• Journal of Microbiology and Biotechnology
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• v.19 no.10
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• pp.1103-1108
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• 2009

The human immunodeficiency virus (HIV)-l protein Tat acts as a transcription transactivator that stimulates expression of the infected viral genome. It is released from infected cells and can similarly affect neighboring cells. The nucleocapsid is an important protein that has a related significant role in early mRNA expression, and which contributes to the rapid viral replication that occurs during HIV-1 infection. To investigate the interaction between the Tat and nucleocapsid proteins, we utilized cDNA micro arrays using pTat and flag NC cotransfection in HEK 293T cells and reverse transcription-polymerase chain reaction to validate the micro array data. Four upregulated genes and nine downregulated genes were selected as candidate genes. Gene ontology analysis was conducted to define the biological process of the input genes. A proteomic approach using PathwayStudio determined the relationship between Tat and nucleocapsid; two automatically built pathways represented the interactions between the upregulated and downregulated genes. The results indicate that the up- and downregulated genes regulate HIV-1 replication and proliferation, and viral entry.

• BMB Reports
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• v.54 no.9
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• pp.464-469
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• 2021

Cardiomyocyte differentiation occurs through complex and finely regulated processes including cardiac lineage commitment and maturation from pluripotent stem cells (PSCs). To gain some insight into the genome-wide characteristics of cardiac lineage commitment, we performed transcriptome analysis on both mouse embryonic stem cells (mESCs) and human induced PSCs (hiPSCs) at specific stages of cardiomyocyte differentiation. Specifically, the gene expression profiles and the protein-protein interaction networks of the mESC-derived platelet-derived growth factor receptor-alpha (PDGFRα)⁺ cardiac lineage-committed cells (CLCs) and hiPSC-derived kinase insert domain receptor (KDR)⁺ and PDGFRα⁺ cardiac progenitor cells (CPCs) at cardiac lineage commitment were compared with those of mesodermal cells and differentiated cardiomyocytes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the genes significantly upregulated at cardiac lineage commitment were associated with responses to organic substances and external stimuli, extracellular and myocardial contractile components, receptor binding, gated channel activity, PI3K-AKT signaling, and cardiac hypertrophy and dilation pathways. Protein-protein interaction network analysis revealed that the expression levels of genes that regulate cardiac maturation, heart contraction, and calcium handling showed a consistent increase during cardiac differentiation; however, the expression levels of genes that regulate cell differentiation and multicellular organism development decreased at the cardiac maturation stage following lineage commitment. Additionally, we identified for the first time the protein-protein interaction network connecting cardiac development, the immune system, and metabolism during cardiac lineage commitment in both mESC-derived PDGFRα⁺ CLCs and hiPSC-derived KDR⁺PDGFRα⁺ CPCs. These findings shed light on the regulation of cardiac lineage commitment and the pathogenesis of cardiometabolic diseases.

• The Plant Pathology Journal
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• v.27 no.1
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• pp.26-32
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• 2011

Plant-pathogenic bacteria including Xanthomonas spp. carry genetic diversity in composition of avirulence genes for interaction with their host plants. Previously, we reported genetic diversity of avirulence genes in X. axonopodis pv. glycines. In this study, we determined genetic diversity of five avirulence genes, avrBs1, avrBs2, avrBs3, avrBs4, and avrRxv, in three other Xanthomonas species isolated in Korea by genomic southern hybridization. Although Korean races of X. campestris pv. vesicatoria that were isolated from year 1995 to 2002 had the same avirulence gene patterns as those that already reported, there was race shift from race 3 to race 1 by acquisition of avrBs3 genes. X. campestris pv. campestris isolated from Chinese cabbage, but not from cabbage or radish, carried two avrBs3 genes, and one of them affected HR-eliciting ability of this bacterium in broccoli. X. oryzae pv. oryzae carried eight to thirteen avrBs3 gene homologs, and this bacterium showed dynamic changes of resistance patterns in rice probably by losing or obtaining avrBs3 genes. These results indicate that avrBs3 gene is more diverse in Xanthomonas spp. than other four avirulence genes and also host ranges of these bacteria can be easily changed by loss or acquisition of avrBs3 genes.

• The Plant Pathology Journal
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• v.24 no.4
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• pp.384-391
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• 2008

Rice blast disease, caused by the pathogenic fungus Magnaporthe grisea, is a serious issue in rice (Oryza sativa L.) growing regions of the world. Transcript profiling in rice inoculated with the fungus has been investigated using the transcriptomics technology, serial analysis of gene expression (SAGE). Short sequence tags containing sufficient information which are ten base-pairs representing the unique transcripts were identified by SAGE technology. We identified a total of 910 tag sequences via the GenBank database, and the resulting genes were shown to be up-regulated in all functional categories under the fungal biotic stress. Compared to the compatible interaction, the stress and defense genes in the incompatible interaction appear to be more up-regulated. Particularly, thaumatin-like gene (TLP) was investigated in determining the gene and protein expression level utilizing Northern and Western blotting analyses, resulting in an increase in both the gene and the protein expression level which arose earlier in the incompatible interaction than in the compatible interaction.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.618-627
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• 2020

