• Fisheries and Aquatic Sciences
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• 제18권2호
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• pp.183-193
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• 2015

Several transgenic marine medaka Oryzias dancena strains harboring a green fluorescent protein (GFP) reporter construct regulated by an endogenous ${\beta}$-actin promoter were established and their expression characteristics in relation to transgene copy numbers were examined in 21 transgene genotypes. Most of the transgenic strains displayed transgene insertion patterns typical of microinjection-mediated introduction of foreign DNA into fish embryos, characterized by the random integration of multiple transgene copies (ranging from 1 - 282 copies per cell), often accompanied by the formation of concatemer(s), as assessed by genomic Southern blot hybridization analysis and qPCR. Transgenic strains showed ubiquitous and continued temporal and spatial expression patterns of the transgenic GFP during most of their life cycle, from the embryonic stage to adulthood, enabling assessment of the expression pattern of the endogenous ${\beta}$-actin gene. However, a comparative evaluation of transgene copy numbers and expression levels showed that copy number-dependent expression, the stability of the ubiquitous distribution and expression efficiency per transgene copy varied among the transgenic strains. Fluorescence expression levels were positively correlated with absolute transgene copy numbers, whereas the expression efficiency per transgene copy was inversely related to the number of transgene integrant copies. Data from this study will guide the selection of potentially desirable transgenic strains with ubiquitous expression of a fluorescent transgene, not only in this marine medaka species but also in other related model fish species.

• 한국미생물·생명공학회지
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• 제47권2호
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• pp.296-302
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• 2019

In this study, the effects of ammonium concentration ($117.5-1155.0mg-N{\cdot}l^{-1}$), nitrite concentration ($0-50.0mg-N{\cdot}l^{-1}$), and temperature ($15-35^{\circ}C$) on nitrification performance and its functional genes (amoA-arc, amoA-bac, hao) in an enriched consortium inoculated with humic acid were determined. Notably, the maximum nitrification rate value was observed at $315mg-N{\cdot}l^{-1}$ of ammonium, but the highest functional gene copy numbers were obtained at $630mg-N{\cdot}l^{-1}$ of ammonium. No inhibition of the nitrification rate and functional gene copy numbers was observed via the added nitrites. The optimum temperature for maximum nitrification performance was observed to be $30^{\circ}C$. The amoA-bac copy numbers were also greater than those of amoA-arc under all test conditions. Notably, amoA-arc copy numbers and nitrification efficiency showed a positive relationship in network analysis. These results indicate that ammonium-oxidizing archaea and bacteria play important roles in the nitrification process.

• Asian-Australasian Journal of Animal Sciences
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• 제24권11호
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• pp.1552-1559
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• 2011

Real time PCR was used in this study to determine the effect of triticale dried distillers grains with solubles (TDDGS) as a replacement for grain or barley silage in finishing diets on the presence of six classical ruminal bacterial species (Succinivibrio dextrinosolvens, Selenomonas ruminantium, Streptococcus bovis, Megasphaera elsdenii, Prevotella ruminicola and Fibrobacter succinogenes) within the rumen contents of feedlot cattle. This study was divided into a step-wise adaptation experiment (112 days) that examined the effects of adaptation to diets containing increasing levels of TDDGS up to 30% (n = 4), a short-term experiment comparing animals (n = 16) fed control, 20%, 25% or 30% TDDGS diets over 28 days, and a rapid transition experiment (56 days) where animals (n = 4) were rapidly switched from a diet containing 30% TDDGS to a barley-based diet with no TDDGS. It was found that feeding TDDGS as replacement for barley grain (control vs. 20% TDDGS) decreased 16S rRNA copy numbers of starch-fermenting S. ruminantium and S. bovis (p<0.001 and p = 0.04, respectively), but did not alter 16S rRNA copy numbers of the other rumen bacteria. Furthermore, feeding TDDGS as a replacement barley silage (20% vs. 25% and 30% TDDGS) increased 16S rRNA copy numbers of S. ruminantium, M. elsdenii and F. succinogenes (p<0.001; p = 0.03 and p<0.001, respectively), but decreased (p<0.001) the 16S rRNA copy number of P. ruminicola. Upon removal of 30% TDDGS and return to the control diet, 16S rRNA copy numbers of S. ruminantium, M. elsdenii and F. succinogenes decreased (p = 0.01; p = 0.03 and p = 0.01, respectively), but S. dextrinosolvens and S. bovis increased (p = 0.04 and p = 0.009, respectively). The results suggest that replacement of TDDGS for grain reduces 16S rRNA copy numbers of starch-fermenting bacteria, whereas substitution for barley silage increases 16S rRNA copy numbers of bacteria involved in fibre digestion and the metabolism of lactic acid. This outcome supports the contention that the fibre in TDDGS is highly fermentable.

