• Journal of Life Science
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• v.21 no.6
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• pp.819-828
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• 2011

To inspect norovirus contamination of groundwater in south eastern areas of Korea, a systematic survey of groundwater in Busan, Ulsan, and Gyeongsangnam-do was performed for two years from 2009 to 2010. For this purpose, we first optimized the nested reverse transcription-PCR condition by designing two sets of primers for the detection of norovirus genogroups, GI and GII. Of 145 samples, 21 (25.9%) and 15 (23.4%) were norovirus positive in the dry season (April to June) and wet season (July to August), respectively. The detection frequencies of norovirus in Busan, Ulsan, and Gyeongsangnam-do were 15%, 7%, and 32%, respectively, reflecting a geographical difference in their distribution. The GI and GII isolates were 5 and 31, respectively, indicating the prevalence of GII in the tested areas. According to phylogenetic analysis of their nucleotide sequences, all of the GI isolates were identified to genotype GI.5 whilst the GII isolates were divided into two genotypes, GII.3 and GII.4. Neither physical-chemical parameters such as pH, temperature, oxidation-reduction potential, and dissolved oxygen, nor microbial indicators of water quality such as total bacteria, total coliforms, and Escherichia coli were statistically correlated with contamination of norovirus in the groundwater. Interestingly, however, the presence of norovirus was closely correlated with low turbidity (<0.50 NTU). The present study suggests that periodical monitoring of norovirus in groundwater is necessary to prevent epidemic waterborne diseases and to secure better sanitary conditions for public health.

• Journal of Life Science
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• v.30 no.11
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• pp.947-955
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• 2020

The foot-and-mouth disease virus (FMDV), a member of the Aphthovirus genus in the Picornaviridae family, affects wild and domesticated ruminants and pigs. During replication of the FMDV RNA (ribonucleic acid) genome, FMDV-encoding RNA polymerase 3D acts in a highly location-specific manner. This suggests that specific RNA structures recognized by 3D polymerase within non-coding regions of the FMDV genome assist with binding during replication. One such region is the cis-acting replication element (CRE), which functions as a template for RNA replication. The FMDV CRE adopts a stem-loop conformation with an extended duplex stem, supporting a novel 15-17 nucleotide loop that derives stability from base-stacking interactions, with the exact RNA nucleotide sequence of the CRE producing different RNA secondary structures. Here, we show that CRE sequences of FMDVs isolated in Korea from 2010 to 2017 exhibit A and O genotypes. Interestingly, variations in the RNA secondary structure of the Korean FMDVs are consistent with the phylogenetic relationships between these viruses and reveal the specificity of FMDV infections for particular host species. Therefore, we conclude that each genetic clade of Korean FMDV is characterized by a unique functional CRE and that the evolutionary success of new genetic lineages may be associated with the invention of a novel CRE motif. Therefore, we propose that the specific RNA structure of a CRE is an additional criterion for FMDV classification dependent on the host species. These findings will help correctly analyze CRE sequences and indicate the specificity of host species for future FMDV epidemics.

• Journal of the Korean Society of International Agriculture
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• v.23 no.5
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• pp.546-551
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• 2011

Chrysanthemums, often called mums or chrysanths, belong to the genus Chrysanthemum, which includes about 30 species of perennial flowering plants in the family Asteraceae. We extracted DNA from Dendranthema grandiflorum ('Smileball') to construct a simple sequence repeat (SSR)-enriched library, using a modified biotin-streptavidin capture method. GS FLX (Genome Sequencer FLX System which provides the flexibility to perform the broad range of applications) sequencing (at the 1/8 run specification) resulted in 18.83 mega base pairs (Mbp) with an average read length of 280.06 bp. Sequence analyses of all SSR-containing clones revealed a predominance of di-nucleotide motifs (16,375, 61.5%) followed by tri-nucleotide motifs (6,616, 24.8%), tetra-nucleotide motifs (1,674, 6.3%), penta-nucleotide motifs (1,283, 4.8%), and hexa-nucleotide motifs (693, 2.6%). Among the di-nucleotide motifs, the AC/CA class was the most frequently identified (93.5% of all di-nucleotide types), followed by the GA/AG class (6.1%), the AT/TA class (0.4%), and the CG/GC class (0.03%). When we analyzed the distribution of different repeat motifs and their respective numbers of repeats, regardless of the motif class, of 100 SSR markers, we found a higher number of di-nucleotide motifs with 70 to 80 repeats; we also found two di-nucleotide motifs with 83 and 89 repeats, respectively, but their product lengths were within optimum size (297 and 300 bp). In future work, we will screen for polymorphisms of possible primer pairs. The results will provide a useful tool for assessing molecular diversity and investigating the population structure among and within Chrysanthemum species.

