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송혜정,이정원,김병기,송상용,배덕수,김대식 한국바이오칩학회 2010 BioChip Journal Vol.4 No.3
The aim of this study was to evaluate the recently developed PANArray™ Human papilloma virus (HPV) kit for detection and genotyping of 19 high-risk and 13 low-risk HPV types, and compare it with the commercially available DNA chip kit geno-typing of 24 HPVs. We llected cervical swabs from 741 patients with various stages of invasive cervical carcinoma being treated at the Samsung Medical Center. The overall HPV positivity rate was 73% using PANArray™ HPV and 72.1% with the DNA chip, and no statistically significant differences were found with respect to the cytology grade. Comparing the results of the two chips, concordant results were found in 637/741 samples (85.9%), compatible in 69/741 (9.3%) and discordant in 35/741(4.7%). Type-specific sequencing analysis of all samples revealed a 99.7% confirmation of PANArray™ HPV genotyping results, compared to 91.0% of DNA chip. The PANArray™ HPV test thus proved to be highly sensitive and accurate even when multiple HPV infections were present.
Surface Plasmon Resonance Biosensor Chips
김문일,한상희,신용범,정봉현 한국바이오칩학회 2007 BioChip Journal Vol.1 No.2
In this study, we describe biosensors predicated on surface plasmon resonance (SPR), a phenomenon that has recently become a focus of interest in biomedical science research. SPR has been shown to occur on two-dimensional metal surfaces, which support the SPR-active substrate on a glass prism. The SPR biosensor, which exploits the SPR effect, is a label-free and surface-sensitive spectroscopic system that utilizes measured changes in the local refraction index upon adsorption. Based on the SPR phenomenon, other technologies have been developed, including SPR-MS, SPR microscopy, localized SPR, and SPR imaging. The development of an SPR imaging system has already begun to overcome one of the difficulties inherent to conventional SPR, namely its high-throughput limitation. In this review, the detection principles and properties of SPR biosensors are briefly elucidated, and the possible future biomedical applications of SPR biosensors, including high-throughput screening in drug discovery, analysis of biomolecular interactions, and proteomics research are also discussed. This discussion is particularly salient now that SPR imaging provides another useful tool for the performance of high-throughput assays.
Quantum Mechanical Calculations for Binding Sites of Metalloproteins
조은성 한국바이오칩학회 2008 BioChip Journal Vol.2 No.2
Conventional docking methods which assume fixed charge model from force field parameters fail to predict right binding modes in a few groups of protein targets including metalloproteins. A new novel docking method with combined quantum mechanics / molecular mechanics (QM/MM) method has been applied to docking as a variable charge model and shown to exhibit improvement on the docking accuracy over fixed charge based methods. However, it has also been shown that there are a number of examples for which adoption of variable charge model fails to reproduce the native binding modes. The original implementation of QM/MM docking treated only ligands as quantum regions, which leaves metal ions present in binding sites with non-optimized charges. To address this problem, we extend the QM/MM docking method so that metal ions are included in quantum region, along with ligand atoms. This extension effectively rescales metal ion charge, but the results of docking experiment for binding mode prediction are unsatisfactory. Further analysis suggests that charge on metal ions transfers more greatly to surrounding protein atoms rather than ligand atoms, which explains the apparent over-correction of metal ion charge.
Effect of Quantum Mechanical Charges in Binding Sites of Metalloproteins
조은성 한국바이오칩학회 2007 BioChip Journal Vol.1 No.1
Conventional docking methods assume fixed charge model from force field parameters. Combined quantum mechanics/molecular mechanics (QM/MM) method has been applied to docking as a variable charge model and shown to exhibit improvement on the docking accuracy over fixed-charge-based methods. However, there are a number of examples for which adoption of variable charge model fails to reproduce the native binding mode. In particular, the method fails more often for metal-ion-containing proteins, metalloproteins. This class of proteins has highly polarized binding sites at which high-coordinate-numbered metal ions reside. We examine the docking results of this group of proteins and analyze the detailed interactions involved. We deduce the mechanism for success and failure of variable charge model. It is argued that extension of QM/MM docking method would correct the over-fitted charges so as to lead to better docking accuracy for docking of metalloproteins.
