• Bulletin of the Korean Chemical Society
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• v.26 no.10
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• pp.1539-1542
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• 2005

We have introduced polyelectrolyte micro-patterning technique employing agarose plane stamp and a hard substrate having microscale features on its surface. With this method, chemically micropatterned surfaces with both positive and negative functionalities were successfully embedded in well-defined microstructures, and selective impartment of charge functionalities was confirmed by patterning bead bearing surface charge. Furthermore, this technique allows highly sensitive immobilization of protein onto targeted surface simply by endowing functionalities, which extends the potential of its use as a tool for high-throughput protein microarray and proteomics. Because plane agarose stamp is free of structures on its surface, there is no concern for pattern collapse, and the combination of agarose plane stamp with patterned substrate is more suited for selective protein patterning compared with adopting surface-patterned agarose stamp with flat substrate. Our technique using agarose plane stamp and a substrate having microscale features on its surface suggests a range of possible applications, including the micropatterning of biofunctionalized copolymer having polyelectrolyte block, immobilization of micro- and nanoparticle with biofunctionalities such as biotin and streptavidine, and establishing optoelectronic microstructures with micro-beads on various surfaces.

• Korean Journal of Poultry Science
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• v.28 no.2
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• pp.143-153
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• 2001

Using bioinformatic tools for searching the massive genome databases, it is possible to Identify new genes in few minutes for initial discoveries based on evolutionary conservation, domain homology, and tissue expression patterns, followed by further verification and characterization using the bench-top works. The development of high-density two-dimensional arrays has allowed the analysis of the expression of thousands of genes simultaneously in the humans, mice, rats, yeast, and bacteria to elucidate the genes and pathways involved in physiological processes. In addition, rapid and automated protein identification is being achieved by searching protein and nucleotide sequence databases directly with data generated from mass spectrometry. Recently, analysis at the bio-chemical level such as biochemical screening and metabolic profiling (Biochemical genomics) has been introduced as an additional approach for categorical assignment of gene function. To make advantage of recent achievements in computational approaches for facilitated gene discoveries in the avian model, chicken expression sequence tags (ESTs) have been reported and deposited in the international databases. By searching EST databases, a chicken heparanase gene was identified and functionally confirmed by subsequent experiments. Using combination of sub-tractive hybridization assay and Genbank database searches, a chicken heme -binding protein family (cSOUL/HBP) was isolated in the retina and pineal gland of domestic chicken and verified by Northern blot analysis. Microarrays have identified several host genes whose expression levels are elevated following infection of chicken embryo fibroblasts (CEF) with Marek's disease virus (MDV). The ongoing process of chicken genome projects and new discoveries and breakthroughs in genomics and proteomics will no doubt reveal new and exciting information and advances in the avian research.

• KSBB Journal
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• v.20 no.2 s.91
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• pp.88-92
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• 2005

Phosphorylation of amino acid residues in proteins, plays a major role in biological mechanism. Phosphorylation acts as a process regulating the protein activity in variable pathways such as metabolism, signal transduction and cell division. Therefore the development of ligands for phosphoamino acids are an important work for protein analysis and proteomics studies. In this study, RNA aptamers for o-phosphoserine, o-phosphotyrosine and o-phosphotyrosine which appears frequently in nature were developed by in vitro evolution method. We could obtain similar sequences from random RNAs of 40 mer by SELEX method through 10 cycles. As result, the aptamers for o-phosphoserine and o-phosphothreonine among phosphoamino acids aptamers showed high affinity of Kd=2.60 nM and 2.65 nM for their target molecules, respectively. In addition, these aptamers could be confirmed the high selectivity for their target.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.50-57
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• 2020

Background: The cellular senescence of primary cultured cells is an irreversible process characterized by growth arrest. Restoration of senescence by ginsenosides has not been explored so far. Rg3(S) treatment markedly decreased senescence-associated β-galactosidase activity and intracellular reactive oxygen species levels in senescent human dermal fibroblasts (HDFs). However, the underlying mechanism of this effect of Rg3(S) on the senescent HDFs remains unknown. Methods: We performed a label-free quantitative proteomics to identify the altered proteins in Rg3(S)-treated senescent HDFs. Upregulated proteins induced by Rg3(S) were validated by real-time polymerase chain reaction and immunoblot analyses. Results: Finally, 157 human proteins were identified, and variable peroxiredoxin (PRDX) isotypes were highly implicated by network analyses. Among them, the mitochondrial PRDX3 was transcriptionally and translationally increased in response to Rg3(S) treatment in senescent HDFs in a time-dependent manner. Conclusion: Our proteomic approach provides insights into the partial reversing effect of Rg3 on senescent HDFs through induction of antioxidant enzymes, particularly PRDX3.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2655-2659
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• 2014

Dual specificity protein phosphatase 4 (DUSP4) has been considered a promising target for the development of therapeutics for various human cancers. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule DUSP4 inhibitors. As a consequence of the virtual screening with the modified scoring function to include an effective molecular solvation free energy term, five micromolar DUSP4 inhibitors are found with the associated $IC_{50}$ values ranging from 3.5 to $10.8{\mu}M$. Because these newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of DUSP4 are discussed in detail.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.933-937
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• 2014

