• 원예과학기술지
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• 제31권5호
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• pp.607-616
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• 2013

광은 모든 살아 있는 세포에 있어서 매우 중요한 신호이며 생물체에게 이익이 되면서 동시에 해가 되기도 하는데, 광 환경에 잘 적응한 유기체는 자연에서의 경쟁에서 더 잘 살아남을 수 있다. 광질과 식물 생육에 대한 정보는 LED와 같은 인공광을 효율적으로 사용하게 하여 경제적인 손실을 줄일 수 있다. 초기 1주 동안 단일 광파장에 노출된 배추 유묘의 생장을 보면 백색광 조건에서 생장한 묘와 비교했을 때 적색광과 청색광 조건에서는 유묘의 발달과 생육이 정상이었다. 암조건에서 자란 유묘는 하배축이 길고 황화된 반면, 초적외광 조건에서 자란 유묘는 황화되었으나 하배축이 거의 신장하지 않았다. 마이크로어레이를 이용하여 유전자 대량 발현분석 실험을 수행한 결과, 청색광 조건에서 유묘의 생육이 가장 왕성하였으며 적색광 조건과 비교하여 발현변화를 보인 유전자의 수가 2배 많았다. 각각의 광질 조건에서 발현 증가 된 유전자들을 기능별로 분류해 보면(GO 분석) 적색광과 청색광은 생물학적 과정(biological process)과 관련된 유전자의 발현에 영향을 많이 주었다. 특히 대사과정(metabolic process)과 발달과정(developmental process) 그리고 세포 요소(cellular component) 중 색소체(plastid)나 엽록체(chloroplast)관련 유전자들의 발현이 청색광 조건에서 더 많이 증가하였다. 또한 초적외광 조건에서도 다양한 유전자들이 발현 변화를 보였다. 본 논문은 다양한 배추 유묘의 생장에 대한 광질의 영향을 분자생물학적으로 증명하기 위해 수행되었으며 유묘의 배양에 LED 광원이 효율적으로 이용될 수 있음을 보여 주었다.

• 동의생리병리학회지
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• 제16권5호
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• pp.976-988
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• 2002

The aim of this study was to examine the memory and attention enhancement effect of YMG-1 and YMG-2, which are modified herbal extracts from Yukmijihwang-tang (YMJ). YMJ, composing six herbal medicine, has been used for restoring the normal functions of the body to consolidate the constitution, nourishing and invigorating the kidney functions for hundreds years in Asian countries. A series of studies reported that YMJ and its components enhance memory retention, protects neuronal cell from reactive oxygen attack and boost immune activities. Recently the microarray analysis suggested that YMG-1 protects neurodegeneration through modulating various neuron specific genes. A total of 55 subjects were divided into three groups according to the treatment of YMG-1 (n=20), YMG-2 (n=20) and control (C; n=15) groups. Before treatments, all of subjects were subjected to the assessments on neuropsychological tests of K-WAIS test, Rey-Kim memory test, and psychophysiological test of Event-Related Potential (ERP) during auditory oddball task and repeated word recognition task. They were repeatedly assessed with the same methods after drug treatment for 6 weeks. Although no significant effect of drug was found in Rey-Kim memory test, a significant interaction (P = .010, P < 0.05) between YMG-2 and C groups was identified in the scores digit span and block design, which are the subscales of K-WAIS. The very similar but marginal interaction (P = .064) between YMG-1 and C groups was found too. In ERP analysis, only YMG-1 group showed decreasing tendency of P300 latency during oddball task while the others tended to increase, and it caused significant interaction between session and group (p= .004). This result implies the enhancement of cognitive function in due to consideration of relationship between P300 latency and the speed of information processing. However, no evidence which could demonstrate the significant drug effect was found in neither amplitude or latency. These results come together suggest that YMG-1, 2 may enhance the attention, resulting in enhancement of memory processing. For elucidating detailed mechanism of YMG on learning and memory, the further studies are necessary.

• Asian Pacific Journal of Cancer Prevention
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• 제15권11호
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• pp.4589-4594
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• 2014

