• Biotechnology and Bioprocess Engineering:BBE
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• v.8 no.2
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• pp.64-75
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• 2003

Aptamers are functional nucleic acids that can specially bind to proteins, peptides, amino acids. nucleotides, drugs, vitamins and other organic and inorganic compounds. The aptamers are identified from random DNA or RNA libraries by a SELEX (systematic evolution of ligands by exponential amplification) process. As aptamers have the advantage, and potential ability to be released from the limitations of antibodies, they are attractive to a wide range of therapeutic and diagnostic applications. Aptamers, with a high-affinity and specificity, could fulfil molecular the recognition needs of various fields in biotechnology. In this work, we reviewed some aptamer Selection techniques, properties, medical applications of their molecules and their biotechnological applications, such as ELONA (enzyme linked oligonucleotide assay), flow cytometry, biosensors, electrophoresis, chromatography and microarrays.

• Proceedings of the KSME Conference
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• 2004.04a
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• pp.1286-1291
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• 2004

In order for studying pressure-coupled dynamic responses of droplet vaporization, open-loop experiment of an isolated droplet vaporization exposed to pressure perturbations in stagnant gaseous environment is numerically conducted. Governing equations are solved for flow parameters at gas and liquid phases separately and thermodynamic parameters at the interfacial boundary are matched for problem closure. For high-pressure effects, vapor-liquid interfacial thermodynamics is rigorously treated. A series of parametric calculations in terms of mean pressure level and wave frequencies are carried out employing a n-pentane droplet in stagnant gaseous nitrogen. Results show that wave instability in view of pressure-coupled vaporization response seems more susceptible at higher pressures and higher wave frequencies. Mass evaporation rate responding to pressure waves is amplified with increase in pressure due to substantial reduction in latent heat of vaporization. Augmentation of perturbation frequency also enhances amplification due to the reduction of phase differences between pressure perturbation and surface temperature fluctuation.

• Journal of Microbiology and Biotechnology
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• v.31 no.1
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• pp.123-129
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• 2021

Polyhydroxyalkanoate (PHA) synthase is a key enzyme for PHA production in microorganisms. The class IV PHA synthase is composed of two subunits: PhaC and PhaR. The PhaR subunit, which encodes the phaR gene, is only present in class IV PHA synthases. Therefore, the phaR gene is used as a biomarker for bacteria that contain a class IV PHA synthase, such as some Bacillus spp. The phaR gene was developed to screen phaR-containing Bacillus spp. The phaR screening method involved two steps: phaR gene amplification by PCR and phaR amplicon detection using a DNA lateral flow assay. The screening method has a high specificity for phaR-containing Bacillus spp. The lowest amount of genomic DNA of B. thuringiensis ATCC 10792 that the phaR screening method could detect was 10 pg. This novel screening method improves the specificity and sensitivity of phaR gene screening and reduces the time and cost of the screening process, which could enhance the opportunity to discover good candidate PHA producers. Nevertheless, the screening method can certainly be used as a tool to screen phaR-containing Bacillus spp. from environmental samples.

• Journal of Crop Science and Biotechnology
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• v.11 no.2
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• pp.91-100
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• 2008

Melting curve analysis of fluorescently labeled DNA fragments is used extensively for genotyping single nucleotide polymorphism(SNP). Here, we evaluated a SNP genotyping method by melting curve analysis with the two probe chemistries in a 384-well plate format on a Roche LightCycler 480. The HybProbe chemistry is based on the fluorescence resonance energy transfer(FRET) and the SimpleProbe chemistry uses a terminal self-quenching fluorophore. We evaluated FRET HybProbes and SimpleProbes for two SNP sites closely linked to two quantitative trait loci(QTL) for southern root-knot nematode resistance. These probes were used to genotype the two parents and 94 $F_2$ plants from the cross of PI 96354$\times$Bossier. The SNP genotypes of all samples determined by the LightCycler software agreed with previously determined SSR genotypes and the SNP genotypes determined on a Luminex 100 flow cytometry instrument. Multiplexed HybProbes for the two SNPs showed a 98.4% success rate and 100% concordance between repeats two of the same 96 DNA samples. Also, we developed a HybProbe assay for the Rcs3 gene conditioning broad resistance to the frogeye leaf spot(FLS) disease. The LightCycler 480 provides rapid PCR on 384-well plate and allows simultaneous amplification and analysis in approximately 2 hours without any additional steps after amplification. This allowed for a reduction of the potential contamination of PCR products, simplicity, and enablement of a streamlined workflow. The melting curve analysis on the LightCycler 480 provided high-throughput and rapid SNP genotyping and appears highly effective for marker-assisted selection in soybean.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7409-7414
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• 2015

