• Korean Journal of Clinical Laboratory Science
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• v.41 no.4
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• pp.158-166
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• 2009

On the basis of morphological characteristics, of total 128 strains of from sputum of tuberculos inpatient were identified as A. fumigatus (61 strains), A. niger (37), A. flavus (26), A. versicolor (1), A. nidulans (1), A. clavatus (1) and Neosartorya fennelliae (1). These strains were re-identified according to recent Aspergillus classification system which is mainly based on molecular characteristics. The strains were grouped by randomly amplified polymorphic DNA (RAPD) techniques. The representative strains from each group were sequenced with partial ${\beta}$-tubulin gene and compared with those of reference strains in the Aspergillus and were identified by the sequence. The identification was confirmed by morphology examination. As the results, they are reidentified as A. fumigatus (58), A. niger (11), A. tubingensis (26), A. flavus (27), A. sydowii (3), A. nidulans (1), A. clavatus (1) and Neosatorya fennelliae (1). This is the first report of A. tubuingensis in clinical field in Korea.

• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.129-131
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• 2006

Through molecular phylogenetic analysis using the nef gene sequences of HIV-l isolated from Korean registered in the NCBI GenBank together with 41 reference strains and 94 foreign isolates, we verified that most (${\sim}80%$) of Korean isolates belonged to subtype B and 78% of subtype B were clustered together exclusively of foreign isolates, and this cluster was named Korean clade subtype B ($K_cB$). Similarity study suggested that the $K_cB$ cluster was more homogeneous than and clearly distinctive from the non-Korean subtype B ($NK_cB$). Comparison of the consensus amino acid sequences of the $K_cB\;or\;NK_cB$ revealed characteristic $K_cB$ signature amino acid pattern comprised of 13 amino acid residues. The $K_cB$ signature amino acid residues were critical in separating the $K_cB$ ftom the $NK_cB$, since substitution of the $NK_cB$ sequences with $K_cB$ signature amino acids relocated them to the Koran clade, and vice versa. Synonymous and nonsynonymous substitution rate study suggested positive selection event for the $K_cB$.

• Genomics & Informatics
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• v.8 no.2
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• pp.81-85
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• 2010

The aim of the study was to investigate pig reference families, generated from Korean native pigs (KNP) that were crossed with Yorkshire (YS) breeds, which were used to evaluate genetic markers to select breeding animals with superior pork quality. A set of five candidate genes (PRKAG3, MC4R, CAST, ESR, and PRLR ) was analyzed for association with pork quality traits. PRKAG3 (I199V) SNP genotypes were significantly associated with muscle moisture, protein, and fat contents. The MC4R D298N polymorphism was significantly associated with meat tenderness and color traits. The CAST polymorphism was significantly associated with muscle moisture and crude protein traits. These three genes have been associated with pork quality traits in other pig populations, and some of our results are consistent with earlier studies. In addition, two reproductive candidate genes (ESR and PRLR ) did not have significant associations. These results suggest that further study is warranted to investigate and develop more DNA markers associated with pork quality in our KNP-crossed pig families.

• Korean Journal of Medicinal Crop Science
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• v.18 no.3
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• pp.180-185
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• 2010

We investigated genetic diversity among and within the populations of cultivated ginseng (Panax ginseng C. A. Meyer ) using SRAP profiles. A total of 24 ginseng plants were sampled from the three populations (two from China, one from Korea). Since all these populations are previously shown closely related to each other assister groups, we used Panax quinquefolium L. and wild ginseng as a reference species, which is not "within the sister group". All individuals from the three populations were screened with a total of 36 primer pairs with 26 primers generated from 328 SRAP bands of DNA gels. The mean gene diversity ($H_E$) was estimated to be 0.057 within populations (range 0.032-0.067), and 0.086 at the species level. The genetic differentiation (Gst=0.31) indicates that genetic variation apportioned 30% among populations and 70% within populations. Generally, the result of this study indicates that ginseng contains high molecular variation in its populations.

• Korean Journal of Breeding Science
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• v.40 no.1
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• pp.8-14
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• 2008

A complete diallel cross was performed to determine the inheritance of allelopathic potential and combining ability of six rice germplasm that showed different level of allelopathic potential against barnyardgrass. Parents and F1 of 30 crosses were assessed for allelophatic potential in field condition. Barnyardgrass (Echinochloa crus-galli (L.) Beauv. var. frumentaceae) was used for rice allelopathic potential indicator which was observed in height and shoot dry weight, then suppression percentage were calculated by comparing to barnyardgrass grown in control plot (no rice). It was found that general combining ability showed no significant effect, whereas specific combining ability and reciprocal effect were significant. Variance analysis confirmed that genetic control of allelopathic potential in rice against barnyardgrass was mostly directed by dominance gene effect. The dominant genes were associated with high allelopathic potential and recessive genes were associated with low allelopathic potential. Heritability in broad sense for barnyardgrass dry weight suppression was around 41%; whereas for barnyardgrass height suppression was 51%. However, heritability in narrow sense was very low. The finding suggests that accumulation of genes associated with allelopathic potential would be a strategy to develop promising varieties in reference with the specific combining ability of cross combinations.