• Korean Journal of Poultry Science
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• v.45 no.3
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• pp.155-165
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• 2018

Chicken feathers could be classified into early-feathering (EF) and late-feathering (LF) depending on the development and patterns of the wing and tail feathers. Currently, feather-sexing is a widely used chick sexing method in the industry. This study was carried out to suggest the method of classifying of EF and LF chicks to establish auto-sexing Korean native chicken (KNC) strains. The development and morphology of wing feathers and tail feathers in 856 KNCs from hatching to 55-days old were analyzed to classify EF and LF chicks. We also performed PCR analysis using K-specific gene primers to confirm the agreement between the phenotypes and genotypes of EF and LF chickens. In the results, the EF chicks had long primaries and coverts, and there was a significant difference in length between primaries and coverts. The LF chicks had shorter primaries and coverts than the EF chicks, and showed little difference in the length between primaries and coverts. LF chicks could be classified into four groups: LF-Less, LF-Scant, LF-Equal and LF-Reverse according to their wing feather patterns. EF chicks had 1.5 times longer primaries than LF chicks until they were 15-days old, but the lengths were almost the same at 50-days old. The tail feathers of the EF chicks were apparent at 5-days old, but those of the LF chicks were short and indefinite at that time. When EF and LF chicks were classified by the length of primaries being more or less than 9 mm, the classification accuracies for EF and LF chicks were 96.2% and 85.4%, respectively, compared to the PCR results. In conclusion, juvenile EF and LF KNC showed distinct differences in feather development and morphology, and could be easily distinguished at one day-old.

• Journal of Gastric Cancer
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• v.4 no.2
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• pp.109-120
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• 2004

Purpose: Individual gastric cancers demonstrate complicated genetic alterations. The PCR-based analysis of polymorphic microsatellite sequences on cancer-related chromosomes has been used to detect chromosomal loss and microsatellite instability. For the purpose of preoperative usage, we analyzed the correspondance rate of the microsatellite genotype between endoscopic biopsy and surgical specimens. Materials and Methods: Seventy-three pairs of biopsy and surgical specimens were examined for loss of heterozygosity and microsatellite instability by using 40 microsatellite markers on eight chromosomes. Microsatellite alterations in tumor DNAs were classified into a high-risk group (baselinelevel loss of heterozygosity: 1 chromosomal loss in diffuse type and high-level loss of heterozygosity: 4 or more chromosomal losses) and a low-risk group (microsatellite instability and low-level loss of heterozygosity: 2 or 3 chromosomal losses in diffuse type or $1\∼3$ chromosomal losses in intestinal type) based on the extent of chromosomal loss and microsatellite instability. Results: The chromosomal losses of the biopsy and the surgical specimens were found to be different in 21 of the 73 cases, 19 cases of which were categorized into a genotype group of similar extent. In 100 surgical specimens, the high-risk genotype group showed a high incidence of nodal involvement (19 of 23 cases: $\leq$5 cm; 23 of 24 cases: >5 cm) irrespective of tumor size while the incidence of nodal involvement for the low-risk genotype group depended on tumor size (5 of 26 cases: $\leq$5 cm; 18 of 27 cases: >5 cm). Extraserosal invasion was more frequent in large-sized tumor in both the high-risk genotype group ($\leq$5 cm: 12 of 23 cases; >5 cm: 23 of 24 cases) and the low-risk genotype group ($\leq$5 cm: 7 of 26 cases; >5 cm: 16 of 27 cases). The preoperative prediction of tumor invasion and nodal involvement based on tumor size and genotype corresponded closely to the pathologic tumor stage (ROC area >0.7). Conclusion: An endoscopic biopsy specimen of gastric cancer can be used to make a preoperative genetic diagnosis that accurately reflect the genotype of the corresponding surgical specimen.

• Childhood Kidney Diseases
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• v.5 no.1
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• pp.43-50
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• 2001

Purpose : The urinary tract infection associated with vesicoureteral reflux(VUR) in children may result in serious complications such as renal scarring, hypertension, proteinuria and end stage renal disease. The purpose of this study was to evaluate the factors affecting renal scar such as age, gender, grade of VUR, and ACE gene polymorphism, and body growth in the patients with and those without renal scar associated with VUR Methods : During the period from January 1994 to July 2000, We had 93 children with urinary tract infection associated with VUR who were admitted to the Department of pediatrics of Chonbuk National University Hospital. The patients were divided into two groups according to follow up 99mTc-DMSA renal scan; patients with renal scar group and those with non-scar group. We analyzed and compared the factors associated with renal scarring between the two groups. Results : There were no significant difference in gender, causative organism, ACE gene polymorphism, height and weight at diagnosis between renal scar group and non-scar group. Fifty four patients were in renal scar group and forty seven of them had VUR. The age at diagnosis was significantly higher in renal scar group (2.48${\pm}$2.64yr) than in non renal scar group (1.26${\pm}$1.83yr). Especially, the infants who were less than 1 year of age with VUR developed relatively more renal scar compared with infants older than 1 tear of age. The incidence of renal scarring showed a direct correlation with the severity of VUR. Conclusion : The factors affecting renal scar formation were age at diagnosis, presence and grade of VUR, but the other factors such as gender, causative organism, ACE gene polymorphism were not associated with renal scarring. Therefore, further evaluation about uropathogenic E coli and foflow up study about body growth associated with severity of renal scar would be necessary. (J. Korean Soc Pediatr Nephrol 5 : 43- 50, 2001)

