• KSBB Journal
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• 제19권1호
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• pp.72-77
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• 2004

건강에 대한 관심의 증대로 인한 저염식품의 개발 필요성에 맞추어 오이발효에 염의 농도를 낮추게 되면 정상적 일차발효 후에 이차발효가 진행됨으로써 결국 부패하게 된다. 장기간에 걸쳐 다양한 균의 복합적 작용으로 진행되는 저염 발효오이의 부패 과정을 이해하기 위하여 이에 관련된 균을 분리 동정하였다. 부패발효액을 무기배양하여 균을 분리하고 이들의 16s rRNA 유전자 부분을 universal primer를 이용한 PCR로서 증폭하여 서열분석 하였다. 분석된 800 염기 길이의 서열 전체를 그대로 이용하여 NCBI의 BLAST로서 유사종을 찾고 RDP의 Sequence Aligner와 Sequence Match에서 재확인하여 분리된 균을 3속 8종으로 동정하였다. Database 내의 표준균 서열을 기반으로 한 제한효소 지도와 동정된 균의 PCR 생성묵의 제한효소 처리결과(RFLP)를 비교하여 동정 결과를 실험으로 검정하였다. 동정과정에서 sequencing 결과 전체를 이용하는 점과 RDP를 통한 확인과 RFLP를 이용한 검정은 동정 결과에 대한 신뢰도를 한층 증가시켰다. 또 분리된 8종은 개별적 특징의 조사나 적절한 조합을 이룰 때의 상호 의존도 등을 조사할 수 있게 함으로써 여러 균에 의한 복합적 과정인 부패를 순차적 혹은 요인별로 나누어 살펴보는 연구를 가능하게 한다.

• Journal of Microbiology and Biotechnology
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• 제28권8호
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• pp.1318-1331
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• 2018

Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.

• BMB Reports
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• 제54권12호
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• pp.608-613
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• 2021

Melanoma, the most serious type of skin cancer, exhibits a high risk of metastasis. Although chemotherapeutic treatment for metastatic melanoma improves disease outcome and patient survival, some patients exhibit resistance or toxicity to the drug treatment regime. OTUB1 is a deubiquitinating enzyme overexpressed in several cancers. In this study, we investigated the effects of inhibiting OTUB1 expression on melanoma-cell proliferation and viability and identified the underlying molecular mechanism of action of OTUB1. We did endogenous OTUB1 knockdown in melanoma cells using short interfering RNA, and assessed the resulting phenotypes via MTT assays, Western blotting, and cell-cycle analysis. We identified differentially expressed genes between OTUB1-knockdown cells and control cells using RNA sequencing and confirmed them via Western blotting and reverse transcription polymerase chain reaction. Furthermore, we investigated the involvement of apoptotic and cell survival signaling pathways upon OTUB1 depletion. OTUB1 depletion in melanoma cells decreased cell viability and caused simultaneous accumulation of cells in the sub-G1 phase, indicating an increase in the apoptotic-cell population. RNA sequencing of OTUB1-knockdown cells revealed an increase in the levels of the apoptosis-inducing protein TRAIL. Additionally, OTUB1-knockdown cells exhibited increased sensitivity to PLX4032, a BRAF inhibitor, implying that OTUB1 and BRAF act collectively in regulating apoptosis. Taken together, our findings show that OTUB1 induces apoptosis of melanoma cells in vitro, likely by upregulating TRAIL, and suggest that approaches targeting OTUB1 can be developed to provide novel therapeutic strategies for treating melanoma.

• Journal of Ginseng Research
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• 제46권4호
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• pp.592-600
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• 2022

Background: Di-(2-ethylhexyl) phthalate (DEHP) is the most common endocrine disrupting chemical used as a plasticizer. DEHP is associated with the development of endometrium-related diseases through the induction of inflammation. The major therapeutic approaches against endometrial cancer and endometriosis involve the suppression of inflammatory response. Korean Red Ginseng (KRG) is a natural product with anti-inflammatory and anti-carcinogenic properties. Thus, the purpose of this study is to investigate the effects of KRG on DEHP-induced inflammatory response in endometrial cancer Ishikawa cells and a mouse model of endometriosis. Methods: RNA-sequencing was performed and analyzed on DEHP-treated Ishikawa cells in the presence and absence of KRG. The effects of KRG on DEHP-induced cyclooxygenase-2 (COX-2) mRNA levels in Ishikawa cells were determined by RT-qPCR. Furthermore, the effects of KRG on the extracellular signal-regulated kinases (ERKs) pathway, COX-2, and nuclear factor-kappa B (NF-kB) p65 after DEHP treatment of Ishikawa cells were evaluated by western blotting. In the mouse model, the severity of endometriosis induced by DEHP and changes in immunohistochemistry were used to assess the protective effect of KRG. Results: According to the RNA-sequencing data, DEHP-induced inflammatory response-related gene expression was downregulated by KRG. Moreover, KRG significantly inhibited DEHP-induced ERK1/2/NF-κB/COX-2 levels in Ishikawa cells. In the mouse model, KRG administration significantly inhibited ectopic endometriosis growth after DEHP-induced endometriosis. Conclusions: Overall, these results suggest that KRG may be a promising lead for the treatment of endometrial cancer and endometriosis via suppression of the inflammatory response.

• 운동영양학회지
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• 제25권4호
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• pp.24-37
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• 2021

[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children. [Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou's evenness, and Faith's phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2. [Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R² = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA. [Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.

