hemorrhage syndrome (FLHS) in chickens. Methods: Herein, we constructed the high-fat diet-induced FLHS chicken model to investigate the genome-wide active enhancers and transcriptome by H3K27ac target chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-Seq) profiles of normal and FLHS liver tissues. Concurrently, an integrative analysis combining ChIP-seq with RNA-Seq and a comparative analysis with chicken FLHS, rat non-alcoholic fatty liver disease (NAFLD) and human NAFLD at the transcriptome level revealed the enhancer and super enhancer target genes and conservative genes involved in metabolic processes. Results: In total, 56 and 199 peak-genes were identified in upregulated peak-genes positively regulated by H3K27ac (Cor (peak-gene correlation) ≥0.5 and log2(FoldChange) ≥1) (PP) and downregulated peak-genes positively regulated by H3K27ac (Cor (peak-gene correlation) ≥0.5 and log2(FoldChange)≤-1) (PN), respectively; then we screened key regulatory targets mainly distributing in lipid metabolism (PCK1, APOA4, APOA1, INHBE) and apoptosis (KIT, NTRK2) together with MAPK and PPAR signaling pathway in FLHS. Intriguingly, PCK1 was also significantly covered in up-regulated super-enhancers (SEs), which further implied the vital role of PCK1 during the development of FLHS. Conclusion: Together, our studies have identified potential therapeutic biomarkers of PCK1 and elucidated novel insights into the pathogenesis of FLHS, especially for the epigenetic perspective.

• Journal of Mushroom
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• v.9 no.4
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• pp.180-185
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• 2011

Spent mushroom substrates (SMS) is a by-product remaining after a crop of mushrooms. About four surfactin-producing strains were isolated from SMS (Pleurotus eryngii). Among of them, one isolate, which designated to YJ07, potentially showed the antifungal activity against Aspergillus flavus and Aspergillus ochraceous producing mycotoxin on PDA medium. The biochemical characteristics of the strain YJ07 was similar with Bacillus subtilis and Bacillus amyloliquefaciens by Bacillus ID kit and VITEK 2 system. Comparative 16S rDNA gene sequence analysis of the strain YJ07 also showed that the strain YJ07 was most closely related to Bacillus amyloliquefaciens with sequence similarity of 99.5%. On the basis of their biochemical characteristics and phylogenetic distinctiveness, the strain YJ07 was classified within the genus Bacillus as Bacillus amyloliquefaciens YJ07. The antifungal compound from B. amyloliquefaciens YJ07 was similar to lipopeptide surfactin from Bacillus subtilis by TLC and HPLC analysis.