• Toxicological Research
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• 제29권3호
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• pp.181-185
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• 2013

Aluminum nanoparticles (Al-NPs) are one of the most widely used nanomaterial in cosmetics and medical materials. For this reason, Al-NP exposure is very likely to occur via inhalation in the environment and the workplace. Nevertheless, little is known about the mechanism of Al-NP neurotoxicity via inhalation exposure. In this study, we investigated the effect AL-NPs on the brain. Rats were exposed to Al-NPs by nasal instillation at 1 mg/kg body weight (low exposure group), 20 mg/kg body weight (moderate exposure group), and 40 mg/kg body weight (high exposure group), for a total of 3 times, with a 24-hr interval after each exposure. Inductively coupled plasma mass spectrometry (ICP-MS) analysis indicated that the presence of aluminum was increased in a dose-dependent manner in the olfactory bulb (OFB) and the brain. In microarray analysis, the regulation of mitogen-activated protein kinases (MAPK) activity (GO: 0043405), including Ptprc, P2rx7, Map2k4, Trib3, Trib1, and Fgd4 was significantly over-expressed in the treated mice than in the controls (p = 0.0027). Moreover, Al-NPs induced the activation of ERK1 and p38 MAPK protein expression in the brain, but did not alter the protein expression of JNK, when compared to the control. These data demonstrate that the nasal exposure of Al-NPs can permeate the brain via the olfactory bulb and modulate the gene and protein expression of MAPK and its activity.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 가을 학술발표논문집 Vol.33 No.2 (C)
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• pp.246-251
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• 2006

마이크로어레이 실험은 수 천에서 수 만개의 유전자 발현 결과를 동시에 측정할 수 있어 질병의 발현 형질 분류 등에 유용하게 이용되고 있다. 그러나 마이크로어레이 실험은 동일한 플랫폼의 실험이라 할지라도 환경 등에 따라 그 실험 결과에 차이가 나는 등 오차를 항상 포함하고 있다. 또한 마이크로어레이 실험은 아직 고가의 실험으로 분류되어 다수의 샘플에 대한 반복 실험 결과를 얻기 어려운 상황이다. 따라서 이종의 플랫폼, 데이터 포맷, 정규화 기법 등이 서로 다른 데이터를 효율적으로 통합하여 유용한 정보를 추출하는 새로운 방식의 개발이 필요하다. 본 논문은 이와 같은 문제를 해결하기 위한 기초 단계 연구 결과이다. 마이크로어레이 실험 데이터로부터 통계적 방법을 이용하여 유의(informative) 유전자를 추출하고 유전자 온톨로지(Gene Ontology : GO)와의 연계를 통하여 유전자 정보의 기능적 분류 결과를 사용자에게 제공하는 유전자 기능 분석 시스템의 설계 및 구현 방안을 보인다. 본 시스템의 실험방법에서는 3-Fold Filtering 기법을 통하여 발현 차가 큰 유전자를 추출하고, t-검정 기법에 의하여 이들 유전자를 순위화 하였으며, 이 중 상위 100개의 유전자를 유의 유전자로 추출하였다. 다음, 이 들 유의 유전자의 t-검정 값을 GO의 유전자 기능을 나타내는 해당 텀 (term)에 가중치로 부과하여 각 유전자들과 기능적으로 연관성이 높은 텀들을 추출한다. 또한 본 연구의 유효성을 검증하기 위하여 본 시스템에 의한 마이크로어레이 데이터 분석 결과를 전문가에 의한 유전자 기능 분석 결과와 비교한다.투명성 있는 서비스를 제공하고 높은 신뢰성과 안정성이 확보될 수 있도록 구성하고자 한다. Query 수행을 여러 서버로 분산처리하게 함으로써 성능에 대한 신뢰성을 향상 시킬 수 있는 Load Balancing System을 제안한다.할 때 가장 효과적인 라우팅 프로토콜이라고 할 수 있다.iRNA 상의 의존관계를 분석할 수 있었다.수안보 등 지역에서 나타난다 이러한 이상대 주변에는 대개 온천이 발달되어 있었거나 새로 개발되어 있는 곳이다. 온천에 이용하고 있는 시추공의 자료는 배제하였으나 온천이응으로 직접적으로 영향을 받지 않은 시추공의 자료는 사용하였다 이러한 온천 주변 지역이라 하더라도 실제는 온천의 pumping 으로 인한 대류현상으로 주변 일대의 온도를 올려놓았기 때문에 비교적 높은 지열류량 값을 보인다. 한편 한반도 남동부 일대는 이번 추가된 자료에 의해 새로운 지열류량 분포 변화가 나타났다 강원 북부 오색온천지역 부근에서 높은 지열류량 분포를 보이며 또한 우리나라 대단층 중의 하나인 양산단층과 같은 방향으로 발달한 밀양단층, 모량단층, 동래단층 등 주변부로 NNE-SSW 방향의 지열류량 이상대가 발달한다. 이것으로 볼 때 지열류량은 지질구조와 무관하지 않음을 파악할 수 있다. 특히 이러한 단층대 주변은 지열수의 순환이 깊은 심도까지 가능하므로 이러한 대류현상으로 지표부근까지 높은 지온 전달이 되어 나타나는 것으로 판단된다.의 안정된 방사성표지효율을 보였다. $^{99m}Tc$-transferrin을 이용한 감염영상을 성공적으로 얻을 수 있었으며, $^{67}Ga$-citrate

• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10513-10524
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• 2015

Background: Metastasis is a major reason for poor prognosis in patients with cancer, including hepatocellular carcinoma (HCC). A salient feature is the ability of cancer cells to colonize different organs. Long non-coding RNAs (lncRNAs) play important roles in numerous cellular processes, including metastasis. Materials and Methods: In this study, the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2) were assessed using the Arraystar Human LncRNA Array v2.0, which contains 33,045 lncRNAs and 30,215 mRNAs. Coding-non-coding gene co-expression (CNC) networks were constructed and gene set enrichment analysis (GSEA) was performed to identify lncRNAs with potential functions in organ-specific metastasis. Levels of two representative lncRNAs and one representative mRNA, RP5-1014O16.1, lincRNA-TSPAN8 and TSPAN8, were further detected in HCC cell lines with differing metastasis potential by qRT-PCR. Results: Using microarray data, we identified 1,482 lncRNAs and 1,629 mRNAs that were differentially expressed (${\geq}1.5$ fold-change) between the two HCC cell lines. The most upregulated lncRNAs in H2 were RP11-672F9.1, RP5-1014O16.1, and RP11-501G6.1, while the most downregulated ones were lincRNA-TSPAN8, lincRNA-CALCA, C14orf132, NCRNA00173, and CR613944. The most upregulated mRNAs in H2 were C15orf48, PSG2, and PSG8, while the most downregulated ones were CALCB, CD81, CD24, TSPAN8, and SOST. Among them, lincRNA-TSPAN8 and TSPAN8 were found highly expressed in high lung metastatic potential HCC cells, while lowly expressed in no or low lung metastatic potential HCC cells. RP5-1014O16.1 was highly expressed in high lymphatic metastatic potential HCC cell lines, while lowly expressed in no lymphatic metastatic potential HCC cell lines. Conclusions: We provide the first detailed description of lncRNA expression profiles related to organ-specific metastasis in HCC. We demonstrated that a large number of lncRNAs may play important roles in driving HCC cells to metastasize to different sites; these lncRNAs may provide novel molecular biomarkers and offer a new basis for combating metastasis in HCC cases.

• Molecules and Cells
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• 제37권12호
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• pp.873-880
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• 2014

In our previous study, miRNA-183, a miRNA in the miR-96-182-183 cluster, was significantly over-expressed in esophageal squamous cell carcinoma (ESCC). In the present study, we explored the oncogenic roles of miR-183 in ESCC by gain and loss of function analysis in an esophageal cancer cell line (EC9706). Genome-wide mRNA micro-array was applied to determine the genes that were regulated directly or indirectly by miR-183. 3'UTR luciferase reporter assay, RT-PCR, and Western blot were conducted to verify the target gene of miR-183. Cell culture results showed that miR-183 inhibited apoptosis (p < 0.05), enhanced cell proliferation (p < 0.05), and accelerated G1/S transition (p < 0.05). Moreover, the inhibitory effect of miR-183 on apoptosis was rescued when miR-183 was suppressed via miR-183 inhibitor (p < 0.05). Western blot analysis showed that the expression of programmed cell death 4 (PDCD4), which was predicted as the target gene of miR-183 by microarray profiling and bioinformatics predictions, decreased when miR-183 was over-expressed. The 3'UTR luciferase reporter assay confirmed that miR-183 directly regulated PDCD4 by binding to sequences in the 3'UTR of PDCD4. Pearson correlation analysis further confirmed the significant negative correlation between miR-183 and PDCD4 in both cell lines and in ESCC patients. Our data suggest that miR-183 might play an oncogenic role in ESCC by regulating PDCD4 expression.