• Microbiology and Biotechnology Letters
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• v.46 no.4
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• pp.334-345
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• 2018

Spore-forming Bacillus species are commercially available probiotic formulations for application in humans. They have health benefits and help prevent disease in hosts by combating entero-pathogens and ameliorating antibiotic-associated diarrhea. However, the molecular and cellular mechanisms of these benefits remain unclear. Here, we report the draft genome of a potential probiotic strain of Bacillus clausii B106. We mapped and compared the probiotic profile of B106 with other reference genomes. The draft genome analysis of B106 revealed the presence of ADI pathway genes, indicating its ability to tolerate acidic pH and bile salts. Genes encoding fibronectin binding proteins, enolase, as well as a gene cluster involved in the biosynthesis of exopolysaccharides underscored the potential of B106 to adhere to the intestinal epithelium and colonize the human gut. Genes encoding bacteriocins were also detected, indicating the antimicrobial ability of this isolate. The presence of genes encoding vitamins, including Riboflavin, Folate, and Biotin, also indicated the health-promoting ability of B106. Resistance of B106 to multiple antibiotics was evident from the presence of genes encoding resistance to chloramphenicol, ${\beta}$-lactams, Vancomycin, Tetracycline, fluoroquinolones, and aminoglycosides. The findings indicate the significance of B. clausii B106 administration during antibiotic treatment and its potential value as a probiotic strain to replenish the health-promoting and disease-preventing gut flora following antibiotic treatment.

• Molecules and Cells
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• v.45 no.5
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• pp.343-352
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• 2022

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

• Genomics & Informatics
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• v.20 no.4
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• pp.46.1-46.7
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• 2022

Influenza A virus (IAV) is the most widespread pathogen causing human respiratory infections. Although polymerase chain reaction (PCR)-based methods are currently the most commonly used tools for IAV detection, PCR is not ideal for point-of-care testing. In this study, we aimed to develop a more rapid and sensitive method than PCR-based tools to detect IAV using loop-mediated isothermal amplification (LAMP) technology. We designed reverse-transcriptional (RT)-LAMP primers targeting the hemagglutinin gene. RNAs from reference H1N1 and H3N2 showed specific RT-LAMP signals with the designed primers. We optimized the reaction conditions and developed universal reaction conditions for both LAMP assays. Under these conditions, the detection limit was 50 copies for both RT-LAMP assays. There was no non-specific signal to 19 non-IAV respiratory viruses, such as influenza B virus, coronaviruses, and respiratory syncytial viruses. Regarding the reaction time, a positive signal was detected within 25 min after starting the reaction. In conclusion, our RT-LAMP assay has high sensitivity and specificity for the detection of the H1 and H3 subtypes, making it suitable for point-of-care IAV testing.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.68-68
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• 2022

The pepper mild mottle virus (PMMoV), belonging to the tobamovirus genus, is currently one of the most destructive pathogens in pepper production. Tobamoviruses have been classified in terms of increased pathogenicity as pathotypes P₀, P₁, P_1,2, P_1,2,3 and P_1,2,3,4, based on their ability to infect systemically Capsicum L⁰ , L¹ , L² , L³ and L⁴ resistant plants, respectively. Two hundred eighty pepper germplasms and 5 reference accessions known as resistant L alleles, were analyzed to select the resistance cultivars against PMMoV- P_1,2,3 (CV130614-2) using bioassay and genetic markers. The susceptible accessions showed systemic symptom when inoculated with PMMoV- P_1,2,3. However, accessions including IT223737, were resistant as they developed necrotic local lesions only on inoculated leaves, whereas no symptoms were observed on the upper leaves. Moreover, RT-PCR results for detecting the presence of virus were also negative. Thus, those accessions will be used as a novel source to facilitate introduction the resistant gene into commercial cultivars of pepper.

• Clinical and Experimental Pediatrics
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• v.53 no.2
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• pp.178-183
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• 2010

Purpose : The aim of this study was to identify mutations associated with macrolide resistance in Mycoplasma pneumoniae (MP) and to establish a cultural method to determine antimicrobial susceptibility. Methods : Nasopharyngeal aspirates (NPAs) were collected from 62 children diagnosed with MP pneumonia by a serologic method or polymerase chain reaction. The 23S rRNA and L4 ribosomal protein genes of MP were amplified and sequenced. To identify mutations in these 2 genes, their nucleotide sequences were compared to those of the reference strain M129. MP cultivation was carried out for 32 (28 frozen and 5 refrigerated) NPAs and M129 strain using Chanock's glucose broth and agar plate in a 5% $CO_2$ incubator at $37^{\circ}C$ and examined at 2-3 day intervals for 6 weeks. Results : Among the 62 specimens, 17 had M144V mutations in ribosomal protein L4. The A2064G mutation was observed in 1 specimen; its 23S rRNA gene was successfully sequenced. Culture for MP was successful from the M129 strain and 2 of the 5 NPAs that were refrigerated for no longer than 3 days. However, MP did not grow from the 28 NPAs that were kept frozen at $-80^{\circ}C$ since 2003. Conclusion : We found the M144V mutation of L4 protein to be common and that of domain V of 23S rRNA gene was relatively rare among MP. Studies on the prevalence of macrolide-resistant MP and the relationship between the mutations of 23S rRNA gene and ribosomal protein L4 will aid in understanding the mechanism of macrolide resistance in MP.