• Journal of Ecology and Environment
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• v.34 no.3
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• pp.323-331
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• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• The Plant Pathology Journal
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• v.31 no.1
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• pp.72-77
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• 2015

Spot blotch caused by the hemibiotrophic pathogen Cochliobolus sativus has been the major yield-reducing factor for barley production during the last decade. Monitoring transcriptional reorganization triggered in response to this fungus is an essential first step for the functional analysis of genes involved in the process. To characterize the defense responses initiated by barley resistant and susceptible cultivars, a survey of transcript abundance at early time points of C. sativus inoculation was conducted. A notable number of transcripts exhibiting significant differential accumulations in the resistant and susceptible cultivars were detected compared to the non-inoculated controls. At the p-value of 0.0001, transcripts were divided into three general categories; defense, regulatory and unknown function, and the resistant cultivar had the greatest number of common transcripts at different time points. Quantities of differentially accumulated gene transcripts in both cultivars were identified at 24 h post infection, the approximate time when the pathogen changes trophic lifestyles. The unique and common accumulated transcripts might be of considerable interest for enhancing effective resistance to C. sativus.

• Journal of Microbiology
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• v.45 no.5
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• pp.441-446
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• 2007

HIV-1 coreceptor usage and phenotype mainly determined by V3 loop are associated with the disease progression of AIDS. Predicting HIV-1 coreceptor usage and phenotype facilitates the monitoring of R5-to-X4 switch and treatment decision-making. In this study, we employed random forest to predict HIV-1 biological phenotype, based on 37 random features of V3 loop. In comparison with PSSM method, our RF predictor obtained higher prediction accuracy (95.1% for coreceptor usage and 92.1% for phenotype), especially for non-B non-C HIV-l subtypes (96.6% for coreceptor usage and 95.3% for phenotype). The net charge, polarity of V3 loop and five V3 sites are seven most important features for predicting HIV-1 coreceptor usage or phenotype. Among these features, V3 polarity and four V3 sites (22, 12, 18 and 13) are first reported to have high contribution to HIV-1 biological phenotype prediction.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.1
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• pp.161-166
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• 2014

Lung cancer is the most common causes of cancer-related deaths worldwide, and a lack of effective methods for early diagnosis has greatly impacted the prognosis and survival rates of the affected patients. Tumor-initiating cells (TICs) are considered to be largely responsible for tumor genesis, resistance to tumor therapy, metastasis, and recurrence. In addition to representing a good potential treatment target, TICs can provide clues for the early diagnosis of cancer. MicroRNA (miRNA) alterations are known to be involved in the initiation and progression of human cancer, and the detection of related miRNAs in TICs is an important strategy for lung cancer early diagnosis. As Hsa-miR-155 (miR-155) can be used as a diagnostic marker for non-small cell lung cancer (NSCLC), a smart molecular beacon of miR-155 was designed to image the expression of miR-155 in NSCLC cases. TICs expressing CD133 and CD338 were obtained from A549 cells by applying an immune magnetic bead isolation system, and miR-155 was detected using laser-scanning confocal microscopy. We found that intracellular miR-155 could be successfully detected using smart miR-155 molecular beacons. Expression was higher in TICs than in A549 cells, indicating that miR-155 may play an important role in regulating bio-behavior of TICs. As a non-invasive approach, molecular beacons could be implemented with molecular imaging to diagnose lung cancer at early stages.

• Molecules and Cells
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• v.27 no.3
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• pp.337-343
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• 2009

We developed a novel on-chip activity assay using protein arrays for quantitative and rapid analysis of transglutaminase activity in mammalian cells. Transglutaminases are a family of $Ca^{2+}$-dependent enzymes involved in cell regulation as well as human diseases such as neurodegenerative disorders, inflammatory diseases and tumor progression. We fabricated the protein arrays by immobilizing N,N'-dimethylcasein (a substrate) on the amine surface of the arrays. We initiated transamidating reaction on the protein arrays and determined the transglutaminase activity by analyzing the fluorescence intensity of biotinylated casein. The on-chip transglutaminase activity assay was proved to be much more sensitive than the $[^3H]putrescine$-incorporation assay. We successfully applied the on-chip assay to a rapid and quantitative analysis of the transglutaminase activity in all-trans retinoic acid-treated NIH 3T3 and SH-SY5Y cells. In addition, the on-chip transglutaminase activity assay was sufficiently sensitive to determine the transglutaminase activity in eleven mammalian cell lines. Thus, this novel on-chip transglutaminase activity assay was confirmed to be a sensitive and high-throughput approach to investigating the roles of transglutaminase in cellular signaling, and, moreover, it is likely to have a strong potential for monitoring human diseases.

• Smart Structures and Systems
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• v.8 no.1
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• pp.119-137
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• 2011

A bio-inspired two-mode structural health monitoring (SHM) system based on the Na$\ddot{i}$ve Bayes (NB) classification method is discussed in this paper. To implement the molecular biology based Deoxyribonucleic acid (DNA) array concept in structural health monitoring, which has been demonstrated to be superior in disease detection, two types of array expression data have been proposed for the development of the SHM algorithm. For the micro-vibration mode, a two-tier auto-regression with exogenous (AR-ARX) process is used to extract the expression array from the recorded structural time history while an ARX process is applied for the analysis of the earthquake mode. The health condition of the structure is then determined using the NB classification method. In addition, the union concept in probability is used to improve the accuracy of the system. To verify the performance and reliability of the SHM algorithm, a downscaled eight-storey steel building located at the shaking table of the National Center for Research on Earthquake Engineering (NCREE) was used as the benchmark structure. The structural response from different damage levels and locations was collected and incorporated in the database to aid the structural health monitoring process. Preliminary verification has demonstrated that the structure health condition can be precisely detected by the proposed algorithm. To implement the developed SHM system in a practical application, a SHM prototype consisting of the input sensing module, the transmission module, and the SHM platform was developed. The vibration data were first measured by the deployed sensor, and subsequently the SHM mode corresponding to the desired excitation is chosen automatically to quickly evaluate the health condition of the structure. Test results from the ambient vibration and shaking table test showed that the condition and location of the benchmark structure damage can be successfully detected by the proposed SHM prototype system, and the information is instantaneously transmitted to a remote server to facilitate real-time monitoring. Implementing the bio-inspired two-mode SHM practically has been successfully demonstrated.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7421-7426
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• 2013

