• Journal of Ginseng Research
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• 제44권1호
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• pp.33-43
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• 2020

Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.

• Journal of Microbiology and Biotechnology
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• 제16권10호
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• pp.1650-1655
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• 2006

Bacteria belonging to the genus Paenibacillus are facultatively anaerobic endospore formers and are attracting growing ecological and agricultural interest, yet their genome information is very limited. The present study surveyed the genomic features of P. polymyxa ATCC $842^T$ using pulse-field gel electrophoresis of restriction fragments and sample genome sequencing of 1,747 reads (approximately 17.5% coverage of the genome). Putative functions were assigned to more than 60% of the sequences. Functional classification of the sequences showed a similar pattern to that of B. subtilis. Sequence analysis suggests nitrogen fixation and antibiotic production by P. polymyxa ATCC $842^T$, which may explain its plant growth-promoting effects.

• Mycobiology
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• 제50권6호
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• pp.408-419
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• 2022

Filamentous fungi that could be classified into Aspergillus flavus/oryzae were isolated from traditionally fermented meju commercially available in Korea. The samples were analyzed for aflatoxin B1 and ochratoxin A contamination by HPLC; however, no toxin was detected. In addition, fungal and bacterial metagenomic sequencing were performed to analyze the microbial distribution in the samples. The results revealed that the distribution and abundance of fungi and bacteria differed considerably depending on the production regions and fermentation conditions of the meju samples. Through morphological analysis, ITS region sequencing, and assessment of the aflatoxin-producing ability, a total of 32 A. flavus/oryzae strains were identified. PCR analysis of six regions with a high mutation frequency in the aflatoxin gene cluster (AGC) revealed a total of six types of AGC breaking point patterns. The A. flavus/oryzae strains did not exhibit the high amylase activity detected in the commercial yellow koji strain (starter mold). However, their peptidase and lipase activities were generally higher than that of the koji isolates. We verified the safety of the traditionally fermented meju samples by analyzing the AGC breaking point pattern and the enzyme activities of A. flavus/oryzae strains isolated from the samples. The isolated strains could possibly be used as starter molds for soybean fermentation.

• Genomics & Informatics
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• 제13권4호
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• pp.126-131
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• 2015

Fulminant type 1 diabetes (T1DM) is a distinct subtype of T1DM that is characterized by rapid onset hyperglycemia, ketoacidosis, absolute insulin deficiency, and near normal levels of glycated hemoglobin at initial presentation. Although it has been reported that class II human leukocyte antigen (HLA) genotype is associated with fulminant T1DM, the genetic predisposition is not fully understood. In this study we investigated the HLA genotype and haplotype in 11 Korean cases of fulminant T1DM using imputation of whole exome sequencing data and compared its frequencies with 413 participants of the Korean Reference Panel. The $HLA-DRB1^*04:05-HLA-DQB1^*04:01$ haplotype was significantly associated with increased risk of fulminant T1DM in Fisher's exact test (odds ratio [OR], 4.11; 95% confidence interval [CI], 1.56 to 10.86; p = 0.009). A histidine residue at $HLA-DR{\beta}1$ position 13 was marginally associated with increased risk of fulminant T1DM (OR, 2.45; 95% CI, 1.01 to 5.94; p = 0.054). Although we had limited statistical power, we provide evidence that HLA haplotype and amino acid change can be a genetic risk factor of fulminant T1DM in Koreans. Further large-scale research is required to confirm these findings.

