• 원예과학기술지
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• 제34권1호
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• pp.46-54
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• 2016

2-Oxoglutarate (2OG) acts as a signaling molecule and plays a critical role in secondary metabolism in a variety of organisms, including plants. Six 2-oxoglutarate (2OG) and Fe(II) oxygenase (2OGO) genes, VlCE2OGO1 [Vitis labruscana 2-oxoglutarate (2OG) and Fe(II) oxygenase 1], VlCE2OGO2, VlCE2OGO3, VlCE2OGO4, VlCE2OGO5, and VlCE2OGO6, which show different expression patterns upon transcriptome analysis of 'Campbell Early' grapevine exposed to low temperature for 4 weeks, were analyzed for their structure and expression. Comparison of the deduced amino acid sequences of the 2OGO genes from the V. labruscana transcripts revealed sequence similarities of 38.6% (VlCE2OGO1 and VlCE2OGO2) to 19.2% (VlCE2OGO2 and VlCE2OGO3). The lengths of these genes ranged from 1053 to 2298 bp, and they encoded 316 to 380 amino acids. The prediction of the secondary structure of the encoded proteins by Self-Optimized Prediction Method with Alignment (SOPMA) indicated that all the genes contained alpha helix (23.95 to 41.71%), extended strand (16 to 22.34%), beta turn (6.65 to 9.22%), and random coil (32.97 to 51.58%) in the analysis. Specific primers from unique regions in each gene obtained by alignment of nucleotide sequences were used in real time PCR for analysis of gene expression. All tested genes showed differential expression in grapevines exposed to low temperature. Of the six transcripts, VlCE2OGO1, VlCE2OGO2, and VlCE2OGO3 were up-regulated and VlCE2OGO4, VlCE2OGO5, and VlCE2OGO6 were down-regulated in response to cold treatments at all tested time points. The 2OG genes can be used for elucidation of mechanisms of tolerance to cold and as valuable molecular genetic resources for selection in breeding programs for cold-hardy grapevines.

• Computers and Concrete
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• 제31권3호
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• pp.253-265
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• 2023

In this research, the gene expression programming (GEP) technique was employed to provide a new model for predicting the maximum loading capacity of concrete-encased steel (CES) columns. This model was developed based on 96 CES column specimens available in the literature. The six main parameters used in the model were the compressive strength of concrete (f_c), yield stress of structural steel (f_ys), yield stress of steel rebar (f_yr), and cross-sectional areas of concrete, structural steel, and steel rebar (A_c, A_s and A_r respectively). The performance of the prediction model for the ultimate load-carrying capacity was investigated using different statistical indicators such as root mean square error (RMSE), correlation coefficient (R), mean absolute error (MAE), and relative square error (RSE), the corresponding values of which for the proposed model were 620.28, 0.99, 411.8, and 0.01, respectively. Here, the predictions of the model and those of available codes including ACI ITG, AS 3600, CSA-A23, EN 1994, JGJ 138, and NZS 3101 were compared for further model assessment. The obtained results showed that the proposed model had the highest correlation with the experimental data and the lowest error. In addition, to see if the developed model matched engineering realities and corresponded to the previously developed models, a parametric study and sensitivity analysis were carried out. The sensitivity analysis results indicated that the concrete cross-sectional area (A_c) has the greatest effect on the model, while parameter (f_yr) has a negligible effect.

• BMB Reports
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• 제53권5호
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• pp.266-271
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• 2020

Breast cancer encompasses a major portion of human cancers and must be carefully monitored for appropriate diagnoses and treatments. Among the many types of breast cancers, triple negative breast cancer (TNBC) has the worst prognosis and the least cases reported. To gain a better understanding and a more decisive precursor for TNBC, two major histone modifications, an activating modification H3K4me3 and a repressive modification H3K27me3, were analyzed using data from normal breast cell lines against TNBC cell lines. The combination of these two histone markers on the gene promoter regions showed a great correlation with gene expression. A list of signature genes was defined as active (highly enriched H3K4me3), including NOVA1, NAT8L, and MMP16, and repressive genes (highly enriched H3K27me3), IRX2 and ADRB2, according to the distribution of these histone modifications on the promoter regions. To further enhance the investigation, potential candidates were also compared with other types of breast cancer to identify signs specific to TNBC. RNA-seq data was implemented to confirm and verify gene regulation governed by the histone modifications. Combinations of the biomarkers based on H3K4me3 and H3K27me3 showed the diagnostic value AUC 93.28% with P-value of 1.16e-226. The results of this study suggest that histone modification analysis of opposing histone modifications may be valuable toward developing biomarkers and targets for TNBC.

