• Journal of Institute of Control, Robotics and Systems
• /
• v.11 no.10
• /
• pp.830-836
• /
• 2005

Application of microarray technologies which monitor simultaneously the expression pattern of thousands of individual genes in different biological systems results in a tremendous increase of the amount of available gene expression data and have provided new insights into gene expression during drug development, within disease processes, and across species. There is a great need of data mining methods allowing straightforward interpretation, visualization and analysis of the relevant information contained in gene expression profiles. Specially, classifying biological samples into known classes or phenotypes is an important practical application for microarray gene expression profiles. Gene expression profiles obtained from tissue samples of patients thus allowcancer classification. In this research, molecular classification of microarray gene expression data is applied for multi-class cancer using computational biology such gene selection, principal component analysis and fuzzy clustering. The proposed method was applied to microarray data from leukemia patients; specifically, it was used to interpret the gene expression pattern and analyze the leukemia subtype whose expression profiles correlated with four cases of acute leukemia gene expression. A basic understanding of the microarray data analysis is also introduced.

• Journal of Life Science
• /
• v.32 no.6
• /
• pp.463-467
• /
• 2022

As a result of applying the COG (Cluster of Orthologous Groups of Protein) algorithm to 1,309 species to confirm the conserved genes of prokaryotes, ribosomal protein S11 (COG0100) was identified. The numbers of conservative genes were 2, 5, 5, and 6 in 1,308, 1,307, 1,306, and 1,305 species, respectively. Twenty-nine genes were conserved in over 1,302 species, and they encoded 23 ribosomal proteins, 3 tRNA synthetases, 2 translation factors, and 1 RNA polymerase subunit. Most of them were related to protein production, suggesting the importance of protein expression in prokaryotes. The highest conservative COG was COG0048 (ribosomal protein S12) among the 29 COGs. The 29 conserved genes usually have one protein for each prokaryote. COG0090 (ribosomal protein L2) had not only the lowest conservation value but also the largest standard deviation of phylogenetic distance value. As COG0090 is not only a member of the ribosome, but also a regulator of replication and transcription, it could be inferred that prokaryotes have large variations in COG0090 to survive in various environments. This study could provide data necessary for basic science, tumor control, and development of antibacterial agents.

• Journal of the Society of Cosmetic Scientists of Korea
• /
• v.46 no.2
• /
• pp.105-117
• /
• 2020

Agaricus blazei Murill (Almond mushroom) has many beneficial effects, such as anti-cancer, immuneenhancement, and anti-obesity. Also, its skin benefits have been reported for antioxidant, anti-inflammatory, and whitening. In order to elucidate these effects, many studies have been conducted. In this study, we reconfirmed the skin efficacy of the extract of the mushrooms mushrooms. The Agaricus blazei extract showed inhibition of melanin synthesis, enhancement of collagen synthesis, and up-regulation of gene expression (hyaluronan syntahase-2, 3 and aquaporin-3) at 100 ㎍/mL. and identified the ingredients from the extract. We further investigated them to find an applicability as cosmetic ingredients. The ingredients were confirmed comparison of their spectroscopic data with literature values. They were identified as being ergosterol (1), 5-dihydroergosterol (2), cerevisterol (3), cerebroside B (4), cerebroside D (5), adenosine (6), and benzoic acid (7). Among these compounds, we evaluated skin efficacy for two cerebrosides and three ergosterol derivatives that have not been reported its efficacy. As a result, 5-dihydroergosterol (2) inhibited melanogenesis in B16F10 and promoted collagen biosynthesis in human dermal fibroblast. In addition, cerevisterol (3), cerebroside B (4), and cerebroside D (5) inhibited NO production in RAW 264.7 cell. In particular, cerebroside D (5) increased the expression of hyaluronan synthase-2 and aquaporin-3 genes in HaCaT. These results suggest that Agaricus blazei extract and isolated compounds can be used as cosmetic ingredients.

