• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.375.1-375.1
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• 2016

Polymerase chain reaction (PCR) has revolutionized genetics and become one of the most popular techniques in modern biological and medical sciences. It can be used not only as an in vitro DNA amplification method but also used in many bioassay applications. The PCR can be used to exponentially produce a large number of DNA copies from a small quantity of DNA molecules in a few hours. However, as unwanted DNA fragments are also often manufactured, the amplification efficiency of PCR is decreased. To overcome this limitation, several nanomaterials have been employed to increase the specificity of the PCR reaction. Recently, graphene has attracted a great interest for its excellent electron transfer, thermal and biocompatibility. Especially, gold nanoparticle-coated graphene oxide (GO/AuNPs) led to enhance electron and thermal transfer rate and low-charge transfer resistance. Therefore, we report the development of a demonstration for the PCR efficiency using a large-scale production of the GO and combination of gold nanoparticles. Because a thermal conductivity is an important factor for improving the PCR efficiency in different DNA polymerases and different size samples. When PCR use GO/AuNPs, the result of transmission electron microscopy and real-time quantitative PCR (qPCR) showed an enhanced PCR efficiency. We have demonstrated that GO/AuNPs would be simply outperformed for enhancing the specificity and efficiency of DNA amplification procedure.

• Journal of Environmental Health Sciences
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• v.23 no.1
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• pp.74-80
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• 1997

This study was performed to estimate the ozonation characteristics of phenol wastewater with increasing pH in the continuous packed column reactor (PCR) and the bubble column reactor (BCR). Among various influencing factors that affect phenol on decomposition through the ozonation, pH was chosen as reaction parameter. Upon increasing pH from 3 to 9, the phenol removal efficiency in PCR was improved approximately by 17% while in BCR approximately by 19.2%. The improvements in the phenol removal efficiency by increasing pH caused the enhancements in ozone utilization efficiency reaching almost 100% in PCR at pH 9. In conclusions, ozone has latent power for phenol wastewater treatment, and the performance of PCR was superior to that of BCR in the aspects of phenol removal and ozone utilization efficiency.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.471-479
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• 2017

White spot syndrome virus (WSSV) is a major threat to the shrimp farming industry and so far there is no effective therapy for it, and thus early diagnostic of WSSV is of great importance. However, at the early stage of infection, the extremely low-abundance of WSSV DNA challenges the detection sensitivity and accuracy of PCR. To effectively detect low-abundance WSSV, here we developed a pre-amplification PCR (pre-amp PCR) method to amplify trace amounts of WSSV DNA from massive background genomic DNA. Combining with normal specific PCR, 10 copies of target WSSV genes were detected from ${\sim}10^{10}$ magnitude of backgrounds. In particular, multiple target genes were able to be balanced amplified with similar efficiency due to the usage of the universal primer. The efficiency of the pre-amp PCR was validated by nested-PCR and quantitative PCR, and pre-amp PCR showed higher efficiency than nested-PCR when multiple targets were detected. The developed method is particularly suitable for the super early diagnosis of WSSV, and has potential to be applied in other low-abundance sample detection cases.

• Journal of Microbiology
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• v.41 no.4
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• pp.320-326
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• 2003

In order to identify Vibrio vulnificus in the Yellow Sea near Gunsan, Korea during the early and late summers, the efficiency of the real-time quantitative TaqMan PCR was compared to the efficiency of the conventional PCR and Biolog identification system^TM. Primers and a probe were designed from the hemolysin/cytolysin gene sequence of V. vulnificus strains. The number of positive detections by real-time quantitative TaqMan PCR, conventional PCR, and the Biolog identification system from seawater were 53 (36.8%), 36 (25%), and 10 strains (6.9%), respectively, among 144 samples collected from Yellow Sea near Gunsan, Korea. Thus, the detection method of the real-time quantitative TaqMan PCR assay was more effective in terms of accuracy than that of the conventional PCR and Biolog system. Therefore, our results showed that the real-time TaqMan probe and the primer set developed in this study can be applied successfully as a rapid screening tool for the detection of V. vulnificus.

• Genomics & Informatics
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• v.21 no.4
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• pp.52.1-52.10
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• 2023

Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.

