• Journal of Gastric Cancer
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• 제12권2호
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• pp.73-80
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• 2012

Purpose: The specific aim of this study is to unravel a DNA copy number alterations, and to search for novel genes that are associated with the development of Korean gastric cancer. Materials and Methods: We investigated a DNA copy number changes in 23 gastric adenocarcinomas by array-comparative genomic hybridization and quantitative real-time polymerase chain reaction analyses. Besides, the expression of UQCRFS1, which shows amplification in array-CGH, was examined in 186 gastric cancer tissues by an immunohistochemistry, and in 9 gastric cancer cell lines, as well as 24 gastric cancer tissues by immunoblotting. Results: We found common gains at 48 different loci, and a common loss at 19 different loci. Amplification of UQCRFS1 gene at 19q12 was found in 5 (21.7%) of the 23 gastric cancers in an array-comparative genomic hybridization and DNA copy number were increased in 5 (20.0%) out of the 25 gastric cancer in quantitative real-time polymerase chain reaction. In immunohistochemistry, the overexpression of the protein was detected in 105 (56.5%) out of the 186 gastric cancer tissues. Statistically, there was no significant relationship between the overexpression of UQCRFS1 and clinicopathologic parameters (P>0.05). In parallel, the overexpression of UQCRFS1 protein was confirmed in 6 (66.7%) of the 9 gastric cancer cell lines, and 12 (50.0%) of the 24 gastric cancer tissues by immunoblotting. Conclusions: These results suggest that the overexpression of UQCRFS1 gene may contribute to the development and/or progression of gastric cancer, and further supported that mitochondrial change may serve as a potential cancer biomarker.

• 한국미생물·생명공학회지
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• 제19권6호
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• pp.575-582
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• 1991

글루타치온 생산증대를 도모하기 위하여 글루타치온 합성에 관여하는 효소들인 GSH-I 및 GSH-II 유전자들 pBR322 벡터에 클로닝하였다. gshI 유전자를 클로닝하기 위하여 GSH-I 효소활성이 결여된 GS903 균주를 분리하였다. E. coli K-12 염색체 DNA로부터 분리된 3.6Kb PstI DNA 절편을 pBR322 벡터에 클로닝하였다. gshII 유전자는 2.2Kb PstI-BamHI DNA 절편내에 존재하며 이 절편을 pUC13 벡터에 클로닝하였다. 플라스미드의 copy number와 gsh 유전자들을 포함하고 있는 삽입 DNA의 크기의 차이에 의한 gsh 유전자들의 발현 정도를 조사하기 위하여 pGH1090, pGH101, pGH200, pGH201, pLF4, pLF6 그리고 pGH300같은 여러 플라스미드를 사용함으로써 gshI 유전자의 발현이 의해 2배이상 증가하였다. 그러나 벡터 플라스미드내에 존재하는 gsh 유전자들을 포함하는 삽입 DNA의 크기의 차이에 의해서는 gsh 유전자들의 발현이 영향을 받지 않았다.

• Environmental Engineering Research
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• 제14권1호
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• pp.63-67
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• 2009

Escherichia coli K-12 (E. coli K-12) is a representative indicator globally used for distinguishing and monitoring dynamic fates of pathogenic microorganisms in the environment. This study investigated how to most critically quantify lacZ ($\beta$-galactosidase) gene in E. coli K-12 by two different real-time polymerase chain reaction (real-time PCR) in association with three different DNA extraction practices. Three DNA extractions, i.e., sodium dodecyl sulfate (SDS)/proteinase K, magnetic beads and guanidium thiocyanate (GTC)/silica matrix were each compared for extracting total genomic DNA from E. coli K-12. Among them, GTC/silica matrix and magnetic beads beating similarly worked out to have the highest (22-23 ng/${\mu}L$) concentration of DNA extracted, but employing SDS/proteinase K had the lowest (10 ng/${\mu}L$) concentration of DNA retrieved. There were no significant differences in the quantification of the copy numbers of lacZ gene between SYBR Green I qPCR and QProbe-qPCR. However, SYBR Green I qPCR obtained somewhat higher copy number as $1{\times}10^8$ copies. It was decided that GTC/silica matrix extraction or magnetic beads beating in combination with SYBR Green I qPCR can be preferably applied for more effectively quantifying specific gene from a pure culture of microorganism.