• Journal of the Korean Institute of Intelligent Systems
• /
• v.25 no.6
• /
• pp.529-535
• /
• 2015

Biological networks have been handled with the static concept. However, life phenomena in cells occur depending on the cellular state and the external environment, and only a few proteins and their interactions are selectively activated. Therefore, we should adopt the dynamic network concept that the structure of a biological network varies along the flow of time. This concept is effective to analyze the progressive transition of the disease. In this paper, we applied the proposed method to Alzheimer's disease to analyze the structural and functional characteristics of the disease network. Using gene expression data and protein-protein interaction data, we constructed the sub-networks in accordance with the progress of disease (normal, early, middle and late). Based on this, we analyzed structural properties of the network. Furthermore, we found module structures in the network to analyze the functional properties of the sub-networks using the gene ontology analysis (GO). As a result, it was shown that the functional characteristics of the dynamics network is well compatible with the stage of the disease which shows that it can be used to describe important biological events of the disease. Via the proposed approach, it is possible to observe the molecular network change involved in the disease progression which is not generally investigated, and to understand the pathogenesis and progression mechanism of the disease at a molecular level.

• Korean Journal of Microbiology
• /
• v.41 no.4
• /
• pp.262-268
• /
• 2005

Intoxication of murine macrophages (RAW 264.7) with the anthrax lethal toxin (LeTx 100 ng/ml) results in profound alterations in the host cell gene expression. The role of LeTx in mediating these effects is unknown, largely due to the difficulty in identifying and assigning function to individual proteins. In this study, we have used two-dimensional polyacrylamide gel electrophoresis to analyze the protein profile of murine macrophages treated with the LeTx, and have coupled this to protein identification using MALDI-TOF mass spectrometry. Interpretation of the peptide mass fingerprint data has relied primarily on the ProFound database. Among the differentially expressed spots, cleaved mitogen-activated protein kinase kinase (Mek1) and glucose-6-phosphate dehydrogenase were increased in the LeTx treated macrophages. Mek1 acts as a negative element in the signal transduction pathway, and G6PD plays the role for the protection of the cells from the hyper-production of active oxygen. Our results suggest that this proteomic approach is a useful tool to study protein expression in intoxicated macrophages and will contribute to the identification of a putative substrate for LeTx.

• The Korean Journal of Applied Statistics
• /
• v.22 no.2
• /
• pp.415-424
• /
• 2009

As one of the unsupervised learning neural network methods, self-organizing maps(SOM) are applied to various fields. It reduces the dimension of multidimensional data by representing observations on the low dimensional manifold. On the other hand, the minimal spanning tree(MST) of a graph that achieves the most economic subset of edges connecting all components by a single open loop. In this study, we apply the MST technique to SOM with subnodes. We propose SOM's with embedded MST and a distance measure for optimum choice of the size and shape of the map. We demonstrate the method with Fisher's Iris data and a real gene expression data. Simulated data sets are also analyzed to check the validity of the proposed method.

• Korean Journal of Clinical Laboratory Science
• /
• v.50 no.2
• /
• pp.197-204
• /
• 2018

Multiple myeloma (MM) is the leading cause of death among hematologic neoplasms. Recently, microRNA has been reported to be useful in the diagnosis of multiple myeloma. This study examined whether miR-221 could be used as a diagnostic marker for multiple myeloma. The study was performed on 20 patients with multiple myeloma without any other hematological diseases. MicroRNA extraction was performed using formalin-fixed paraffin-embedded (FFPE) tissues obtained from the bone marrow of patients with multiple myeloma. miR-15a, miR-16, miR-21, miR-181a, and miR-221 were selected as the microRNA target genes for multiple myeloma. The significance of microRNA was based on a fold change of <1.5. To quantify the fold changes, data normalized to the human gene, SNORD43, were used as the values of the patient group. Fold change values greater than 1.5 were defined as "overexpression", whereas values less than -1.5 were defined as "underexpression". Of note, 65.0% (13/20) of samples showed significant "overexpression" in the levels of miR-221 expression and plasma cells with a group of more and less than 30% in MM patients did not show any significance of plasma cell (P<0.05). The results of other studies showing a correlation between the expression of miR-221 and MM in Caucasians were confirmed. These results suggest that miR-221 may be a useful indicator for diagnosing patients with MM. In conclusion, miR-221 is useful in the diagnosis and determining the prognosis of multiple myeloma in Koreans.

