• Korean Journal of Microbiology
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• v.32 no.2
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• pp.115-119
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• 1994

Replication control region of pSBK203, a chloramphenicol acetyltransferase conferring plasmid from Staphylococus aureus was cloned and its nucleotide sequence has been determined. Base sequence homology of this copy control region with those of plasmids belonging to pT181 family was obtained and analyzed. Copy number of four copy mutants derived by addtion or deletion of nucleotides in unique XbaI recognition site in copy control region of pSBK203 was also determined.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.1
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• pp.225-229
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• 2012

Background: Males have a higher prevalence of hepatocellular carcinoma (HCC) than females in general, but the reasons for the sex disparity are still obscure. DNA copy number alteration (CNA) is a major feature of solid tumors including HCC, but whether CNA plays a role in sex-related differences in HCC development has never been evaluated. Methods: High-resolution array comparative genomic hybridization (CGH) was used to examine 17 female and 46 male HCC patients with chronic hepatitis B virus (HBV) infection in Shanghai, China. Two-tailed Fisher's exact or ${\chi}^2$ tests was used to compare CNAs between females and males. Results: The overall frequencies and patterns of CNAs in female and male cases were similar. However, female HCC tumors presented more copy number gains compared to those in males on 1q21.3-q22 (76.5% vs. 37.0%, P = 0.009), 11q11 (35.3% vs. 0.0%, P = 0.0002) and 19q13.31-q13.32 (23.5% vs. 0.0%, P = 0.004), and loss on 16p11.2 (35.3% vs. 6.5%, P = 0.009). Relative to females, male cases had greater copy number loss on 11q11 (63.0% vs. 17.6%, P = 0.002). Further analyses showed that 11q11 gain correlated with 19q13.31-q13.32 gain (P = 0.042), 11q11 loss (P = 0.011) and 16p11.2 loss (P = 0.033), while 1q21.3-q22 gain correlated with 19q13.31-q13.32 gain (P = 0.046). Conclusions: These findings suggest that CNAs may play a role in sex-related differences in HBVassociated HCC development.

• Korean Journal of Poultry Science
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• v.41 no.4
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• pp.305-311
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• 2014

Copy number variation (CNV) is a form of structural variation that shows various numbers of copies in segments of the DNA. It has been shown to account for phenotypic variations in human diseases and agricultural production traits. Currently, most of chicken breeds in the poultry industry are based on European-origin breeds that have been mostly provided from several international breeding companies. Therefore, National Institute of Animal Science, RDA has been trying to restore and improve Korean native chicken breeds (12 lines of 5 breeds) for about 20 years. Thanks to the recent advance of sequencing technologies, genome-wide CNV can be accessed in the higher resolution throughout the genome of species of interest. However, there is no systematic study available to dissect the CNV in the native chicken breed in Korea. Here, we report genome-wide copy number variations identified from a genome of Korean native chicken (Line L) by comparing between the chicken reference sequence assembly (Gallus gallus) and a de novo sequencing assembly of the Korean native chicken (Line L). Throughout all twenty eight chicken autosomes, we identified a total of 501 CNVs; defined as gain and loss of duplication and deletion respectively. Furthermore, we performed gene ontology (GO) analysis for the putative CNVs using DAVID, leading to 68 GO terms clustered independently. Of the clustered GO terms, genes related to transcription and gene regulation were mainly detected. This study provides useful genomic resource to investigate potential biological implications of CNVs with traits of interest in the Korean native chicken.

• Korean Journal of Organic Agriculture
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• v.23 no.4
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• pp.847-858
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• 2015

Bacillus amyloliquefaciens GR4-5 was isolated from the rhizosphere soil of Korean ginseng and displayed broad-spectrum suppression of ginseng root rot pathogens. The survivability of B. amyloliquefaciens GR4-5 in soil was investigated under three different conditions; indoor, outdoor - of which soil was put in 14 mL tube after treatment - and field environments. Soil samples were collected over a four-week period from three experimental designs, and assessed for 16S rRNA gene copy number by quantitative polymerase chain reaction (qPCR). In outdoor condition, the 16S rRNA gene copy number of Bacillus spp. was 8.35 log copies g $soil^{-1}$ immediately after the GR4-5 treatment. Two weeks later, the 16S rRNA gene copy number of Bacillus spp. (6.70 log copies g $soil^{-1}$) was similar to that of the control (6.38 log copies g $soil^{-1}$). In indoor condition, the 16S rRNA gene copy number of Bacillus spp. maintained in a certain level for a longer period than those in outdoor and field. The 16S rRNA gene copy number of Bacillus spp. in field experiment was reduced faster than that of outdoor condition. Our results show that B. amyloliquefaciens GR4-5 can survive in bulk soil for 1 week, indicating its potential use as a biocontrol agent following 7 day application intervals. This study presents that outdoor microcosm system design could be a useful method to assess easily the survivability of beneficial microorganisms.

• Journal of Aquaculture
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• v.11 no.4
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• pp.457-463
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• 1998

An expression vector, pUC19N6-luc, containing nuclear matrix attachment region(MAR) isolated from Misgurnus mizolepis liver and control expressino vector, pUC19-luc, were constructed. After these vectors were transferred into CHSE-214 cell line by electroporation, the expression rate of luckferase gens, copy number of vectors and chromosome integration of vectors were analyzed by using assay of luciferase activity, PCR and Southern blotting. While the expression pattern of luciferase gene of pUC19-luc was shown in typicla transient ecpression pattern, that of pUC19N6-luc was highly increased at the 5 days after transfectrion. Although the cope number of pUC19N6-luc vector was higher than that of pUC19-luc vector, these vectors were integrated into chromosome at the same time point in the transfected CHSE-214 cells. In conclusion, the increase of luciferase gene expression of pUC19N6-luc was resulted from not the maintaining of the high copy number but the formation of transcription-favorable structure by MAR effect after chromosomal integration.

