• Molecules and Cells
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• v.37 no.12
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• pp.873-880
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• 2014

In our previous study, miRNA-183, a miRNA in the miR-96-182-183 cluster, was significantly over-expressed in esophageal squamous cell carcinoma (ESCC). In the present study, we explored the oncogenic roles of miR-183 in ESCC by gain and loss of function analysis in an esophageal cancer cell line (EC9706). Genome-wide mRNA micro-array was applied to determine the genes that were regulated directly or indirectly by miR-183. 3'UTR luciferase reporter assay, RT-PCR, and Western blot were conducted to verify the target gene of miR-183. Cell culture results showed that miR-183 inhibited apoptosis (p < 0.05), enhanced cell proliferation (p < 0.05), and accelerated G1/S transition (p < 0.05). Moreover, the inhibitory effect of miR-183 on apoptosis was rescued when miR-183 was suppressed via miR-183 inhibitor (p < 0.05). Western blot analysis showed that the expression of programmed cell death 4 (PDCD4), which was predicted as the target gene of miR-183 by microarray profiling and bioinformatics predictions, decreased when miR-183 was over-expressed. The 3'UTR luciferase reporter assay confirmed that miR-183 directly regulated PDCD4 by binding to sequences in the 3'UTR of PDCD4. Pearson correlation analysis further confirmed the significant negative correlation between miR-183 and PDCD4 in both cell lines and in ESCC patients. Our data suggest that miR-183 might play an oncogenic role in ESCC by regulating PDCD4 expression.

• Journal of the Korean Society of Radiology
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• v.9 no.7
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• pp.425-431
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• 2015

Measurement accuracy was evaluated for the respiratory air flow transducer developed for applications under emergent situations. Pressure-Flow calibration equation was obtained by acquisition of air flow signals from the transducer in response to 6 flow waveforms, similar to those of artificial ventilation, generated by the standard flow generator system. Tidal volume and maximal flow rate were calculated on the flow signal then compared with the error-free data obtained by the linear displacement transducer of the flow generator system. Mean relative error of the tidal volume was within 3% and that of the maximal flow rate, approximately 5%, demonstrating accurate enough measurements. Therefore, the transducer could be applied to emergent situations to monitor the respiratory air flow signal as well as diagnostic parameters in real time.

• Interdisciplinary Bio Central
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• v.1 no.3
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• pp.9.1-9.6
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• 2009

Introduction: In the mass spectrometry-based proteomics, biological samples are analyzed to identify proteins by mass spectrometer and database search. Database search is the process to select the best matches to the experimental mass spectra among the amino acid sequence database and we identify the protein as the matched sequence. The match score is defined to find the matches from the database and declare the highest scored hit as the most probable protein. According to the score definition, search result varies. In this study, the difference among search results of different search engines or different databases was investigated, in order to suggest a better way to identify more proteins with higher reliability. Materials and Methods: The protein extract of human mesenchymal stem cell was separated by several bands by one-dimensional electrophorysis. One-dimensional gel was excised one by one, digested by trypsin and analyzed by a mass spectrometer, FT LTQ. The tandem mass (MS/MS) spectra of peptide ions were applied to the database search of X!Tandem, Mascot and Sequest search engines with IPI human database and SwissProt database. The search result was filtered by several threshold probability values of the Trans-Proteomic Pipeline (TPP) of the Institute for Systems Biology. The analysis of the output which was generated from TPP was performed. Results and Discussion: For each MS/MS spectrum, the peptide sequences which were identified from different conditions such as search engines, threshold probability, and sequence database were compared. The main difference of peptide identification at high threshold probability was caused by not the difference of sequence database but the difference of the score. As the threshold probability decreases, the missed peptides appeared. Conversely, in the extremely high threshold level, we missed many true assignments. Conclusion and Prospects: The different identification result of the search engines was mainly caused by the different scoring algorithms. Usually in proteomics high-scored peptides are selected and low-scored peptides are discarded. Many of them are true negatives. By integrating the search results from different parameter and different search engines, the protein identification process can be improved.

• Interdisciplinary Bio Central
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• v.3 no.3
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• pp.10.1-10.8
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• 2011

