• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.47-47
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• 2005

There are many different surface technologies currently applied for preparation of protein chips. However, it requires innovative surface chemistry for capture proteins to be immobilized on chip surface keeping their conformation and activity intact and their orientation right, while they bind tightly and densely in a given array spot. Proteogen has developed 'ProteoChip BP' coated with novel proprietary linker molecules $(ProLinker^{TM})$ for efficient and robust immobilizations of capture proteins by improving surface properties of molecular captures. It was demonstrated that $ProLinker^{TM}$ gave the best surface performance in preparation of protein microarray chip base plates among others currently available on the market. In particular, the $ProLinker^{TM}-based$ surface chemistry has demonstrated to provide excellent performance in preparation of 'Antibody Chip' for analysis of biomarkers as well as proteome expression profiles. The linker molecule has also shown to be well applicable for development of biosensors and micro-beads as well as protein microarray and nano-array. ProteoChip BP can be used either for preparation of high-density array by using a microarrayer or for preparation of 'Well-on-a-Chip' with low density array, which is better applicable for quantitative analysis of biomarkers or protein-protein interactions. The biomarker assay can be performed either by direct or sandwich methods of fluorescence immunoassay. Application of ProteoChip BP has been well demonstrated by the extensive studies of 1) tumor-marker assays, 2) new drug screening by using 'Integrin Chip' and 3) protein expression profile analysis. Some of experimental results will be presented.

• The Journal of the Korea Contents Association
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• v.7 no.1
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• pp.40-47
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• 2007

In the protein macro array image, it is important to find out the feature of the each protein chip. A decision error by the personal sense of sight occurred from long time observation while making an experiment in many protein chip image. So the feature extraction is needed by a simulator. In the case of feature analysis for macro array scan image the efficiency is maximized. In the fluorescence scan image, the response for each cell have been depend on R, G, B distribution of color image. But it is difficult to be classified as one color feature in the case of mixed color image. In this paper, the response color of a protein chip is classified according to the fuzzy integral value with respect to fuzzy measure as the user desired color. The result of the experiment for the macro array fluorescence image with the Scan Array 5000 shows that the proposed method using the fuzzy integral is important fact to be make decision for the ambiguous color.

• 대한예방의학회:학술대회논문집
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• 2002.10a
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• pp.542-542
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• 2002

• Journal of Korean Society of Occupational and Environmental Hygiene
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• v.20 no.1
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• pp.29-40
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• 2010

This study was aimed at investigating the gene expression profile in basal ganglia of cadmium exposed rat based on cDNA array analysis. For cDNA array analysis, adult Sprague-Dawley male rats (350 ${\pm}$ 25 g) were intraperitoneally injected with 2.0 mg/kg body weight/day of CdCl2 (0.3 ml) for 5 days. For doserelated gene expression analysis rats were intraperitoneally injected with 0.0, 0.1, 0.3, 1.0 mg/kg body weight/day of CdCl$_2$ for 5 days. Control rats were injected with equal volume of saline. Cadmium concentration of brain was analyzed by atomic absorption spectrophotometer. For cDNA array, RNA samples were extracted from basal ganglia and reverse-transcribed in the presence of [${\alpha}$32P]-dATP. Membrane sets of the Atlas Rat 1.2 array II and Toxicology array 1.2 (Clontech, Palo Alto, CA) were hybridized with cDNA probe sets. RT-PCR was employed to validate the relative gene expression patterns obtained from the cDNA array. Northern blot hybridization methods were employed to assess the dose-related gene expression. Among the 2352 cDNAs, 671 genes were detected in both array sets and 63 genes of 38 classes showed significant (more than two fold) changes in expression. Thirty five of these genes were up-regulated and twenty eight were down-regulated in the cadmium exposed group. According to the dose-related gene expression analysis, heat shock 27 kDa protein (HSP27), neurodegeneration-associated protein 1 (Neurodap 1) genes were significantly up-regulated and melatonin receptor 1a (Mel1a), Kinesin family member 3C (KIF3C), novel kinesinrelated protein (KIF1D) genes were significantly downregulated even in the low-dose of cadmium exposed group (0.1 mg/kg body weight/day). Conclusions Sixty three genes detected in this study can give some more useful informations about the cadmium-induced neurotoxicity in the basal ganglia. As well as, HSP27, Neurodap1, Mel1a, KIF3C and KIF1D genes may be useful for the study of the cadmium-induced neurotoxicity because these genes showed dramatic changes of mRNA levels in response to the low dose of cadmium exposure.

