• Journal of Genetic Medicine
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• 제19권2호
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• pp.63-75
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• 2022

Purpose: Osteoporosis is a common calcium and metabolic skeletal disease which is characterized by decreased bone mass, microarchitectural deterioration of bone tissue and impaired bone strength, thereby leading to enhanced risk of bone fragility. In this study, we aimed to identify novel genes for susceptibility to osteoporosis and/or bone density. Materials and Methods: To identify differentially expressed genes (DEGs) between control and osteoporosis-induced cells, annealing control primer-based differential display reverse-transcription polymerase chain reaction (RT-PCR) was carried out in pre-osteoblast MC3T3-E1 cells. Expression levels of the identified DEGs were evaluated by quantitative RT-PCR. Association studies for the quantitative bone density analysis and osteoporosis case-control analysis of single nucleotide polymorphism (SNPs) were performed in Korean women (3,570 subjects) from the Korean Association REsource (KARE) study cohort. Results: Comparison analysis of expression levels of the identified DEGs by quantitative RT-PCR found seven genes, Anxa6, Col5a1, Col6a2, Eno1, Myof, Nfib, and Scara5, that showed significantly different expression between the dexamethason-treated and untreated MC3T3-E1 cells and between the ovariectomized osteoporosis-induced mice and sham mice. Association studies revealed that there was a significant association between the SNPs in the five genes, ANXA6, COL5A1, ENO1, MYOF, and SCARA5, and bone density and/or osteoporosis. Conclusion: Using a whole-genome comparative expression analysis, gene expression evaluation analysis, and association analysis, we found five genes that were significantly associated with bone density and/or osteoporosis. Notably, the association P-values of the SNPs in the ANXA6 and COL5A1 genes were below the Bonferroni-corrected significance level.

• 한국발생생물학회지:발생과생식
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• 제8권1호
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• pp.35-42
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• 2004

미성숙의 Germinal Vesicle(GV 단계에서 성숙한 Metaphase II(MII) 단계가 되는 난자성숙 과정은 핵과 세포질의 성숙을 통해 이루어지며, 이를 통해 수정과 배 발달을 할 수 있는 능력을 갖게 된다. GV 난자는 prophase I 단계에 arrest 되어 있다가 meiosis 과정을 거쳐 성숙한 MII로 되는데 이를 조절하는 기작에 대해서는 거의 알려져 있지 않다. 따라서 본 연구는 미성숙 난자와 성숙 난자간의 유전자 발현의 차이를 동정함으로써 난자성숙에 관여하는 유전인자를 밝히고자 하였다. GV와 MII 난자에서 mRNA를 정제한 후 ACP System을 이용하여 두 그룹간의 유전자 발현 차이를 분석하여 양적으로 서로 다르게 발현하거나 한쪽에서만 특이적으로 발현하는 유전자를 cloning하여 Sequencing과 BLAST search를 통해 분석하였다. ACP 1번부터 20번까지를 사용하여 32개의 유전자를 찾았으며 이중 26개가 기능적으로 알려진 유전자였다. Pscd2를 포함한 4개의 유전자는 GV에 특이적으로 발현하였고, PKD2와 CSN3를 포함하는 10개의 유전자는 GV에서 더 높게 발현하였으며 Diva를 포함하는 12개의 유전자는 MII에서 더 높게 발현하였다. 본 연구를 통해 분석된 모든 유전자는 난자에서의 발현은 보고되지 않은 것으로 ACP System을 통해 최초로 동정되었으며 특히 PKD-CSN Signaling pathway가 난자에서 발현함을 알 수 있었다. 본 연구는 난자 성숙 과정에서 서로 다르게 발현하는 유전인자를 성공적으로 동정하였으며 향후 이들의 기능을 연구함으로써 난자성숙 조절기전을 연구하는데 기여할 것으로 사료된다.

• Molecules and Cells
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• 제28권6호
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• pp.565-573
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• 2009

The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds.

• 환경생물
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• 제27권4호
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• pp.391-396
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• 2009

The biological effects of carcinogenic polycyclic aromatic hydrocarbons (cPAHs) including benzo[a]pyrene (BaP), dibenzo[a,h]anthracene (DBA), benzo[a]anthracene (BaA), benzo[b] fluoranthene (BbF), benzo[k]fluoranthene (BkF), and indeno[1,2,3-c, d]pyrene (InP) on transcriptomic changes were determined in the liver of Oryzias latipes. Differentially expressed genes (DEGs) by binary exposure to cPAHs (BaP+BaA, BaP+BbF, BaP+BkF, BaP+DbA, BaP+InP) were screened by annealing control primers-based polymerase chain reaction followed by sequence analysis and BLAST searching. The results showed that four DEGs were commonly expressed by cPAHs and they were identified as ribosomal protein S4, coagulation factor II, elongation factor 1 beta, and a predicted protein similar to human immunodeficiency virus type I enhancer binding protein 3. This finding suggests that binary exposure to cPAHs interferes protein synthesis required for fundamental liver functions in fish.