• 한국임상수의학회지
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• 제23권4권
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• pp.405-410
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• 2006

피부사상균증이 있는 개와 고양이에서 분리한 9주의 Microsporum canis와 5주의 Microsporum gypseum에서 ribosomal DNA를 추출하여 internal transcribed spacer 1 (ITS1) gene을 PCA로 증폭한 후 sequencing을 실시하여, 각 사상균의 계통학적 관계를 조사하였다. M canis 분리주 9주의 ITS1 gene의 nucleotide sequence는 100% 일치하였으며 M gypseum 분리주 5주의 nucleotide sequence도 100% 일치하였다. M canis 분리주 9주의 계통분석 결과 미국, 일본, 호주 및 유럽에서 분리된 M canis와 같은 cluster에 속하였으며 다른 Microsporum spp와는 유전적으로 다른 cluster를 형성하였다. 그러나 M canis와 M distortum, M equinum, M ferrugineum은 유전적으로 매우 가까운 위치에 있었다. M gypseum 분리주는 M canis와는 다른 cluster를 형성하였다. ITS1 gene의 분자생물학적 분석은 Microsporum spp를 확인하고 그들의 유전학적 관계를 이해하는 유용한 정보를 제공하는 것으로 생각된다.

• Animal cells and systems
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• 제8권1호
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• pp.49-55
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• 2004

In vertebrates, multisubunit cofactors regulate gene expression through interacting with cell-type- and gene-specific DNA-binding proteins in a chromatin-selective manner. ADD1/SREBP1c regulates fatty acid metabolism and insulin-dependent gene expression through binding to SRE and E-box motif with dual DNA binding specificity. Although its transcriptional and post-translational regulation has been extensively studied, its regulation by interacting proteins is not well understood. To identify cellular proteins that associate with nuclear form of ADD1/SEBP1c, we employed the GST pull-down system with Hela cell nuclei extract. In this study, we demonstrated that Ku proteins interact specifically with ADD1/SREP1c protein. GST pull-down combined with peptide sequencing analysis revealed that Ku80 binds to ADD1/SREBP1c in vitro. Additionally, western blot analysis showed that Ku70, a heterodimerizing partner of Ku80, also associates with ADD1/SREBP1c. Furthermore, co-transfection of Ku70/Ku80 with ADD1/SREBP1c enhanced the transcriptional activity of ADD1/SREBP1c. Taken together, these results suggest that the Ku proteins might be involved in the lipogenic and/or adipogenic gene expression through interacting with ADD1/SREBP1c.

• 대한의생명과학회지
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• 제28권1호
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• pp.9-24
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• 2022

The aim of this study was to identify the expression of zinc finger E-box binding homeobox 1 (ZEB1), its prognostic significance, and correlation between ZEB1 and infiltrating immune cells in lung cancer. Correlation between ZEB1 and telomerase was also analyzed in different types of cancers. RNA sequencing analysis and survival rates of patients were confirmed by Gene Expression Profiling Interactive Analysis (GEPIA). The Kaplan-Meier plotter and PrognoScan databases were used to analyze the prognostic value of ZEB1 in various cancers. The Tumor IMmune Estimation Resource (TIMER) was used to determine the correlation between ZEB1 and infiltrating immune cells. Lower ZEB1 expression was lower in lung cancer and was related to poor prognosis in lung adenocarcinoma (LUAD). ZEB1 expression exhibited a significantly positive correlation with infiltration levels of immune cells in LUAD and lung squamous cell carcinoma. Furthermore, we found that the ZEB1 expression correlated with subunits of telomerase. Our findings suggest ZEB1 as a potential biomarker to be used for prognostic significance and tumor immunology in lung cancer. The correlation between the expression of ZEB1 and telomere-related gene will help in understand the cancer-promoting mechanisms.

• Asian-Australasian Journal of Animal Sciences
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• 제18권4호
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• pp.483-489
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• 2005

