• Bulletin of the Korean Chemical Society
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• 제28권3호
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• pp.386-390
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• 2007

By use of a simple two-point extrapolation scheme estimating the correlation energies of the molecules along with the basis sets specifically targeted for extrapolation, we have shown that the MP2 basis set limit binding energies of large hydrogen-bonded complexes can be accurately predicted with relatively small amount of computational cost. The basis sets employed for computation and extrapolation consist of the smallest correlation consistent basis set cc-pVDZ and another basis set made of the cc-pVDZ set plus highest angular momentum polarization functions from the cc-pVTZ set, both of which were then augmented by diffuse functions centered on the heavy atoms except hydrogen in the complex. The correlation energy extrapolation formula takes the (X+1)-3 form with X corresponding to 2.0 for the cc-pVDZ set and 2.3 for the other basis set. The estimated MP2 basis set limit binding energies for water hexamer, hydrogen fluoride pentamer, alaninewater, phenol-water, and guanine-cytosine base pair complexes of nucleic acid by this method are 45.2(45.9), 36.1(37.5), 10.9(10.7), 7.1(6.9), and 27.6(27.7) kcal/mol, respectively, with the values in parentheses representing the reference basis set limit values. A comparison with the DFT results by B3LYP method clearly manifests the effectiveness and accuracy of this method in the study of large hydrogen-bonded complexes.

• BMB Reports
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• 제39권6호
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• pp.686-695
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• 2006

Interleukin-2 enhancer binding factor 2 (ILF2) was reported to regulate transcription of interleukin-2 (IL-2), a central cytokine in the regulation of T-cell responses. This property of ILF2 was well characterized in human and mammals, but little is known in bony fish. In this paper, an ILF2 homologue was cloned and well characterized from Tetraodon nigrovirid is for the further investigation of the function of ILF2 in bony fish. The full-length Tetraodon ILF2 cDNA was 1380 bp in size and contained an open reading frame (ORF) of 1164 bp that translates into a 387 amino-acid peptide with a molecular weight of 42.9 kDa, a 5' untranslated region (UTR) of 57 bp, and a 3' UTR of 159 bp containing a poly A tail. The deduced peptide of Tetraodon ILF2 shared an overall identity of 58%~93% with other known ILF2 sequences, and contained two N-glycosylation sites, two N-myristoylation sites, one RGD cell attachment sequence, six protein kinase C phosphorylation sites, one amino-terminal RGG-rich single-stranded RNA-binding domain, and a DZF zinc-finger nucleic acid binding domain, most of which were highly conserved through species compared. Constitutive expression of Tetraodon ILF2 was observed in all tissues examined, including gill, gut, head kidney, spleen, liver, brain and heart. The highest expression was detected in heart, followed by liver, head kidney and brain. Stimulation with LPS did not significantly alter the expression of Tetraodon ILF2. Gene organization analysis showed that the Tetraodon ILF2 gene have fifteen exons, one more than other known ILF2 genes in human and mouse. Genes up- and down-stream from the Tetraodon ILF2 were Rpa12, Peroxin-11b, Smad4, Snapap and Txnip homologue, which were different from that in human and mouse.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2004년도 춘계학술대회 학술발표 논문집 제14권 제1호
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• pp.97-100
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• 2004

The identification of the DNA structure as a double-stranded helix consting of two nucleotide chain molecules was a milestone in modern molecular biology. The DNA chip technology is based on reverse hybridization that follows the principle of complementary binding of double-stranded DNA. DNA chip can be described as the deposition of defined nucleic acid sequences, probes, on a solid substrate to form a regular array of elements that are available for hybridization to complementary nucleic acids, targets. DNA chips based on cDNA clons, oligonucleotides and genomic clons have been developed for gene expression studies, genetic variation analysis and genomic changes associated with disease including cancers and genetic diseases. DNA chips for gene expression profiling can be used for functional analysis in human eel Is and animal models, disease-related gene studies, assessment of gene therapy, assessment of genetically modified food, and research for drug discovery. DNA chips for genetic variation detection can be used for the detection of mutations or chromosomal abnormalities in cnacers, drug resistances in cancer cells or pathogenic microbes, histocompatibility analysis for transplantation, individual identification for forensic medicine, and detection and discrimination of pathogenic microbes. The DNA chip will be generalized as a useful tool in clinical diagnostics in near future. Lab-on-a chip and informatics will facilitate the development of a variety of DNA chips for diagnostic purpose.

