• BMB Reports
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• 제41권8호
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• pp.609-614
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• 2008

The concentrations and catalytic activities of enzymes control metabolic rates. Previous studies have focused on enzyme concentrations because there are no genome-wide techniques used for the measurement of enzyme activity. We propose a method for evaluating the significance of enzyme activity by integrating metabolic network topologies and genome-wide microarray gene expression profiles. We quantified the enzymatic activity of reactions and report the 388 significant reactions in five perturbation datasets. For the 388 enzymatic reactions, we identified 70 that were significantly regulated (P-value < 0.001). Thirty-one of these reactions were part of anaerobic metabolism, 23 were part of low-pH aerobic metabolism, 8 were part of high-pH anaerobic metabolism, 3 were part of low-pH aerobic reactions, and 5 were part of high-pH anaerobic metabolism.

• Reproductive and Developmental Biology
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• 제37권4호
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• pp.185-192
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• 2013

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network analysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like reproduction.

• Genomics & Informatics
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• 제15권2호
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• pp.56-64
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• 2017

We have previously reported that NS-398, a cyclooxygenase-2 (COX-2)-selective inhibitor, inhibited replicative cellular senescence in human dermal fibroblasts and skin aging in hairless mice. In contrast, celecoxib, another COX-2-selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. The data showed that several senescence-related gene sets were regulated by the inhibitor treatment. NS-398 up-regulated gene sets involved in the tumor necrosis factor ${\beta}$ receptor pathway and the fructose and mannose metabolism, whereas it down-regulated a gene set involved in protein secretion. Celecoxib up-regulated gene sets involved in G2M checkpoint and E2F targets. Aspirin up-regulated the gene set involved in protein secretion, and down-regulated gene sets involved in RNA transcription. These results suggest that COX inhibitors modulate cellular senescence by different mechanisms and will provide useful information to understand senescence-modulating mechanisms of COX inhibitors.

• Biomolecules & Therapeutics
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• 제25권2호
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• pp.177-185
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• 2017

Auranofin has been developed as antirheumatic drugs, which is currently under clinical development for the treatment of chronic lymphocytic leukemia. Previous report showed that auranofin induced apoptosis by enhancement of annexin A5 expression in PC-3 cells. To understand the role of annexin A5 in auranofin-mediated apoptosis, we performed microarray data analysis to study annexin A5-controlled gene expression in annexin A5 knockdown PC-3 cells. Of differentially expressed genes, plasminogen activator inhibitor (PAI)-2 was increased by annexin A5 siRNA confirmed by qRT-PCR and western blot. Treatment with auranofin decreased PAI-2 and increased annexin A5 expression as well as promoting apoptosis. Furthermore, auranofin-induced apoptosis was recovered by annexin A5 siRNA but it was promoted by PAI-2 siRNA. Interestingly, knockdown of annexin A5 rescued PAI-2 expression suppressed by auranofin. Taken together, our study suggests that induction of annexin A5 by auranofin may enhance apoptosis through suppression of PAI-2 expression in PC-3 cells.

• 한국초지조사료학회지
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• 제41권4호
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• pp.242-249
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• 2021

Forage crop management is severely challenged by global warming-induced climate changes representing diverse a/biotic stresses. Thus, screening of valuable genetic resources would be applied to develop stress-tolerant forage crops. We isolated two NAC (NAM, ATAF1, ATAF2, CUC2) transcription factors (ANAC032 and ANAC083) transcriptionally activated by multi-abiotic stresses (salt, drought, and cold stresses) from Arabidopsis by microarray analysis. The NAC family is one of the most prominent transcription factor families in plants and functions in various biological processes. The enhanced expressions of two ANACs by multi-abiotic stresses were validated by quantitative RT-PCR analysis. We also confirmed that both ANACs were localized in the nucleus, suggesting that ANAC032 and ANAC083 act as transcription factors to regulate the expression of downstream target genes. Promoter activities of ANAC032 and ANAC083 through histochemical GUS staining again suggested that various abiotic stresses strongly drive both ANACs expressions. Our data suggest that ANAC032 and ANAC083 would be valuable genetic candidates for breeding multi-abiotic stress-tolerant forage crops via the genetic modification of a single gene.