To understand the molecular mechanisms that regulate intramuscular fat deposition and its release, cDNA clones expressed in adipose tissues of Korean cattle were identified by differential screening from adipose tissue cDNA library. By partial nucleotide sequencing of 486 clones and a search for sequence similarity in NCBI nucleotide databases, 245 clones revealed unique clones. By a functional grouping of the clones, 14% of the clones were categorized to metabolism and enzyme-related group (stearoyl CoA desaturase, lactate dehydrogenase, fatty acid synthase, ATP citrate lyase, lipoprotein lipase, acetyl CoA synthetase, etc), and 6% to signal transduction/cell cycle-related group (C/EBP, cAMP-regulated phosphoprotein, calmodulin, cyclin G1, cyclin H, etc), and 4% to cytoskeleton and extracellular matrix components (vimentin, ankyrin 2, gelosin, syntenin, talin, prefoldin 5). The obtained 245 clones will be useful to study lipid metabolism and signal transduction pathway in adipose tissues and to study obesity in human. Some clones were subjected to full-sequencing containing open reading frame. The cDNA clone of bovine homolog of human prefoldin 5 gene had a total length of 959 nucleotides coding for 139 amino acids. Comparison of the deduced amino acid sequences of bovine prefoldin 5 with those of human and mouse showed over 95% identity. The cDNA clone of bovine homolog of human ubiquitin-like/S30 ribosomal fusion protein gene had a total length of 484 nucleotides coding for 133 amino acids. Comparison of the deduced amino acid sequences of bovine ubiquitin-like/S30 ribosomal fusion protein gene with those of human, rat and mouse showed over 97% identity. The cDNA clone of bovine homolog of human proteolipid protein 2 mRNA had a total length of 928 nucleotides coding for 152 amino acids. Comparison of the deduced amino acid sequences of bovine proteolipid protein 2 with those of human and mouse showed 87.5% similarity. The cDNA clone of bovine homolog of rat thymosin beta 4 had a total length of 602 nucleotides coding for 44 amino acids. Comparison of the deduced amino acid sequences of bovine thymosin beta 4 gene with those of human, mouse and rat showed 93.1% similarity. The cDNA clone of bovine homolog of human myotrophin mRNA had a total length of 790 nucleotides coding for 118 amino acids. Comparison of the deduced amino acid sequences of bovine myotrophin gene with those of human, mouse and rat showed 83.9% similarity. The functional role of these clones in adipose tissues needs to be established.

• 생명과학회지
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• 제30권1호
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• pp.64-69
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• 2020

꿀벌(Apis mellifera)에는 많은 항균성 펩티드가 있습니다. 그러나 아직 많은 종류의 펩티드를 기능을 알려지지 않았다. 따라서, 알려지지 않은 기능성 펩티드의 특성화가 필요하다. 그래서 우리는 새로운 항균성 펩티드(AMP)를 분석 하였다. 우리는 Apis mellifera에서 total RNA를 분리하고 Illumina HiSeq 2500 차세대 시퀀싱(NGS) 기술을 사용하여 15,314 개의 펩티드 서열을 생성하여 새로운 AMP를 선발 하였다. AMP로서 기능을 가지는 AMP를 선발 하기 위해 AMP 서열의 특성 과 특징을 분석을 기초로 하여 알려지지 않은 펩티드 및 알려진 44 개의 펩티드가 확인 되었다. 그 중에서도 AMP5라는 특성화 되지 않은 펩티드를 선발 하였다. AMP5는 표피, 지방체, 독낭에서 발현된다. 항균 활성을 분석하기 위해 Gram-negative bacteria Escherichia coli KACC 10005 및 Bacillus thuringiensis KACC 10168에 대한 항균 활성을 합성한 AMP5 처리하여 시험 하였다. AMP5는 Gram-negative bacteria Escherichia coli에 대한 항균 활성을 나타냈다(MIC₅₀ = 22.04±0.66 μM). 일벌에 Escherichia coli을 주사했을 때 AMP5는 체내에서 항균성 펩티드로 발현이 높아졌다. 이러한 결과는 Escherichia coli에 대한 항균 활성을 나타냄을 확인하였다.

• The Plant Pathology Journal
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• 제39권5호
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• pp.430-448
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• 2023

Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil Bacillus spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of Fol by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, F. oxysporum f. sp. cubense race 1 (Foc), Sclerotium rolfsii, Colletotrichum musae, and C. gloeosporioides were noted for these isolates. These two Bacillus isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as Bacillus stercoris by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of B. stercoris strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.