• 생명과학회지
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• 제31권12호
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• pp.1057-1065
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• 2021

위암 환자에서 미토콘드리아 DNA (mtDNA)의 양적 변화가 보고 되고 있으며 이러한 변화가 위암의 발암이나 진행에 관여되는 것으로 추정되고 있다. 그리나 위암에서 미토콘드리아 단백질이나 mtDNA에 의해 암호화된 산화적 인산화(OXPHOS) 단백질의 양적 변화에 관한 연구는 아직까지 미비한 실정이다. 본 연구에서는 위암환자 조직 및 세포주를 이용하여 mtDNA 양 그리고 미토콘드리아 단백질 및 OXPHOS 단백질의 양을 분석하였다. 또한, mtDNA 양적 변화와 위암 환자의 임상병리학적 특징을 연관 분석하였다. MtDNA 양을 분석하기 위하여 qPCR 기법을 그리고 단백질 분석에는 Western blot 기법을 각각 활용하였다. 총 27개의 위암 환자 샘플에서 약 80%에 해당하는 22개의 환자 위암조직에서 정상조직에 비해 mtDNA 양이 감소하였으며, 나머지 환자에서는 mtDNA 양이 증가하였다. 이러한 mtDNA 양이 감소한 위암 조직 샘플에서는 미토콘드리아 단백질 및 OXPHOS 단백질의 양도 같이 감소하였다. 한편, 본 연구에 사용된 총 5개의 위암 세포주 모두에서 mtDNA 양이 감소하였다 그러나 위암 세포주에서는 mtDNA 양적 감소와 미토콘드리아 단백질 및 OXPHOS 단백질의 양적 감소가 항상 일치하지는 않았다. 이러한 연구결과는 위암 조직 및 세포주에서 mtDNA 양의 감소가 흔하며 이는 mtDNA 양적 변화가 위암의 생성에 관여함을 제시한다.

• 한국미생물·생명공학회지
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• 제42권1호
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• pp.32-40
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• 2014

본 연구에서는 도심 학교 운동장(soil A)과 화단(soil B, C, & D)에서 채취한 토양의 잠재적인 메탄 산화 및 생성능을 평가하였다. 토양 원시료 중 메탄 산화균 수를 정량 분석한 결과, 운동장 토양(soil A)는 $6.1{\times}10^3$ gene copy number/g dry weight soil이었으나, 화단 토양(soil B~D)는 $1.6-1.9{\times}10^5$ gene copy number/g dry weight soil이었다. 토양을 넣은 혈청병에 메탄 가스를 주입하여 잠재 메탄 산화능을 평가한 결과, 운동장 토양은 다른 토양보다 메탄을 산화하기까지 긴 유도기를 보였으나, 유도기 이후에는 화단 토양과 거의 유사한 메탄 산화능을 나타냈다. 또한 운동장 토양의 메탄 산화균 수는 $2.3{\times}10^7$ gene copy number/g dry weight soil까지 증가하여 화단 토양의 메탄 산화균 수($1.2-2.8{\times}10^8$ gene copy number/g dry weight soil)과 유의적 차이를 보이지 않았다. 교정에서 채취한 토양의 메탄 생성 거동도 메탄 산화와 유사한 패턴을 보였다. 토양 원시료의 메탄 생성균 수는 화단 토양($1.3-3.4{\times}10^7$ gene copy number/g dry weight soil)에 비해 운동장 토양($1.7{\times}10^5$ gene copy number/g dry weight soil)이 훨씬 적었다. 그러나 토양에 유기물을 첨가한 후 메탄 생성 현상이 발휘된 후에는 메탄 생성 균수는 운동장 토양과 화단토양 모두 $10^7$ gene copy number/g dry weight soil 수준이었다. 본 연구를 통해 도심 교정에서 채취한 네 종류의 토양은 모두 메탄 산화균 및 생성균을 가지고 있으며, 메탄 산화와 생성에 적합한 조건이 되면, 메탄 산화균 및 생성균의 개체군이 증가하여 메탄을 산화하거나 생성할 수 있는 잠재력을 지니고 있음을 알 수 있었다.

