• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.711-717
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• 2016

Toxoplasma gondii is an obligate intracellular parasite that stimulates production of high levels of proinflammatory cytokines, which are important for innate immunity. NLRs, i.e., nucleotide-binding oligomerization domain (NOD)-like receptors, play a crucial role as innate immune sensors and form multiprotein complexes called inflammasomes, which mediate caspase-1-dependent processing of $pro-IL-1{\beta}$. To elucidate the role of inflammasome components in T. gondiiinfected THP-1 macrophages, we examined inflammasome-related gene expression and mechanisms of inflammasome-regulated cytokine $IL-1{\beta}$ secretion. The results revealed a significant upregulation of $IL-1{\beta}$ after T. gondii infection. T. gondii infection also upregulated the expression of inflammasome sensors, including NLRP1, NLRP3, NLRC4, NLRP6, NLRP8, NLRP13, AIM2, and NAIP, in a time-dependent manner. The infection also upregulated inflammasome adaptor protein ASC and caspase-1 mRNA levels. From this study, we newly found that T. gondii infection regulates NLRC4, NLRP6, NLRP8, NLRP13, AIM2, and neuronal apoptosis inhibitor protein (NAIP) gene expressions in THP-1 macrophages and that the role of the inflammasome-related genes may be critical for mediating the innate immune responses to T. gondii infection.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.5977-5982
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• 2014

Research over the years has progressively shown substantial broadening of the tumor necrosis factor alpha-related apoptosis-inducing ligand (TRAIL)-mediated signaling landscape. Increasingly it is being realized that pancreatic cancer is a multifaceted and genomically complex disease. Suppression of tumor suppressors, overexpression of oncogenes, epigenetic silencing, and loss of apoptosis are some of the extensively studied underlying mechanisms. Rapidly accumulating in vitro and in vivo evidence has started to shed light on the resistance mechanisms in pancreatic cancer cells. More interestingly a recent research has opened new horizons of miRNA regulation by DR5 in pancreatic cancer cells. It has been shown that DR5 interacts with the core microprocessor components Drosha and DGCR8, thus impairing processing of primary let-7. Xenografting DR5 silenced pancreatic cancer cells in SCID-mice indicated that there was notable suppression of tumor growth. There is a paradigm shift in our current understanding of TRAIL mediated signaling in pancreatic cancer cells that is now adding new layers of concepts into the existing scientific evidence. In this review we have attempted to provide an overview of recent advances in TRAIL mediated signaling in pancreatic cancer as evidenced by findings of in vitro and in vivo analyses. Furthermore, we discuss nanotechnological advances with emphasis on PEG-TRAIL and four-arm PEG cross-linked hyaluronic acid (HA) hydrogels to improve availability of TRAIL at target sites.

• Journal of Applied Biological Chemistry
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• v.60 no.3
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• pp.257-263
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• 2017

A cellulolytic strain Y2 was isolated from soil obtained in the Canadian Alpine region. The isolate was identified as Paenibacillus sp. Y2 by 16S rRNA sequencing. When grown in LB medium supplemented with carboxymethyl-cellulose (CMC), CMCase production increased to 122.0% of that observed in LB without CMC. Culture supernatant was concentrated by ultrafiltration and 80% ammonium sulfate precipitates were separated by Hi-Trap Q and CHT-II chromatography. The purified enzyme (EG-PY2) showed a homogeneous single band and the molecular mass was estimated to be 38 kDa by SDS-PAGE. Optimum pH and temperature of the enzyme were 4.5 and $30^{\circ}C$, respectively. The half-life of enzyme activity at 50 was 140.7 min, but the enzyme was drastically inactivated within 5 min at $55^{\circ}C$. The enzyme was highly activated to 135.7 and 126.7% by 5.0 mM of $Cu^{2+}$ or $Mg^{2+}$ ions, respectively, and moderately activated by $Ba^{2+}$ and $Ca^{2+}$ ions, whereas it was inhibited to 76.8% by $Fe^{2+}$, and to ${\leq}50%$ by $Mn^{2+}$, $Co^{2+}$, $Zn^{2+}$, and EDTA. The enzyme was activated to 211.5% in the presence of 0.5 M of NaCl and greatly tolerant to 3.15M of NaCl. The enzyme showed 2.98 times higher ${\beta}$-glucanase activity than CMCase activity. Based on these results, it can be concluded that EG-PY2 is an acidophilic, cold-active, and halotolerant endoglucanase. The authors suggest it is considered to be useful for various industrial applications, such as, fruit juice clarification, acidic deinking processes, high-salt food processing, textile and pulp industries, and for biofuel production from seaweeds.