• 한국가금학회지
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• 제50권4호
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• pp.193-202
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• 2023

인플루엔자 A 바이러스(IAVs)는 많은 조류 종의 호흡 기관에 감염되며 사람을 비롯한 다른 동물로 전파될 수 있는 포장된 음극성 역전사 RNA 바이러스이다. 이 연구에서는 이전 연구의 마이크로어레이 데이터를 다시 분석하여 닭에서 공통 및 특이하게 발현되는 유전자(DEG) 및 그들의 생물학적 활동을 식별하였다. 고병원성(HPAIV) 및 저병원성(LPAIV) 인플루엔자 A 바이러스 감염된 닭 세포에서 각각 760개와 405개의 DEG가 발굴되다. HPAIV 및 LPAIV는 각각 670개와 315개의 DEG를 가지고 있으며, 이 중 90개의DEG가 두 바이러스에서 공유된다. HPAIV 감염으로 인해DEG의 기능 주석에 따르면 세포 주기의 기본적인 생물학적 기능과 연관된 다양한 유전자가 발굴되었다. 대상 유전자중에서 CDC Like Kinase 3(CLK3), Nucleic Acid Binding Protein 1(NABP1), Interferon-Inducible Protein 6(IFI6), PIN2 (TERF1) Interacting Telomerase Inhibitor 1(PINX1), 그리고Cellular Communication Network Factor 4(WISP1)의 발현은 polyinosinic:polycytidylic acid(PIC)로 처리된 DF-1 세포에서 변화되었다. 이것은 toll-like receptor 3(TLR3) 리간드인 TLR3 신호에 의해 이러한 유전자의 전사가 조절될 수 있음을 시사하며, 닭에서 AIV의 병리 생리학에 대한 더 나은 이해를 얻기 위해서는 AIV 감염 과정 중에 호스트 반응을 조절할 수 있는 메커니즘을 구명하는 데 더 많은 연구에 초점을 맞추는 것이 필요하다고 사료된다. 이러한 메커니즘에 대한 이해는 신규 치료 전략 개발에 활용될 수 있다.

• 한방안이비인후피부과학회지
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• 제21권3호
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• pp.52-68
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• 2008

Objectives and Methods : Salviae miltiorrhizae Radix (SMR) promotes blood circulation to remove blood stasis, cools the blood to relieve carbuncle, clears away heat from the heart and tranquilizes the mind. This study was designed to investigate the effects of SMR on immuno-potentiative action in terms of changes in the genetic profile of dendritic cells (DC) using by microarray analysis. Results and Conclusion: In this experiment, treatments with more than 250 ${\mu}g/ml$ upto 1000 ${\mu}g/ml$ of SMR elevated the proliferation rates of DC. Microscopic observations confirmed the tendency on proliferation rates. Expression levels of genes related with cellular methabolic process, cell communication, and macromolecule metabolic process were elevated by treatment with SMR in comparison of functional distribution in a Biological Process. In molecular functions, expression levels of genes related with receptor activation, nucleotide binding and nucleic acid binding were elevated. In cellular components, expression levels of genes related to cellular membrane-bound organelles were elevated. In addition, expression levels of genes related to Wnt signalling pathways and the glycerophospholipid metabolism were elevated through analysis using pathway analysis between up-and down-regulated genes in cells treated with SMR. Finally, genes related to JAK2, GRB2, CDC42, SMAD4, B2M, FOS and ESRI located the center of Protein interaction network of genes through treatment with SMR.

• 대한수의학회지
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• 제52권2호
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• pp.99-104
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• 2012

The present study was performed to evaluate the relationship between the neurotoxicity of acrylamide and the differential gene expression pattern in mice. Both locomotor test and rota-rod test showed that the group treated with higher than 30 mg/kg/day of acrylamide caused impaired motor activity in mice. Based on cDNA microarray analysis of mouse brain, myelin basic protein gene, kinesin family member 5B gene, and fibroblast growth factor (FGF) 1 and its receptor genes were down-regulated by acrylamide. The genes are known to be essential for neurofilament synthesis, axonal transport, and neuroprotection, respectively. Interestingly, both FGF 1 and its receptor genes were down-regulated. Genes involved in nucleic acid binding such as AU RNA binding protein/enoyl-coA hydratase, translation initiation factor (TIF) 2 alpha kinase 4, activating transcription factor 2, and U2AF 1 related sequence 1 genes were down-regulated. More interesting finding was that genes of both catalytic and regulatory subunit of protein phosphatases which are important for signal transduction pathways were down-regulated. Here, we propose that acrylamide induces neurotoxicity by regulation of genes associated with neurofilament synthesis, axonal transport, neuro-protection, and signal transduction pathways.