• Clinical and Experimental Pediatrics
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• v.48 no.8
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• pp.871-876
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• 2005

Purpose : Recently, it was reported that tumor necrosis factor(TNF) and $lymphotoxin-{\alpha}$($LT-{\alpha}$) gene regions might be a susceptible loci to type 1 diabetes in Japanese. The purpose of this study was to investigate the association of TNF and $LT-{\alpha}$ gene polymorphisms with disease susceptibility in Korean children with type 1 diabetes. Methods : Forty-nine Korean children with type 1 diabetes(29 girls and 20 boys) and 94 healthy Koreans were investigated in this study. Genotyping for -857T/C polymorphism in the TNF promoter region and $LT-{\alpha}$ gene polymorphism were performed by PCR-RFLP(restriction fragment length polymorphism). TNF promoter -1031C/T polymorphism was detected by allele-specific PCR. Results : The distribution of the -857T/C and -1031C/T genotype in the TNF promoter region was not different between diabetic children and the controls. The frequency of TT genotype in the distribution of TNF -1031C/T polymorphism in diabetic children with diabetic ketoacidosis(DKA) at diagnosis was significantly lower than those without DKA(P<0.05). No significant difference in the distribution of $LT-{\alpha}$ gene polymorphism was observed between diabetic children and the controls. There was no association between clinical characteristics of type 1 diabetes and $LT-{\alpha}$ gene polymorphisms. Conclusion : These results suggest that TNF promoter -857T/C and $LT-{\alpha}$ gene polymorphisms are not associated with susceptibility to type 1 diabetes in Korean children. TNF promoter -1031C/T polymorphism might be related to clinical manifestations(DKA) of type 1 diabetes.

• Journal of Life Science
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• v.26 no.8
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• pp.904-910
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• 2016

Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The gene network analysis has been performed by diverse types of methods such as gene co-expression, gene regulatory relationships, protein-protein interaction (PPI) and genetic networks. Moreover, the network-based methods were described for predicting gene functions such as graph theoretic method, neighborhood counting based methods and weighted function. However, there are a limited number of researches in livestock. The present study systemically analyzed genes associated with 102 types of economic traits based on the Animal Trait Ontology (ATO) and identified their relationships based on the gene co-expression network and PPI network in cattle. Then, we constructed the two types of gene network databases and network visualization system (http://www.nabc.go.kr/cg). We used a gene co-expression network analysis from the bovine expression value of bovine genes to generate gene co-expression network. PPI network was constructed from Human protein reference database based on the orthologous relationship between human and cattle. Finally, candidate genes and their network relationships were identified in each trait. They were typologically centered with large degree and betweenness centrality (BC) value in the gene network. The ontle program was applied to generate the database and to visualize the gene network results. This information would serve as valuable resources for exploiting genomic functions that influence economically and agriculturally important traits in cattle.

• Korean Journal of Microbiology
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• v.50 no.4
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• pp.285-295
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• 2014

This study was conducted to survey the epidemiological characteristics and the isolated strains for pathogenic E. coli which was the major causative organisms for food poisoning occurred at school food services in the Gyeonggi-do area during the past three years. We investigated 19 accidents of food-borne disease outbreaks by pathogenic E. coli at school food services from 2010 to 2012. Food-borne disease outbreaks by pathogenic E. coli were usually occurred at direct management type (18 accidents, 95%) and high schools. For the seasonal factors, 13 accidents (65%) were occurred in June to September, especially the end of August and September after the summer holidays. The first patients were occurred on Wednesday (7 accidents, 37%) and Thursday (7 accidents, 37%), and they were mainly reported on Thursday (7 accidents, 37%) and Friday (5 accidents, 26%). The exposure of risk was estimated in Monday (4 accidents, 21%), Tuesday (7 accidents, 37%) and Wednesday (4 accidents, 21%), and kimchi (5 accidents, 50%) was estimated as the food of the high risk responsible for the outbreaks. 98 isolates of pathogenic E. coli consisted of PEC (50%), ETEC (34%), EAEC (15%), and EHEC (1%). The antibiotic resistance of pathogenic E. coli showed in the descending order of ampicilline (40%), nalidixic acid (37%), trimethoprim/sulfamethoxazole (24%), and tetracycline (19%). The antibiotics of second and third generation cephalosporins, cabarpenem, aminoglycosides, and second generation quinolones had antimicrobial susceptibilities and cefalotin, ampicillin/sulbactam and chloramphenicol showed medium resistance at 29%, 25%, and 6% respectively, and 70% of isolates were resistant to more than one antibiotic. By the PFGE analysis, they were classified into nine major groups and 31 profiles with 57% pattern similarity. It was very difficult to find the correlation of antimicrobial susceptibilities and genotype in the small scale-food poisoning, but the similarity of antimicrobial resistance and PFGE patterns in the large scale-food poisoning enabled the outbreaks to estimate the same pathotype of E. coli derived from identical origins.