• The Plant Pathology Journal
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• v.30 no.3
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• pp.236-244
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• 2014

The plant pathogen Fusarium graminearum causes Fusarium head blight in cereal crops and produces mycotoxins that are harmful to animals and humans. For the initiation and spread of disease, asexual and sexual reproduction is required. Therefore, studies on fungal reproduction contribute to the development of new methods to control and maintain the fungal population. Screening a previously generated transcription factor mutant collection, we identified one putative $C_2H_2$ zincfinger transcription factor, pcs1, which is required for both sexual and asexual reproduction. Deleting pcs1 in F. graminearum resulted in a dramatic reduction in conidial production and a complete loss of sexual reproduction. The pathways and gene ontology of pcs1-dependent genes from microarray experiments showed that several G-protein related pathways, oxidase activity, ribosome biogenesis, and RNA binding and processing were highly enriched, suggesting that pcs1 is involved in several different biological processes. Further, overexpression of pcs1 increased conidial production and resulted in earlier maturation of ascospores compared to the wild-type strain. Additionally, the vegetative growth of the overexpression mutants was decreased in nutrient-rich conditions but was not different from the wild-type strain in nutrient-poor conditions. Overall, we discovered that the pcs1 transcription factor positively regulates both conidiation and sexual reproduction and confers nutrient condition-dependent vegetative growth.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.248-255
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• 2005

To understand the response of cancer cells to anticancer drugs at the gene expression level, we examined the gene expression changes in response to five anticancer drugs, 5-fluorouracil, cytarabine, cisplatin, paclitaxel, and cytochalasin D in NCI-H460 human lung cancer cells. Of the five drugs, 5-fluorouracil had the most distinctive gene expression signature. By clustering genes whose expression changed significantly, we identified three clusters with unique gene expression patterns. The first cluster reflected the up-regulation of gene expression by cisplatin, and included genes involved in cell death and DNA repair. The second cluster pointed to a general reduction of gene expression by most of the anticancer drugs tested. A number of genes in this cluster are involved in signal transduction that is important for communication between cells and reception of extracellular signals. The last cluster represented reduced gene expression in response to 5-fluorouracil, the genes involved being implicated in DNA metabolism, the cell cycle, and RNA processing. Since the gene expression signature of 5-fluorouracil was unique, we investigated it in more detail. Significance analysis of microarray data (SAM) identified 808 genes whose expression was significantly altered by 5-fluorouracil. Among the up-regulated genes, those affecting apoptosis were the most noteworthy. The down-regulated genes were mainly associated with transcription-and translation-related processes which are known targets of 5-fluorouracil. These results suggest that the gene expression signature of an anticancer drug is closely related to its physiological action and the response of caner cells.

• Korean Journal of Plant Resources
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• v.19 no.1
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• pp.174-179
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• 2006

A cDNA library was constructed from leaf samples of 4-year-old Panax ginseng cultured in a field. 3,000 EST from a size selected leaf cDNA library were analyzed. The 349 of 2,896 cDNA clones has related with energy metabolism genes. The 349 known genes were categorized into nine groups according to their functional classification, aerobic respiration(48.4%), accessory proteins of electron transport and membrane associated energy conservation(17.2%), glycolysis and gluconeogenesis(3.4%), electron transport and membrane associated energy conservation(2.9%), respiration(2.0%), glycolysis methylglyoxal bypass(1.7%), metabolism of energy reserves(0.6%) and alcohol fermentation(0.3%).

