• Asian Pacific Journal of Cancer Prevention
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• v.14 no.2
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• pp.915-921
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• 2013

Background: Hepatocellular carcinoma is one of the leading causes of mortalities worldwide. The search for new therapeutic targets is of utmost importance for improved treatment. Altered expression of HDAC1 in hepatocellular carcinoma (HCC) and its requirement for liver formation in zebrafish, suggest that it may regulate key events in liver carcinogenesis and organogenesis. However, molecular mechanisms of HDAC1 action in liver carcinogenesis are largely unknown. The present study was conducted to identify HDAC1 interacting proteins in HepG2 cells using modified SH-double-affinity purification coupled with liquid mass spectrophotemetery. Materials and Methods: HepG2 cells were transfected with a construct containing HDAC1 with a C-terminal strepIII-HA tag as bait. Bait proteins were confirmed to be expressed in HepG2 cells by western blotting and purified by double affinity columns and protein complexes for analysis on a Thermo LTQ Orbitrap XL using a C18 nano flow ESI liquid chromatography system. Results: There were 27 proteins which showed novel interactions with HDAC1 identified only in this study, while 14 were among the established interactors. Various subunits of T complex proteins (TCP1) and prefoldin proteins (PFDN) were identified as interacting partners that showed high affinity with HDAC1 in HepG2 cells. Conclusions: The double affinity purification method adopted in this study was very successful in terms of specificity and reproducibility. The novel HDAC1 complex identified in this study could be better therapeutic target for treatment of hepatocellular carcinoma.

• Journal of Korea Multimedia Society
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• v.11 no.9
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• pp.1302-1309
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• 2008

Traditional clustering methods, like k-means or fuzzy clustering, are prototype-based methods which are applicable only to convex clusters. On the other hand, spectral clustering tries to find clusters only using local similarity information. Its ability to handle concave clusters has gained the popularity recent years together with support vector machine (SVM) which is a kernel-based classification method. However, as is in SVM, the kernel width plays an important role and has a great impact on the result. Several methods are proposed to decide it automatically, it is still determined based on heuristics. In this paper, we proposed an adaptive method deciding the kernel width based on distance histogram. The proposed method is motivated by the fact that the affinity matrix should be formed into a block diagonal matrix to generate the best result. We use the tradition Euclidean distance together with the random walk distance, which make it possible to form a more apparent block diagonal affinity matrix. Experimental results show that the proposed method generates more clear block structured affinity matrix than the existing one does.

• Membrane Journal
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• v.8 no.1
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• pp.50-58
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• 1998

Protein affinity membranes were prepared via coating of chitosan gel on the porous flat and hollow-fiber polysulfone membranes, followed by the immobilization of the reactive dye (Cibacron Blue 3GA) to the chitosan gel. Maximum protein binding capacity of these affinity membranes was about 70 $\mu{g/cm}^2$. Using the affinity flat membrane module, the elution chromatography of human serum albumin (HSA) was performed to determine the optimum condition of eluent buffer. The optimum condition of eluent was the universal buffer solution of 0.06 M concentration containing 1 M KCl at pH 10. For the frontal chromatography of HSA using the flat module, the dynamic protein binding capacity was rapidly decreased from the equilibrium values with increasing flow rate and HSA concentration of the loading solution. However, in the case of hollow-fiber module, the dynamic binding capacity was maintained an equilibrium value without depending on the operating conditions. These results showed that the hollow-fiber module was more effective than the flat module as an affinity chromatography column.

• KSBB Journal
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• v.14 no.4
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• pp.396-402
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• 1999

To verify enchancing effect of polycation of polycation on the retroviral infecivity, we directly measured the binding affinity of retroviruses to the target cells in the presence or in the absence of polybrene with R18 fluorescence assay and examined the effect of the polymers on the relationship between the host cell and the retroviral infecity. There was no difference in the effect of the types of charge of the polymer on the binding affinity. However, polycations, in general, show effect on the retrovirus infecity. This results suggest that the enhancing effect of polybrene and other polycations on the infecity is not due to the binding step but due to the post-binding steps, especially the internalization step. With the result of the internalization of FITC-labeled poly-L-lysine into the host cells, it is suggested that the uptake of polycations into the host cells would play a crucial role in the intermalization of retroviruses.

• Biotechnology and Bioprocess Engineering:BBE
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• v.6 no.2
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• pp.144-149
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• 2001

For the production and purification of a single chain human insulin precursor, four types of fusion peptides $\beta$-galactosidase (LacZ), maltose binding protein (MBP), glutathione-S-transferase (GST), and (His)(sub)6-tagged sequence (HTS) were investigated. Recombinant E. coli harboring hybrid genes was cultivated at 37$\^{C}$ for 1h, and gene induction occurred when 0.2mM of isopropyl-D-thiogalactoside (IPTG) was added to the culture broth, except for E. coli BL21 (DE3) pLysS harboring a pET-BA cultivation with 1.0mM IPTG, followed by a longer than 4h batch fermentation respectively. DEAE-Sphacel and Sephadex G-200 gel filtration chromatography, amylose affinity chromatography, glutathione-sepharose 4B affinity chromatography, and a nickel chelating affinity chromatography system as a kind of immobilized metal ion affinity chromatography (IMAC) were all employed for the purification of a single chain human insulin precursor. The recovery yields of the HTS-fused, GST-fused, MBP-fused, and LacZ-fused single chain human insulin precursors resulted in 47%, 20%, 20%, and 18% as the total protein amounts respectively. These results show that a higher recovery yield of the finally purified recombinant peptides was achieved when affinity column chromatography was employed and when the fused peptide had a smaller molecular weight. In addition the pET expression system gave the highest productivity of a fused insulin precursor due to a two-step regulation of the gene expression, and the HTS-fused system provided the highest recovery of a fused insulin precursor based on a simple and specific separation using the IMAC technique.

