• Journal of Microbiology and Biotechnology
• /
• v.17 no.2
• /
• pp.271-279
• /
• 2007

Black rice (Oryza sativa L. var. japonica) has been used in folk medicine in Asia. To understand the effects of black rice hydrolyzed peptides (BRP) from germinated black rice, we assessed the expression levels of about 20,000 transcripts in BRP-treated HaCaT keratinocytes using human 1A oligo microarray analysis. As a result, the BRP treatment showed a differential expression ratio of more than 2-fold: 745 were activated and 1,011 were repressed. One of the most interesting findings was a 2-fold increase in hyaluronan synthase 2 (HAS2) gene expression by BRP. Semiquantitative RT-PCR showed that BRP increased HAS2 mRNA in dose-dependent manners. ELISA showed that BRP effectively increased hyaluronan (HA) production in HaCaT keratinocytes.

• Structural Engineering and Mechanics
• /
• v.54 no.4
• /
• pp.793-807
• /
• 2015

Constructing the influence lines of forces of statically indeterminate structures is a traditional issue in structural engineering and mechanics. However, the existing kinematic method for establishing these force influence lines is an indirect or mixed approach by combining the force method with the theorem of reciprocal displacements, which is yet inconsistent with the kinematic method for statically determinate structure. This paper proposes the direct kinematic method in conjunction with the load-displacement differential relation for exactly constructing influence lines of reaction and internal forces of indeterminate structures. Firstly, through applying the principle of virtual displacement, the formula for influence lines of reaction and internal forces of indeterminate structure via direct kinematic method is derived based on the released structure. Then, a computational approach with a clear concept and unified procedure as well as wide applicability based on the load-displacement differential relation of beam is suggested to achieve conveniently the closed-form expression of force influence lines, and exactly draw them. Finally, three representative examples for constructing force influence lines of statically indeterminate beams and frame illustrate the superiority of the proposed method.

• Clinical and Experimental Pediatrics
• /
• v.64 no.7
• /
• pp.355-363
• /
• 2021

Background: Nephrotic syndrome (NS) is a common renal disorder in children attributed to podocyte injury. However, children with the same diagnosis have markedly variable treatment responses, clinical courses, and outcomes, suggesting molecular heterogeneity. Purpose: This study aimed to explore the molecular responses of podocytes to nephrotic plasma to identify specific genes and signaling pathways differentiating various clinical NS groups as well as biological processes that drive injury in normal podocytes. Methods: Transcriptome profiles from immortalized human podocyte cell line exposed to the plasma of 8 subjects (steroid-sensitive nephrotic syndrome [SSNS], n=4; steroid-resistant nephrotic syndrome [SRNS], n=2; and healthy adult individuals [control], n=2) were generated using microarray analysis. Results: Unsupervised hierarchical clustering of global gene expression data was broadly correlated with the clinical classification of NS. Differential gene expression (DGE) analysis of diseased groups (SSNS or SRNS) versus healthy controls identified 105 genes (58 up-regulated, 47 down-regulated) in SSNS and 139 genes (78 up-regulated, 61 down-regulated) in SRNS with 55 common to SSNS and SRNS, while the rest were unique (50 in SSNS, 84 genes in SRNS). Pathway analysis of the significant (P≤0.05, -1≤ log2 FC ≥1) differentially expressed genes identified the transforming growth factor-β and Janus kinase-signal transducer and activator of transcription pathways to be involved in both SSNS and SRNS. DGE analysis of SSNS versus SRNS identified 2,350 genes with values of P≤0.05, and a heatmap of corresponding expression values of these genes in each subject showed clear differences in SSNS and SRNS. Conclusion: Our study observations indicate that, although podocyte injury follows similar pathways in different clinical subgroups, the pathways are modulated differently as evidenced by the heatmap. Such transcriptome profiling with a larger cohort can stratify patients into intrinsic subtypes and provide insight into the molecular mechanisms of podocyte injury.

• Journal of Mushroom
• /
• v.2 no.3
• /
• pp.145-148
• /
• 2004

This study was carried out to screen the fruiting body formation-specific genes from the medicinal mushroom Cordyceps militaris. A cDNA synthesized using total RNA from 4 stages of mushroom development, mycelium, primordium, immature fruiting body and mature fruiting body. Differential expression gene screening was performed by DD-PCR(Differential Display Arbitrary Primer PCR) with cDNA, we sequenced partial 6 genes using pGEM cloning vector. The DNA Sequence of the six DD-PCR products derived from differentially expressed genes was compared to that in the GenBank database by using the NCBI BLAST search to identify similarities to known sequences. Sequence analysis showed that six of DD-PCR products have unknown sequence.

