• Tuberculosis and Respiratory Diseases
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• v.79 no.2
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• pp.85-90
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• 2016

Background: Lung cancer is the most common cause of cancer related death. Alterations in gene sequence, structure, and expression have an important role in the pathogenesis of lung cancer. Fusion genes and alternative splicing of cancer-related genes have the potential to be oncogenic. In the current study, we performed RNA-sequencing (RNA-seq) to investigate potential fusion genes and alternative splicing in non-small cell lung cancer. Methods: RNA was isolated from lung tissues obtained from 86 subjects with lung cancer. The RNA samples from lung cancer and normal tissues were processed with RNA-seq using the HiSeq 2000 system. Fusion genes were evaluated using Defuse and ChimeraScan. Candidate fusion transcripts were validated by Sanger sequencing. Alternative splicing was analyzed using multivariate analysis of transcript sequencing and validated using quantitative real time polymerase chain reaction. Results: RNA-seq data identified oncogenic fusion genes EML4-ALK and SLC34A2-ROS1 in three of 86 normal-cancer paired samples. Nine distinct fusion transcripts were selected using DeFuse and ChimeraScan; of which, four fusion transcripts were validated by Sanger sequencing. In 33 squamous cell carcinoma, 29 tumor specific skipped exon events and six mutually exclusive exon events were identified. ITGB4 and PYCR1 were top genes that showed significant tumor specific splice variants. Conclusion: In conclusion, RNA-seq data identified novel potential fusion transcripts and splice variants. Further evaluation of their functional significance in the pathogenesis of lung cancer is required.

• BMB Reports
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• v.43 no.5
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• pp.369-374
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• 2010

The PC12 is the widely used cell line to study neuronal differentiation. We had extensively investigated the details of protein expression in differentiated PC12 cells by proteomic analysis. The cells were incubated at the presence of nerve growth factor. We had analyzed the expression changes in the differentiating PC12 cells by 2-dimensional electrophoresis and the identification of the proteins using MALDI-TOF MS. By comparing expression pattern in the time course, we identified the candidate genes which are associated with neuronal differentiation. Among these genes, we performed real-time PCR analysis to validate $Idh3{\alpha}$ expression by the time course. To identify the function of $Idh3{\alpha}$ in neuronal differentiation stage, the transfection of $Idh3{\alpha}$ to PC12 cells was performed. As a result, we proved that up-regulation of $Idh3{\alpha}$ causes reduction in neural differentiation of PC12 cells. Based on these data, we suggest that $Idh3{\alpha}$ plays a role to the neuronal differentiation.

• International Journal of Industrial Entomology and Biomaterials
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• v.31 no.1
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• pp.14-19
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• 2015

In a previous report, we identified several candidate antimicrobial peptides through de novo RNA sequencing of the centipede Scolopendra subspinipes mutilans. Here, we identify and characterize one of these peptides, Scolopendrasin I. We identified the centipede antimicrobial peptide Cecropin from the centipede transcriptome using an SVM algorithm, and subsequently analyzed the amino acid sequence for predicted secondary structure using a GOR algorithm. We identified an alpha helical region of Cecropin and named it Scolopendrasin I. We then assessed antimicrobial and hemolytic activity of Scolopendrasin I. Scolopendrasin I showed antimicrobial activity against various microbes, including antibiotic-resistant Gram-negative bacteria, in a radial diffusion assay. Scolopendrasin I had potent antibacterial activity against acne-associated microbes in a colony count assay and showed no hemolytic activity in a hemolysis assay. In addition, we confirmed that Scolopendrasin I bound to the surface of bacteria via a specific interaction with lipoteichoic acid and lipopolysaccharide, two components of bacterial cell membranes. In conclusion, the results presented here provide evidence that this is an efficient strategy for antimicrobial peptide candidate identification and that Scolopendrasin I has potential for successful antibiotic development.