• Asian Pacific Journal of Cancer Prevention
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• 제15권4호
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• pp.1863-1869
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• 2014

The amplification of telomerase component (TERC) gene could play an important role in generation and treatment of haematological malignancies. This present study was aimed to investigate copy number amplification status of TERC gene in chronic myeloid leukaemia (CML) patients who were being treated with imatinib mesylate (IM). Genomic DNA was extracted from peripheral blood of CML-IM Resistant (n=63), CML-IM Respond (n=63) and healthy individuals (n=30). TERC gene copy number predicted (CNP) and copy number calculated (CNC) were determined based on $Taqman^{(R)}$ Copy Number Assay. Fluorescence in situ hybridization (FISH) analysis was performed to confirm the normal signal pattern in C4 (calibrator) for TERC gene. Nine of CML patients showed TERC gene amplification (CNP=3), others had 2 CNP. A total of 17 CML patients expressed CNC>2.31 and the rest had 2.31>CNC>1.5. TERC gene CNP value in healthy individuals was 2 and their CNC value showed in range 1.59-2.31. The average CNC TERC gene copy number was 2.07, 1.99 and 1.94 in CML-IM Resistant patients, CML-IM Respond and healthy groups, respectively. No significant difference of TERC gene amplification observed between CML-IM Resistant and CML-IM Respond patients. Low levels of TERC gene amplification might not have a huge impact in haematological disorders especially in terms of resistance towards IM treatment.

• 대한의생명과학회지
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• 제28권3호
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• pp.157-169
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• 2022

DNA typing is the typical technology in the forensic science and plays a significant role in the personal identification of victims and suspects. Short tandem repeat (STR) is the short tandemly repeated DNA sequence consisting of 2~7 bp DNA units in specific loci. It is disseminated across the human genome and represents polymorphism among individuals. Because polymorphism is a key feature of the application of DNA typing STR analysis, STR analysis becomes the standard technology in forensics. Therefore, the DNA database (DNA-DB) was first introduced with 4 essential STR markers for the application of forensic science; however, the number of STR markers was expanded from 4 to 13 and 13 to 20 later to counteract the continuously increased DNA profile and other needed situations. After applying expanded STR markers to the South Korean DNA-DB system, it positively affected to low copy number analysis that had a high possibility of partial DNA profiles, and especially contributed to the theft cases due to the high portion of touch DNA evidence in the theft case. Furthermore, STR marker expansion not only contributed to the resolution of cold cases but also increased kinship index indicating the potential for improved kinship test accuracy using extended STR markers. Collectively, the expansion of the STR locus was considered to be necessary to keep pace with the continuously increasing DNA profile, and to improve the data integrity of the DNA-DB.

• 한국미생물·생명공학회지
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• 제31권4호
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• pp.322-328
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• 2003

TAR(Transformation-Associated Recombination) cloning 법은 복잡한 고등생물의 게놈으로부터 유전자나 특정 염색체 부위를 선별적 분리를 가능하게 한다. 이 방법은 목적으로 하는 염색체 부위의 주변에 존재하는 비교적 짧은 게놈 염기서열에 대한 정보를 필요로 하며, spheroplast 형질전환 과정에서 게놈 DNA와 5'-와 3'-표적배열을 지닌 TAR vector 사이에서 일어나는 상동성 재조합과정에 의해 이루어진다. 본 연구에서는 single-copy 유전자의 클론닝에 필요한 specific hook의 최소 크기를 조사하였고, 서로 다른 TAR vector(radial과 unique vector)의 유용성을 조사하기 위해 동일한 single-copy 유전자의 클론닝을 통해 비교하였다. 그 결과, hHPRT 유전자에 대한 TAR cloning의 빈도는 hook의 길이가 750 bp∼63 bp의 범위에서 동일하게 나타났다. radial hook을 사용한 경우보다 unique hook을 사용하였을 경우 형질전환체의 수는 약 20배정도의 감소를 보였으나 목적으로 하는 재조합체의 분리 빈도는 두 배 이상 증가하였다. 그러므로 본 연구에서 two-unique TAR vector는 선별력이 높으므로 일반적 TAR cloning에 사용할 수 있으며, radial TAR vector의 경우는 병리학적 표본과 같이 제한된 게놈 DNA를 사용하는 경우에 더 적합하다고 볼 수 있다. 또한, single-copy 유전자의 분리에 필요로 하는 specific hoot의 최소 길이는 약 60 bp로도 가능하다는 것을 확인하였다.

