• Molecules and Cells
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• 제23권3호
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• pp.357-362
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• 2007

There is an increasing demand for high throughput (HTP) methods for gene analysis on a genome-wide scale. However, the current repertoire of HTP detection methodologies allows only a limited range of cellular phenotypes to be studied. We have constructed two HTP-optimized expression vectors generated from the red fluorescent reporter protein (RFP) gene. These vectors produce RFP-tagged target proteins in a multiple expression system using gateway cloning technology (GCT). The RFP tag was fused with the cloned genes, thereby allowing us localize the expressed proteins in mammalian cells. The effectiveness of the vectors was evaluated using an HTP-screening system. Sixty representative human C2 domains were tagged with RFP and overexpressed in HiB5 neuronal progenitor cells, and we studied in detail two C2 domains that promoted the neuronal differentiation of HiB5 cells. Our results show that the two vectors developed in this study are useful for functional gene analysis using an HTP-screening system on a genome-wide scale.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2001년도 발생공학 국제심포지움 및 학술대회 발표자료집
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• pp.53-54
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• 2001

Expression of HAND genes in sympathetic adrenal lineage suggests that HAND genes may regulate Mash-I independent neuronal genes. HAND genes are also expressed in other cell types, e.g. Cardiac cells, trophoblasts, and decidua, suggesting that HAND genes are not cell fate determination factors. It is unclear how HAND genes function specifically in different types of cells. Combinational actions of HANDs with other cell-lineage specific transcription factor may determine each cell fate and differentiation processes. Identifying the transcription target genes of HANDs and Mash-I will be important to elucidate the function of these bHLH factors in SNS factors in SNS development. (omitted)

• Molecules and Cells
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• 제40권10호
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• pp.737-751
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• 2017

Histone-modifying enzymes are key players in the field of cellular differentiation. Here, we used GSK-J4 to profile important target genes that are responsible for neural differentiation. Embryoid bodies were treated with retinoic acid ($10{\mu}M$) to induce neural differentiation in the presence or absence of GSK-J4. To profile GSKJ4-target genes, we performed RNA sequencing for both normal and demethylase-inhibited cells. A total of 47 and 58 genes were up- and down-regulated, respectively, after GSK-J4 exposure at a log2-fold-change cut-off value of 1.2 (p-value < 0.05). Functional annotations of all of the differentially expressed genes revealed that a significant number of genes were associated with the suppression of cellular proliferation, cell cycle progression and induction of cell death. We also identified an enrichment of potent motifs in selected genes that were differentially expressed. Additionally, we listed upstream transcriptional regulators of all of the differentially expressed genes. Our data indicate that GSK-J4 affects cellular biology by inhibiting cellular proliferation through cell cycle suppression and induction of cell death. These findings will expand the current understanding of the biology of histone-modifying enzymes, thereby promoting further investigations to elucidate the underlying mechanisms.

• Journal of the Korean Society for Industrial and Applied Mathematics
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• 제9권2호
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• pp.83-89
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• 2005

In this paper a new algorithm of learning and evolving artificial neural networks using gene expression programming (GEP) is presented. Compared with other traditional algorithms, this new algorithm has more advantages in self-learning and self-organizing, and can find optimal solutions of artificial neural networks more efficiently and elegantly. Simulation experiments show that the algorithm of evolving weights or thresholds can easily find the perfect architecture of artificial neural networks, and obviously improves previous traditional evolving methods of artificial neural networks because the GEP algorithm imitates the evolution of the natural neural system of biology according to genotype schemes of biology to crossover and mutate the genes or chromosomes to generate the next generation, and the optimal architecture of artificial neural networks with evolved weights or thresholds is finally achieved.

• International Journal of Oral Biology
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• 제35권4호
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• pp.209-214
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• 2010

Cells that have endogenous multipotent properties can be used as a starting source for the generation of induced pluripotent cells (iPSC). In addition, small molecules associated with epigenetic reprogramming are also widely used to enhance the multi- or pluripotency of such cells. Skinderived precursor cells (SKPs) are multipotent, sphereforming and embryonic neural crest-related precursor cells. These cells can be isolated from a juvenile or adult mammalian dermis. SKPs are also an efficient starting cell source for reprogramming and the generation of iPSCs because of the high expression levels of Sox2 and Klf4 in these cells as well as their endogenous multipotency. In this study, valproic acid (VPA), a histone deacetylase (HDAC) inhibitor, was tested in the generation of iPSCs as a potential enhancer of the reprogramming potential of SKPs. SKPs were isolated from the back skins of 5-6 week old C57BL/6 X DBA/2 F1 mice. After passage 3, the SKPs was treated with 2 mM of VPA and the quantitative real time RT-PCR was performed to quantify the expression of Oct4 and Klf4 (pluripotency specific genes), and Snai2 and Ngfr (neural crest specific genes). The results show that Oct4 and Klf4 expression was decreased by VPA treatment. However, there were no significant changes in neural crest specific gene expression following VPA treatment. Hence, although VPA is one of the most potent of the HDAC inhibitors, it does not enhance the reprogramming of multipotent skin precursor cells in mice.