Introduction: Hash functions are computer algorithms that protect information and secure transactions. In response to the NIST's "International Call for Hash Function", we developed a biological hash function using the computing capabilities of bacteria. We designed a DNA-based XOR logic gate that allows bacterial colonies arranged in a series on an agar plate to perform hash function calculations. Results and Discussion: In order to provide each colony with adequate time to process inputs and perform XOR logic, we designed and successfully demonstrated a system for time-delayed bacterial growth. Our system is based on the diffusion of ${\ss}$-lactamase, resulting in destruction of ampicillin. Our DNA-based XOR logic gate design is based on the op-position of two promoters. Our results showed that $P_{lux}$ and $P_{OmpC}$ functioned as expected individually, but $P_{lux}$ did not behave as expected in the XOR construct. Our data showed that, contrary to literature reports, the $P_{lux}$ promoter is bidirectional. In the absence of the 3OC6 inducer, the LuxR activator can bind to the $P_{lux}$ promoter and induce backwards transcription. Conclusion and Prospects: Our system of time delayed bacterial growth allows for the successive processing of a bacterial hash function, and is expected to have utility in other synthetic biology applications. While testing our DNA-based XOR logic gate, we uncovered a novel function of $P_{lux}$. In the absence of autoinducer 3OC6, LuxR binds to $P_{lux}$ and activates backwards transcription. This result advances basic research and has important implications for the widespread use of the $P_{lux}$ promoter.

• Parasites, Hosts and Diseases
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• v.53 no.4
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• pp.403-411
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• 2015

Plasmodium falciparum can invade all stages of red blood cells, while Plasmodium vivax can invade only reticulocytes. Although many P. vivax proteins have been discovered, their functions are largely unknown. Among them, P. vivax reticulocyte binding proteins (PvRBP1 and PvRBP2) recognize and bind to reticulocytes. Both proteins possess a C-terminal hydrophobic transmembrane domain, which drives adhesion to reticulocytes. PvRBP1 and PvRBP2 are large (>326 kDa), which hinders identification of the functional domains. In this study, the complete genome information of the P. vivax RBP family was thoroughly analyzed using a prediction server with bioinformatics data to predict B-cell epitope domains. Eleven pvrbp family genes that included 2 pseudogenes and 9 full or partial length genes were selected and used to express recombinant proteins in a wheat germ cell-free system. The expressed proteins were used to evaluate the humoral immune response with vivax malaria patients and healthy individual serum samples by protein microarray. The recombinant fragments of 9 PvRBP proteins were successfully expressed; the soluble proteins ranged in molecular weight from 16 to 34 kDa. Evaluation of the humoral immune response to each recombinant PvRBP protein indicated a high antigenicity, with 38-88% sensitivity and 100% specificity. Of them, N-terminal parts of PvRBP2c (PVX_090325-1) and PvRBP2 like partial A (PVX_090330-1) elicited high antigenicity. In addition, the PvRBP2-like homologue B (PVX_116930) fragment was newly identified as high antigenicity and may be exploited as a potential antigenic candidate among the PvRBP family. The functional activity of the PvRBP family on merozoite invasion remains unknown.

• Animal cells and systems
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• v.16 no.1
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• pp.11-19
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• 2012

A major concern regarding the collection and storage of biodiversity information is the inefficiency of conventional taxonomic approaches in dealing with a large number of species. This inefficiency has increased the demand for automated, rapid, and reliable molecular identification systems and large-scale biological databases. DNA-based taxonomic approaches are now arguably a necessity in biodiversity studies. In particular, DNA barcoding using short DNA sequences provides an effective molecular tool for species identification. We constructed a large-scale database system that holds a collection of 5531 barcode sequences from 2429 Korean species. The Korea Barcode of Life database (KBOL, http://koreabarcode.org) is a web-based database system that is used for compiling a high volume of DNA barcode data and identifying unknown biological specimens. With the KBOL system, users can not only link DNA barcodes and biological information but can also undertake conservation activities, including environmental management, monitoring, and detecting significant organisms.

• Journal of Life Science
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• v.30 no.11
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• pp.1012-1020
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• 2020

Remicade is a therapeutic biosimilar natural antibody in which the mouse variable domain has been linked to the human constant domain. It is a chimeric monoclonal antibody specific to tumor necrosis factor-alpha (TNF-α) and has been developed for the treatment of rheumatoid arthritis. To investigate the biological activity of the Remicade antibody, we carried out a bioinformatics study using a protein data bank to characterize the TNF-α antigen binding mechanism of the Remicade natural antibody. Because the production of the Remicade antibody is often limited by genetic instability of the natural antibody-producing cell, we generated a Remicade single-chain variable domain fragment antibody (Remicade) in which a heavy chain variable domain (VH) is joined with a light chain variable domain (VL) by a polypeptide linker. Furthermore, Remicade was fused to a leucine zipper (RemicadeScZip) for higher production and higher antigen-binding activity than Remicade. The Remicade and Remicade ScZip were expressed in Escherichia coli and purified by a Ni⁺-NTA-agarose column. As expected, the purified proteins had migrated as 28.80 kDa and 33.96 kDa in sodium dodecyl sulfate-polyacrylamide electrophoresis. The TNF-α antigen binding activity of Remicade was not observed by ELISA and western blot. In contrast, RemicadeScZip showed antigen-binding activity. Additional bio-layer interferometry analysis confirmed the antigen-binding activity of RemicadeScZip, suggesting that the leucine zipper stabilized the folding of RemicadeScZip in a denatured condition and improved the TNF-α antigenbinding activity.