• Genomics & Informatics
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• 제8권2호
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• pp.76-80
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• 2010

Although autism spectrum disorder (ASD) has been thought to have a substantial genetic background, major contributing genes have yet to be identified or successfully replicated. Immunological dysfunction has been suggested to be associated with ASD, and T cell-mediated immunity was considered important for the development of ASD. In this study, we analyzed 163 ASD subjects and 97 normal controls by genomic quantitative PCR to evaluate the association between the copy number variation of the 7q34 locus, harboring the TCRB gene, and ASDs. As a result, there was no significant difference of the frequency distribution of TCRB copy numbers between ASD cases and normal controls. TCRB gene copy numbers ranged from 0 to 5 copies, and the frequency distribution of each copy number was similar between the two groups. The proportion of the individuals with <2 copies of TCRB was 52.8% (86/163) in ASD cases and 57.1% (52/91) in the control group (p=0.44). The proportion of individuals with >2 copies of TCRB was 11.7% (19/163) in ASD cases and 12.1% (11/91) in the control group (p=0.68). After the effects of sex were adjusted by logistic regression, ORs for individuals with <2 copies or >2 copies showed no significant difference compared with the diploid copy number as reference (n=2). Although we could not see the positive association, our results will be valuable information for mining ASD-associated genes and for exploring the role of T cell immunity further in the pathogenesis of ASD.

• Environmental Engineering Research
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• 제20권1호
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• pp.51-57
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• 2015

As expected, the expression of denitrifying genes in a Typha wetland (relatively stagnant compared to other ponds), showing higher nitrogen removal efficiency in summer, was affected by temperature. The abundance and gene transcripts of nitrate reductase (narG), nitrite reductase (nirS), nitric oxide reductase (norB), and nitrous oxide reductase (nosZ) genes in seasonal sediment samples taken from the Acorus and Typha ponds of free surface flow constructed wetlands were investigated using quantitative polymerase chain reaction (Q-PCR) and quantitative reverse transcription PCR (Q-RT-PCR). Denitrifying gene copy numbers ($10^5-10^8$ genes $g^{-1}$ sediment) were found to be higher than transcript numbers-($10^3-10^7$ transcripts $g^{-1}$ sediment) of the Acorus and Typha ponds, in both seasons. Transcript numbers of the four functional genes were significantly higher for Typha sediments, in the warm than in the cold season, potentially indicating greater bacterial activity, during the relatively warm season than the cold season. In contrast, copy numbers and expression of denitrifying genes of Acorus did not provide a strong correlation between the different seasons.

• 한국CDE학회논문집
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• 제13권4호
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• pp.273-285
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• 2008

In this paper we propose an engineering bill of materials (E-BOM) copy method that can be utilized to manage the product information for each equipment during building a product lifecycle management (PLM) system in the order-specific semiconductor equipment manufacturer. The previous works studied on an E-BOM creation and management method for the mass manufacturing and production. The method is difficult to apply to an environment in which many engineering changes occur and the different specification to each equipment is required such as semiconductor equipments and facilities adopting built-to-order instead of built for inventory. Moreover the method is known to be the major drawback to deteriorate the design efficiency. Our E-BOM copy method enables users efficiently to manage the specification of a product and shortens the product development cycle. To implement the E-BOM copy method in the PLM environment, we developed the E-BOM copy system that automatically generates new parts and their numbers according to the numbering rule while copying the E-BOM from existing semiconductor equipments and then can apply the parts for reuse to new semiconductor equipments. This system can duplicate not only 3D CAD data but also technical documents.

