• Bulletin of the Korean Chemical Society
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• 제34권9호
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• pp.2725-2730
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• 2013

Single C-reactive protein (CRP) molecules, which are non-specific acute phase markers and products of the innate immune system, were quantitatively detected on a gold-nanopatterned biochip using evanescent field-enhanced fluorescence imaging. The $4{\times}5$ gold-nanopatterned biochip (spot diameter of 500 nm) was fabricated by electron beam nanolithography. Unlabeled CRP molecules in human serum were identified with single-molecule sandwich immunoassay by detecting secondary fluorescence generated by total internal reflection fluorescence (TIRF) microscopy. With decreased standard CRP concentrations, relative fluorescence intensities reduced in the range of 33.3 zM-800 pM. To enhance fluorescence intensities in TIRF images, the distance between biochip surface and CRP molecules was optimally adjusted by considering the quenching effect of gold and the evanescent field intensity. As a result, TIRF only detected one single-CRP molecule on the biochip the first time.

• Biotechnology and Bioprocess Engineering:BBE
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• 제9권2호
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• pp.143-146
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• 2004

A surface plasmon resonance (SPR) imaging system was constructed and used to detect the hexahistidine-ubiquitin-tagged human parathyroid hormone fragment (His$\sub$6/-Ub-hPTHF(1-34)) expressed in Escherichia coli. The hexahistidine-specific antibody was immobilized on a thin gold film coated with ProLinker$\^$TM/ B, a novel calixcrown derivative with a bifunctional coupling property that permits efficient immobilizaton of capture proteins on solid matrices. The soluble and insoluble fractions of an E. coli cell lysate were spotted onto the antibody-coated gold chip, which was then washed with buffer (pH 7.4) solution and dried. SPR imaging measurements were carried out to detect the expressed His$\sub$6/-Ub-hPTHF(1-34). There was no discernible protein image in the uninduced cell lysate, indicating that non-specific binding of contaminant proteins did not occur on the gold chip surface. It is expected that the approach used here to detect affinity-tagged recombinant proteins using an SPR imaging technique could be used as a powerful tool for the analyses of a number of proteins in a high-throughput mode.

• Bulletin of the Korean Chemical Society
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• 제28권5호
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• pp.783-790
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• 2007

The immobilization of proteins and their molecular interactions on various polymer-modified glass substrates [i.e. 3-aminopropyltriethoxysilane (APTS), 3-glycidoxypropyltrimethoxysilane (GPTS), poly (ethylene glycol) diacrylate (PEG-DA), chitosan (CHI), glutaraldehyde (GA), 3-(trichlorosilyl)propyl methacrylate (TPM), 3'-mercaptopropyltrimethoxysilane (MPTMS), glycidyl methacrylate (GMA) and poly-l-lysine (PL).] for potential applications in a nanoarray protein chip at the single-molecule level was evaluated using prismtype dual-color total internal reflection fluorescence microscopy (dual-color TIRFM). A dual-color TIRF microscope, which contained two individual laser beams and a single high-sensitivity camera, was used for the rapid and simultaneous dual-color detection of the interactions and colocalization of different proteins labeled with different fluorescent dyes such as Alexa Fluor® 488, Qdot® 525 and Alexa Fluor® 633. Most of the polymer-modified glass substrates showed good stability and a relative high signal-to-noise (S/N) ratio over a 40-day period after making the substrates. The GPTS/CHI/GA-modified glass substrate showed a 13.5-56.3% higher relative S/N ratio than the other substrates. 1% Top-Block in 10 mM phosphate buffered saline (pH 7.4) showed a 99.2% increase in the blocking effect of non-specific adsorption. These results show that dual-color TIRFM is a powerful methodology for detecting proteins at the single-molecule level with potential applications in nanoarray chips or nano-biosensors.

• Journal of Information Processing Systems
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• 제8권3호
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• pp.459-470
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• 2012

Recently, high-throughput technologies such as the two-hybrid system, protein chip, Mass Spectrometry, and the phage display have furnished a lot of data on protein-protein interactions (PPIs), but the data has not been accurate so far and the quantity has also been limited. In this respect, computational techniques for the prediction and validation of PPIs have been developed. However, existing computational methods do not take into account the fact that a PPI is actually originated from the interactions of domains that each protein contains. So, in this work, the information on domain modules of individual proteins has been employed in order to find out the protein interaction relationship. The system developed here, WASPI (Web-based Assistant System for Protein-protein interaction Inference), has been implemented to provide many functional insights into the protein interactions and their domains. To achieve those objectives, several preprocessing steps have been taken. First, the domain module information of interacting proteins was extracted by taking advantage of the InterPro database, which includes protein families, domains, and functional sites. The InterProScan program was used in this preprocess. Second, the homology comparison with the GO (Gene Ontology) and COG (Clusters of Orthologous Groups) with an E-value of $10^{-5}$, $10^{-3}$ respectively, was employed to obtain the information on the function and annotation of each interacting protein of a secondary PPI database in the WASPI. The BLAST program was utilized for the homology comparison.