Loop-mediated isothermal amplification (LAMP) developed by Notomi et al. (2000) has made it possible to amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. The ultimate products of LAMP are stem-loop structures with several inverted repeats of the target sequence and cauliflower-like patterns with multiple loops shaped by annealing between every other inverted repeats of the amplified target in the similar strand. Because the amplification process in LAMP is achieved by using four to six distinct primers, it is expected to amplify the target region with high selectivity. However, evaluation of reaction accuracy or quantitative inspection make it necessary to append other procedures to scrutinize the amplified products. Hitherto, various techniques such as turbidity assessment in the reaction vessel, post-reaction agarose gel electrophoresis, use of intercalating fluorescent dyes, real-time turbidimetry, addition of cationic polymers to the reaction mixture, polyacrylamide gel-based microchambers, lateral flow dipsticks, fluorescence resonance energy transfer (FRET), enzyme-linked immunosorbent assays and nanoparticle-based colorimetric tests have been utilized for this purpose. In this paper, we reviewed the best-known techniques for evaluation of LAMP amplicons and their applications in molecular biology beside their advantages and deficiencies. Regarding the properties of each technique, the development of innovative prompt, cost-effective and precise molecular detection methods for application in the broad field of cancer research may be feasible.

• Journal of Korea Soil Environment Society
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• v.5 no.1
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• pp.3-12
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• 2000

The multi-region model, to describe preferential flow, is an equation representing solute transport in soils by dividing soil into numerous pore groups and using the hydraulic properties of the soil. As the model partial differential equation (PDE) is solved numerically with finite difference methods. a modified equivalent partial differential equation(MEPDE) of the partial differential equation of the multi-region model is derived to analyze the accuracy and consistency of the solution of the model PDE and the Von Neumann method is used to analyze the stability of the finite difference scheme. The evaluation obtained from the MEPDE indicated that the finite difference scheme was found to be consistent with the model PDE and had the second order accuracy The stability analysis is performed to analyze the model PDE with the amplification ratio and the phase lag using the Von Neumann method. The amplification ratio of the finite difference scheme gave non-dissipative results with various Peclet numbers and yielded the most high values as the Peclet number was one. The phase lag showed that the frequency component of the finite difference scheme lagged the true solution. From the result of the stability analysis for the model PDE, it is analyzed that the model domain should be discretized in the range of Pe < 1.0 and Cr < 2.0 to obtain the more accurate solution.

• Proceedings of the KSME Conference
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• 2004.11a
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• pp.1122-1127
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• 2004

an isolated droplet combustion exposed to pressure perturbations in stagnant gaseous environment is numerically conducted. Governing equations are solved for flow parameters at gas and liquid phases separately and thermodynamic parameters at the interfacial boundary are matched for problem closure. For high-pressure effects, vapor-liquid interfacial thermodynamics is rigorously treated. A series of parametric calculations in terms of mean pressure level and wave frequencies are carried out employing a n-pentane droplet in stagnant gaseous air. Results show that the operating pressure and driving frequency have an important role in determining the amplitude and phase lag of a combustion response. Mass evaporation rate responding to pressure waves is amplified with increase in pressure due to substantial reduction in latent heat of vaporization. Phase difference between pressure and evaporation rate decreases due to the reduced thermal inertia at high pressure. In addition to this, augmentation of perturbation frequency also enhances amplification of vaporization rate because the time period for the pressure oscillation is much smaller than the liquid thermal inertia time. The phase of evaporation rate shifts backward due to the elevated thermal inertia at high acoustic frequency.