• Applied Biological Chemistry
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• v.49 no.3
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• pp.180-185
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• 2006

${\alpha}$-Galactosidase was partially purified from the culture filtrate of Debaryomyces sp. by Mannobiose-Sepharose affinity column chromatography. The galactosidase exhibited maximum activity at pH 4.0 and $60^{\circ}C$, and was stable in the pH and temperature ranges of 3 to 4.5 and 30 to $50^{\circ}C$, respectively. The enzyme was inhibited by $Hg^{2+}\;and\;Ag^{2+}$. The enzyme activity was not affected considerably by treatment with other metal compounds. The enzyme hydrolyzed melibiose to galactose and glucose, raffinose to galactose and sucrose, and $Gal^3Man_3$ ($6^3-{\alpha}$-galactosyl-1,4-mannotriose) to galactose and mannotriose. On the contrary, it could not hydrolyze $Gal^3Man_4$ ($6^3-{\alpha}$-galactosyl-1,4-mannotetraose).

• Journal of KIISE:Databases
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• v.28 no.4
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• pp.715-722
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• 2001

Mobile computing has become a reality thank to the convergence of two technologies :powerful portable computers and the wireless networks. The restrictions of wireless network such as bandwidth and energy limitations make data broadcasting an attractive data communication method. This paper addresses the clustering of wireless broadcast data for multipoint queries. By effective clustering of broadcast data the mobile client can access the data on the air in short latency In the paper we define the data affinity and segment affinity measures. The data affinity is the degree that two data objects are accessed by queries, and the segment affinity is the degree that two sets of data (i.e segments) are accessed by queries Our method clusters data objects based on data and segment affinity measures we show that the performance of our method is scarcely infuenced by the growth of the number of queries.

• Biomolecules & Therapeutics
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• v.31 no.2
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• pp.176-182
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• 2023

Among 14 subtypes of serotonin receptors (5-HTRs), 5-HT_2AR plays important roles in drug addiction and various psychiatric disorders. Agonists for 5-HT_2AR have been classified into three structural groups: phenethylamines, tryptamines, and ergolines. In this study, the structure-activity relationship (SAR) of phenethylamine and tryptamine derivatives for binding 5-HT_2AR was determined. In addition, functional and regulatory evaluation of selected compounds was conducted for extracellular signal-regulated kinases (ERKs) and receptor endocytosis. SAR studies showed that phenethylamines possessed higher affinity to 5-HT_2AR than tryptamines. In phenethylamines, two phenyl groups were attached to the carbon and nitrogen (R³ ) atoms of ethylamine, the backbone of phenethylamines. Alkyl or halogen groups on the phenyl ring attached to the β carbon exerted positive effects on the binding affinity when they were at para positions. Oxygen-containing groups attached to R³ exerted mixed influences depending on the position of their attachment. In tryptamine derivatives, tryptamine group was attached to the β carbon of ethylamine, and ally groups were attached to the nitrogen atom. Oxygen-containing substituents on large ring and alkyl substituents on the small ring of tryptamine groups exerted positive and negative influence on the affinity for 5-HT_2AR, respectively. Ally groups attached to the nitrogen atom of ethylamine exerted negative influences. Functional and regulatory activities of the tested compounds correlated with their affinity for 5-HT_2AR, suggesting their agonistic nature. In conclusion, this study provides information for designing novel ligands for 5-HT_2AR, which can be used to control psychiatric disorders and drug abuse.

• Progress in Superconductivity and Cryogenics
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• v.25 no.4
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• pp.60-64
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• 2023

The manufacturing process of antibody drugs comprises two main stages: the upstream process for antibody cultivation and the downstream process for antibody extraction. The domestic bio industry has excellent technology for the upstream process. However, it relies on the technology of foreign countries to execute downstream process such as affinity chromatography. Furthermore, there are no domestic companies capable of producing the equipment for affinity chromatography. High gradient magnetic separation technology using a high temperature superconducting magnet as a novel antibody separation and purification technology is introduced to substitute for the traditional technology of affinity chromatography. A specially designed magnetic filter was equipped in the bore of the superconducting magnet enabling the continuous magnetic separation of nano-sized paramagnetic beads that can be used as affinity magnetic nano beads for antibodies. To optimize the magnetic filter that captures superparamagnetic nanoparticles effectively, various shapes and materials were examined for the magnetic filter. The result of magnetic separation experiments show that the maximum separation and recovery ratio of superparamagnetic nanoparticles are 99.2 %, and 99.07 %, respectively under magnetic field (3 T) and flow rate (600 litter/hr).

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2723-2725
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• 2014

Recently we have reported a novel class of anion receptors which are based on 2n-crown-n topology. Trioxane derivatives are capable of anion sensing through pure aliphatic C-H hydrogen bonding. In this work, we highlight another interesting property, i.e., they can also recognize cations as normal crown ethers (3n-crown-n topology). Since the same functional moiety can recognize anions and cations, these coronands are predicted to be amphi-ionophores. However, we could not detect cations even in the gas phase. Considering trioxane is analogous to [$1_6$]starand, this was rather counter-intuitive. The calculation results show that these coronands can detect alkali metals with very low affinity. The low affinity toward cations should be responsible for this failure of experimental detection. With careful theoretical study, we found that this low affinity toward cations could be explained by the unfavorable charge-dipolar moiety orientations as proposed by Cui et al. As in the case of [$1_6$]starand, this is an example that underscores the importance of charge-dipolar moiety orientation in supramolecular interactions.