Effect of Food Sensitivity on Overweight Assessed Using Food-Specific Serum Immunoglobulin G Levels
이민형,길현민,Eugene Cheon,김소연,Jeahee Ryu,Hayoung Khil,강충원,박승일,강석성,금나나,권영은 한국바이오칩학회 2021 BioChip Journal Vol.15 No.3
Food sensitivity is considered to be implicated in obesity via chronic inflammation. Obesity has become a global epidemic, and overweight is a gateway to obesity. Hence, understanding the effect of food sensitivity on overweight is important for public health. To examine the association between food sensitivity and overweight, we compared the levels of diverse serological IgGs (total IgG, food-specific IgG [sIgG], and total food-sIgG [the sum of food-sIgG]) between overweight and lean Korean adults. A total of 164 Koreans aged 19–29 years participated in the study. We collected serum samples, information on frequency of food consumption, and height and weight measures to calculate body mass index (BMI). Immunoassays were performed using protein microarrays to determine total IgG, food-sIgG for each of the 68 food antigens, and the total food-sIgG. Participants were classified as overweight (BMI ≥ 25 kg/m 2 ) or lean (BMI < 25 kg/m 2 ). The Wilcoxon rank-sum test was used to compare the decile scores of IgG values between the groups. The total IgG ( P = 0.58) and total food-sIgG scores ( P = 0.27) did not differ significantly between the groups, precluding chronic inflammation as the cause of overweight. However, in the overweight group, food-sIgG scores against dairy products and seafood were significantly higher ( P < 0.05), whereas those against fruit and vegetables were significantly lower ( P < 0.05). In overweight individuals, food-sIgG scores against milk were not associated with the actual consumption ( P = 0.76), suggesting higher food-sIgG as an indicator of higher sensitivity than of higher consumption. Higher sensitivity to dairy foods and seafood and lower sensitivity to fruit and vegetables are likely associated with weight gain. Future studies are warranted to understand the heterogeneous associations between food-sIgGs and overweight.
Gene Expression Profiles of Nonylphenol as Representative EDCs in Normal Human Kidney HK-2 Cells
김승준,오문주,박혜원,김준섭,Saswati Paul,하정미,김연정,류재천,이철우,김현미,최경희,황승용 한국바이오칩학회 2008 BioChip Journal Vol.2 No.2
Nonylphenol (NP) is an organic compound of the wider family of alkylphenols and is a product of industrial synthesis formed during the alkylation process of phenols, particularly in the synthesis of polyethoxylate detergents. NP is an endocrine disruptors. Endocrine-disrupting chemicals (EDCs) are exogenous compounds that have the potential to hamper with hormonal regulations and the normal endocrine system and consequently cause health effects. In numerous chemical substances, the action mechanism of an endocrine disruptor is not clearly understood. In the present study, in vitro gene expression profiles were analyzed in nonylphenol-treated HK-2 cells using an Agilent Human 4×44 K whole genome array including 41,000 transcripts. Gene expression profiles were analyzed 3 and 48 hrs after exposure to NP with 2 different doses. We analyzed the gene expression profiles in order to understand the biological effects at level of gene functions and their time-dependent effects. A total of 1,727 genes were identified as being either over or down-expressed over 2-fold changes (P-value⁄0.05) in NP treated HK-2 cells. The functional classification of differentially expressed genes showed that cell death related genes were regulated by NP in HK-2 cells. 79 genes were time-dependent and differentially expressed, while 259 genes were concentration-dependent, all of which were selected using an ANOVA method. These data may support the understanding of the toxicity of nonylphenol in normal human kidney cells.