• Journal of Microbiology and Biotechnology
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• v.19 no.10
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• pp.1103-1108
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• 2009

The human immunodeficiency virus (HIV)-l protein Tat acts as a transcription transactivator that stimulates expression of the infected viral genome. It is released from infected cells and can similarly affect neighboring cells. The nucleocapsid is an important protein that has a related significant role in early mRNA expression, and which contributes to the rapid viral replication that occurs during HIV-1 infection. To investigate the interaction between the Tat and nucleocapsid proteins, we utilized cDNA micro arrays using pTat and flag NC cotransfection in HEK 293T cells and reverse transcription-polymerase chain reaction to validate the micro array data. Four upregulated genes and nine downregulated genes were selected as candidate genes. Gene ontology analysis was conducted to define the biological process of the input genes. A proteomic approach using PathwayStudio determined the relationship between Tat and nucleocapsid; two automatically built pathways represented the interactions between the upregulated and downregulated genes. The results indicate that the up- and downregulated genes regulate HIV-1 replication and proliferation, and viral entry.

• Molecules and Cells
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• v.20 no.1
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• pp.97-104
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• 2005

To investigate apoptosis in HC11 mammary epithelial cells, we compared the gene expression profiles of actively growing and serum-starved apoptotic cells using a mouse apoptosis gene array and $^{33}P$-labeled cDNA prepared from the RNA of the two cultures. Analysis of the arrays showed that expression of several genes such as clusterin, secreted frizzled related protein mRNA (sFRP-1), CREB-binding protein (CBP), and others was higher in the apoptotic cells whereas expression of certain genes including survivin, cell division cycle 2 homolog A (CDC2), and cyclin A was lower. These expression patterns were confirmed by RT-PCR and/or Northern analyses. We compared the expression of some of these genes in the mouse mammary gland under various physiological conditions. The expression levels of genes (clusterin, CBP, and M6P-R) up-regulated in apoptotic conditions were higher at involution than during lactation. On the other hand, genes (Pin, CDC2) downregulated in apoptotic conditions were relatively highly expressed in virgin and pregnant mice. We conclude that certain genes such as clusterin, sFRP-1, GAS1 and CBP are induced in apoptotic mammary epithelial cells, and others are repressed. Moreover, the apoptosis array is an efficient technique for comparing gene expression profiles in different states of the same cell type.

• Journal of Computing Science and Engineering
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• v.4 no.4
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• pp.350-367
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• 2010

Microarray technology is an interdisciplinary technique that promises a revolutionary progress toward better health and improved quality of life. The paper focuses on the development of an efficient software package, equipped with already well-known methods; also some new methods are proposed that will allow the processing and analysis of thousands of genes on microarray images. The microarray analysis software package (called SmartArray), newly proposed in this paper verifies, through microarray analysis, dramatic changes in the mRNA, protein, and activity level in the rat retina during light deprivation, which have been demonstrated in previous biological experiments. The analysis results demonstrate that SmartArray can successfully find many changes in gene expression levels in each subarray and classify them according to their significance.

• IMMUNE NETWORK
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• v.6 no.3
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• pp.128-137
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• 2006