• Asian Pacific Journal of Cancer Prevention
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• 제13권12호
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• pp.6101-6104
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• 2012

Background: Breast cancer accounts about one million from total annual ten million new diagnosed cases of neoplasia worldwide and is the main cause of death due to cancer in women. Tamoxifen is the most popular selective estrogen receptor modulator used in anti estrogen treatments. Tamoxifen must be converted into its metabolite endoxifen for biologic effects; this conversion process is catalysed by highly polymorphic cytochrome P450 2D6 (CYP2D6). This study surveyed copy number variation of the CYP2D6 gene and its possible correlation with Tamoxifen resistance in breast cancer patients. Methods: This case control study was performed on samples taken from 79 patients with breast cancer who used tamoxifen in Yazd and Tehran Cities, Iran. Real time reactions were conducted for 10 healthy samples using the comparative $C_t$ (Cycles threshold) method, each pair of genes being compared and samples with ratios around 1 were taken as control samples. Proliferation reactions were done by Real-Time PCR ABI Prism 7500. All registered data were transformed into SPSS 15 program and analyzed. Results: Efficiency of PCR for both CYP2D6 and ALB genes was 100%. From all 23 drug resistant patients 21.7% had one copy, 47.8% two copies and 30.4% had three copies. Also from all 56 drug sensitive patients, 26.8% had one copy, 51.8% two copies and 21.4% had three copies. The percentage of patients with one and two copies was similar between two groups but patients with three copies were more likely to belong to the drug resistant group more. Odd ratios for one and two copies were 0.759 and 0.853 respectively, indicating possible protective effects while that for three copies was 1.604. Conclusions: Based on our study there is no significant link between CYP2D6 gene copy numbers and tamoxifen resistance in women with breast cancer. But more studies considering other influencing factors appear warranted.

• Journal of Animal Science and Technology
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• 제65권4호
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• pp.767-778
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• 2023

The aim of the research is to identify that porcine oocytes can function as recipients for interspecies cloning and have the ability to develop to blastocysts. Furthermore each mitochondrial DNA (mtDNA) in interspecises cloned embryos was analyzed. For the study, mouse-porcine and porcine-porcine cloned embryos were produced with mouse fetal fibroblasts (MFF) and porcine fetal fibroblasts (PFF), respectively, introduced as donor cells into enucleated porcine oocytes. The developmental rate and cell numbers of blastocysts between intraspecies porcine-porcine and interspecies mouse-porcine cloned embryos were compared and real-time polymerase chain reaction (PCR) was performed for the estimate of mouse and porcine mtDNA copy number in mouse-porcine cloned embryos at different stages.There was no significant difference in the developmental rate or total blastocyst number between mouse-porcine cloned embryos and porcine-porcine cloned embryos (11.1 ± 0.9%, 25 ± 3.5 vs. 10.1 ± 1.2%, 24 ± 6.3). In mouse-porcine reconstructed embryos, the copy numbers of mouse somatic cell-derived mtDNA decreased between the 1-cell and blastocyst stages, whereas the copy number of porcine oocyte-derived mtDNA significantly increased during this period, as assessed by real-time PCR analysis. In our real-time PCR analysis, we improved the standard curve construction-based method to analyze the level of mtDNA between mouse donor cells and porcine oocytes using the copy number of mouse beta-actin DNA as a standard. Our findings suggest that mouse-porcine cloned embryos have the ability to develop to blastocysts in vitro and exhibit mitochondrial heteroplasmy from the 1-cell to blastocyst stages and the mouse-derived mitochondria can be gradually replaced with those of the porcine oocyte in the early developmental stages of mouse-porcine cloned embryos.