• 한국동물학회지
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• 제22권4호
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• pp.141-152
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• 1979

고양이 백혈병 바이러스에서 reverse transcriptase를 분리하여 생화학적 및 면역학적 연구를 하였다. 분자량은 72,000이고, DNA polymerase와 RNase H의 활성은 0.05-1 mM $M_n^2+$와 50-80 mM KCl에서 가장 좋았다. DNA polymerase와 RNase H는 같은 단백질 분자에 있으며, chymotrypsin 처리로서 RNase H를 쪼개낼 수 있으며, 이 RNase H도 reverse transcriptase의 항체에 의해서 활성이 거의 억제 된다. Reverse transcriptase의 항체 결합위치와 활성을 내는 위치는 다른 것 같다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.482-483
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• 2011

Graphene is a good candidate for the future nano-electronic materials because it has excellent conductivity, mobility, transparency, flexibility and others. Until now, most graphene researches are focused on the nano electronic device applications, however, biological application of graphene has been relatively less reported. We have fabricated a deoxyribonucleic acid (DNA) conjugated graphene field-effect transistor (FET) and measured the electrical transport characteristics. We have used graphene sheets grown on Ni substrates by chemical vapour deposition. The Raman spectra of graphene sheets indicate high quality and only a few number of layers. The synthesized graphene is transferred on top of the substrate with pre-patterned electrodes by the floating-and-scooping method [1]. Then we applied adhesive tapes on the surface of the graphene to define graphene flakes of a few micron sizes near the electrodes. The current-voltage characteristic of the graphene layer before stripping shows linear zero gate bias conductance and no gate operation. After stripping, the zero gate bias conductance of the device is reduced and clear gate operation is observed. The change of FET characteristics before and after stripping is due to the formation of a micron size graphene flake. After combined with 30 base pairs single-stranded poly(dT) DNA molecules, the conductance and gate operation of the graphene flake FETs become slightly smaller than that of the pristine ones. It is considered that DNA is to be stably binding to the graphene layer due to the ${\pi}-{\pi}$ stacking interaction between nucleic bases and the surface of graphene. And this binding can modulate the electrical transport properties of graphene FETs. We also calculate the field-effect mobility of pristine and DNA conjugated graphene FET devices.

• Biotechnology and Bioprocess Engineering:BBE
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• 제8권4호
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• pp.263-267
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• 2003

Magnetic nanoparticles prepared from an alkaline solution of divalent and trivalent iron ions could covalently bind protein via the activation of Nethyl-N-(3-dimethylaminopropyl) carbodiimide (EDC). Trypsin and avidin were taken as the model proteins for the formation of protein-nanoparticle conjugates. The immobilized yield of protein increased with molar ratio of EDC/nanoparticie. Higher concentrations of added protein could yield higher immobilized protein densities on the particles. In contrast to EDC, the yields of protein immobilization via the a ctivation of cyanamide were relatively lower. Nanoparticles bound with avidin could attach a single-stranded DNA through the avidin-biotin interaction and hybridize with a DNA probe. The DNA hybridization was confirmed by fluorescence microscopy observations. Immobilized DNA on nanoparticles by this technique may have widespread applicability to the detection of specific nucleic acid sequence and targeting of DNA to particular cells.

• Molecules and Cells
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• 제40권12호
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• pp.889-896
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• 2017

Nuclear bodies are subnuclear, spheroidal, and membraneless compartments that concentrate specific proteins and/or RNAs. They serve as sites of biogenesis, storage, and sequestration of specific RNAs, proteins, or ribonucleoprotein complexes. Recent studies reveal that a subset of nuclear bodies in various eukaryotic organisms is constructed using architectural long noncoding RNAs (arcRNAs). Here, we describe the unifying mechanistic principles of the construction and function of these bodies, especially focusing on liquid-liquid phase separation induced by architectural molecules that form multiple weakly adhesive interactions. We also discuss three possible advantages of using arcRNAs rather than architectural proteins to build the bodies: position-specificity, rapidity, and economy in sequestering nucleic acid-binding proteins. Moreover, we introduce two recently devised methods to discover novel arcRNA-constructed bodies; one that focuses on the RNase-sensitivity of these bodies, and another that focuses on "semi-extractability" of arcRNAs.