A derivative of Mycobacterium bovis Bacillus Calmette-Guerin (BCG) has been used for the preparation of tuberculosis vaccines. To establish a Korean tuberculosis vaccine derived from BCG-Pasteur $1173P_2$, genome sequencing of a BCG-Korea strain was completed by Joung and coworkers. A comparison analysis of the genome sequences of the BCG-Pasteur $1173P_2$ and BCG-Korea strains showed marginal increases in the total genome length (~0.05%) and the number of genes (~4%) in the BCG-Korea genome. However, how the genomic changes affect the BCG-Korea protein expression levels remains unknown. Here, we provide evidence of the proteomic alterations in the BCG-Korea strain by using a SWATH-based mass spectrometric approach (Sequential Window Acquisition of all THeoretical mass spectra). Twenty BCG proteins were selected by top-rank identification in the BCG proteome analysis and the proteins were quantified by the SWATH method. Thirteen of 20 proteins showing significant changes were enough to discriminate between the two BCG proteomes. The SWATH method is very straightforward and provides a promising approach owing to its strong reliability and reproducibility during the proteomic analysis.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.845-850
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• 2014

The rapid development of shotgun proteomics is paving the way for extensive proteome profiling, while providing extensive information on various post translational modifications (PTMs) that occur to a proteome of interest. For example, the current phosphoproteomic methods can yield more than 10,000 phosphopeptides identified from a proteome sample. Despite these developments, it remains a challenging issue to pinpoint the true phosphorylation sites, especially when multiple sites are possible for phosphorylation in the peptides. We developed the Phospho-UMC filter, which is a simple method of localizing the site of phosphorylation using unique mass classes (UMCs) information to differentiate phosphopeptides with different phosphorylation sites and increase the confidence in phosphorylation site localization. The method was applied to large scale phosphopeptide profiling data and was demonstrated to be effective in the reducing ambiguity associated with the tandem mass spectrometric data analysis of phosphopeptides.

• Bulletin of the Korean Chemical Society
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• v.31 no.1
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• pp.92-99
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• 2010

Photoexcitation of a precursor ion inside a cell floated at high voltage installed in a tandem time-of-flight (TOF) mass spectrometer provides triple tandem mass spectrometric information and allows kinetic and mechanistic studies. In this work, the factors affecting, or downgrading, the performance of the technique were identified. Ion-optical and computational analyses showed that an optimum instrument could be designed by utilizing a reflectron with linear-plus-quadratic potential inside. Theoretical predictions were confirmed by tests with instruments built with different ion-optical layout. With optimized instruments, masses of intermediate ions in the consecutive dissociation of a precursor ion could be determined with the maximum error of $\pm5$ Da. We also observed excellent agreement in dynamical parameters (critical energy and entropy) for the dissociation of a model peptide ion determined by instruments with different ion-optical layout operated under optimum conditions. This suggests that these parameters can be determined reliably by the kinetic method developed previously when properly designed and operated tandem TOF instruments are used.

• Korean Journal of Materials Research
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• v.32 no.4
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• pp.186-192
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• 2022

Collagen is one of the most widely used biological materials in medical design. Collagen extracted from marine organisms can be a good biomaterial for tissue engineering applications due to its suitable properties. In this study, collagen is extracted from fish skin of Ctenopharyngodon Idella; then, the freeze drying method is used to design a porous scaffold. The scaffolds are modified with the chemical crosslinker N-(3-Dimethylaminopropyl)-N'-ethyl carbodiimide hydrochloride (EDC) to improve some of the overall properties. The extracted collagen samples are evaluated by various analyzes including cytotoxicity test, SDS-PAGE, FTIR, DSC, SEM, biodegradability and cell culture. The results of the SDS-PAGE study demonstrate well the protein patterns of the extracted collagen. The results show that cross-linking of collagen scaffold increases denaturation temperature and degradation time. The results of cytotoxicity show that the modified scaffolds have no toxicity. The cell adhesion study also shows that epithelial cells adhere well to the scaffold. Therefore, this method of chemical modification of collagen scaffold can improve the physical and biological properties. Overall, the modified collagen scaffold can be a promising candidate for tissue engineering applications.

• Macromolecular Research
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• v.14 no.2
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• pp.121-128
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• 2006

Microfluidic systems have attracted much research attention recently in the areas of genomics, proteomics, pharmaceutics, clinical diagnostics, and analytical biochemistry, as they provide miniaturized platforms for conventional analysis techniques. The microfluidic systems allow faster and cheaper analysis using much smaller amounts of sample and reagent than conventional methods. Polymers have recently found useful applications in microfluidic systems due to the wide range of available polymeric materials and the relative ease of chemical modification. This paper discusses the fundamentals of microfluidic systems and the roles, essential properties and various forms of polymers used as solid supports in microfluidic systems, based on the recent advances in the use of polymers for microfluidic chips.