• Genomics & Informatics
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• 제17권1호
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• International Journal of Industrial Entomology and Biomaterials
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• 제8권1호
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• pp.117-121
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• 2004

Soluble proteins of silkworm hemolymph were investigated by means of isoelectric focusing (IEF). The protein spectra during ontogenesis of races and inter-races hybrids kept in Bulgaria was studied. A total of 51 protein bands in the hemolymph from fourth larval instar to imago were ascertained. Stage specific expression was established. The specific expression of some protein bands in the individual spectra manifest phenotype of gene determinate polymorphism (HP F, HP J, HP K, HP L, HP Q - in the zone with pH gradient 3.5-6.2 and HP K, HP L, HP N, HP P, HP T - in the zone with pH gradient 9.5 - 6.2). Breed specific expression was observed. On the basis of the obtained results, it was established that the investigated breeds are heterogeneous and the isoelectric focusing method is successful when specifying the inner-race and inter-race polymorphism in silkworm.

• Biotechnology and Bioprocess Engineering:BBE
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• 제9권3호
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• pp.184-190
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• 2004

The influences of impeller types on morphology and protein expression were investigated in a submerged culture of Aspergillus oryzae. The impeller types strongly affected mycelial morphology and protein production in batch and fed-batch fermentations. Cells that were cultured by propeller agitation grew in the form of a pellet, whereas cells that were cultured by turbine agitation grew in a freely dispersed-hyphal manner and in a clumped form. Pellet-grown cells showed high levels of protein production for both the intracellularly heterologous protein (${\beta}$-glucuronidase) and the extracellularly homologous protein (${\alpha}$-amylase). The feeding mode of the carbon source also influenced the morphological distribution and protein expression in fed-batch fermentation of A. oryzae. Pulsed-feeding mainly showed high protein expression and homogeneous distribution of pellet whereas continuous feeding resulted in less protein expression and heterogeneous distribution with pellet and dispersed-hyphae. The pellet growth with propeller agitation paralleling with the pulsed-feeding of carbon source showed a high level of protein production in the submerged fed-batch fermentation of recombinant A. oryzae.

• 농업과학연구
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• 제38권1호
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• pp.65-70
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• 2011

Development of mouse fetus brains can be defined morphologically and functionally by three developmental stages, embryo day (ED) 16, postnatal stage one week and eight weeks. These defined stages of brain development may be closely associated with differential gene expression rates due to limited cellular resources such as energy, space, and free water. Complex patterns of expressed genes and proteins during brain development suggests the changes in relative concentrations of proteins rather than the increase in numbers of new gene products. This study was designed to evaluate early protein expression pattern in mouse fetus brain. The mouse brain proteome of fetus at ED 15.5, and 19.5 was obtained using 2-dimensional gel electrophoresis (DE). Analysis of the 2-DE gels in pH 3-10 range revealed the presence of 15 differentially expressed spots, of which 11 spots were identified to be known proteins following MALDI-TOF analysis; 3 spots were up-regulated and 8 spots were down-regulated in the mouse fetus brain at ED 15.5. UP-regulated proteins were identified as MCG18238, isoform M2 of pyruvate kinase isozymes M1/M2, isoform 2 of heterogeneous nuclear ribonucleoprotein K, heterogeneous nuclear ribonucleoprotein H2, creatine kinase B-type, 40S ribosomal protein SA and hemoglobin subunit beta-H1. Down-regulated proteins were putative uncharacterized protein, lactoylglutathione lyase and secreted acidic cysteine rich glycoprotein. Our results revealed composite profiles of mouse fetus brain proteins related to mouse fetus development by 2-DE analysis implying possible roles of these proteins in neural differentiation.

• Food Science and Biotechnology
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• 제14권6호
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• pp.854-859
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• 2005

Although action modes of equol and genistein have been extensively studied, their precise roles in tumor cells remain elusive. To address possible effects of these compounds on protein expression in mammary tumor cells, proteins modulated in MCF-7 mammary tumor cells when incubated in absence and presence of 10 uM equol or genistein were identified through 2-dimensional gel electrophoresis, MALDI-TOF MS/MS, and NCBInr database search using Mascot software. Most proteins differentially expressed in MCF-7 cells after treatment with 10 uM genistein or equol were identified as being the same. Exposure to both compounds caused decreased cellular expression of RNA-binding protein regulatory subunit and oncogene DJ1 tubulin beta-1 chain, and increased expression of heterogeneous ribonucleoproteins F and L, KH-type splicing regulatory protein, and translation elongation factor EF-Tu precursor. Genistein and equol at dose used in this study showed common action mechanism.

• 한국어병학회지
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• 제16권3호
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• pp.147-152
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• 2003

The CMV promoter driven luciferase reporter gene coding plasmid (pcDNA-luc) was constructed and used as a model for DNA immunization study. Expression of the recombinant luciferase protein was confirmed in vitro in RTG-2 cell line before using in vivo study in olive flounder. In dose response study, the maximum expression of the luciferase gene was found in the group injected with 10-15μg of plasmid DNA. The kinetic study showed that the luciferase gene expression was reached at the maximum level at one day after injection and slightly decreased after then but significantly high level of expression was sustained until the conducted experiment of 7 days. In the study of tissue distribution of gene expression, it was found that luciferase gene was expressed at the significant level in immune organs such as gill and spleen, located far from the injected site, suggesting the systemic distribution of the intramuscularly injected DNA in olive flounder.