• Nuclear Engineering and Technology
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• 제54권8호
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• pp.3027-3033
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• 2022

Background: In this study, various types of deep-learning models for predicting in vitro radiosensitivity from gene-expression profiling were compared. Methods: The clonogenic surviving fractions at 2 Gy from previous publications and microarray gene-expression data from the National Cancer Institute-60 cell lines were used to measure the radiosensitivity. Seven different prediction models including three distinct multi-layered perceptrons (MLP), four different convolutional neural networks (CNN) were compared. Folded cross-validation was applied to train and evaluate model performance. The criteria for correct prediction were absolute error < 0.02 or relative error < 10%. The models were compared in terms of prediction accuracy, training time per epoch, training fluctuations, and required calculation resources. Results: The strength of MLP-based models was their fast initial convergence and short training time per epoch. They represented significantly different prediction accuracy depending on the model configuration. The CNN-based models showed relatively high prediction accuracy, low training fluctuations, and a relatively small increase in the memory requirement as the model deepens. Conclusion: Our findings suggest that a CNN-based model with moderate depth would be appropriate when the prediction accuracy is important, and a shallow MLP-based model can be recommended when either the training resources or time are limited.

• Journal of Plant Biotechnology
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• 제49권4호
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• pp.292-2999
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• 2022

Anthocyanin, an important component in the grape berry skin, strongly affects grape quality. The transcription factors VvMYBA1 and VvMYBA2 (VvMYBA1/2) control anthocyanin biosynthesis. In addition, cultivation and environmental factors, such as light, influence anthocyanin accumulation. The present study aimed to clarify the effect of shading (reduced light condition) on the transcriptomic regulation of anthocyanin biosynthesis using a red-wine grape cultivar, Vitis vinifera 'Pinot Noir', and its white mutant, 'Pinot Blanc', caused by the deletion of the red allele of VvMYBA1/2. The grape berry skins were analyzed for anthocyanin content and global gene transcription accumulation. The microarray data were later validated by quantitative real-time PCR. A decisive influence of VvMYBA1/2 on the expression of an anthocyanin-specific gene, UDP glucose: flavonoid 3-O-glucosyltransferase, was observed as expected. In contrast, upstream genes of the pathway, which are shared by other flavonoids, were also expressed in 'Pinot Blanc', and the mRNA levels of some of these genes decreased in both cultivars on shading. Thus, the involvement of light-sensitive transcription factor(s) other than VvMYBA1/2 was suggested for the expression control of the upstream genes of the anthocyanin biosynthetic pathway. Furthermore, it was suggested that the effects of these factors are different among isogenes.

• IMMUNE NETWORK
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• 제11권5호
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• pp.258-267
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• 2011

Background: Current management strategies attempt to diagnose rheumatoid arthritis (RA) at an early stage. Transcription profiling is applied in the search for biomarkers for detecting early-stage disease. Even though gene profiling has been reported using several animal models of RA, most studies were performed after the development of active arthritis, and conducted only on the peripheral blood and joint. Therefore, we investigated gene expression during the initial phase of collagen-induced arthritis (CIA) before the arthritic features developed in the thymus in addition to the peripheral blood and synovium. Methods: For gene expression analysis using cDNA microarray technology, samples of thymus, blood, and synovium were collected from CIA, rats immunized only with type II collagen (Cll), rats immunized only with adjuvant, and unimmunized rats on days 4 and 9 after the first immunization. Arrays were scanned with an Illumina bead array. Results: Of the 21,910 genes in the array, 1,243 genes were differentially expressed at least 2-fold change in various organs of CIA compared to controls. Among the 1,243 genes, 8 encode T-cell receptors (TCRs), including CD3${\zeta}$, CD3${\delta}$, CD3${\varepsilon}$, CD8${\alpha}$, and CD8${\beta}$ genes, which were down-regulated in CIA. The synovium was the organ in which the genes were differentially expressed between CIA and control group, and no difference were found in the thymus and blood. Further, we determined that the differential expression was affected by adjuvant more than Cll. The differential expression of genes as revealed by real-time RT-PCR, was in agreement with the microarray data. Conclusion: This study provides evidence that the genes encoding TCRs including CD3${\zeta}$, CD3${\delta}$, CD3${\varepsilon}$, CD8${\alpha}$, and CD8${\beta}$ genes were down-regulated during the initial phase of CIA in the synovium of CIA. In addition, adjuvant played a greater role in the down-regulation of the CD3 complex compared to CII. Therefore, the down-regulation of TCR gene expression occurred dominantly by adjuvant could be involved in the pathogenesis of the early stage at CIA.