• Journal of Microbiology and Biotechnology
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• v.16 no.3
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• pp.457-464
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• 2006

Three extracellular proteases (Vpr, peptidase T, and subtilisin) were identified from the culture supernatant of Bacillus subtilis KCTC 3014. All the proteins were partially purified as a mature form by using a DEAE-cellulose ion-exchange column chromatography. Their activities were determined by using zymography and densitometry. The relative molecular masses of Vpr and peptidase T (PepT) were determined to be 68 and 48 kDa by SDS-PAGE and zymography, respectively. However, subtilisin formed a 'binding mode' at the top of the separating gel. After denaturation by boiling at $100^{\circ}C$ for 5 min, its molecular mass was determined to be 29 kDa, whereas its activity was lost. The optimal pH of Vpr, PepT, and subtilisin were 9.0, 6.0-7.0, and 7.0-8.0, respectively. The optimal temperature of Vpr, PepT, and subtilisin was 40, 50, and $40^{\circ}C$, respectively. Inhibitor test revealed that Vpr and subtilisin were serine proteases and that PepT was a metalloprotease. Interestingly, we found that Vpr showed no enzyme activity on a 2DE zymogram gel. Three genes, vpr, pepT, and apr (encoding subtilisin protein), were cloned and their nucleotide and deduced amino acid sequences were determined.

• Structural Engineering and Mechanics
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• v.27 no.5
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• pp.625-638
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• 2007

The damage detection process may appear difficult to be implemented for truss structures because not all degrees of freedom in the numerical model can be experimentally measured. In this context, the damage locating vector (DLV) method, introduced by Bernal (2002), is a useful approach because it is effective when operating with an arbitrary number of sensors, a truncated modal basis and multiple damage scenarios, while keeping the calculation in a low level. In addition, the present paper also evaluates the noise influence on the accuracy of the DLV method. In order to verify the DLV behavior under different damages intensities and, mainly, in presence of measurement noise, a parametric study had been carried out. Different excitations as well as damage scenarios are numerically tested in a continuous Warren truss structure subjected to five noise levels with a set of limited measurement sensors. Besides this, it is proposed another way to determine the damage locating vectors in the DLV procedure. The idea is to contribute with an alternative option to solve the problem with a more widespread algebraic method. The original formulation via singular value decomposition (SVD) is replaced by a common solution of an eigenvector-eigenvalue problem. The final results show that the DLV method, enhanced with the alternative solution proposed in this paper, was able to correctly locate the damaged bars, using an output-only system identification procedure, even considering small intensities of damage and moderate noise levels.

• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.36 no.3
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• pp.238-243
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• 2008

Several experimental techniques for identifying the noise sources distributed over a moving vehicle have been developed recently and are used to design a low noise vehicle. The beamforming method, which uses phase information between several microphones to localize the source position, is proved to be one of the promising techniques applicable even under complicated test environments. In this study a beamforming algorithm is developed and applied to measure the dominant noise sources on a passenger car passing by. Unlike the acoustic signals from a stationary noise source, the sound generated from a moving source is distorted due to the Doppler effects. The information about the speed and relative position of the vehicle are used to eliminate the Doppler effects from the measured acoustic signal by using a de-Dopplerization algorithm. The noise generated from a moving vehicle can be grouped in many ways, however, tire noise and the noise generated from the engine are distinguishable at the speeds being tested.

• Journal of Microbiology and Biotechnology
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• v.16 no.6
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• pp.911-920
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• 2006

[ $CD8^+$ ] T Iymphocytes with the cytotoxic activity and capability to release various cytokines are the major players in immune responses against viral infection and cancer. To identify the proteins specific to resting or activated human CD8$^+$ T cells, human CD8$^+$ T cells were activated with anti-CD3+anti-CD28 mAb in the presence of IL-2. The solubilized proteins from resting and activated human CD8$^+$ T cells were separated by high-resolution two-dimensional polyacrylamide gel electrophoresis, and their proteomes were analyzed. Proteomic analysis of resting and activated T cells resulted in identification of 35 proteins with the altered expression. Mass spectrometry coupled with Profound and SWISS-PROT database analysis revealed that these identified proteins are to be functionally associated with cell proliferation, metabolic pathways, antigen presentation, and intracellular signal transduction pathways. We also identified six unknown proteins predicted from genomic DNA sequences specific to resting or activated CD8$^+$ T cells. Protein network studies and functional characterization of these novel proteins may provide new insight into the signaling transduction pathway of CD8$^+$ T cell activation.

• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.659-665
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• 2016

The oligosaccharides in human milk constitute a major innate immunological mechanism by which breastfed infants gain protection against infectious diarrhea. Clostridium difficile is the most important cause of nosocomial diarrhea, and the C-terminus of toxin A with its carbohydrate binding site, TcdA-f2, demonstrates specific abolishment of cytotoxicity and receptor binding activity upon diethylpyrocarbonate modification of the histidine residues in TcdA. TcdA-f2 was cloned and expressed in E. coli BL21 (DE3). A human milk oligosaccharide (HMO) mixture displayed binding with TcdA-f2 at 38.2 respond units (RU) at the concentration of 20 μg/ml, whereas the eight purified HMOs showed binding with the carbohydrate binding site of TcdA-f2 at 3.3 to 14 RU depending on their structures via a surface plasma resonance biosensor. Among them, Lacto-N-fucopentaose V (LNFPV) and Lacto-N-neohexaose (LNnH) demonstrated tight binding to TcdA-f2 with docking energy of −9.48 kcal/mol and −12.81 kcal/mol, respectively. It displayed numerous hydrogen bonding and hydrophobic interactions with amino acid residues of TcdA-f2.

• Proceedings of the Korea Contents Association Conference
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• 2009.05a
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• pp.993-997
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• 2009

Designs in the modernism era were produced for the purpose of standardization of items and devices centered on efficiency and functions, and the will of design consumers in the industrial era, when consumption exceeded production, was limited to the objects of consumption. But, after the post-modernism era, design consumers have started to entail acts of exclusive possession such as participation in the design idolization, partipation, tuning, control and parody as design consumers in the digital environment do not passively accept what is given to them anymore, and aggressively intervene in the process of design production and management. It is expected that designs will change from the system in which only professionals can produce and manage its production to that of cooperating with consumers to produce designs, and various forms of consumers' exclusive possession will change all sort of design environments including production methods surrounding design products and distribution. Therefore, this study seeks to induce efficient design production by understanding changes of consumers' cultural environment resisting standardization and structuralization with smoothy perception between producers and consumers through classification of consumers' appropriation into de-construction, re-signification and self-identification.

• Journal of Chest Surgery
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• v.47 no.5
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• pp.458-464
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• 2014

Background: The effort to detect lung cancer in ever-earlier stages leads to the identification of an increasing number of patients without preoperative histological diagnosis. The aim of this study is to determine the prevalence and characteristics of benign lesions excised in the context of lung cancer surgery. Methods: We retrospectively analyzed data from 125 surgical procedures. We compared the preoperative clinical or cyto-histological diagnosis with the surgical-pathologic diagnosis in order to identify the percentage of benign lesions excised. Furthermore, other parameters were analyzed, such as age, sex, tumor size, the presence of calcification, and the type of surgery according to subgroup. Results: Of the 125 patients included in the study, 63 (50.4%) had a preoperative histological diagnosis of malignancy, corresponding to 56 cases (44.8%) of primary lung cancer and 7 cases (5.6%) of metastases. The 62 (49.6%) remaining cases without preoperative histological diagnosis were divided among 50 (40%) solitary pulmonary nodules and 12 (9.6%) pulmonary masses. According to the postoperative pathologic examination, we identified 12 (9.6%) benign lesions excised during lung cancer surgery. There were no statistically significant differences by subgroups with respect to age or sex. We found statistically significant evidence regarding the size and wedge resection as the surgical technique of choice for this type of benign lesion. Conclusion: Our study obtained results similar to those published by other groups regarding the resection of benign lesions in lung cancer surgery. This percentage could be a quality management index of indeterminate lung lesions.