• Genomics & Informatics
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• 제3권2호
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• pp.66-72
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• 2005

The epidermis is a physiological barrier to protect organisms against environment. During the aging process, skin tissues undergo various changes including morphological and functional changes. The transcriptional regulation of genes is part of cellular reaction of aging process. In order to examine the changes of gene expression during the aging process, we used the primary cell culture system of human keratinocytes. Since UV radiation is the most important environmental skin aggressor, causing skin cancer and other problems including premature skin aging, we examined the changes of gene expression in human keratinocytes after UV irradiation using oligonucleotide microarray containing over 10,000 genes. We also compared the gene expression patterns of the senescent and UV treated cells. Expression of the variety of genes related to transcription factors, cell cycle regulation, immune response was altered in human keratinocytes. Some of down-regulated genes are represented in both senescent and UV treated cells. The results may provide a new view of gene expression following UVB exposure and aging process in human keratinocytes.

• Genomics & Informatics
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• 제4권1호
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• pp.23-32
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• 2006

In order to investigate the molecular basis of the aging process in brain, we have employed high-density oligonucleotide microarrays providing data on 10,108 gene clusters to define transcriptional patterns in three brain regions, cerebral cortex, cerebellum, and hippocampus. Comparison of the expression patterns between young (6-week-old) and aged (17-month-old) C57BL/6 male micerevealed that about ten percent (1098) of the genes showed a significant change in the expression level in at least one of the three tissues. Among them, 23 genes were upregulated and 62 genes were downregulated in all three tissues of the old mice. The number of genes upregulated exclusively in hippocampus (337) was much larger compared to other tissues. Gene ontology-based analysis showed the genes related with signal transduction or molecular transports are more likely to be upregulated than downregulated in the aging process of hippocampus. These data may provide some useful means for elucidating the molecular aspect of aging in hippocampus and other regions in brain.

• BMB Reports
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• 제44권5호
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• pp.291-297
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• 2011

Aging is one of the most complicated biological processes in all species. A number of different model organisms from yeast to monkeys have been studied to understand the aging process. Until recently, many different age-related genes and age-regulating cellular pathways, such as insulin/IGF-1-like signal, mitochondrial dysfunction, Sir2 pathway, have been identified through classical genetic studies. Parallel to genetic approaches, genome-wide approaches have provided valuable insights for the understanding of molecular mechanisms occurring during aging. Gene expression profiling analysis can measure the transcriptional alteration of multiple genes in a genome simultaneously and is widely used to elucidate the mechanisms of complex biological pathways. Here, current global gene expression profiling studies on normal aging and age-related genetic/environmental interventions in widely-used model organisms are briefly reviewed.

• Genomics & Informatics
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• 제2권2호
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• pp.92-98
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• 2004

A cDNA microarray experiment is one of the most useful high-throughput experiments in medical informatics for monitoring gene expression levels. Statistical analysis with a cDNA microarray medical data requires a normalization procedure to reduce the systematic errors that are impossible to control by the experimental conditions. Despite the variety of normalization methods, this. paper suggests a more general and synthetic normalization algorithm with a control gene set based on previous studies of normalization. Iterative normalization method was used to select and include a new control gene set among the whole genes iteratively at every step of the normalization calculation initiated with the housekeeping genes. The objective of this iterative normalization was to maintain the pattern of the original data and to keep the gene expression levels stable. Spatial plots, M&A (ratio and average values of the intensity) plots and box plots showed a convergence to zero of the mean across all genes graphically after applying our iterative normalization. The practicability of the algorithm was demonstrated by applying our method to the data for the human photo aging study.