• Clinical and Experimental Reproductive Medicine
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• 제47권3호
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• pp.194-206
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• 2020

Objective: The aim of this study was to investigate microRNAs (miRNAs) related to follicle-stimulating hormone (FSH) responsiveness using miRNA microarrays and to identify their target genes to determine the molecular regulatory pathways involved in FSH signaling in KGN cells. Methods: To change the cellular responsiveness to FSH, KGN cells were treated with FSH receptor (FSHR)-specific small interfering RNA (siRNA) followed by FSH. miRNA expression profiles were determined through miRNA microarray analysis. Potential target genes of selected miRNAs were predicted using bioinformatics tools, and their regulatory function was confirmed in KGN cells. Results: We found that six miRNAs (miR-1261, miR-130a-3p, miR-329-3p, miR-185-5p, miR-144-5p and miR-4463) were differentially expressed after FSHR siRNA treatment in KGN cells. Through a bioinformatics analysis, we showed that these miRNAs were predicted to regulate a large number of genes, which we narrowed down to cytochrome P450 family 19 subfamily A member 1 (CYP19A1) and estrogen receptor alpha (ESR1) as the main targets for miR-4463. Functional analysis revealed that miR-4463 is a regulatory factor for aromatase expression and function in KGN cells. Conclusion: In this study, we identified differentially expressed miRNAs related to FSH responsiveness. In particular, upregulation of miR-4463 expression by FSHR deficiency in human granulosa cells impaired 17β-estradiol synthesis by targeting CYP19A1 and ESR1. Therefore, our data might provide novel candidates for molecular biomarkers for use in research into poor responders.

• 원예과학기술지
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• 제33권4호
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• pp.575-584
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• 2015

건조 스트레스는 작물의 생존과 생산성을 결정하는데 매우 중요한 환경요인이다. 본 연구의 목적은 배추에서 신규 건조 스트레스 저항성 유전자를 동정 검정하는 것이다. 건조 스트레스 하에서 생육된 지부('Chiifu') 배추를 이용하여 제작된 KBGP-24K 마이크로어레이 데이터 분석을 통해 738개의 건조 반응 유전자 중 기능은 밝혀져 있지 않지만, 건조 스트레스 하에서 발현량이 6배 이상 크게 증가한 1개의 유전자를 선발하여 BrDSR(B. rapa Drought Stress Resistance)이라 명명하였다. 이의 검정을 위해 내혼계배추('CT001')에서 BrDSR을 동정한 결과 438bp의 오픈리딩프레임과 145개의 아미노산을 가지고 있음을 확인하였고, 동정된 완전장의 cDNA 염기서열은 형질전환용 과발현 vector인 'pSL100' 제작에 이용하였다. BrDSR이 식물체에서 건조 스트레스 저항성을 향상시켜줄 수 있는지 분석하기 위해 담배 형질전환을 수행하였다. PCR과 DNA 블롯 분석으로 선발된 T1 세대 담배 형질전환체들을 대상으로 quantitative real-time RT PCR 분석을 수행한 결과, 형질전환체의 BrDSR 발현량은 비형질 전환체 보다 2.6배까지 증가하였다. 또한 건조처리 10일째 수행한 표현형 분석에서 BrDSR이 발현되는 담배 형질전환체들이 비형질전환체들 보다 우수한 건조 저항성을 보였다. 연구 결과들을 종합하면 BrDSR은 건조 스트레스 하에서 식물의 생장과 생존에 효과적인 저항성 기능을 할 것으로 기대된다.

• Animal cells and systems
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• 제14권4호
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• pp.275-282
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• 2010

Chunghyul-dan (CHD) is a combinatorial drug known to exert anti-inflammatory effects in endothelial cells. In this study, we employed global transcriptional profiling using cDNA microarrays to identify molecular mechanisms responsible for the anti-inflammatory activity of CHD in endothelial cells. An analysis of the microarray data revealed that transcript levels of monocyte chemotactic protein-1 (MCP-1), vascular cell-adhesion molecule-1 (VCAM-1) and activated leukocyte cell-adhesion molecule were dramatically altered in CHD-treated endothelial cells. These changes in gene expression were confirmed by RT-PCR, Western blotting and ELISA. Chronic CHD treatment also appeared to decrease MCP-1 secretion, probably as a result of decreased MCP-1 expression. In addition, we determined that chronic CHD treatment inhibited lipopolysaccharide-stimulated adhesion of THP-1 leukocytes to endothelial cells. The inhibitory effect of CHD on LPS-stimulated adhesion resulted from downregulation of VCAM-1 expression. Transmigration of THP-1 leukocytes through endothelial cells was also inhibited by chronic CHD treatment. In conclusion, CHD controls a variety of inflammatory activities by regulating MCP-1 and VCAM-1 gene expression.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2004년도 춘계 학술대회지
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• pp.12-27
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• 2004