Xin Qiao,Silian Zhu,Shujiao Zhang,Hongmei Dong 한국바이오칩학회 2017 BioChip Journal Vol.11 No.1
To identify disrupted pathways associated with neonatal sepsis, we performed a research based on the combination of protein-protein interactions (PPIs) and pathway data. Firstly, a total of 23,292 genes, 787,896 PPIs and 1,675 human pathways were obtained, respectively. Then, under the threshold value of false discovery rate (FDR)<0.05 and a delta cut-off value >4.36, a total of 986 differentially expressed genes (DEGs) were identified. In the following, by degree centrality for the objective PPI network, 20 hub genes were obtained. Finally, pathway enrichment analysis and randomization tests indicated that pathways of gene expression, immune system and innate immune system were with remarkable significance in neonatal sepsis. Therefore, in the present study, we presented a novel pathway method, and we successfully identified several pathways in neonatal sepsis, which might be underlying indicators in the detection and treatment of neonatal sepsis.
Recent Development of Aptasensor for Influenza Virus Detection
김수민,김진명,노승우,손희상,이택 한국바이오칩학회 2020 BioChip Journal Vol.14 No.4
In nowadays, we have entered the new era of pandemics and the significance of virus detection deeply impacts human society. Viruses with genetic mutations are reported nearly every year, and people have prepared tools to detect the virus and vaccines to ensure proper treatments. Influenza virus (IV) is one of the most harmful viruses reporting various mutations, sub-types, and rapid infection speed for humans and animals including swine and poultry. Moreover, IV infection presents several harmful symptoms including cough, fever, diarrhea, chills, even causing death. To reduce the IV-induced harm, its proper and rapid detection is highly required. Conventional techniques were used against various IV sub-types including H1N1, H3N2, and H5N1. However, some of the techniques are time-consuming, expensive, or labor-intensive for detecting IV. Recently, the nucleic acid-based aptamer has gained attention as a novel bioprobe for constructing a biosensor. In this review, the authors discuss the recent progress in aptasensors for detecting IV in terms of an electrochemical and an optical biosensor.
The Fabrication of Cell Chips for Use as Bio-sensors
예철헌,민준홍,최정우 한국바이오칩학회 2007 BioChip Journal Vol.1 No.4
The development of biosensors for the detection of chemicals that are used by cells is of great interest to the pharmaceutical and environmental fields because of the potential for biosensors to measure unknown materials that cannot be detected based on their DNA or protein reactions. However, various problems associated with the introduction of cells to micro-devices, such as low reproducibility and sensitivity, must be overcome before biosensors can be used on a commercial scale. Here, we briefly discuss the cultivation of cells within microchips <i>in vitro</i> as well as the biosensor technologies that allow detection of cell properties and subsequent evaluation of specific analytes.
Immunosensors for Point-of-Care Testing
백세환,조정환,조일훈,오병근,김영기 한국바이오칩학회 2007 BioChip Journal Vol.1 No.1
Although immuno-chromatographic assays on membrane strips have been employed at points of care for more than 20 years, their applications have become limited to qualitative analyses of the analytes present at relatively high concentrations in samples. An evolution of technology in this field will be required in order to achieve the capability of detection sufficient for early diagnosis as well as a degree of quantification sufficient to allow for the monitoring of the sease progress, a digital display of analytical results, and automatic recording and correlation in a database. In order to attain proper sensitivity, the colloidal gold normally used as a tracer for colorimetry may be replaced with different signal generators, including fluorophores, magnetic beads, electrochemiluminescent substances, and enzymes. The means by which ntigen-antibody binding in the assay can be quantified as a measurable signal also varies, depending on the tracer employed and the transduction technology available. Indeed, we have devoted ourselves for more than ten years to the investigation of combinatorial substitutes onsisting of novel immunosensors that fulfill the demands inherent to medical diagnostics. In this review, selected immunosensor technologies developed in our laboratories are introduced, along with their detection principles and analytical characteristics.