• Toxicological Research
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• 제31권2호
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• pp.173-180
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• 2015

Extract from Gryllus bimaculatus crickets inhibits oxidation at the DNA level, with reduced production of 8-hydroxy-2'-deoxyguanosine (8-OHdG). Microarray analyses were performed with a rat 28K cDNA clone set array to identify the gene expression profiles of aged (10 months old) Wistar Kyoto rats treated for one month with 100 mg/kg G. bimaculatus ethanol extract to assess the effects. The extract produced a meaningful anti-edema effect, evident by the inhibition of creatinine phosphokinase activity. The weights of abdominal and ovarian adipose tissues were reduced and the proportion of unsaturated fatty acids in adipose tissues was increased in an extract dose-dependent manner. Compared with untreated control rats, rats treated with the extract displayed the upregulation of 1053 genes including Fas (tumor necrosis factor receptor superfamily, member 6), Amigo3 (adhesion molecule with an immunoglobulin-like domain), Reticulon 4, 3-hydroxy-3-methylglutaryl-coenzyme (Hmgcr; a reductase), related anti-fatigue (enzyme metabolism), and Rtn antioxidant, and the downregulation of 73 genes including Ugt2b (UDP glycosyltransferase 2 family), Early growth response 1, and Glycoprotein m6a. Data suggest that G. bimaculatus extract may have value in lessening the effects of aging, resulting in a differential gene expression pattern indicative of a marked stress response and lower expression of metabolic and biosynthetic genes.

• 한국한의학연구원논문집
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• 제8권1호
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• pp.109-126
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• 2002

The herbal extract (YMT_02) is a modified herbal extracts from Yukmijihwangtang (YMJ) to promote memory-enhancing. The YMJ extracts has been widely used as an anti-aging herbal medicine for hundred years in Asian countries. The purpose of this study is to; 1) quantitatively evaluate the memory-enhancing effect of YMT_02 by hehavior task, 2) identify candidate genes responsible for enhancing memory by cDNA microarray and 3) assess the anti-oxidant effect of YMT_02 on PC12 cell. Memory retention abilities are addressed by passive avoidance task with Sprague-Dawley (SD) male rat. Before the training session, the rats are subdivided into four groups and administrated with YMT_02, Ginkgo biloba, Soya lecithin and normal saline for 10 days. The retention test was performed. 24 hours after the training session. The retention time of the YMT_02 group was significantly (p<0.05) delayed $({\sim}100%)$, whereas Ginkgo biloba and Soya lecithin treatment delayed 20% and 10% respectively. The hippocampi of YMT_02 and control group were dissected and mRNA was further purified. After synthesizing cDNA using oligo-dT primer, the cDNA were applied and mRNA was further purified. After synthesizing cDNA using oligo-dT primer, the cDNA were applied to Incyte rat GEMTM 2 cDNA microarray. The microarray results show that prealbumin(transthyretin), phosphotidy lethanolamine N-methyltransferase, and PEP-19 are expressed abundantly in the YMT_02 treated group. Especially, PEP-19 is a neuron-specific protein, which inhibits apoptotic processes in neuronal cell. On the other hand, transcripts of RAB15, glutamate receptor subunit 2 and CDK 108 are abundant in control group. Besides, neuronal genes involved in neuronal death or neurodegeneration such as neuronal-pentraxin and spectrin are abundantly expressed in control group. Additionally, the YMT_02 shows an anti oxidative effect in the PC12 cell. The list of differentially expressed genes may implicate further insight on the action and mechanism behind the memory-enhancing effect of herbal extracts YMT_02, for example, anti-apoptotic, anti-oxidative, and neuroprotective effects.

• 융합정보논문지
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• 제11권2호
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• pp.201-210
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• 2021

본 연구는 메밀 추출물과 비텍신을 이용하여 UVB 손상 개선에 대한 효과를 알아보기 위해 Microarray 분석, 세포의 증식, 세포 상처 회복, 세포주기, 마이크로파지의 생성 양상, 단백질 분석 등을 실시하였다. Microarray 분석 결과는 DRAM1, Atg2a 및 Atg13 유전자에서 UVB에 의해 증가 된 양상을 메밀 에탄올추출물과 비텍신에서 감소시켰다. 세포의 증식, 상처 회복, 주기 및 마이크로파지 양상에서는 메밀 에탄올추출물과 비텍신에서 정상 세포와 유사하게 개선되었으며, 단백질 분석에서 DRAM1, Beclin-1 및 LC3 I/II 모두 비텍신 처리군에서 감소하였고, p-mTOR 및 Survivin은 모두 증가 되었다. UVB에 의한 손상에서 메밀 에탄올추출물과 비텍신은 DRAM1, Atg2a 및 Atg13을 같이 컨트롤 하고 세포 증식, 상처 회복 및 주기를 정상으로 회복하며 UVB에 의한 세포 노화 발생원인 중 하나인 오토파지를 조절하여 세포의 사멸억제 및 재생하므로 기능성 화장품 성분으로 활용가능할 것으로 사료 된다.