• The Korean Journal of Mycology
• /
• v.27 no.3 s.90
• /
• pp.187-190
• /
• 1999

A cDNA library was constructed using mRNA from the cells of 7-day-old cultures of Flammulina velutipes after induction of fruiting treatment. A cDNA clone, FVFD16 (Flammulina velutipes fruiting body differentiation), was selected by differential screening. The expression property of the FVFD16 gene was examined by Northern blot analysis. FVFD16 represents mRNA that is specifically expressed during differentiation of fruit bodies. The conspicuous accumulation of the FVFD16 mRNA was detected in 4-day-old and 1-day-old cultures. The nucleotide sequence of the FVFD16 gene was determined and the mRNA contained an open reading frame that encoded a putative protein of 128 amino acid residues (13.5 kDa).

• Journal of Microbiology and Biotechnology
• /
• v.17 no.12
• /
• pp.2005-2017
• /
• 2007

Diabetic nephropathy remains a major cause of morbidity and mortality in the diabetic population and is the leading cause of end-stage renal failure. Despite current therapeutics including intensified glycemic control and blood pressure lowering agents, renal disease continues to progress relentlessly in diabetic patients, albeit at a lower rate. Since synthetic drugs for diabetes are known to have side effects, fungal mushrooms as a natural product come into preventing the development of diabetes. Our previous report showed the hypoglycemic effect of extracellular fungal polysaccharides (EPS) in streptozotocin (STZ)-induced diabetic rats. In this study, we analyzed the differential expression patterns of rat kidney proteins from normal, STZ-induced diabetic, and EPS-treated diabetic rats, to discover diabetes-associated proteins in rat kidney. The results of proteomic analysis revealed that up to 500 protein spots were visualized, of which 291 spots were differentially expressed in the three experimental groups. Eventually, 51 spots were statistically significant and were identified by peptide mass fingerprinting. Among the differentially expressed renal proteins, 10 were increased and 16 were decreased significantly in diabetic rat kidney. The levels of different proteins, altered after diabetes induction, were returned to approximately those of the healthy rats by EPS treatment. A histopathological examination showed that EPS administration restored the impaired kidney to almost normal architecture. The study of protein expression in the normal and diabetic kidney tissues enabled us to find several diabetic nephropathy-specific proteins, such as phospholipids scramblase 3 and tropomyosin 3, which have not been mentioned yet in connection with diabetes.

• Genomics & Informatics
• /
• v.10 no.1
• /
• pp.16-22
• /
• 2012

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by formation of multiple fluid-filled cysts that expand over time and destroy renal architecture. The proteins encoded by the $PKD1$ and $PKD2$ genes, mutations in which account for nearly all cases of ADPKD, may help guard against cystogenesis. Previously developed mouse models of $PKD1$ and $PKD2$ demonstrated an embryonic lethal phenotype and massive cyst formation in the kidney, indicating that $PKD1$ and $PKD2$ probably play important roles during normal renal tubular development. However, their precise role in development and the cellular mechanisms of cyst formation induced by $PKD1$ and $PKD2$ mutations are not fully understood. To address this question, we presently created $Pkd2$ knockout and $PKD2$ transgenic mouse embryo fibroblasts. We used a mouse oligonucleotide microarray to identify messenger RNAs whose expression was altered by the overexpression of the $PKD2$ or knockout of the $Pkd2$. The majority of identified mutations was involved in critical biological processes, such as metabolism, transcription, cell adhesion, cell cycle, and signal transduction. Herein, we confirmed differential expressions of several genes including aquaporin-1, according to different $PKD2$ expression levels in ADPKD mouse models, through microarray analysis. These data may be helpful in $PKD2$-related mechanisms of ADPKD pathogenesis.