• 대한의생명과학회지
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• 제24권4호
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• pp.426-429
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• 2018

Chronic eosinophilic leukemia (CEL) is characterized by eosinophilia and organ damage. Imatinib is widely used for treating CEL, chronic myeloid leukemia (CML) and acute myeloid leukemia (AML). Unfortunately, the cancer cells gain resistance against the drug after prolonged molecular-targeted therapies. Imatinib-resistant EoL-1 (EoL-1-IR) cells were produced from chronic eosinophilic leukemia cells (EoL-1) after treatment with imatinib for a long duration. Two-dimensional electrophoresis (2-DE) analysis revealed numerous protein variations in the EoL-1 and EoL-1-IR sub-types. Compared to the EoL-1 cells, expression levels of TIP49, RBBP7, ${\alpha}$-enolase, adenosine deaminase, C protein, galactokinase, eukaryotic translation initiation factor, $IFN-{\gamma}$, and human protein homologous to DROER were increased, whereas core I protein, proteasome subunit p42, heterogeneous ribonuclear particle protein, chain B, and nucleoside diphosphate were decreased in the EoL-1-IR cells. Taken together, these results contribute to understanding the pathogenic mechanism of drug-resistant diseases.

• Journal of Periodontal and Implant Science
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• 제34권1호
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• pp.205-221
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• 2004

Periodontal ligament(PDL) cells have been known as playing an important roles in periodontal regeneration and gingival fibroblasts are also important to periodontal regeneration by forming connective tissue attachment. There were rare studies about the gene expression patterns of PDL cells and gingival fibroblasts, therefore in this study, we tried cDNA microarray-based gene expression monitoring to explain the functional differences of PDL cells and gingival fibroblasts in vivo and to confirm the characteristics of PDL cells. Total RNA were extracted from PDL cells and gingival fibroblasts of same person and same passages, and mRNA were isolated from the total RNA using Oligotex mRNA midi kit(Qiagen) and then fluorescent cDNA probe were prepared. And microarray hybridization were performed. The gene expression patterns of PDL cells and gingival fibroblasts were quite different. About 400 genes were expressed more highly in the PDL cells than gingival fibroblasts and about 300 genes were more highly expressed in the gingival fibroblasts than PDL cells. Compared growth factor- and growth factor receptor-related gene expression patterns of PDL cells with gingival fibroblasts, IGF-2, IGF-2 associated protein, nerve growth factor, placental bone morphogenic protein, neuron-specific growth- associated protein, FGF receptor, EGF receptor-related gene and PDGF receptor were more highly expressed in the PDL cells than gingival fibroblasts. The results of collagen gene expression patterns showed that collagen type I, type III, type VI and type VII were more highly expressed in the PDL cells than gingival fibroblasts, and in the gingival fibroblasts collagen type V, XII were more highly expressed than PDL cells. The results of osteoblast-related gene expression patterns showed that osteoblast specific cysteine-rich protein were more highly expressed in the PDL cells than gingival fibroblasts. The results of cytoskeletal proteins gene expression patterns showed that a-smooth muscle actin, actin binding protein, smooth muscle myosin heavy chain homolog and myosin light chain were more highly expressed in the PDL cells than gingival fibrobalsts, and ${\beta}-actin$, actin-capping protein(${\beta}$ subunit), actin- related protein Arp3(ARP) and myosin class I(myh-1c) were more highly expressed in the gingival fibroblasts than PDL cells. Osteoprotegerin/osteoclastogenesis inhibitory factor(OPG/OCIF) was more highly expressed in the PDL cells than gingival fibroblasts. According to the results of this study, PDL cells and gingival fibroblasts were quite different gene expression patterns though they are the fibroblast which have similar shape. Therefore PDL cells & gingival fibroblasts are heterogeneous populations which represent distinct characteristics. If more studies about genes that were differently expressed in each PDL cells & gingival fibroblasts would be performed in the future, it would be expected that the characteristics of PDL cells would be more clear.

• Journal of the Korean Wood Science and Technology
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• 제46권6호
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• pp.670-680
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• 2018

Acanthophysium sp. KMF001, a wood rotting fungus, produces a strong crude enzyme complex that efficiently produces simple sugars from wood. The transcriptomic analysis of Acanthophysium sp. KMF001 identified 14 genes for putative glycoside hydrolases. Among them, isotig01043 was expressed heterogeneously in Escherichia coli BL21(DE3), and the expressed protein exhibited an endo-${\beta}$-1,4-xylanase activity which showed the optimum reaction at pH 5.0 and $30^{\circ}C$. The enzyme kinetic values of $K_m$ and $V_{max}$ were 25.92 mg/ml and $0.628{\mu}mole/mg/ml$, respectively. The enzymatic characteristics of the expressed xylanase showed a typical fungal xylanase. However, the bioinformatics analysis suggested that the protein encoded by isotig01043 was a novel xylanase based on a low identity when it was compared with the closest protein in the NCBI database and a similar protein domain with GH16_fungal_Lam16A_glucanase, which had not been earlier suggested as a xylanase.

• The Plant Pathology Journal
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• 제21권3호
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• pp.195-206
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• 2005

Spatial and temporal expression of pathogenesis-related (PR) gene and proteins has been recognized as inducible defense response in pepper plants. Gene expression and/or protein accumulation of PR-1, $\beta-1,3-glucanase$ and chitinase was predominantly found in pepper plants during the inoculations by Xanthomonas campestris pv. vesicatoria, Phytophthora capsici and Colletotrichum coccodes. PR-1 and chitinase genes were also induced in pepper plants in response to environmental stresses, such as high salinity and drought. PR-1 and chitinase gene expressions by biotic and abiotic stresses were regulated by their own promoter regions containing several stress-related cis-acting elements. Overexpression of pepper PR-1 or chitinase genes in heterogeneous transgenic plants showed enhanced disease resistance as well as environmental stress tolerances. In this review, we focused on the putative function of pepper PR-1, $\beta-1,3-glucanase$ and chitinase proteins and/or genes at the biochemical, molecular and cytological aspects.