• BMB Reports
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• 제42권1호
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• pp.6-15
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• 2009

The most common genetic disorder Down syndrome (DS) displays various developmental defects including mental retardation, learning and memory deficit, the early onset of Alzheimer's disease (AD), congenital heart disease, and craniofacial abnormalities. Those characteristics result from the extra-genes located in the specific region called 'Down syndrome critical region (DSCR)' in human chromosome 21. In this review, we summarized the recent findings of the DYRK1A and RCAN1 genes, which are located on DSCR and thought to be closely associated with the typical features of DS patients, and their implication to the pathogenesis of neural defects in DS. DYRK1A phosphorylates several transcriptional factors, such as CREB and NFAT, endocytic complex proteins, and AD-linked gene products. Meanwhile, RCAN1 is an endogenous inhibitor of calcineurin A, and its unbalanced activity is thought to cause major neuronal and/or non-neuronal malfunction in DS and AD. Interestingly, they both contribute to the learning and memory deficit, altered synaptic plasticity, impaired cell cycle regulation, and AD-like neuropathology in DS. By understanding their biochemical, functional and physiological roles, we hope to get important molecular basis of DS pathology, which would consequently lead to the basis to develop the possible therapeutic tools for the neural defects in DS.

• 대한한방내과학회지
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• 제32권2호
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• pp.301-321
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• 2011

Objectives : The purpose of this investigation was to evaluate the effects of Coptidis chinesis FRANCH. on the alteration of gene expression in a hypoxic model using cultured rat cortical cells. Methods : E18 rat cortical cells were grown in neurobasal medium containing B27 supplement. On 12 DIV, water extract from Coptidis chinesis FRANCH. was added ($20{\mu}g/ml$) to the culture media 4 hrs. On 14 DIV, cells were given hypoxic insult (2% $O_2$/5% $CO_2$, $37^{\circ}C$, 3 hrs), returned to normoxia and cultured for another 24 hrs. Total RNA was extracted from Coptidis chinesis FRANCH. treated and untreated cultures and alterations in the gene expression were analysed by microarray using rat 5K-TwinChips. Results : Effects on some of the genes whose functions were implicated in neural viability were as follows: the expression of apoptosis-related genes such as Clu (Global M = 1.3), of presynaptic inhibition's genes such as Penk-rs (Global M = 1.97), and of innate immuniti's such as Crp (Global M = 1.95), Defensin (Global M = 2.14), and Dnase1l3 (Global M = 1.57) increased. The expression of neurotrophic genes such as S100b (Global M = 1.42), and $NF{\kappa}B$ (Global M = 2.04) increased. Conclusions : Analysing the genes expressed on microarray, shows Coptidis chinesis FRANCH.protects cells by increasing viability and neural nutrition.

• 한국정보통신학회논문지
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• 제12권12호
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• pp.2259-2264
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• 2008

정보력 있는 유전자는 특정한 실험 조건의 특성을 나타내주는 발현수준의 유전자를 의미한다. 이 유전자들은 여러 집단 간의 발현수준에서 유의한 차이를 보여주며, 실제로 집단 간의 차이를 유발하는 유전자일 확률이 높아 특정 생물학적 현상과 관련 있는 정보적 유전자를 찾는 연구에 이용될 수 있다. 본 논문에서는 먼저 그 동안 제안된 여러 표준화 방법들 중에서 가장 널리 사용되고 있는 방법들을 이용하여 데이터를 표준화 한 후 제안한 유사성 척도 조합 방법으로 정보력 있는 유전자들을 추출할 수 있는 시스템을 고안하였다. 다층퍼셉트론 신경망 분류기를 이용하여 각 표준화 방법들의 성능을 비교분석하였다. 그 결과 Lowess 표준화 후 피어슨 적률 상관 계수와 유클리디안 거리 계수 조합을 이용하여 선택된 200 유전자들을 멀티퍼셉트론 신경망 분류기로 분류한 결과 93.84%의 향상된 분류 성능을 보였다.

• 한국수정란이식학회:학술대회논문집
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• 한국수정란이식학회 2006년도 The 6th Intermational Symposium on Developmental Biotechnology
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• pp.10-10
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• 2006

• Molecules and Cells
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• 제43권6호
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• pp.551-571
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• 2020

Nuclear receptor-related 1 (Nurr1) protein has been identified as an obligatory transcription factor in midbrain dopaminergic neurogenesis, but the global set of human NURR1 target genes remains unexplored. Here, we identified direct gene targets of NURR1 by analyzing genome-wide differential expression of NURR1 together with NURR1 consensus sites in three human neural stem cell (hNSC) lines. Microarray data were validated by quantitative PCR in hNSCs and mouse embryonic brains and through comparison to published human data, including genome-wide association study hits and the BioGPS gene expression atlas. Our analysis identified ~40 NURR1 direct target genes, many of them involved in essential protein modules such as synapse formation, neuronal cell migration during brain development, and cell cycle progression and DNA replication. Specifically, expression of genes related to synapse formation and neuronal cell migration correlated tightly with NURR1 expression, whereas cell cycle progression correlated negatively with it, precisely recapitulating midbrain dopaminergic development. Overall, this systematic examination of NURR1-controlled regulatory networks provides important insights into this protein's biological functions in dopamine-based neurogenesis.