Although limited progress have been made about pathogen system of Hibiscus rosa-sinensis and Hibiscus latent Fort Pierce virus (HLFPV), interaction between plant host and pathogen remain largely unknown, which led to deficiency of effective measures to control disease of hibiscus plants caused by HLFPV. In this study, infection of HLFPV in Hibiscus rosa-sinensis was firstly confirmed for the first time by traditional electron microscopy, modern reverse transcription polymerase chain reaction and RNA-seq methods in China (HLFPV-Ch). Sequence properties analyzing suggested that the full-length sequences (6,465 nt) of HLFPV-Ch had a high sequence identity and a similar genomic structure with other tobamoviruses. It includes a 5'-terminal untranslated region (UTR), followed by four open reading frames encoding for a 128.5-kDa replicase, a 186.5-kDa polymerase, a 31-kDa movement protein, 17.6-kDa coat protein, and the last a 3'-terminal UTR. Furthermore, HLFPV-Ch-derived virus-derived siRNAs (vsiRNAs) ant its putative target genes, reported also for the first time, were identified and characterized from disease Hibiscus rosa-sinensis through sRNA-seq and Patmatch server to investigate the interaction in this pathogen systems. HLFPV-Ch-derived vsiRNAs demonstrated several general and specific characteristics. Gene Ontology classification revealed predicted target genes by vsiRNAs are involved in abroad range of cellular component, molecular function and biological processes. Taken together, for first time, our results certified the HLFPV infection in China and provide an insight into interaction between HLFPV and Hibiscus rosa-sinensis.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.13-13
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• 2014

Species belonging to the genus Fusarium are widely distributed and cause diseases in many plants. Isolation of fungal strains from air or cereals is necessary for disease forecasting, disease diagnosis, and population genetics [1]. Previously we showed that Fusarium species are resistant to toxoflavin produced by the bacterial rice pathogen Burkholderia glumae while other fungal genera are sensitive to the toxin, resulting in the development of a selective medium for Fusarium species using toxoflavin [2]. In this study, we have tried to elucidate the resistant mechanism of F. graminearum against toxoflavin and interaction between the two pathogens in nature. To test whether B. glumae affects the development of F. graminearum, the wild-type F. graminearum strains were incubated with either the bacterial strain or supernatant of the bacterial culture. Both conditions increased the conidial production five times more than when the fungus was incubated alone. While co-incubation resulted in dramatic increase of conidial production, conidia germination delayed by either the bacterial strain or supernatant. These results suggest that certain factors produced by B. glumae induce conidial production and delay conidial germination in F. graminearum. To identify genes related to toxoflavin resistance in F. graminearum, we screened the transcriptional factor mutant library previously generated in F. graminearum [3] and identified one mutant that is sensitive to toxoflavin. We analyzed transcriptomes of the wild-type strain and the mutant strain under either absence or presence of toxoflavin through RNAseq. Expression level of total genes of 13,820 was measured by reads per kilobase per million mapped reads (RPKM). Under the criteria with more than two-fold changes, 1,440 genes were upregulated and 1,267 genes were down-regulated in wild-type strain than mutant strain in response to toxoflavin treatment. A comparison of gene expression profiling between the wild type and mutant through gene ontology analysis showed that genes related to metabolic process and oxidation-reduction process were highly enriched in the mutant strain. The data analyses will focus on elucidating the resistance mechanism of F. graminearum against toxoflavin and the interaction between the two pathogens in rice. Further evolutionary history will be traced through figuring out the gene function in populations and in other filamentous fungi.

• Animal Bioscience
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• v.37 no.8
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• pp.1345-1354
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• 2024

Objective: The objective of this study was to identify candidate genes that play important roles in skeletal muscle development in ducks. Methods: In this study, we investigated the transcriptional sequencing of embryonic pectoral muscles from two specialized lines: Liancheng white ducks (female) and Cherry valley ducks (male) hybrid Line A (LCA) and Line C (LCC) ducks. In addition, prediction of target genes for the differentially expressed mRNAs was conducted and the enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes signaling pathways were further analyzed. Finally, a protein-to-protein interaction network was analyzed by using the target genes to gain insights into their potential functional association. Results: A total of 1,428 differentially expressed genes (DEGs) with 762 being up-regulated genes and 666 being down-regulated genes in pectoral muscle of LCA and LCC ducks identified by RNA-seq (p<0.05). Meanwhile, 23 GO terms in the down-regulated genes and 75 GO terms in up-regulated genes were significantly enriched (p<0.05). Furthermore, the top 5 most enriched pathways were ECM-receptor interaction, fatty acid degradation, pyruvate degradation, PPAR signaling pathway, and glycolysis/gluconeogenesis. Finally, the candidate genes including integrin b3 (Itgb3), pyruvate kinase M1/2 (Pkm), insulin-like growth factor 1 (Igf1), glucose-6-phosphate isomerase (Gpi), GABA type A receptor-associated protein-like 1 (Gabarapl1), and thyroid hormone receptor beta (Thrb) showed the most expression difference, and then were selected to verification by quantitative real-time polymerase chain reaction (qRT-PCR). The result of qRT-PCR was consistent with that of transcriptome sequencing. Conclusion: This study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.21 no.3
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• pp.52-68
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• 2008