• Molecular & Cellular Toxicology
• /
• v.5 no.4
• /
• pp.310-316
• /
• 2009

Some environmental chemicals have been shown to cause liver-toxicity as the result of bioaccumulation. Particularly, fungicides have been shown to cause varying degrees of hepatictoxicity and to disrupt steroid hormone homeostasis in in vivo models. The principal objective of this study was to evaluate the liver-toxic responses of environmental chemicals-in this case selected fungicides and parasiticides-in order to determine whether or not this agent differentially affected its toxicogenomic activities in hepatic tumor cell lines. To determine the gene expression profiles of 3 fungicides (triadimefon, myclobutanil, vinclozolin) and 1 parasiticide (dibutyl phthalate), we utilized a modified HazChem human array V2. Additionally, in order to observe the differential alterations in its time-dependent activities, we conducted two time (3 hr, 48 hr) exposures to the respective IC20 values of four chemicals. As a result, we analyzed the expression profiles of a total of 1638 genes, and we identified 70 positive significant genes and 144 negative significant genes using four fungicidic and parasiticidic chemicals, using SAM (Significant Analysis of Microarray) methods (q-value<0.5%). These genes were analyzed and identified as being related to apoptosis, stress responses, germ cell development, cofactor metabolism, and lipid metabolism in GO functions and pathways. Additionally, we found 120 genes among those time-dependently differentially expressed genes, using 1-way ANOVA (P-value<0.05). These genes were related to protein metabolism, stress responses, and positive regulation of apoptosis. These data support the conclusion that the four tested chemicals have common toxicogenomic effects and evidence respectively differential expression profiles according to exposure time.

• Journal of Veterinary Science
• /
• v.22 no.5
• /
• pp.61.1-61.13
• /
• 2021

Background: Hepatocellular carcinoma is the most common primary hepatic malignancy in humans and dogs. Several differentially expressed molecules have been studied and reported in human hepatocellular carcinoma and non-neoplastic liver lesions. However, studies on the features of canine hepatocellular carcinoma are limited, especially related to the differential characteristics of neoplastic and non-neoplastic lesions. Objectives: The study's objective was 1) to examine and evaluate the expression of arginase-1, P-glycoprotein, and cytokeratin 19 in canine liver tissues and 2) to investigate the differential features of hepatocellular carcinomas, liver tissue with non-neoplastic lesions, and paracancerous liver tissues in dogs. Methods: The expression levels of three markers underwent immunohistochemical analysis in 40 non-neoplastic liver tissues, 32 hepatocellular carcinoma tissues, and 11 paracancerous liver tissues. Scoring of each marker was performed semi-quantitatively. Results: Arginase-1 and P-glycoprotein were significantly downregulated in hepatocellular carcinoma, compared with hepatic tissues with non-neoplastic diseases (p < 0.001). Expression levels of arginase-1 and P-glycoprotein were also significantly lower in hepatocellular carcinoma than in paracancerous liver tissues (arginase-1, p = 0.0195; P-glycoprotein, p = 0.047). Few cytokeratin 19-positive hepatocytes were detected and only in one hepatocellular carcinoma and one cirrhotic liver sample. Conclusions: The results of this study suggest that downregulation of arginase-1 and P-glycoprotein is a feature of canine hepatocellular carcinoma; thus, those markers are potential candidates for use in differentiating hepatocellular carcinomas from non-neoplastic liver lesions in dogs.

• Journal of Korean Neurosurgical Society
• /
• v.38 no.1
• /
• pp.12-15
• /
• 2005

Objective : Cerebral edema develops in the brain tumors by loosening of the endothelial tight junction. Tight junction[TJ] proteins, such as occludin and claudin bind adjacent cells tightly. Authors examine the expression rate of occludin in human brain tumors to evaluate the effect of altered expression of occludin on cerebral edema. Methods : Seventy surgical specimens stored at $-70^{\circ}C$ were used. It included 14 astrocytic tumors, 27 meningiomas, 12 scwannomas, 7 pituitary adenomas, 6 hemangioblastomas. and 4 craniopharyngiomas. After protein extraction, expression of occludin was investigated by Western blot analysis. The tumors were classified according to World Health Organization[WHO] classification. Results : The expression rates of occludin in brain tumors were : glioma [8/14=57.1%]. meningioma [16/27=59.3%], schwannoma [10/12=83.3%], pituitary adenoma [6/7=85.7%], hemangioblastoma [6/6=100%], and craniopharyngioma [3/4=75.0%]. The expression rate in glioma and meningioma was lower than other brain tumors. In gliomas, high grade tumor [1/4=25.0%] exhibited lower expression rate of occludin than low grade one [7/10=70.0%]. Conclusion : These results suggest that the expression of occludin is different among the various kinds of brain tumors. In gliomas, its expression is correlated with the histological grade. It may indicate that occludin plays a role in the development of edema in the brain tumors.