• 대한의생명과학회지
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• 제28권4호
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• pp.317-321
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• 2022

Due to COVID-19 pandemic, wearing face masks is obligatory to prevent respiratory virus transmissions in the community. However, there are few studies of the desirable number of wearing a face mask, and how to store them for reuse. Therefore, in this study, a survey was conducted among 208 healthy adults, and 27 kf-94 masks worn for 1, 2, and 3 days were collected. To estimate the risk of bacterial contamination, we analyzed the extent of bacterial contamination of the BHI medium and 16S rRNA gene sequencing. With an increase in the number of days of using the mask, the degree of bacterial contamination of the used mask gradually increased. As a result of 16S rRNA PCR performed for strain identification, Staphylococcus, known as a pathogenic bacterium, was identified the most. In conclusion, we found that wearing a cotton KF mask provides an optimal environment for microbes, which are related to the skin and respiratory system, to thrive. Therefore, it is also important to reduce the risk of bacterial infection of the face mask with appropriate sterilization methods.

• BMB Reports
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• 제55권9호
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• pp.465-471
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• 2022

Understanding and monitoring virus-mediated infections has gained importance since the global outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Studies of high-throughput omics-based immune profiling of COVID-19 patients can help manage the current pandemic and future virus-mediated pandemics. Although COVID-19 is being studied since past 2 years, detailed mechanisms of the initial induction of dynamic immune responses or the molecular mechanisms that characterize disease progression remains unclear. This study involved comprehensively collected biospecimens and longitudinal multi-omics data of 300 COVID-19 patients and 120 healthy controls, including whole genome sequencing (WGS), single-cell RNA sequencing combined with T cell receptor (TCR) and B cell receptor (BCR) sequencing (scRNA(+scTCR/BCR)-seq), bulk BCR and TCR sequencing (bulk TCR/BCR-seq), and cytokine profiling. Clinical data were also collected from hospitalized COVID-19 patients, and HLA typing, laboratory characteristics, and COVID-19 viral genome sequencing were performed during the initial diagnosis. The entire set of biospecimens and multi-omics data generated in this project can be accessed by researchers from the National Biobank of Korea with prior approval. This distribution of large-scale multi-omics data of COVID-19 patients can facilitate the understanding of biological crosstalk involved in COVID-19 infection and contribute to the development of potential methodologies for its diagnosis and treatment.

• Molecules and Cells
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• 제27권1호
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• pp.47-54
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• 2009

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.

• 한국식물병리학회지
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• 제10권3호
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• pp.228-234
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• 1994

Genomic RNA was extracted from Cy strain of odontoglossum ringspot tobamovirus (ORSV-Cy) isolated from infected leaves of tobacco cv. Samsun. Size of the genomic RNA was about 6.6 kb in length. The genomic RNA was fractionated using Sephadex G-50 column chromatography into 2 fractions. They were polyadenylated at their 3'-end using E. coli poly(A) polymerase. Polyadenylated viral RNA was recovered by oligo (dT) primer adapter containing NotI restriction site and Moloney murine leukemia virus SuperScript reverse transcriptase (RNase H-). Second-strand cDNA was synthesized by using E. coli DNA ligase, E. coli DNA polymerase I and E. coli RNase H. Recombinant plasmids containing cDNAs for ORSV-Cy RNA ranged from about 800 bp to 3,000 bp. Among the selected 238 recombinants, pORCY-124 clone was the largest one covering 3'-terminal half of the viral RNA. This clone contained two restriction sites for EcoRI and XbaI and one site for AccI, AvaI, BglII, BstXI, HindIII, PstI, and TthIII 1. respectively. The clone contained partial viral replicase, a full-length movement protein and a complete coat protein genes followed by a 3' untranslated region of 414 nucleotides based on restriction mapping and nucleotide sequencing analyses. Clones pORCY-028, -068, -072, -187 and -224 were overlapped with the pORCY-124. Clones pORCY-014 and -095 covered 5' half upstream from the middle region of the viral RNA, which was estimated based on restriction mapping and partial sequence analysis. Constructed cDNA library covered more than 90% of the viral genome.

• Animal Systematics, Evolution and Diversity
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• nspc3호
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• pp.139-146
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• 1992

중합효소연쇄반응(PCR)을 이용한 클로닝 기법과 Taq 염기서열분석법을 사용하여 갑각류에 속하는 뿔물맞이게(Pugettia quadridens)(십각 목, 범배 아목, 게 하목)에 대한 18S 리보솜 RNA 유전자의 1차염기서열을 밝혔다. 본 종의 18S 리보솜 RNA 유전자는 십각류에 속하는 또 다른 종인 두드러기어리게(Oedignathus inermis)보다 46개가 짧은 1837개의 염기로 이루어져 있었다. 염기가 삽입되거나 결실된 부분을 고려하지 않았을때에 두 종간에 염기서열 유사도는 90.8%이었다. 염기서열이 가장 보존적인 부위는 1137-1206(70개) 분위로 이 부위에서는 두 종이 완전히 동일한 염기서열을 보이고 있었고, 변이가 연속적으로 가장 큰 부위는 46-55 부위였고 399-407 부위가 그 다음으로 많은 연속적 변이를 가지고 있었다. 18S 리보솜 RNA 유전자의 1차구조에 있어서 염기서열의 변이는 이 유전자 전체를 통해 고르게 분포하지 않았다.