• Korean Journal of Environmental Biology
• /
• v.40 no.4
• /
• pp.464-476
• /
• 2022

In recent years, macroalgal bloom occurs frequently in coastal oceans worldwide. It might be attributed to accelerating climate change. "Green tide" events caused by proliferation of green macroalgae (Ulva spp.) not only damage the local economy, but also harm coastal environments. These nuisance events have become common across several coastal regions of continents. In Korea, green tide incidences are readily seen throughout the year along the coastlines of Jeju Island, particularly the northeastern coast, since the 2000s. Ulva species are notorious to be difficult for morphology-based species identification due to their high degrees of phenotypic plasticity. In this study, to investigate temporal variation in Ulva community structure on Jeju Island between 2015 and 2020, chloroplast barcode tufA gene was sequenced and phylogenetically analyzed for 152 specimens from 24 sites. We found that Ulva ohnoi and Ulva pertusa known to be originated from subtropical regions were the most predominant all year round, suggesting that these two species contributed the most to local green tides in this region. While U. pertusa was relatively stable in frequency during 2015 to 2020, U. ohnoi increased 16% in frequency in 2020 (36.84%), which might be associated with rising sea surface temperature from which U. ohnoi could benefit. Two species (Ulva flexuosa, Ulva procera) of origins of Europe should be continuously monitored. The findings of this study provide valuable information and molecular genetic data of genus Ulva occurring in southern coasts of Korea, which will help mitigate negative influences of green tide events on Korea coast.

• Korean Journal of Breeding Science
• /
• v.49 no.3
• /
• pp.129-140
• /
• 2017

This study was carried out to develop of environmental risk assessments and the biosafety guide for Vitamin E enhanced transgenic soybean at LMO (Living Modified Organism) isolation field. In LMO quarantine area of National Institute of Agricultural Sciences, insect species diversities and population densities on vitamin E enhanced transgenic soybean and non-GM soybeans (Willams 82 and Seoritae) were investigated. A total of 17,717 individuals of 77 species from 8 orders were collected in LMO isolation field. In three type soybeans field, total of 5,250 individuals in Vitamin E enhanced transgenic soybean, 5,510 individuals in Willams 82, and 6,957 individuals in Seoritae were collected, respectively. There was no difference between the population densities of insect pests, natural enemies and other insects on Vitamin E enhanced transgenic soybean and Willams 82, while natural enemies density on Seoritae was higher than on Vitamin E enhanced transgenic soybean, but insect pests density on Vitamin E enhanced transgenic soybean was higher. These results provided the insects diversity for risk assessment survey of Vitamin E enhanced transgenic soybean and suggested that the guideline could be useful to detect LMO crops.

• The Korean Journal of Nuclear Medicine
• /
• v.38 no.4
• /
• pp.288-293
• /
• 2004

Purpose: increased uptake of wrist and hand joints in three phase bone scintigraphy (TPBS) have been used in the detection of reflex sympathetic dystrophy syndrome (RSDS). TPBS frequently shows increased shoulder uptake in the hemiplegic RSDS patients. We investigated the significance of the shoulder uptake in the detection of these patients. Materials and Methods: Twenty three patients who had hemiplegia due to brain stroke and diagnosed as RSD were enrolled in this study (M:F=16:7, R:L=11:12). The mean age was $63{\pm}10$ yrs. Ter normal volunteer (mean age: $60{\pm}5$, M:F=1:9) data was used as control group. TPBS was performed $59{\pm}32$ days after stoke (acute stage). We obtained the count ratios of bilateral hands by drawing a region of interest (ROI) in three phase images and compared to the count ratios of shoulders in the delayed image. Hand ROI included an ipsilateral wrist. Sensitivity of detecting the affected limb was defined using the right/left count ratio of normal control. Results: Sensitivities using count ratios of hand blood flow, blood pool and delayed image were 45%, 76% and 78%, respectively. Sensitivity of shoulder count ratio was 74%. Log of right/left counts of hand delayed image and that of shoulder delayed image were correlated well with statistical significance (Spearman's R=0.824, p<0.001). Conclusion: Shoulder uptake showed good correlation with hand uptake in the delayed image of TPBS. Shoulder uptake maybe helpful in the diagnosis of reflex sympathetic dystrophy syndrome in patients with hemiplegia.