• Biomolecules & Therapeutics
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• 제30권3호
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• pp.238-245
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• 2022

Previous reports have demonstrated that genetic mechanisms greatly mediate responses to drugs of abuse, including methamphetamine (METH). The circadian gene Period 2 (Per2) has been previously associated with differential responses towards METH in mice. While the behavioral consequences of eliminating Per2 have been illustrated previously, Per2 overexpression has not yet been comprehensively described; although, Per2-overexpressing (Per2 OE) mice previously showed reduced sensitivity towards METH-induced addiction-like behaviors. To further elucidate this distinct behavior of Per2 OE mice to METH, we identified possible candidate biomarkers by determining striatal differentially expressed genes (DEGs) in both drug-naïve and METH-treated Per2 OE mice relative to wild-type (WT), through RNA sequencing. Of the several DEGs in drug naïve Per2 OE mice, we identified six genes that were altered after repeated METH treatment in WT mice, but not in Per2 OE mice. These results, validated by quantitative real-time polymerase chain reaction, could suggest that the identified DEGs might underlie the previously reported weaker METH-induced responses of Per2 OE mice compared to WT. Gene network analysis also revealed that Asic3, Hba-a1, and Rnf17 are possibly associated with Per2 through physical interactions and predicted correlations, and might potentially participate in addiction. Inhibiting the functional protein of Asic3 prior to METH administration resulted in the partial reduction of METH-induced conditioned place preference in WT mice, supporting a possible involvement of Asic3 in METH-induced reward. Although encouraging further investigations, our findings suggest that these DEGs, including Asic3, may play significant roles in the lower sensitivity of Per2 OE mice to METH.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.261-261
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• 2022

Cowpea [Vigna unguiculata (L.) Walp] is one of the most important grain legumes that enhance soil fertility and is well-adapted to various abiotic stress. Also, it is cultivated worldwide as a tropical annual crop, and the semi-arid regions are known as the main cowpea-produced regions. However, accumulation of soil salinity induced by low rainfall in these regions is reducing crop yields and quality. In general, plants exposed to soil salinity cause an accumulation of high ion chloride, which leads to the degradation of root and leaf proteins. In this study, we identified candidate genes associated with salinity tolerance through an analysis of differentially expressed genes (DEGs) in four cowpea germplasms with contrasting salinity tolerance. A total of 553,776,035 short reads were obtained using the Illumina Novaseq 6000 platform for RNA-Seq, which were subsequently aligned to the reference genome of cowpea Vunguiculata v1.2. A total of9,806 DEGs were identified between NaCl treatment and control of four cowpea germplasms. Among these DEGs, functions related to salt stress such as calcium transporter and cytochrome-450 family were associated with salt stress. In GO analysis and KEGG analysis, these DEGs were enriched in terms such as the "phosphorylation", ''extracellular region", and "ion binding". These RNA-seq results will improve the understanding of the salt tolerance of cowpea and can be used as useful basic data for molecular breeding technology in the future.

• Journal of Korean Neurosurgical Society
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• 제65권5호
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• pp.697-709
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• 2022

Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

• 한국발생생물학회지:발생과생식
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• 제18권1호
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• pp.1-11
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• 2014

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(-/-) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within -500 bp of DEG's promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.354-362
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• 2018

Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.

• Molecules and Cells
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• 제39권4호
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• pp.337-344
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• 2016

Intravenous administration of mesenchymal stem cells (IV-MSC) protects the ischemic rat brain in a stroke model, but the molecular mechanism underlying its therapeutic effect is unclear. We compared genomic profiles using the mRNA microarray technique in a rodent stroke model. Rats were treated with $1{\times}10^6$ IV-MSC or saline (sham group) 2 h after transient middle cerebral artery occlusion (MCAo). mRNA microarray was conducted 72 h after MCAo using brain tissue from normal rats (normal group) and the sham and MSC groups. Predicted pathway analysis was performed in differentially expressed genes (DEGs), and functional tests and immunohistochemistry for inflammation-related proteins were performed. We identified 857 DEGs between the sham and normal groups, with the majority of them (88.7%) upregulated in sham group. Predicted pathway analysis revealed that cerebral ischemia activated 10 signaling pathways mainly related to inflammation and cell cycle. IV-MSC attenuated the numbers of dysregulated genes in cerebral ischemia (118 DEGs between the MSC and normal groups). In addition, a total of 218 transcripts were differentially expressed between the MSC and sham groups, and most of them (175/218 DEGs, 80.2%) were downregulated in the MSC group. IV-MSC reduced the number of Iba-$1^+$ cells in the peri-infarct area, reduced the overall infarct size, and improved functional deficits in MCAo rats. In conclusion, transcriptome analysis revealed that IV-MSC attenuated postischemic genomic alterations in the ischemic brain. Amelioration of dysregulated inflammation- and cell cycle-related gene expression in the host brain is one of the molecular mechanisms of IV-MSC therapy for cerebral ischemia.