• Molecules and Cells
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• 제43권5호
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• pp.469-478
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• 2020

Hepatitis C virus (HCV) propagation is highly dependent on cellular proteins. To identify the host factors involved in HCV propagation, we previously performed protein microarray assays and identified the LIM and SH3 domain protein 1 (LASP-1) as an HCV NS5A-interacting partner. LASP-1 plays an important role in the regulation of cell proliferation, migration, and protein-protein interactions. Alteration of LASP-1 expression has been implicated in hepatocellular carcinoma. However, the functional involvement of LASP-1 in HCV propagation and HCV-induced pathogenesis has not been elucidated. Here, we first verified the protein interaction of NS5A and LASP-1 by both in vitro pulldown and coimmunoprecipitation assays. We further showed that NS5A and LASP-1 were colocalized in the cytoplasm of HCV infected cells. NS5A interacted with LASP-1 through the proline motif in domain I of NS5A and the tryptophan residue in the SH3 domain of LASP-1. Knockdown of LASP1 increased HCV replication in both HCV-infected cells and HCV subgenomic replicon cells. LASP-1 negatively regulated viral propagation and thereby overexpression of LASP-1 decreased HCV replication. Moreover, HCV propagation was decreased by wild-type LASP-1 but not by an NS5A binding-defective mutant of LASP-1. We further demonstrated that LASP-1 was involved in the replication stage of the HCV life cycle. Importantly, LASP-1 expression levels were increased in persistently infected cells with HCV. These data suggest that HCV modulates LASP-1 via NS5A in order to regulate virion levels and maintain a persistent infection.

• 생명과학회지
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• 제20권2호
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• pp.213-218
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• 2010

본 연구에서는 대장암 세포주 모델에서 파이토케미칼 capsaicin에 의한 항 생장 활성과 유전체 수준에서의 유전자 발현 변화를 연구하였다. 그 결과, 처리한 capsaicin 농도 의존적으로 세포 생존율이 감소함을 확인하였고, capsaicin은 다양한 유전자의 발현 변화를 유도하였다. DNA microarray 실험결과 $100\;{\mu}M$ capsaicin의 처리에 의해 2배 이상 증가되는 유전자 103개가 확인된 반면, 2배 이상 발현이 감소되는 유전자 153개가 확인되었다. 발현이 증가되는 유전자 중 4개(NAG-1, DDIT3, GADD45A 그리고 PCK2)를 선택하여 RT-PCR을 수행한 결과, DNA micorarray 실험과 일치함을 확인하였다. 또한 $100\;{\mu}M$ capsaicin의 처리에 의해 암 억제유전자인 p53의 발현이 증가됨을 RT-PCR과 real-time PCR 방법으로 확인하였다. 게다가, NAG-1, DDIT3 그리고 GADD45A 유전자는 p53의 존재에 관계없이 발현이 증가되는 반면, PCK2 유전자는 반드시 p53에 의해 발현이 유도됨을 확인할 수 있었다. 이러한 연구는 대장암 세포주에서 capsaicin에 의한 항암 기전을 이해하는데 도움을 줄 것으로 기대된다.