The mammalian target of rapamycin (mTOR) signaling pathway is upregulated in the pathogenesis of many cancers, including colorectal cancer (CRC). DEPTOR is an mTOR inhibitor whose expression is negatively regulated by mTOR. However, the role of DEPTOR in the development of CRC is not known. The aim of this study was to investigate the expression of DEPTOR and mTORC1 activity (P-S6) in a subset of CRC patients and determine their relation to tumor differentiation, invasion, nodal metastasis and disease-free survival. Here, Immunohistochemical expression of P-S6 (S235/236) and DEPTOR were evaluated in 1.5 mm tumor cores from 90 CRC patients and in 90 samples of adjacent normal mucosa by tissue microarray. The expression of P-S6 (S235/236) was upregulated in CRC, with the positive rate of P-S6 (S235/236) in CRC (63.3%) significantly higher than that in control tissues (36.7%, 30%) (p<0.05). P-S6 (S235/236) also correlated with high tumor histologic grade (p=0.002), and positive nodal metastasis (p=0.002). In contrast, the expression level of DEPTOR was correlated with low tumor histological grade (p=0.006), and negative nodal metastasis (p=0.001). Interestingly, P-S6 (S235/236) expression showed a significant negative association with the expression of DEPTOR in CRC (p=0.011, R= -0.279). However, upregulation of P-S6 (S235/236) (p=0.693) and downregulation of DEPTOR (p=0.331) in CRC were not significantly associated with overall survival. Thus, we conclude that expression of DEPTOR negatively correlates with mTORC1 activity and tumor progression in CRC. DEPTOR is a potential marker for prognostic evaluation and a target for the treatment of CRC.

• 한국정보과학회논문지:소프트웨어및응용
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• 제37권1호
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• pp.1-8
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• 2010

최근 마이크로어레이 데이터를 기반으로 두 개의 샘플 그룹간에 유의한 발현 차이를 나타내는 생물학적 기능 그룹을 검출하기 위한 유전자 집합 분석(gene set analysis) 연구가 많은 주목을 받고 있다. 기존의 유의 유전자 검출 연구와는 달리, 유전자 집합 분석 연구는 유의한 유전자 집합과 이들의 기능적 특징을 함께 검출할 수 있다는 장점이 있다. 이러한 이유로 최근에는 PAGE, GSEA 등과 같은 다양한 통계적 방식의 유전자 집합 분석 방법들이 소개되고 있다. 특히, PAGE의 경우 두 샘플 그룹간의 유전자 발현 차이를 나타내는 스코어의 분포가 정규 분포임을 가정하는 모수적 접근 방식을 취하고 있다. 이러한 방법은 GSEA 등과 같은 비모수적 방식에 비해 계산량이 적고 성능이 비교적 우수한 장점이 있다. 하지만, PAGE에서 유전자 발현 차이를 정량화하기 위한 메트릭으로 사용하고 있는 AD(average difference)의 경우, 두 그룹간에 절대적 평균 발현 차이만을 고려하기 때문에 실제 유전자의 발현값 크기나 분산의 크기에 따른 상대적 중요성을 반영하지 못하는 문제가 있다. 본 논문에서는 이를 보완하기 위해 실제 유전자의 발현값 크기나 그룹 내 샘플들의 분산 정보 등을 스코어 계산에 함께 반영하는 WAD(weighted average difference), FC(Fisher's criterion), 그리고 Abs_SNR(Absolute value of signal-to-noise ratio)을 모수적 방식의 유전자 집합 분석에 적용하고 이에 따른 유의 유전자 집합 검출 결과를 실험을 통해 비교 분석하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• 생명과학회지
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• 제22권11호
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• pp.1500-1506
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• 2012

Transforming growth factor-${\beta}$ (TGF-${\beta}$)에 의해 유도되는 세포사멸 과정은 간에서 손상 받은 조직이나 비정상적인 조직을 제거하는데 중요한 역할을 담당한다. 간세포에서 TGF-${\beta}$에 의해 유도되는 세포사멸 과정 동안 중요한 기능을 담당하는 유전자를 탐색하고자 쥐의 간세포인 AML12 세포를 이용하여 TGF-${\beta}$ 처리 전후에 발현이 변화되는 유전자를 microarray analysis를 통해 확인하였다. TGF-${\beta}$에 의해 여러 가지 유전자들의 발현이 변화됨을 확인하였는데, 그 가운데 여러 가지 세포사멸 인자들의 활성을 억제하여 세포사멸을 억제한다고 알려져 있는 SGK1의 발현 감소를 확인하였다. TGF-${\beta}$에 의해 SGK1의 mRNA와 단백질 level이 모두 감소함을 확인하였고, 항상 active한 형태의 SGK1 (CA-SGK1)을 발현시켰을 때 TGF-${\beta}$에 의한 세포사멸이 억제됨을 확인하였다. 이러한 결과들은 간세포에서 SGK1의 발현 감소가 TGF-${\beta}$에 의한 세포사멸을 유도하는데 중요한 기능을 담당할 가능성이 높음을 의미하는 것이다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.83-89
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• 2006