• KSBB Journal
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• v.24 no.5
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• pp.432-438
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• 2009

Here, we demonstrated simple nucleic acid, RNA, concentration method using polymer micro chip containing glass bead ($100\;{\mu}m$). Polymer micro chip was fabricated by PDMS ($1.5\;cm\;{\times}\;1.5\;cm$, $100\;{\mu}m$ in the height) including pillar structure ($160\;{\mu}m\;(I)\;{\times}\;80\;{\mu}m\;(w)\;{\times}\;100\;{\mu}m\;(h)$, gap size $50\;{\mu}m$) for blocking micro bead. RNA could be adsorbed on micro glass bead at low pH by hydrogen bonding whereas RNA was released at high pH by electrostatic force between silica surface and RNA. Amount of glass beads and flow rate were optimized in aspects of adsorption and desorption of RNA. Adsorption and desorption rate was measured with real time PCR. This concentrated RNA was applied to amplification micro chip in which NASBA (Nucleic Acid Sequence Based Amplification) was performed. As a result, E.coli O157 : H7 in the concentration of 10 c.f.u./10 mL was successfully detected by these serial processes (concentration and amplification) with polymer micro chips. It implies this simple concentration method using polymer micro chip can be directly applied to ultra sensitive method to measure viable bacteria and virus in clinical samples as well as environmental samples.

• Proceedings of the Korean Society of Propulsion Engineers Conference
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• 2004.03a
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• pp.155-164
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• 2004

In order for studying pressure-coupled dynamic responses of droplet vaporization, open-loop experiment of an isolated droplet vaporization exposed to pressure perturbations in stagnant gaseous environment is numerically conducted, Governing equations are solved for flow parameters at gas and liquid phases separately and thermodynamic parameters at the interfacial boundary are matched for problem closure. For high-pressure effects, vapor-liquid interfacial thermodynamics is rigorously treated. A series of parametric calculations in terms of mean pressure level and wave frequencies are carried out employing a n-pentane droplet in stagnant gaseous nitrogen. Results show that wave instability in view of pressure-coupled vaporization response seems more susceptible at higher pressures and higher wave frequencies. Mass evaporation rate responding to pressure waves is amplified with increase in pressure due to substantial reduction in latent heat of vaporization. Augmentation of perturbation frequency also enhances amplification due to the reduction of phase differences between pressure perturbation and surface temperature fluctuation.

• Journal of The Korean Astronomical Society
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• v.45 no.5
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• pp.127-138
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• 2012

We explore how wave-particle interactions affect diffusive shock acceleration (DSA) at astrophysical shocks by performing time-dependent kinetic simulations, in which phenomenological models for magnetic field amplification (MFA), Alfv$\acute{e}$nic drift, thermal leakage injection, Bohm-like diffusion, and a free escape boundary are implemented. If the injection fraction of cosmic-ray (CR) particles is ${\xi}$ > $2{\times}10^{-4}$, for the shock parameters relevant for young supernova remnants, DSA is efficient enough to develop a significant shock precursor due to CR feedback, and magnetic field can be amplified up to a factor of 20 via CR streaming instability in the upstream region. If scattering centers drift with Alfv$\acute{e}$n speed in the amplified magnetic field, the CR energy spectrum can be steepened significantly and the acceleration efficiency is reduced. Nonlinear DSA with self-consistent MFA and Alfv$\acute{e}$nic drift predicts that the postshock CR pressure saturates roughly at ~10 % of the shock ram pressure for strong shocks with a sonic Mach number ranging $20{\leq}M_s{\leq}100$. Since the amplified magnetic field follows the flow modification in the precursor, the low energy end of the particle spectrum is softened much more than the high energy end. As a result, the concave curvature in the energy spectra does not disappear entirely even with the help of Alfv$\acute{e}$nic drift. For shocks with a moderate Alfv$\acute{e}$n Mach number ($M_A$ < 10), the accelerated CR spectrum can become as steep as $E^{-2.1}$ - $E^{-2.3}$, which is more consistent with the observed CR spectrum and gamma-ray photon spectrum of several young supernova remnants.