• 한국산학기술학회논문지
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• 제12권1호
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• pp.312-317
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• 2011

캡사이신 채널로 알려진 바닐로이드 수용체 TRPV1 (캡사이신채널, Transient Receptor Potential Vanilloid 1)은 통증발현에서 중요한 역할을 하는 것으로 알려져 있다. 하지만 TRPV1의 활성조절에 관여하는 단백질에 대하여는 알려진 바가 많지 않다. 최근 rat TRPV1과 직접적으로 결합하는 단백질을 탐색하여 mouse Rab11-FIP3 (rab11-family interaction protein 3)가 rat TRPV1과 직접적으로 결합한다는 것이 보고되었다. Rab11은 여러 가지의 세포내 이동에 관여하는 것으로 보고되었다. 그러므로 Rab11-FIP3과의 결합을 통해 TRPV1의 세포막으로의 이동에 관여할 것으로 추측할 수 있다. 본 연구에서는 전에 보고된 연구가 mouse와 rat 이라는 다른 종의 단백질끼리의 결합이기 때문에 같은 종에서의 상호작용을 확인하고 Rab11-FIP3의 TRPV1의 세포막으로의 이동에서의 역할을 알아보고자 현재까지 동정되지 않은 rat의 Rab11-FIP3의 유전자를 GenBank 서열을 바탕으로 rat 뇌의 RNA 로부터 cDNA 를 클로닝하여 유전자를 분리하고 TRPV1 과의 관계를 세포생물학적으로 알아보았다. 연구결과 rat의 Rab11-FIP3는 489개의 아미노산 서열을 가지고 있으며 human과는 80%, mouse와는 90% 이상 아미노산 서열의 상동성을 보였다. 조직별 분포는 심장, 뇌, 간, 콩팥, 정소에서 발현되고 있는 것을 northern blot assay와 western blot assay 로 확인하였다. rat 의 뇌조직에서 TRPV1 과 Rab11-FIP3 단백질이 결합하여 colocalize 하는 것을 면역화학방법으로 확인하였다. 이 결합은 같은 family 의 TRPV2 와는 결합하지 않는 특이적 결합이므로 Rab11-FIP3 가 TRPV1 과 상호작용하여 세포막으로의 이동에 관여할 것이라는 것을 시사한다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권4호
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• pp.462-469
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• 2017

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

• IMMUNE NETWORK
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• 제5권4호
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• pp.237-246
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• 2005

Background: Little information is available on the identification and characterization of the upstream regulators of the signal transduction cascades for Mycobacterium tuberculosis (M. tbc)-induced ERK 1/2 activation and chemokine expression. We investigated the signaling mechanisms involved in expression of CCL3 /MIP-1 and CCL4/MIP-1 in human primary monocytes infected with M. tbc. Methods: MAP kinase phosphorylation was determined using western blot analysis with specific primary antibodies (ERK 1/2, and phospho-ERK1/2), and the upstream signaling pathways were further investigated using specific inhibitors. Results: An avirulent strain, M. tbc H37Ra, induced greater and more sustained ERK 1/2 phosphorylation, and higher CCL3 and CCL4 production, than did M. tbc H37Rv. Specific inhibitors for mitogen-activated protein kinase (MAPK) kinase (MEK; U0126 and PD98059) significantly inhibited the expression of CCL3 and CCL4 in human monocytes. Mycobactetia-mediated expression of CCL3 and CCL4 was not inhibited by the Ras inhibitor manumycin A or the Raf-1 inhibitor GW 5074. On the other hand, phospholipase C (PLC) inhibitor (U73122) and protein kinase C (PKC)specific inhibitors ($G\ddot{o}6976$ and Ro31-8220) significantly reduced M. tbc-induced activation of ERK 1/2 and chemokine synthesis. Conclusion: These results are the first to demonstrate that the PLC-PKC-MEK-ERK, not the Ras-Raf-MEK-ERK, pathway is the major signaling pathway inducing M. tbc-mediated CCL3 and CCL4 expression in human primary monocytes.

• Journal of Biomedical and Translational Research
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• 제19권4호
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• pp.116-124
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• 2018

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP ${\times}$ Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (${\left|log2FC\right|}$ > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

• Molecules and Cells
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• 제46권6호
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• pp.360-373
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• 2023

Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid carcinoma. Despite a good prognosis, approximately a quarter of PTC patients are likely to relapse. Previous reports suggest an association between S-phase kinase-associated protein 2 (SKP2) and the prognosis of thyroid cancer. SKP1 is related to apoptosis of PTC cells; however, its role in PTC remains largely elusive. This study aimed to understand the expression and molecular mechanism of SKP2 in PTC. SKP2 expression was upregulated in PTC tissues and closely associated with clinical diagnosis. In vitro and in vivo knockdown of SKP2 expression in PTC cells suppressed cell growth and proliferation and induced apoptosis. SKP2 depletion promoted cell autophagy under glucose deprivation. SKP2 interacted with PH domain leucine-rich repeat protein phosphatase-1 (PHLPP1), triggering its degradation by ubiquitination. Furthermore, SKP2 activates the AKT-related pathways via PHLPP1, which leads to the cytoplasmic translocation of SKP2, indicating a reciprocal regulation between SKP2 and AKT. In conclusion, the upregulation of SKP2 leads to PTC proliferation and survival, and the regulatory network among SKP2, PHLPP1, and AKT provides novel insight into the molecular basis of SKP2 in tumor progression.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.278-283
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• 2005

Cell cycle is regulated cooperatively by several genes. The dynamic regulatory mechanism of protein interaction network of cell cycle will be presented taking the budding yeast as a sample system. Based on the mathematical model developed by Chen et at. (MBC, 11,369), at first, the dynamic role of the feedback loops is investigated. Secondly, using a bifurcation diagram, dynamic analysis of the cell cycle regulation is illustrated. The bifurcation diagram is a kind of ‘dynamic road map’ with stable and unstable solutions. On the map, a stable solution denotes a ‘road’ attracting the state and an unstable solution ‘a repelling road’ The ‘START’ transition, the initiation of the cell cycle, occurs at the point where the dynamic road changes from a fixed point to an oscillatory solution. The 'FINISH' transition, the completion of a cell cycle, is returning back to the initial state. The bifurcation analysis for the mutants could be used uncovering the role of proteins in the cell cycle regulation network.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2002년도 생물공학의 동향 (X)
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• pp.30-33
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• 2002

We have shown that it is possible to form a fibrilar network of fibronectin on a polyelectrolyte polymer film whose dimensions are similar to those reported on the extra cellular matrix. The fibronectin network was observed to form only when the charge density of the polymer was in excess of the natural charge density of the cell wall. Furthermore, the self-organized fibronectin layer was much thicker than the polymer film, indicating that long ranged interaction may playa key role in the assembly process. It is therefore important to understand the structure of the polymer layer/protein interface. Here we report on a neutron reflectivity study where we explore the structure of the polyelectrolyte layer, in this case sulfonated polystyrene (PSSx,), with varying degree of sulfonation (x<30%), as a function of sulfur content and counter ion concentration. These results are then correlated with systemic study of the adsorption and the multilayer formation of fibronectin as a function of incubation time for various sulfonation levels of $PSSx.^1$

• Preventive Nutrition and Food Science
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• 제3권2호
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• pp.128-132
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• 1998

7S globulin has been isolate from the defatted soybean meal(glycine max,. merill) by Sepharose-6B column chromatography and CM-Sephadex column chromatography. Coagulum of 7S globulin formed at a temperature of $65^{\circ}C$ in microbial enzyme treatment. In order to characterize the structure of the coagulum, three kinds of coagulum (enzyme-, calcium-and acid-induced coagulum)were compared througth the Scanning Electron Microscope(SEM). The network structure was found to be of two levels. First, there was an appearance on the molecular level in the form of strands. Second, there was a denser network with a fine structure.

• 디지털산업정보학회논문지
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• 제15권2호
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• pp.19-28
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• 2019

The purpose of this study is to examine the trends on machine learning and deep learning research in the published journals from the Web of Science Database. To achieve the study purpose, we used the abstracts of 20,664 articles published between 1990 and 2017, which include the word 'machine learning', 'deep learning', and 'artificial neural network' in their titles. Twenty major research topics were identified from topic modeling analysis and they were inclusive of classification accuracy, machine learning, optimization problem, time series model, temperature flow, engine variable, neuron layer, spectrum sample, image feature, strength property, extreme machine learning, control system, energy power, cancer patient, descriptor compound, fault diagnosis, soil map, concentration removal, protein gene, and job problem. The analysis of the time-series linear regression showed that all identified topics in machine learning research were 'hot' ones.

• International Journal of Computer Science & Network Security
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• 제21권3호
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• pp.31-36
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• 2021

RNA sequencing (RNA-Seq) is a technology that facilitates transcriptome analysis using next-generation sequencing (NSG) tools. Information on the quantity and sequences of RNA is vital to relate our genomes to functional protein expression. RNA-Seq data are characterized as being high-dimensional in that the number of variables (i.e., transcripts) far exceeds the number of observations (e.g., experiments). Given the wide range of dimensionality reduction techniques, it is not clear which is best for RNA-Seq data analysis. In this paper, we study the effect of three dimensionality reduction techniques to improve the classification of the RNA-Seq dataset. In particular, we use PCA, SVD, and SOM to obtain a reduced feature space. We built nine classification models for a cancer dataset and compared their performance. Our experimental results indicate that better classification performance is obtained with PCA and SOM. Overall, the combinations PCA+KNN, SOM+RF, and SOM+KNN produce preferred results.