• Journal of fish pathology
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• v.34 no.2
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• pp.161-168
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• 2021

Quantitative analysis of myxosporean parasites (Enteromyxum leei and Parvicapsula anisocaudata) were performed using real-time PCR on the internal organs (head kidney, body kidney, intestine, spleen, brain, liver, heart, muscle, blood, and eye) of emaciated Paralichthys olivaceus from farm-A. The highest DNA copy number of E. leei was shown in the intestine (1.3 × 10⁸ copies/mg tissue) of emaciatied P. olivaceus and DNA copy number in the other internal organs (1.3 × 10³~4.6 × 10⁵ copies/mg tissue) showed lower than in intestine. From the result of real-time PCR for P. anisocaudata, it was considered mildly infected, due to the low DNA copy numbers of the head kidney (1.3 × 10³ copies/mg tissue) and body kidney (9.1 × 10³ copies/mg tissue). In order to investigate whether myxosporean parasites can be detected in a non-invasive way, quantitative analysis of E. leei and P. anisocaudata from rearing water of three farms were performed by real-time PCR. The DNA copy number of E. leei from rearing water of farm-A and farm-B were 8 × 10⁴ and 5 × 10⁵ copies/L, respectively. However, it was not detected in farm-C. For P. anisocaudata from rearing water, farm-A, farm-B and farm-C showed 0, 2.0 × 10⁶ and 5.1 × 10⁶ copies/L, respectively.

• Journal of fish pathology
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• v.36 no.2
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• pp.229-238
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• 2023

In this study, the correlation between clinical changes and RSIV genome copy number was investigated to determine the quantitative criteria for the characteristics of RSIV infection. The rock bream (Oplegnathus fasciatus) was intraperitoneally injected with three different doses (1.0×10¹, 1.0×10³ and 1.0×10⁵ viral genome copies/fish) as low, medium, and high doses, respectively. The clinical signs (spleen enlargement, death) observation and real-time PCR were conducted at 5, 10 and 14 days post-injection. During the experiment, spleen index as a quantitative indicator for spleen enlargement was continuously increased in the medium- (up to 2.26) and high-dose (up to 4.99) challenge groups, respectively. Notably, when the spleen index was over 1.5, 2.0, 2.5 and 3.0, a positive correlation was revealed with average viral genome copy numbers of 2.51, 3.37, 4.97 and 5.43×10⁷ viral genome copies/mg, respectively. Moreover, the threshold of spleen index over 1.5 was 1.0×10⁶ viral genome copies/mg, while the thresholds of spleen index over 2.0 and dead was 2.51×10⁷ viral genome copies/mg and the thresholds of spleen index over 2.5 and 3 was 3.98×10⁷ viral genome copies/mg. These findings suggest the possibility of quantitatively analyzing the characteristics and development process of RSIV infection.

• Journal of Korean society of Dental Hygiene
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• v.20 no.5
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• pp.743-752
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• 2020

Objectives: The objectives of this study were to investigate the distribution and level of periodontopathic bacteria with the general characteristics and oral health condition of the elderly. Methods: A total of 335 elderly individuals aged 65 years or older who lived in Ganghwa-gun, Incheon, were included in the study. Oral examination, investigation through a questionnaire, and collection of saliva were carried out. The collected saliva was analyzed for the distribution and levels of bacteria (red and orange complex bacteria) by real-time polymerase chain reaction. Statistical analyses were performed using chi-square test, t-test, one-way analysis of variance, and Pearson's correlation coefficient with SAS statistical software version 9.4. Results: Among the general characteristics, there were significant differences in the distribution of Porphyromonas gingivalis, Treponema denticola, and Parvimonas micra depending on sex, age, and dental visits (p<0.05). The number of remaining teeth and denture use were related to the distribution of periodontopathic bacteria, except T. denticola (p<0.05). Additionally, periodontitis was related to the distribution of P. gingivalis (p<0.05). As the number of remaining teeth increased, the copy number of red and orange complex bacteria also increased (p<0.05). Those individuals who did not use dentures and had periodontal disease had more periodontopathic bacteria (p<0.05). Conclusions: The distribution and copy number of periodontopathic bacteria in the elderly were more related to oral health condition than to general characteristics. In particular, the distribution and copy number of periodontopathic bacteria were higher in subjects with multiple remaining teeth, no dentures, and periodontal disease.

• The Korea Genome Conference
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• 2006.09a
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• pp.79-79
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• 2006

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1353-1358
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• 2005

A rapid and quantitative real-time PCR was developed to target the invasion A (invA) gene of Salmonella spp. We developed quantitative standard curves based on plasmids containing the invA gene. Based on these curves, we detected Salmonella spp. in artificially contaminated buffered peptone water (BPW) and milk samples. We were able to determine the invA gene copy number per ml of food samples, with the minimum detection limit of $4.1{\times}10^{3}$ copies/ml of BPW and $3.3{\times}10^{3}$ copies/ml of milk. When applied directly to detect and quantify Salmonella spp. in BPW and milk, the present real-time PCR assay was as sensitive as the plate count method; however, copy numbers were one to two logs higher than the colony-forming units obtained by the plate count methods. In the present work, the real-time PCR assay was shown to significantly reduce the total time necessary for the detection of Salmonella spp. in foods and to provide an important model for other foodborne pathogens.