• 생명과학회지
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• 제26권12호
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• pp.1367-1375
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• 2016

Cilostazol은 phosphodiesterase III의 선택적 저해제로 알려져 있으며, 뇌졸중 치료에 일반적으로 사용되고 있다. Cilostazol을 처리한 경우, 국소 뇌허혈이 발생한 후에 혈관신생을 통해서 혈관형성이 향상된다는 것을 본 연구자들이 발표하였다. 혈관신생은 조직의 허혈상태를 극복하기 위해서 혈관재생을 촉진하는 중요한 과정으로써, 혈관내피세포의 증식, 이동, 모세관구조 형성의 다단계 과정으로 구성되어 있다. 이에 본 연구에서는 인간 뇌혈관내피세포를 이용하여 cilostazol이 혈관신생의 각 단계들에 어떤 영향을 미치는지 조사하였다. Cilostazol은 농도의존적으로 뇌혈관내피세포의 이동성을 촉진하였으나, 뇌혈관내피세포의 증식과 모세관구조 형성에는 영향을 미치지 않았다. Cilostazol이 세포이동을 조절하는 기전을 분석하기 위해서 cDNA microarray를 수행하였고, 세포이동에 관련성이 있는 5종의 후보 유전자들을 선택하여 real-time PCR을 통해 해당 유전자의 발현을 검증하였다. Cilostazol에 의해서 발현양이 조절되는 유전자들로써, phosphoserine aminotransferase 1 (PSAT1)와 CCAAT/enhancer binding protein ${\beta}$ ($C/EBP{\beta}$)은 발현이 증가하였고, tissue factor pathway inhibitor 2 (TFPI2), retinoic acid receptor responder 1 (RARRES1), RARRES3는 발현이 감소하였다. 이상의 결과를 통해서 cilostazol이 혈관내피세포의 이동을 촉진하여 혈관신생을 향상시킬 수 있음을 제안할 수 있으며, 뇌혈관내피세포에 대한 cilostazol의 조절기전에 대해서 더욱 상세히 규명을 한다면 혈관형성을 통하여 허혈성 질환을 치료할 수 있는 유용한 정보가 될 것으로 기대한다.

• 대한화장품학회:학술대회논문집
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• 대한화장품학회 2003년도 IFSCC Conference Proceeding Book I
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• pp.741-762
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• 2003

Ginsenosides, the major active ingredients of ginseng, show a variety of biomedical efficacies such as anti-aging, anti oxidation and anti-inflammatory activities. To understand the effects of compound K (20-O-D-glucopyranosyl-20 (S)-protopanaxadiol), one of the major metabolite of ginsenosides on the skin, we assessed the expression level of ∼ 100 transcripts in compound K-treated HaCaT cells using cDNA microarray analysis. Compound K treatment induced differential expression of 21 genes, which have been reported to be involved in the organization of ECM structure as well as defense responses in human skin cells. One of the most interesting findings is 2-fold increase in hyaluronan synthase2 (HAS2) gene expression by compound K. We found that change in expression of HAS2 gene represents a specific response of HaCaT cells to compound K because hyaluronan synthase 1, 3 was not changed by treatment with compound K. We also demonstrated that the compound K effectively induced hyaluronan synthesis in human skin cells and hairless mouse skin. The human clinical study indicates that topical application of compound K-containing oil-in-water emulsion showed improvement of xerosis, wrinkle and fine lines in the aged skin. We concluded that compound K has anti-aging effects by the induction of HAS2 gene expression and following hyaluronan synthase.

• Genomics & Informatics
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• 제17권3호
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• pp.28.1-28.9
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• 2019

Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up-and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 ㎛, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 ㎛, 48K) could represent ~10,000 up-/ down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58℃ for both tags. Intriguingly, up-tags required 3× higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25℃) was optimal for cultivation instead of a normal temperature (30℃) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.