• 한국고분자학회:학술대회논문집
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• 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
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• pp.306-306
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• 2006

We immobilized and patterned PDA vesicles on solid substrate using micro arrayer, which have moieties to react with chemical and biological materials. Immobilized vesicle system was developed since it possesses many advantages in multiple screening, durable stability, and higher sensitivity. We applied polydiacetylene supramolecules to chemical and biological sensors for detection of ${\alpha}-cyclodextrin$ and E.coli cell selectively. This detection method could be applied as DNA chip, protein chip, and cell chip for multiple screening as well as chemical sensor by modifying the functional groups of diacetylene monomer.

• BMB Reports
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• 제46권10호
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• pp.490-494
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• 2013

The phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor-suppressing lipid phosphatase that is frequently absent in breast tumors. Thus, the stability of PTEN is essential for tumor prevention and therapy. The ubiquitin-proteasome pathway has an important role in regulating the functions of PTEN. Specifically, carboxyl terminus Hsp70-interacting protein (CHIP), the E3 ubiquitin ligase of PTEN, can regulate PTEN levels. In this study, we report that BCL-2-associated athanogene 5 (BAG5), a known inhibitor of CHIP activity, reduces the degradation of PTEN and maintains its levels via an ubiquitylation-dependent pathway. BAG5 is identified as an antagonist of cell tumorigenicity.

• Bulletin of the Korean Chemical Society
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• 제23권12호
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• pp.1724-1728
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• 2002

The adsorption of proteins on the surface of glass slides is essential for the construction of protein chips. Here, we report that a Histidine (His)-tagged protein protein has been efficiently adsorbed on glass coated with nickel. A variety of nickel chloride-coated plates were prepared by the spin-coating method and adsorbed to the His-tagged protein. When the protein was adsorbed onto the surface of a variety of nickel chloride-coated glass slides, the efficiency of protein adsorption was dependent upon the coating conditions such as nickel chloride concentration, the spin speed and the drying temperature. The slides appropriate for protein adsorption were obtained when the slides were coated with 11%(w/w) of $NiCl_2$ at the spin speed of 4000 rpm for 20 sec and then dried at higher than 40°C. The physical properties of their nickel chloride thin layer were characterized by scanning electron microscopy. x-ray diffraction and atomic force microscopy, finding that the nickel chloride particles were around 10 nm in diameter and uniformly crystallized at 101 faces. These results show that nickel chloride-coated slides prepared by the spin-coating method are utilizable for the construction of Histagged protein chips.

• Journal of Plant Biotechnology
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• 제43권2호
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• pp.231-239
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• 2016

담배에서 후성유전관련 유전자의 발현연구를 위해 담배유래 시토신 DNA 탈메틸화 관련 NtROS2a 유전자를 과발현 및 RNAi 식물체를 육성하였다. 이들 형질전환체들은 고염 및 산화 스트레스하에서 내성이 증진되었으며, 다양한 표현형변이를 보였다(Lee et al. 2015). 본연구에서는 선발된 과발현 (OX1), RNAi 식물체(RNAi 13) 및 대조식물체(WT)를 이용하여 Agilent Tobacco 4 X 44K Oligo chip으로 microarray분석을 수행하였다. OX1과 RNAi13 계통을 이용하여 WT과 함께 비교 분석한 결과, 대부분 세포 내 이온 수송, 영양 공급 등과 같은 물질대사와 생물적 비생물적 스트레스 및 methylation과 관련되어 영향을 주는 유전자들에서 up-regulation 되었고, 물질대사관련 유전자와 세포 내 기능유전자의 역할을 담당하는 조효소, 그리고 다양한 스트레스 및 메틸레이션 관련 유전자군에서 또한 down-regulation되었다. 각각의 up-, down-regulation된 유전자들을 WT과 비교하여 qRT-PCR을 수행한 결과, KH domain-containing protein, MADS-box protein 및 Zinc phosphodiesterase ELAC protein 유전자들에서 발현이 높게 나타났으며, 반면에 pentatricopeptide (PPR) repeat-containing protein, histone deacetylase HDAC3 protein 및 protein kinase는 0.4 ~ 1.0-fold 발현양이 감소되었다. 따라서 DNA glycosylase를 암호화하는 NtROS2a 유전자는 demethylation과 관련되어 담배 식물체에서 다양한 전사레벨을 조절하는 것으로 판단된다.