• Asian-Australasian Journal of Animal Sciences
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• 제30권8호
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• pp.1183-1189
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• 2017

Objective: Owing to the public availability of complete genome sequences, including avian species, massive bioinformatics analyses may be conducted for computational gene prediction and the identification of gene regulatory networks through various informatics tools. However, to evaluate the biofunctional activity of a predicted target gene, in vivo and in vitro functional genomic analyses should be a prerequisite. Methods: Due to a lack of quail genomic sequence information, we first identified the partial genomic structure and sequences of the quail SH3 domain containing ring finger 2 (SH3RF2) gene. Subsequently, SH3RF2 was knocked out using clustered regularly interspaced short palindromic repeat/Cas9 technology and single cell-derived SH3RF2 mutant sublines were established to study the biofunctional activity of SH3RF2 in quail myoblast (QM7) cells during muscle differentiation. Results: Through a T7 endonuclease I assay and genotyping analysis, we established an SH3RF2 knockout (KO) QM7#4 subline with 61 and 155 nucleotide deletion mutations in SH3RF2. After the induction of myotube differentiation, the expression profiles were analyzed and compared between regular QM7 and SH3RF2 KO QM7#4 cells by global RNA sequencing and bioinformatics analysis. Conclusion: We did not detect any statistically significant role of SH3RF2 during myotube differentiation in QM7 myoblast cells. However, additional experiments are necessary to examine the biofunctional activity of SH3RF2 in cell proliferation and muscle growth.

• Asian Pacific Journal of Cancer Prevention
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• 제16권18호
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• pp.8467-8471
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• 2016

Background: One of the major mechanisms for drug resistance is associated with altered anticancer drug transport, mediated by the human-adenosine triphosphate binding cassette (ABC) transporter superfamily proteins. The overexpression of adenosine triphosphate binding cassette, sub-family B, member 1 (ABCB1) by multidrug-resistant cancer cells is a serious impediment to chemotherapy. In our study we have studied the possibility that structural single-nucleotide polymorphisms (SNP) are the mechanism of ABCB1 overexpression. Materials and Methods: A total of 101 gastric cancer multidrug resistant cases and 100 controls were genotyped with sequence-specific primed PCR (SSP-PCR). Gene expression was evaluated for 70 multidrug resistant cases and 54 controls by real time PCR. The correlation between the two groups was based on secondary structures of RNA predicted by bioinformatics tool. Results: The results of genotyping showed that among 3 studied SNPs, rs28381943 and rs2032586 had significant differences between patient and control groups but there were no differences in the two groups for C3435T. The results of real time PCR showed over-expression of ABCB1 when we compared our data with each of the genotypes in average mode. Prediction of secondary structures in the existence of 2 related SNPs (rs28381943 and rs2032586) showed that the amount of ${\Delta}G$ for original mRNA is higher than the amount of ${\Delta}G$ for the two mentioned SNPs. Conclusions: We have observed that 2 of our studied SNPs (rs283821943 and rs2032586) may elevate the expression of ABCB1 gene, through increase in mRNA stability, while this was not the case for C3435T.

• 생물정신의학
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• 제23권4호
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• pp.140-147
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• 2016

Objectives To determine the relationship between the Alu insertion/deletion (I/D) polymorphism in the tissue-type plasminogen activator (tPA) gene and the clinical outcome of mirtazapine treatment in Korean major depressive disorder (MDD) patients. Methods We enrolled 422 patients in this study. Symptoms were evaluated using the 21-item Hamilton Depression Rating (HAMD-21) Scale. After 1, 2, 4, and 8 weeks of mirtazapine treatment, the association between the Alu I/D polymorphism in the tPA gene and remission/response outcomes were evaluated. Results The proportion of I/I homozygotes in responders was higher than that in non-responders, whereas the proportion of D/D homozygotes in responders was lower than that in non-responders at 8 weeks of treatment (p = 0.032, OR = 1.57). The percentage decline of HAMD-21 scores in I allele carriers was larger than that of D/D homozygotes at 2 and 8 weeks of treatment (p = 0.035 and 0.007, respectively). I allele carriers were associated with remission at 8 weeks of treatment (p = 0.047, OR = 2.2). Conclusions These results show that treatment response and remission to mirtazapine were associated with the Alu I/D polymorphism of the tPA gene. This suggests the Alu I/D polymorphism may be a potential genetic marker for the prediction of therapeutic response to mirtazapine treatment in patients with MDD.