Background: Apoptosis is a physiologic phenomenon involved in development, elimination of damaged cells, and maintenance of cell homeostasis. Deregulation of apoptosis may cause diseases, such as cancers, immune diseases, and neurodegenerative disorders. The mouse myeloma cell P3-X63-Ag8.653 (v653) is an HGPRT deficient $(HGPRT^-)$ mutant strain. High dependency on de novo transcription and translation of aminopterin induced apoptosis of this cell seems to be an ideal experimental system for searching apoptosis-induced genes. Methods & Results: For searching apoptosis-related genes we carried out GE-array (dot blot), Affymetrix GeneChip analysis, Northern analysis and differential display-PCR techniques. The chip data were analyzed with three different programs. 66 genes were selected through Affymetrix GeneChip analyses. All genes selected were classified into 8 groups according to their known functions. They were Genes of 1) Cell growth/maintenance/death/enzyme, 2) Cell cycle, 3) Chaperone, 4) Cancer/disease-related genes, 5) Mitochondria, 6) Membrane protein/signal transduction, 7) Nuclear protein/nucleic acid binding/transcription binding and 8) Translation factor. Among these groups number of genes were the largest in the genes of cell growth/maintenance/death/enzyme. Expression signals of most of all groups were peaked at 3 hour of apoptosis except genes of Nuclear protein/nucleic acid binding/transcription factor which showed maximum signal at 1 hour. Conclusion: This study showed induction of wide range of proapoptotic factors which accelerate cell death at various stage of cell death. In addition apoptosis studied in this research can be classified as a type 2 which involves cytochrome c and caspase 9 especially in early stages of death. But It also has progressed to type 1 in late stage of the death process.

• Mass Spectrometry Letters
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• v.15 no.1
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• pp.1-25
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• 2024

Protein glycosylation, a highly significant and ubiquitous post-translational modification (PTM) in eukaryotic cells, has attracted considerable research interest due to its pivotal role in a wide array of essential biological processes. Conducting a comprehensive analysis of glycoproteins is imperative for understanding glycoprotein bio-functions and identifying glycosylated biomarkers. However, the complexity and heterogeneity of glycan structures, coupled with the low abundance and poor ionization efficiencies of glycopeptides have all contributed to making the analysis and subsequent identification of glycans and glycopeptides much more challenging than any other biopolymers. Nevertheless, the significant advancements in enrichment techniques, chromatographic separation, and mass spectrometric methodologies represent promising avenues for mitigating these challenges. Numerous substrates and multifunctional materials are being designed for glycopeptide enrichment, proving valuable in glycomics and glycoproteomics. Mass spectrometry (MS) is pivotal for probing protein glycosylation, offering sensitivity and structural insight into glycopeptides and glycans. Additionally, enhanced MS-based glycopeptide characterization employs various separation techniques like liquid chromatography, capillary electrophoresis, and ion mobility. In this review, we highlight recent advances in enrichment methods and MS-based separation techniques for analyzing different types of protein glycosylation. This review also discusses various approaches employed for glycan release that facilitate the investigation of the glycosylation sites of the identified glycoproteins. Furthermore, numerous bioinformatics tools aiding in accurately characterizing glycan and glycopeptides are covered.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1619-1619
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• 2001

Ourwork aims to assess the content of dry matter, protein, cell wall parameters and water soluble carbohydrates in forages without having to handle samples, transport them to a laboratory, dry, grind and chemically analyze them. for this purpose, the concept of fresh forage analysis under field conditions by means of compact integrated NIRS InGaAs-diode array instruments on small plot harvesters is being evaluated for plant breeding trials. This work was performed with the world first commercial experimental forage plot harvester equipped with a NIRS module for the collection, compression, and scanning of forage samples (including automatic referencing and dark current measure ments). It was used for harvesting and analyzing a number of typical forage grass and forage legume plot trials. After NIRS measurements in the field each sample was again analyzed in the laboratory by means of a conventional grating spectrometer equipped with Si-and PbS-detectors. Conventional laboratory analysis of the samples was restricted to dry matter (DM) content by means of oven drying at 105. Routine chemometric procedures were then employed to assess the comparative accuracy and precision of the DM assessments in the spectral range between 950 and 1650nm by the NIRS diode array as well as by the conventional NIRS scanning instrument. The results of this study confirmed that the type of NIRS diode array instrument employed here functioned well even in rugged field operations. further refinements proved to be necessary for optimizing the automatic filling of the sample compartment to adjust for the wide variation in forage material under conditions of extremely low or high harvest yields. The error achieved in calibrating the apparatus for forages of typical DM content proved to be satisfactory (SECV < 1.0). Possibly as a consequence of higher sampling errors, its performance in atypical forages with elevated DM contents was less satisfactory. The error level obtained on the conventional grating NIR spectrometer was similar to that of the diode array instrument for both types of forage.