Objectives and Methods : Salviae miltiorrhizae Radix (SMR) promotes blood circulation to remove blood stasis, cools the blood to relieve carbuncle, clears away heat from the heart and tranquilizes the mind. This study was designed to investigate the effects of SMR on immuno-potentiative action in terms of changes in the genetic profile of dendritic cells (DC) using by microarray analysis. Results and Conclusion: In this experiment, treatments with more than 250 ${\mu}g/ml$ upto 1000 ${\mu}g/ml$ of SMR elevated the proliferation rates of DC. Microscopic observations confirmed the tendency on proliferation rates. Expression levels of genes related with cellular methabolic process, cell communication, and macromolecule metabolic process were elevated by treatment with SMR in comparison of functional distribution in a Biological Process. In molecular functions, expression levels of genes related with receptor activation, nucleotide binding and nucleic acid binding were elevated. In cellular components, expression levels of genes related to cellular membrane-bound organelles were elevated. In addition, expression levels of genes related to Wnt signalling pathways and the glycerophospholipid metabolism were elevated through analysis using pathway analysis between up-and down-regulated genes in cells treated with SMR. Finally, genes related to JAK2, GRB2, CDC42, SMAD4, B2M, FOS and ESRI located the center of Protein interaction network of genes through treatment with SMR.

• Journal of Microbiology and Biotechnology
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• v.25 no.6
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• pp.903-909
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• 2015

Indole-3-acetic acid (IAA) production is a typical mechanism of plant growth promotion by some rhizobacteria. However, a functional genomic study is necessary to unravel the function and mechanism of IAA signaling during rhizobacteria-plant interactions. In this study, the expression of SlIAA1 and SlIAA9 among the auxin response genes in tomato was examined during the interaction between IAA-producing Acinetobacter guillouiae SW5 and tomato plants. When 3-day grown tomato seedlings were treated for 30 min with 10~100 µM of IAA produced by bacteria from tryptophan, the relative mRNA levels of SlIAA1 and SlIAA9 increased significantly compared with those of the control, demonstrating that IAA produced by this bacterium can induce the expressions of both genes. Inoculation of live A. guillouiae SW5 to tomato seedlings also increased the expressions of SlIAA1 and SlIAA9, with more mRNA produced at higher bacterial density. In contrast, treatment of tomato seedlings with dead A. guillouiae SW5 did not significantly affect the expression of SlIAA1and SlIAA9. When 3-day bacterial culture in tomato root exudates was administered to tomato seedlings, the relative mRNA level of SlIAA1 increased. This result indicated that the plant may take up IAA produced by bacteria in plant root exudates, which may increase the expression of the auxin response genes, with resulting promotion of plant growth.

• The Journal of Korean Obstetrics and Gynecology
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• v.23 no.2
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• pp.71-84
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• 2010

Purpose: In the theory of traditional medicine, Glenditsia spina(GS) can resolve carbuncle, relive swelling, dispel wind and destroy parasites. This study was designed to investigate the effects of GS on gene expression of ovarian tissue in polycystic ovary syndrome(PCOS) rats. Methods: In this experiment, female rats injected with a single dose of 2 mg estradiol valerate(EV) and GS was given for 5 weeks. The genetic profile for the effects on ovarian tissue in PCOS rats was measured using microarray technique, and the functional analysis on these genes was conducted. Results: 985 genes were increased in control and restored to normal level in GS group. (B), 733 genes were decreased in control group and restored to normal level in GS group. (F). Metabolic pathways related in B group genes were Graft-versus-host disease, Allograft rejection, Autoimmune thyroid disease, Cytokine-cytokine receptor interaction, Small cell lung cancer, Type I diabetes mellitus. Metabolic pathways related in F group genes were Antigen processing and present, Adipocytokine signalling pathway, Focal adhesion, ECM-receptor interaction, Pancreatic cancer, Notch signalling pathway, Tight junction. The network of total protein interactions was measured using cytoscape program, and some key molecules, such as c-Fos, c-Myc, ABL1 related in B group, MAPK8, RASA1, CALR related in F group that can be used for elucidation of therapeutical mechanism of medicine in future were identified. Conclusion: These results suggest possibility of GS as anti-cancer and anti-hyperplasia drug in PCOS. In addition, the present author also suggests that related mechanisms are involved in suppression of proto-oncogene such as c-Fos, c-Myc and ABL1, and in regulation of cell cycle such as RASA1.