• Biomolecules & Therapeutics
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• 제15권3호
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• pp.156-161
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• 2007

Rapid advances in pharmacogenomic research have provided important information to improve drug selection, to maximize drug efficacy, and to minimize drug adverse reaction. The SNPs that are the most abundant type of genetic variants have been proven as valid biomarkers to give information on the prediction of pharmacokinetic/pharmacodynamic properties of drugs based on genotype. In order to elucidate a correlation between SNPs of calcium channel encoding gene and adverse reactions of calcium channel blockers, we investigated SNPs in CACNA1C gene known as a binding site of calcium channel blocker. 96 patients with hypertension who had taken or are taking an antihypertensive drug, 1,4-dihydropyridine (DHP) were included for analysis. These patients were composed of 47 patients with adverse drug reactions (ADR) such as edema from calcium channel blockers and 49 patients without ADR as a control group. The exons encoding the drug binding sites were amplified by PCR using specific primers, and SNPs were analyzed by direct sequencing. We found that there was no SNP in the exons encoding DHP binding site, but four novel SNPs in the exon-intron junction region. However, four novel SNPs were not associated with the ADR of calcium channel blockers. In conclusion, this study showed that ADR from calcium channel blockers may not be caused by SNPs of the binding sites of calcium channel blockers in CACNA1C gene.

• 한국지능시스템학회논문지
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• 제19권6호
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• pp.802-808
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• 2009

마이크로어레이 데이터의 클러스터링 성능을 향상시키기 위하여 유전자 온톨로지(GO)를 활용하는 연구가 최근 진행 중에 있다. 그 중 Biological Process(BP) GO를 활용한 Kustra et al.의 연구가 2006년에 소개된 바 있다. 본 연구는 Kustra et al.의 연구를 확장하여 일반적이고 실질적인 GO의 활용 방안을 위한 분석 결과를 제시하기 위하여 다양한 활용 방법을 적용한다. (1) GO의 거리를 측정하기 위하여 Lin et al, Resnik et al과 Jiang et al의 방법을 적용하였으며, (2) BP를 포함한 세 가지 GO 유형의 구조에 대해 적용하여 각 방법에 따른 성능 향상 정도를 분석한다. 각 방법에 대한 성능 분석 비교를 위하여 효모 유전자를 관측하여 형성한 데이터를 활용한다. 실험 결과를 통하여 GO 정보를 클러스터링에 적용하면 전반적으로 성능 향상을 유도하지만, 활용 방법에 따라서 성능 개선 정도의 차이가 발생한다. 그 중 Resnik의 거리 측정 척도와 BP GO를 활용하였을 때, 가장 개선된 성능을 유도함을 볼 수 있다.

• 한국정보통신학회논문지
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• 제23권8호
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• pp.903-909
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• 2019

치주질환은 상당수의 성인들이 가지고 있는 질환이지만 아직 분자적인 수준에서의 발생 기작과 치료 방법에 대해서는 많은 것이 밝혀져 있지 않다. 본 연구에서는 치주질환 조직과 정상 조직에서 얻어진 유전자 발현 데이터를 이용하여 치주질환 조직과 정상 조직 사이에 분자적 차이가 있는지를 확인한다. 특히 기계학습 알고리즘을 이용하여 유전자 발현양 기반 치주질환 조직과 정상 조직의 분류가 가능한지를 확인하고, 각 조직에서 발현양 차이가 나는 유전자들이 주로 어떤 기능을 하는 것인지 살펴본다. t-SNE를 이용한 분석 결과 정상 조직과 치주질환 조직 샘플이 명확히 구분되어 군집화 될 수 있음이 확인되었다. 또한, 결정 트리, 랜덤 포레스트, 서포트 벡터 머신을 이용한 분류 알고리즘을 적용한 결과 불균형 데이터임에도 높은 정확도와 민감도, 특이도를 보였으며, 염증 반응 및 면역 반응 관련 유전자들이 주로 두 집단 간에 차이를 보임이 확인되었다.

• The Plant Pathology Journal
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• 제35권2호
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• pp.172-177
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• 2019

A duplex PCR method was developed for simultaneous detection and identification of tobacco root rot pathogens Phytophthora nicotianae and Thielaviopsis basicola. The specific primers for P. nicotianae were developed based on its internal transcribed spacer (ITS) regions of ribosomal gene, ras gene and hgd gene, while the specific primers for T. basicola were designed based on its ITS regions and ${\beta}$-tubulin gene. The specificity of the primers was determined using isolates of P. nicotianae, T. basicola and control samples. The results showed that the target pathogens could be detected from diseased tobacco plants by a combination of the specific primers. The sensitivity limitation was $100fg/{\mu}l$ of pure genomic DNA of the pathogens. This new assay can be applied to screen out target pathogens rapidly and reliably in one PCR and will be an important tool for the identification and precise early prediction of these two destructive diseases of tobacco.