Cellular functions are carried out by a concerted action of biochemical pathways whose components have genetic interactions. Abnormalities in the activity of the genes that constitute or modulate these pathways frequently have oncogenic implications. Therefore, identifying the upstream regulatory genes for major biochemical pathways and defining their roles in carcinogenesis can have important consequences in establishing an effective target-oriented antitumor strategy We have analyzed the gene expression profiles of human liver cancer samples using cDNA microarray chips enriched in liver and/or stomach-expressed cDNA elements, and identified groups of genes that can tell tumors from non-tumors or normal liver, or classify tumors according to clinical parameters such as tumor grade, age, and inflammation grade. We also set up a high-throughput cell-based assay system (cell chip) that can monitor the activity of major biochemical pathways through a reporter assay. Then, we applied the cell chip platform for the analysis of the HCC-associated genes discovered from transcriptome profiling, and found a number of cancer marker genes having a potential of modulating the activity of cancer-related biochemical pathways such as E2F, TCF, p53, Stat, Smad, AP-1, c-Myc, HIF and NF-kB. Some of these marker genes were previously blown to modulate these pathways, while most of the others not. Upon a fast-track phenotype analysis, a subset of the genes showed increased colony forming abilities in soft agar and altered cell morphology or adherence characteristics in the presence of purified matrix proteins. We are currently analyzing these selected marker genes in more detail for their effects on various biological Processes and for Possible clinical roles in liver cancer development.

• Journal of Periodontal and Implant Science
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• 제49권5호
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• pp.270-286
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• 2019

Purpose: Despite the well-known anti-inflammatory effects of vitamin D in periodontal health, its mechanism has not been fully elucidated. In the present study, the effect of vitamin D on strengthening E-cadherin junctions (ECJs) was explored in human gingival keratinocytes (HGKs). ECJs are the major type of intercellular junction within the junctional epithelium, where loose intercellular junctions develop and microbial invasion primarily occurs. Methods: HOK-16B cells, an immortalized normal human gingival cell line, were used for the study. To mimic the inflammatory environment, cells were treated with tumor necrosis factor-alpha ($TNF-{\alpha}$). Matrix metalloproteinases (MMPs) in the culture medium were assessed by an MMP antibody microarray and gelatin zymography. The expression of various molecules was investigated using western blotting. The extent of ECJ development was evaluated by comparing the average relative extent of the ECJs around the periphery of each cell after immunocytochemical E-cadherin staining. Vitamin D receptor (VDR) expression was examined via immunohistochemical analysis. Results: $TNF-{\alpha}$ downregulated the development of the ECJs of the HGKs. Dissociation of the ECJs by $TNF-{\alpha}$ was accompanied by the upregulation of MMP-9 production and suppressed by a specific MMP-9 inhibitor, Bay 11-7082. Exogenous MMP-9 decreased the development of ECJs. Vitamin D reduced the production of MMP-9 and attenuated the breakdown of ECJs in the HGKs treated with $TNF-{\alpha}$. In addition, vitamin D downregulated $TNF-{\alpha}$-induced nuclear factor kappa B ($NF-{\kappa}B$) signaling in the HGKs. VDR was expressed in the gingival epithelium, including the junctional epithelium. Conclusions: These results suggest that vitamin D may avert $TNF-{\alpha}$-induced downregulation of the development of ECJs in HGKs by decreasing the production of MMP-9, which was upregulated by $TNF-{\alpha}$. Vitamin D may reinforce ECJs by downregulating $NF-{\kappa}B$ signaling, which is upregulated by $TNF-{\alpha}$. Strengthening the epithelial barrier may be a way for vitamin D to protect the periodontium from bacterial invasion.

• 한방재활의학과학회지
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• 제33권3호
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• pp.1-15
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• 2023

Objectives We aimed to find out the improvement effect of Baekhogainsam-tang (Baihu Jia Renshen-tang, BIT) on metabolic syndrome and alteration of microbiota and gene expression. Methods We used male C57BI/6 mice and randomly assigned them into three groups. Normal control group was fed 10% kcal% fat diet, high-fat diet (HFD) group was fed 45% kcal% fat diet and 10% fructose water. BIT group was fed same diet as HFD group and treated by BIT for once daily, 6 days per week, total 8 weeks. We measured their body weight and food intake every week and performed oral glucose tolerance test 1 week before the end of the study. Then we collected the blood sample to measure triglyceride, total cholesterol, high-density lipoprotein cholesterol, insulin, and hemoglobin A1c. We harvested tissue of liver, muscle, fat, and large intestine for quantitative polymerase chain reaction (qPCR) and histopathological examination. Fresh fecal samples were collected from each animal to verify alterations of gut microbiota and we used RNA from liver tissue for microarray analysis. Results The body weight and fat weight of BIT group were reduced compared to HFD group. The qPCR markers usually up-regulated in metabolic syndrome were decreased in BIT group. Bacteroides were higher in BIT group than other groups. There were also differences in gene expressions between two groups such as Cyp3a11 and Scd1. Conclusions We could find out BIT can ameliorate metabolic syndrome and suggest its effect is related to gut microbiota composition and gene expression pattern.