• Journal of Environmental Health Sciences
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• v.21 no.2
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• pp.12-19
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• 1995

The objectives of this research prograln were to study the ozonation characteristics of phenol contaminated wastewater in the continuous packed column reactor (PCR) and the bubble column reactor (BCR) using ozone that has a strong oxidizing potential, and to provide the fundamentals of ozonizing the phenol contaminated wastewater. Among various influencing factors on phenol decomposition through the oxidation by ozone, phenol/ozone mde ratio was chosen as reaction parameters. Concerning the phenol/ozone mde ratio, as the influent phenol concentration increased from 30 mg/l to 150 mg/l, the phenol removal efficiency decreased from 99% for 30 mg/l to 83.7% for 150 mg/l, in PCR. PCR also showed higher treatment efficiency than BCR by 1% for 30 mg/l and 2.2% for 150 mg/l, respectively. The ozone utilization efficiency of PCR for the phenol concentration 30 mg/l was higher than that of BCR while the efficiency of both reactors was 99.9% for the phenol concentration of 150 mg/l.

• Journal of Environmental Health Sciences
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• v.22 no.1
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• pp.57-64
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• 1996

The main objectives of this research program were to study the ozonation characteristics of phenol wastewater in the continuous packed colamn reactor(PCR) and the bubble column reactor (BCR) using ozone and to provide the fundamentals of ozonizing the phenol wastewater. Among various influencing factors that affect on phenol decomposition through the oxidation by ozone, contacting method, and ozone flow rate were chosen as reaction parameters. The results were obtained from two different types of contacting methods where the countercurrent flow was more efficient than the cocurrent flow in both the phenol removal efficiency and the ozone utilization efficiency. Furthermore, PCR showed the phenol removal efficiency 1.6 to 3% higher than that of BCR in both contacting methods, as well as the ozone utilization efficiency, suggesting that the countercurrent flow is more efficient than the cocurrent flow. The phenol removal efficiency and the ozone utilization efficiency were reduced in both reactors as the influent ozone flow rate increased. Upon varing flow rate from 0.5l/min to 2.0 l/min by 0.5 l/min, the phenol removal efficiency was reduced approximately from 8.5% to 10.5% and the ozone utilization efficiency was reduced approximately from 6% to 8% in both reactors. The performance of PCR was superior to that of BCR in the aspects of phenol removal and ozone utilization efficiency.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.204-205
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• 2001

Milk is easily contaminated by pathogenic microorganisms and contains many ingredients that inhibit normal PCR. In this study, we developed a detection mothed for pathogenic microorganisms existing in milk by usting PCR. 'Sample pretreatment prior to PCR were compared to overcome the inhibition. A high PCR efficiency was achieved by SDS lysis pretreatment. without further purification of DNA for PCR.

• Fisheries and Aquatic Sciences
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• v.17 no.3
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• pp.339-344
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• 2014

PCR amplification with universal primer is a useful tool for speciation of symbionts in marine eukaryote coupled with robust separation method such as denaturing high performance chromatography (DHPLC). To overcome the biased amplification, clamping PCR is recommended to suppress the amplification of host gene. In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis: C3 linked nucleotide (C3) and peptide nucleic acid (PNA). PNA was 3-4 orders of magnitude higher than that of C3 tested in clamping efficiency and rare gene detection. This represented that PNA could be a more competent clamping probe for the enhancement of PCR amplification for rare symbiont genes.

• Food Science of Animal Resources
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• v.41 no.1
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• pp.85-94
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• 2021

A pig-specific real-time PCR assay based on the mitochondrial ND5 gene was developed to detect porcine material in food and other products. To optimize the performance of assay, seven commercial TaqMan master mixes and two real-time PCR platforms (Applied Biosystems StepOnePlus and Bio-rad CFX Connect) were used to evaluate the limit of detection (LOD) as well as the PCR efficiency and specificity. The LODs and PCR efficiencies for the seven master mixes on two platforms were 0.5-5 pg/reaction and 84.96%-108.80%, respectively. Additionally, non-specific amplifications of DNA from other animal samples (human, dog, cow, and chicken) were observed for four master mixes. These results imply that the sensitivity and specificity of a real-time PCR assay may vary depending on master mix and platform used. The best combination of master mix and real-time PCR platform can accurately detect 0.5 pg porcine DNA, with a PCR efficiency of 100.49%.