• Genomics & Informatics
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• v.4 no.3
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• pp.110-117
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• 2006

In microarray technology, many diverse experimental features can cause biases including RNA sources, microarray production or different platforms, diverse sample processing and various experiment protocols. These systematic effects cause a substantial obstacle in the analysis of microarray data. When such data sets derived from different experimental processes were used, the analysis result was almost inconsistent and it is not reliable. Therefore, one of the most pressing challenges in the microarray field is how to combine data that comes from two different groups. As the novel trial to integrate two data sets with batch effect, we simply applied standardization to microarray data before the significant gene selection. In the gene selection step, we used new defined measure that considers the distance between a gene and an ideal gene as well as the between-slide and within-slide variations. Also we discussed the association of biological functions and different expression patterns in selected discriminative gene set. As a result, we could confirm that batch effect was minimized by standardization and the selected genes from the standardized data included various expression pattems and the significant biological functions.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.784-791
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• 2007

The present work aims to use a biofilter technology(aerated submerged filters) for the aerobic transformation at laboratory-scale of olive washing water(OWW) generated in the first steps of olive oil processing, as well as the genetic profiling and identification to the species level of the bacteria involved in the formation of the biofilm, by means of TGGE. Chemical parameters, such as biological oxygen demand at five days($BOD_5$) and chemical oxygen demand(COD), decreased markedly(up to 90 and 85%, respectively) by the biological treatment, and the efficiency of the process was significantly affected by aeration and inlet flow rates. The total polyphenol content of inlet OWW was only moderately reduced(around 50% decrease of the inlet content) after the biofilter treatment, under the conditions tested. Partial 16S rRNA genes were amplified using total DNA extracted from the biofilm and separated by TGGE. Sequences of isolated bands were mostly affiliated to the $\alpha-subclass$ of Proteobacteria, and often branched in the periphery of bacteria] genera commonly present in soil(Rhizobium, Reichenowia, Agrobacterium, and Sphingomonas). The data obtained by the experimentation at laboratory scale provided results that support the suitability of the submerged filter technology for the treatment of olive washing waters with the purpose of its reutilization.

• The Plant Pathology Journal
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• v.33 no.4
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• pp.370-381
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• 2017

Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R. tritici NCPPB 1953 with diverse features of this strain. The whole genome consists of one circular chromosome of 3,354,681 bp with a GC content of 69.48%. A total of 2,979 genes were predicted, comprising 2,866 protein coding genes and 49 RNA genes. The comparative genomic analyses between R. tritici NCPPB 1953 and R. toxicus strains identified 1,052 specific genes in R. tritici NCPPB 1953. Using the BlastKOALA database, we revealed that the flexible genome of R. tritici NCPPB 1953 is highly enriched in 'Environmental Information Processing' system and metabolic processes for diverse substrates. Furthermore, many specific genes of R. tritici NCPPB 1953 are distributed in substrate-binding proteins for extracellular signals including saccharides, lipids, phosphates, amino acids and metallic cations. These data provides clues on rapid and stable colonization of R. tritici for disease mechanism and nematode association.

• The Korean Journal of Food And Nutrition
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• v.32 no.5
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• pp.408-416
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• 2019

This study investigated the anti-inflammatory effects of processed (Beopje) curly dock (Rumex crispus L.) in LPS (lipopolysaccharide)-stimulated murine RAW 264.7 cells. The experimental group was classified into five groups : LPS no treatment, CD (curly dock), CD-B (CD processed through Beopje), LPS, LPS+CD-B (LPS+CD processed through Beopje) and LPS+CD (LPS+CD). Treatment of the Raw 264.7 cell lines using LPS led to a significant increase in NO production, pro-inflammatory cytokines ($TNF-{\alpha}$, IL-6 and $IL-1{\beta}$), and inflammation related genes (COX-2 and iNOS). Investigation of the inhibitory effects of CD and processed CD on NO production and expression of iNOS and COX-2 was done in LPS-induced RAW 264.7 cells. There was significant inhibition of NO production by LPS+CD and LPS+CD-B in a dose-dependent manner (p<0.05). Particularly, LPS+CD-B exhibited reduced mRNA expression of iNOS and COX-2 and NO production as compared to LPS+CD in Raw 264.7 cell lines (p<0.05). These results may explain some known biological activities of curly dock including the anti-inflammatory effects. CD-B in particular exhibited the highest anti-inflammatory effects of inhibiting production of NO, through the regulation of inflammatory related genes and pro-inflammatory cytokines. These results of Beopje processing might help decrease the anti-biological effects and increase several active substances of curly dock.