• Korean Journal of Microbiology
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• v.50 no.4
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• pp.360-367
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• 2014

Candida albicans is an opportunistic and the most prevalent fungal pathogen that can cause superficial and systemic infections in immunocompromised patients. C. albicans can promote the transition from budding yeast to filamentous form, generating biofilms. Infections associated with C. albicans biofilms are frequently resistant to conventional antifungal therapy. Therefore, the development of more effective antifungal drugs related with biofilm formation is required urgently. The roots of Rheum undulatum have been used for medicinal purposes in Korea and China traditionally. The aim of present study was to evaluate the effect of R. undulatum extract upon preformed biofilms of 12 clinical C. albicans isolates and the antifungal activities. Its effect on preformed biofilms was evaluated using XTT reduction assay, and metabolic activity of all tested strains was reduced significantly ($49.4{\pm}6.0%$) at 0.098 mg/ml R. undulatum. The R. undulatum extract blocked the adhesion of C. albicans biofilms to polystyrene surfaces, and damaged the cell membrane integrity of C. albicans which was analyzed by CFDA, AM, and propidium iodide double staining. It caused cell lysis which was observed by Confocal laser scanning and phase contrast microscope after propidium iodide and neutral red staining, respectively. Membrane permeability was changed as evidenced by crystal violet uptake. The data suggest that R. undulatum inhibits biofilm formation by C. albicans, which can be associated with the damage of the cell membrane integrity, the changes in the membrane permeability and the cell lysis of C. albicans.

• Journal of Sensor Science and Technology
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• v.14 no.2
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• pp.69-77
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• 2005

The electronic nose (e-nose) has been used in food industry and quality controls in plastic packaging. Recently it finds its applications in medical diagnosis, specifically on detection of diabetes, pulmonary or gastrointestinal problem, or infections by examining odors in the breath or tissues with its odor characterizing ability. Moreover, the use of portable e-nose enables the on-site measurements and analysis of vapors without extra gas-sampling units. This is expected to widen the application of the e-nose in various fields including point-of-care-test or e-health. In this study, a PDA-based portable e-nose was developed using micro-machined gas sensor array and miniaturized electronic interfaces. The rich capacities of the PDA in its computing power and various interfaces are expected to provide the rapid and application specific development of the diagnostic devices, and easy connection to other facilities through information technology (IT) infra. For performance verification of the developed portable e-nose system, Six different vapors were measured using the system. Seven different carbon-black polymer composites were used for the sensor array. The results showed the reproducibility of the measured data and the distinguishable patterns between the vapor species. Additionally, the application of two typical pattern recognition algorithms verified the possibility of the automatic vapor recognition from the portable measurements. These validated the portable e-nose based on PDA developed in this study.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.4
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• pp.269-274
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• 2014

Series of field experiments were conducted to evaluate the long term effect of gypsum and crop residue on crop yield and soil health in rice-wheat crop rotation system in salt affected soil. A saline-sodic field having $EC_e$ (electrical conductivity of the saturation extract) 4.77 ($dSm^{-1}$); pH ($H_2O$) 8.96; SAR 43.78 ($mmol\;L^{-1}$) and gypsum requirement (G.R.) 2.86 (Mg $acre^{-1}$) was selected on Soil Salinity Research Institute Farm. Five treatments consisting of ($T_1$) control, ($T_2$) gypsum at 100% G.R., ($T_3$) gypsum at 25% G.R. + wheat straw at $3Mg\;ha^{-1}$, ($T_4$) gypsum at 25% G.R. + rice straw at $3Mg\;ha^{-1}$, ($T_5$) gypsum at 25% G.R.+ rice and wheat straw at $3Mg\;ha^{-1}$ were replicated four times under completely randomized block design. The data indicated that grain and straw yield of rice and wheat was significantly (P<0.05) increased by all the amendments used either single or in combination. $T_2$ (gypsum at 100% G.R.) significantly (P<0.05) increased grain and straw yield of rice and wheat crops followed by $T_3$ (gypsum at 25% G.R. + wheat straw at $3Mg\;ha^{-1}$) when compared with control. Soil properties were also improved by used amendments, pronounced decreased in $EC_e$, $pH_s$ and SAR were recorded in $T_2$ followed by $T_3$. The efficiency of the treatments could be arranged in following order gypsum at 100% G.R.> gypsum at 25% G.R. + wheat straw at $3Mg\;ha^{-1}$ > gypsum at 25% G.R. + rice and wheat straw at $3Mg\;ha^{-1}$ > gypsum at 25% G.R. + rice straw at $3Mg\;ha^{-1}$ > control.