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant sciences. Plant proteomics would be most useful when combined with other functional genomics tools and approaches. A combination of microarray and proteomics analysis will indicate whether gene regulation is controlled at the level of transcription or translation and protein accumulation. In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is a most prevalent technique to identify rapidly a large of proteins in proteome analysis. However, the conventional Western blotting/sequencing technique us still used in many laboratories. As a first step to efficiently construct protein data-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein spots are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins (i. e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 30% of total rice cDNA have been deposited in the database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that fumed out to be calreticulin, gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activate in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins (http://genome .c .kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Recently, we are separated proteins from grain filling and seed maturation in rice to perform ESI-Q-TOF/MS and MALDI-TOF/MS. This experiment shows a possibility to easily and rapidly identify a number of 2-DE separated proteins of rice by ESI-Q-TOF/MS and MALDI-TOF/MS. Therefore, the Information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful in the plant molecular breeding. Also, information from our study could provide a venue to plant breeder and molecular biologist to design their research strategies precisely.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2019년도 추계학술대회
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• pp.73-73
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• 2019

Angelica gigas Nakai (Korean danggui), a member of the Umbelliferae family, is a Korean traditional medicinal plant whose roots have been used for treating gynecological diseases. Transcriptomics is the study of the transcriptome, which is the complete set of RNA transcripts that are produced by the genome, using high-throughput methods, such as microarray analysis. In this study, transcriptome analysis of A.gigas Nakai was carried out. Transcriptome sequencing and assembly was carried out by using Illumina Hiseq 2500, Velvet and Oases. A total of 109,591,555 clean reads of A. gigas Nakai was obtained after trimming adaptors. The obtained reads were assembled with an average length of 1,154 bp, a maximum length of 13,166 bp, a minimum length of 200 pb, and N50 of 1,635 bp. Functional annotation and classification was performed using NCBI NR, InterprotScan, KOG, KEGG and GO. Candidate genes for phenylpropanoid biosynthesis were obtanied from A.gigas transcriptome and the genes and its proteins were confirmed through the NCBI homology BLAST searches, revealing high identity with other othologous genes and proteins from various plants pecies. In RNA sequencing analysis using an Illumina Next-Seq2500 sequencer, we identified a total 94,930 transcripts and annotated 71,281 transcripts, which provide basic information for further research in A.gigas Nakai. Our transcriptome data reveal that several differentially expressed genes related to flower color in A.gigas Nakai. The results of this research provide comprehensive information on the A.gigas Nakai genome and enhance our understanding of the flower color related gene pathways in this plant.

• Journal of Ginseng Research
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• 제45권1호
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• pp.183-190
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• 2021

Background: The circadian rhythm is the internal clock that controls sleep-wake cycles, metabolism, cognition, and several processes in the body, and its disruption has been associated with aging. The differentiated embryo chondrocyte (Dec) gene is related to circadian rhythm. To our knowledge, there are no reports of the relationship between dec gene expression and KRG effect. Therefore, we treated Dec gene knockout (KO) aging mice with KRG to study anti-aging related effects and possible mechanisms. Methods: We evaluated KRG and expression of Dec genes in an ototoxicity model. Dec genes expression in livers of aging mice was further analyzed. Then, we assessed the effects of DEC KO on hearing function in mice by ABR. Finally, we performed DNA microarray to identify KRG-related gene expression changes in mouse liver and assessed the results using KEGG analysis. Results: KRG decreased the expression of Dec genes in ototoxicity model, which may contribute to its anti-aging efficacy. Moreover, KRG suppressed Dec genes expression in liver of wild type indicating inhibition of senescence. ABR test indicated that KRG improved auditory function in aging mouse, demonstrating KRG efficacy on aging related diseases. Conclusion: Finally, in KEGG analysis of 238 genes that were activated and 158 that were inhibited by KRG in DEC KO mice, activated genes were involved in proliferation signaling, mineral absorption, and PPAR signaling whereas the inhibited genes were involved in arachidonic acid metabolism and peroxisomes. Our data indicate that inhibition of senescence-related Dec genes may explain the anti-aging efficacy of KRG.