• Genomics & Informatics
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• 제18권1호
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• pp.3.1-3.8
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• 2020

Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic survey with a large number of cases is yet missing in lung cancer. Here we report the comparison of genomic characters between mouse and patient tumor tissues in lung cancer based on exome sequencing data. We established PDX mouse models for 132 lung cancer patients and performed whole exome sequencing for trio samples of tumor-normal-xenograft tissues. Then we computed the somatic mutations and copy number variations, which were used to compare the PDX and patient tumor tissues. Genomic and histological conclusions for validity of PDX models agreed in most cases, but we observed eight (~7%) discordant cases. We further examined the changes in mutations and copy number alterations in PDX model production and passage processes, which highlighted the clonal evolution in PDX mouse models. Our study shows that the genomic characterization plays complementary roles to the histological examination in cancer studies utilizing PDX mouse models.

• ALGAE
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• 제32권3호
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• pp.189-197
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• 2017

To quantify the abundance of the harmful dinoflagellate Cochlodinium polykrikoides in natural seawaters, we developed the innovative procedure using a droplet digital PCR (ddPCR) with C. polykrikoides-specific primers targeting the internal transcription sequence (ITS). The abundance of C. polykrikoides was estimated by the specific copy number of target ITS DNA segments per cell in cultures and natural water samples. The copy number per C. polykrikoides cell as acquired by ddPCR was $157{\pm}16$, which was evaluated against known cell numbers through a simplified protocol preparing DNAs. The abundances of C. polykrikoides in the waters of different locations estimated by ddPCR agreed with the number of cells visually counted under a microscope. This protocol was used to measure the abundance of C. polykrikoides close to and further off the southern coast of Korea in August of 2016 and 2017. The practical application showed that this method can reduce time for analysis and increase accuracy.

• Journal of Periodontal and Implant Science
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• 제48권4호
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• pp.261-271
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• 2018

Purpose: Few studies have examined periodontal pathogens from saliva samples in periodontally healthy young adults. The purposes of this study were to determine the prevalence of periodontopathic bacteria and to quantify periodontal pathogens in saliva samples using real-time polymerase chain reaction (PCR) assays in periodontally healthy Korean young adults under 35 years of age. Methods: Nine major periodontal pathogens were analyzed by real-time PCR in saliva from 94 periodontally healthy young adults. Quantification of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Prevotella intermedia, Fusobacterium nucleatum, Campylobacter rectus, Peptostreptococcus anaerobius, and Eikenella corrodens was performed by DNA copy number measurement. Results: F. nucleatum and E. corrodens were detected in all subjects; the numbers of positive samples were 87 (92.6%), 91 (96.8%), and 90 (95.7%) for P. gingivalis, P. anaerobius, and C. rectus, respectively. Other pathogens were also detected in periodontally healthy subjects. Analysis of DNA copy numbers revealed that the most abundant periodontal pathogen was F. nucleatum, which was significantly more prevalent than all other bacteria (P<0.001), followed by P. anaerobius, P. gingivalis, E. corrodens, C. rectus, and T. denticola. There was no significant difference in the prevalence of each bacterium between men and women. The DNA copy number of total bacteria was significantly higher in men than in women. Conclusions: Major periodontal pathogens were prevalent in the saliva of periodontally healthy Korean young adults. Therefore, we suggest that the development of periodontal disease should not be overlooked in periodontally healthy young people, as it can arise due to periodontal pathogen imbalance and host susceptibility.

• 한국미생물·생명공학회지
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• 제16권6호
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• pp.476-483
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• 1988

효모 유전자 운반체의 유형을 특징지우는 ARS1 (autonomous replicating sequence), CEN3 (centromere), 2 $\mu$m OR (yeast plasmid의 origin of replication)의 DNA 절편을 재조합하여 만든 유전자 운반체들의 형질전환력, 안정도 및 운반체 수를 효모균주 SHY4(cir$^+$)와 NNY1(cir$^{\circ}$)에서 비교 조사하였다. CEN3를 갖는 유전자 운반체는 매우 안정하나 세포당 수가 하나로 매우 낮으며 2 $\mu$m OR과 ARS1 을 동시에 갖는 유전자 운반체는 안정할 뿐만 아니라 세포당 수도 높으며 균주내에 존재하는 2 $\mu$m 플라스미드는 2 $\mu$m OR을 가지는 유전자 운반체의 복제에 영향을 준다는 사실을 알 수 있었다.