Background: Colorectal cancer is the fourth most common cancer worldwide and the second leading cause of cancer-related death. FOLFOX is the most common regimen used in the first-line chemotherapy in advanced colorectal cancer, but only half of the patients respond to this regimen and we have almost no clue in predicting resistance in such first-line application. Methods: To explore the potential molecular biomarkers predicting the resistance of FOLFOX regimen as the first-line treatment in advanced colorectal cancer, we screened microRNAs in serum samples from drug-responsive and drug-resistant patients by microarrays. Then differential microRNA expression was further validated in an independent population by reverse transcription and quantitative real-time PCR. Results: 62 microRNAs expressing differentially with fold-change >2 were screened out by microarray analysis. Among them, 5 (miR-221, miR-222, miR-122, miR-19a, miR-144) were chosen for further validation in an independent population (N=72). Our results indicated serum miR-19a to be significantly up-regulated in resistance-phase serum (p=0.009). The ROC curve analysis showed that the sensitivity of serum miR-19a to discriminate the resistant patients from the response ones was 66.7%, and the specificity was 63.9% when the AUC was 0.679. We additionally observed serum miR-19a had a complementary value for cancer embryonic antigen (CEA). Stratified analysis further revealed that serum miR-19a predicted both intrinsic and acquired drug resistance. Conclusions: Our findings confirmed aberrant expression of serum miR-19a in FOLFOX chemotherapy resistance patients, suggesting serum miR-19a could be a potential molecular biomarker for predicting and monitoring resistance to first-line FOLFOX chemotherapy regimens in advanced colorectal cancer patients.

• Journal of the Korean Electrochemical Society
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• v.18 no.4
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• pp.137-142
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• 2015

$Mn_{1+X}Co_{2-X}O_4$ solid solutions with various Mn/Co ratios were synthesized by a combustion method, and used as cathode catalysts for lithium/air secondary battery. Their electrochemical and physicochemical properties were investigated. The morphology was examined by transmission electron microscopy (TEM), and the crystallinity was confirmed by X-ray diffraction (XRD) analyses. For the measurement of electrochemical properties, charge and discharge measurements were carried out at a constant current density of $0.2mA/cm^2$, monitoring the voltage change. Electrochemical impedance spectroscopy (EIS) analyses were also employed to examine the change in charge transfer resistance during charge-discharge process. $Mn_{1+X}Co_{2-X}O_4$ solid solutions showed enhanced cycleability as a cathode of Li/air secondary battery, and the performance was found to be strongly dependent on Mn/Co ratio. Among synthesized catalysts, $Mn_{1.5}Co_{1.5}O_4$ exhibited the best performance and cycleability, due to high charge transfer rate.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.806-811
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• 2007

Bacillus anthracis is a soil pathogen capable of causing anthrax that is closely related to several environmental species, including B. cereus, B. mycoides, and B. thuringiensis. DNA homology studies showed that B. anthracis, B. cereus, B. mycoides, and B. thuringiensis are closely related, with a high sequence homology. To establish a method to specifically detect B. anthracis in situations such as environmental contamination, we initially performed RAPD-PCR with a 10-mer random primer and confirmed the presence of specific PCR bands only in B. anthracis species. One region specific for B. anthracis was cloned and sequenced, and an internal primer set was designed to amplify a 241-bp DNA fragment within the sequenced region. The PCR system involving these specific primer sets has practical applications. Using lyses methods to prepare the samples for PCR, it was possible to quickly amplify the 241-bp DNA segment from samples containing only a few bacteria. Thus, the PCR detection method developed in this study is expected to facilitate the monitoring of environmental B. anthracis contamination.

• Journal of Korean Society on Water Environment
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• v.39 no.6
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• pp.465-474
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• 2023

The chemical composition and molecular weight characteristics of dissolved organic matter (DOM) exert a profound influence on the efficiency of organic matter removal in water treatment systems, acting as efficiency predictive indicators. This research evaluated the primary chemical and molecular weight properties of DOM derived from diverse sources, including rivers, lakes, and biomasses, and assessed their relationship with the efficiency of coagulation/flocculation treatments. Dissolved organic carbon (DOC) removal efficiency through coagulation/flocculation exhibited significant correlations with DOM's hydrophobic distribution, the ratio of humic-like to protein-like fluorescence, and the molecular weight associated with humic substances (HS). These findings suggest that the DOC removal rate in coagulation/flocculation processes is enhanced by a higher presence of HS in DOM, an increased influence of externally sourced DOM, and more presence of high molecular weight compounds. The results of this study further posit that the efficacy of water treatment processes can be more accurately predicted when considering multiple DOM characteristics rather than relying on a singular trait. Based on major results from this study, a predictive model for DOC removal efficiency by coagulation/flocculation was formulated as: 24.3 - 7.83 × (fluorescence index) + 0.089 × (hydrophilic distribution) + 0.102 × (HS molecular weight). This proposed model, coupled with supplementary monitoring of influent organic matter, has the potential to enhance the design and predictive accuracy for coagulation/flocculation treatments targeting DOC removal in future applications.