• Clinical and Experimental Pediatrics
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• 제48권7호
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• pp.779-788
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• 2005

목 적 : Echinacea는 면역증강제로 이미 사용되고 있는 재래 식물로서 최근에 Echinacea의 추출물로 단구를 중심으로 면역세포들에 의한 면역증강효과에 대한 연구가 이루어지고 있다. 본 연구는 단구와 수지상세포에서 Echinacea에 의해 유전자의 발현이 증가되는 면역관련 유전자들을 cDNA microarray chip을 사용하여 선별하고 이들을 토대로 Echinacea의 면역증강 효과에 대한 연구를 할 때 기초 자료가 되고자 하였다. 방 법 : 실험 1과 2는 3명의 공여자의 말초혈 단구로 실험하였는데 실험 1은 단구에 최종 농도가 $50{\mu}g/mL$ 되게 Echinacea를 첨가하여 1일간 배양하였고, 실험 2는 실험 1의 대조군으로서 Echinacea를 첨가하지 않고 배양하였다. 실험 3과 4는 2명의 공여자의 단구로 실험하였는데 실험 3은 GM-CSF와 IL-4를 첨가하여 5일간 배양시켜 수지상세포로 분화시킨 뒤 Echinacea를 첨가하여 1일간 더 배양시켰고, 실험 4는 실험 3의 대조군으로서 수지상세포로 분화시킨 뒤 Echinacea를 첨가하지 않고 1 일간 더 배양하였다. Echinacea에 의한 단구와 수지상세포의 유전자발현 효과를 알아보기 위해서 cDNA microarray chip을 이용하여 대조군에 대한 실험군의 각 유전자의 발현비를 구하였다. Echinacea를 첨가하지 않은 단구(실험 2의 단구)에 대한 Echinacea를 첨가한 단구(실험 1의 단구)의 각 유전자들의 발현 비를 구하였고, Echinacea를 첨가하지 않은 수지상세포(실험 4의 수지상세포)에 대한 Echinacea를 첨가한 수지상세포(실험 3의 수지상세포)의 각 유전자들의 발현비를 구하였다. 여기서 실험 1과 2에서는 세 공여자의 단구에서 나온 유전자 발현비의 결과를, 실험 3과 4에서는 두 공여자의 수지상세포에서 나온 유전자 발현비의 결과를 평균하여 그 발현비가 2.5 이상 되는 것을 의미있게 발현된 유전자로 보았다. 결 과 : Echinacea를 첨가하지 않은 단구를 대조군으로 하여 Echinacea를 첨가한 단구의 유전자 발현비가 2.5 이상으로 증가한 것들 중 면역과 관계된 유전자들은 17개였다. Echinacea를 첨가하지 않은 수지상세포를 대조군으로 하여 Echinacea를 첨가한 수지상세포의 유전자 발현비가 2.5 이상으로 증가한 것들 중 면역과 관계된 유전자들은 24개였고, 실험에 사용한 수지상세포들은 모두 미성숙 수지상세포의 특징적인 표면항원들을 가지고 있음을 유세포 분석으로 확인하였다. Echinacea가 단구와 수지상세포 둘 다에서 의미있게 유전자발현비가 증가된 것들이 7개 있었는데, 이들은 CD44, IFI 30, MRC 1, CCR 7, CLK 2, syntenin, cytochrome C oxidase subunit VIII 등의 유전자들이었다. 특히 발현비가 3.5 이상으로 높은 유전자들을 그 발현비 순으로 나열하면 단구에서는 IFI 30, CLK 2, syntenin, superoxide dismutase 2 등 4개의 유전자들이 있었고, 수지상세포에서는 somatomedin A, methyl-CpG binding domain protein 3, IFI 30, small inducible cytokine subfamily A(Cys-Cys), member 22, ubiquitin-conjugating enzyme E2L 6, hexosaminidase B, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor epsilon, CCR 7 등 8개의 유전자들이 있었다. 결 론 : 본 연구는 Echinacea가 $CD14^+$ 단구 및 수지상세포에서 발현을 증가시키는 면역관련 유전자들을 cDNA microarray chip을 이용하여 검색하였고, 향후 이 유전자들을 기초로 정량적이고 기능적으로 분석할 수 있는 토대를 마련하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제19권3호
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• pp.368-375
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• 2006

Four rumen-fistulated dairy steers were randomly assigned according to a $4{\times}4$ Latin square design to investigate effects of supplementation levels of sodium dl-malate in concentrates on rumen ecology, ruminal fermentation, nitrogen balance, feed intake and digestibility of nutrients and ruminal microbial protein synthesis. The dietary treatments were cassava concentrate-based, containing sodium dl-malate supplementation at 0, 9, 18 and 27 g/hd/d with urea-treated rice straw (UTS) fed ad libitum. The experiment was conducted for four periods, each period lasting 21 days. Ruminal pH increased with incremental addition of malate (p<0.05). Additionally, molar proportions of propionate were higher in supplemented groups and was highest at 18 g/hd/d of malate supplement (p<0.05). Microbial protein synthesis tended to be higher in dairy steers receiving sodium dl-malate supplements and also was the highest at 18 g/hd/d. Variable bacterial populations, such as amylolytic, proteolytic and cellulolytic species were increased (p<0.05). Furthermore, protozoal populations were decreased significantly (p<0.05), while fungal zoospores were dramatically increased in dairy steers receiving sodium dl-malate supplement (p<0.05). These results suggested that supplementation of concentrate containing a high level of cassava chip at 18 g/hd/d with UTS in dairy steers could improve rumen fermentation efficiency and rumen microbial protein synthesis.