• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7645-7652
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• 2014

Neuroblastoma (NB), the most common extracranial solid tumor, accounts for 10% of childhood cancer. To date, scientists have gained quite a lot of knowledge about microRNAs (miRNAs) and their genes in NB. Discovering inner regulation networks, however, still presents problems. Our study was focused on determining differentially-expressed miRNAs, their target genes and transcription factors (TFs) which exert profound influence on the pathogenesis of NB. Here we constructed three regulatory networks: differentially-expressed, related and global. We compared and analyzed the differences between the three networks to distinguish key pathways and significant nodes. Certain pathways demonstrated specific features. The differentially-expressed network consists of already identified differentially-expressed genes, miRNAs and their host genes. With this network, we can clearly see how pathways of differentially expressed genes, differentially expressed miRNAs and TFs affect on the progression of NB. MYCN, for example, which is a mutated gene of NB, is targeted by hsa-miR-29a and hsa-miR-34a, and regulates another eight differentially-expressed miRNAs that target genes VEGFA, BCL2, REL2 and so on. Further related genes and miRNAs were obtained to construct the related network and it was observed that a miRNA and its target gene exhibit special features. Hsa-miR-34a, for example, targets gene MYC, which regulates hsa-miR-34a in turn. This forms a self-adaption association. TFs like MYC and PTEN having six types of adjacent nodes and other classes of TFs investigated really can help to demonstrate that TFs affect pathways through expressions of significant miRNAs involved in the pathogenesis of NB. The present study providing comprehensive data partially reveals the mechanism of NB and should facilitate future studies to gain more significant and related data results for NB.

• Development and Reproduction
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• v.7 no.2
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• pp.119-126
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• 2003

In the previous study, we obtained list of differentially expressed genes between postnatal day 1 and day 5 mouse ovaries using suppression subtractive hybridization(SSH) and found that MT Oansposon-like element, clone MTi7(MTi7) was one of the highly expressed genes in the day 5 mouse ovary(Park et at., 2002). Results of in situ hybridization and RNA interference revealed that the expression of MTi7 is oocyte-specific in the ovary and may be involved in the regulation of oocyte maturation(Park et at., 2003). At present, MTi7 sequence has been known only in the mouse. Therefore, the present study was accomplished 1) to identify MTi7 sequence in the other mammalian species, such as bovine, porcine, rat, and human, and 2) to evaluate the flanking sequence of the mouse MTi7 since it has transposon characteristics. Using ovarian cDNAs derived from low different species, we cloned and identified new MTi7 sequence showing a high degree of sequence homology with the mouse MTi7(87∼98%). By using inverse PCR, we found that the mouse MTi7 may intercalated the beta-carotene 15, 15'-monooxygenase(Bcdo) gene and/or serine protease inhibitor, Kunitz Dpe I(Spint 1) gene. By finding the MTi7 sequences in the other mammalian species and the flanking gene of the MTi7 in mouse, it is expected to reveal the role(s) of MTi7 in the oogenesis as well as folliculogenesis in the near future.

• The Plant Pathology Journal
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• v.16 no.5
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• pp.269-279
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• 2000

Alfalfa mosaic alfamoviruses(AIMV) were isolated from infected potato (Solanum tuberosum) and azuki bean (Paseolus angularis) in Korea. Two AIMV isolated from potatoes were named as strain KR (AIMV-KR1 and KR2) and AIMV isolated from azuki bean was named as strain Az (AIMV-Az). Each isolated AIMV strain was characterized by using their host ranges, symptom developments, serological relations and nucleotide sequence analysis of coat protein (CP) gene. Strains KR1, KR2, and Az were readily transmitted to 20 of 22 inoculated plant species including bean, cowpea, tomato, tobacco, and potato. AIMV-KR1 and KR2 produced the typical symptoms like chlorotic or necrotic spots in Chenopodium quinoa and Solanum tuberosum cv. Superior. AIMV-Az caused bright yellow mosaic symptom and leaf malformation in Nicotiana glauca, which were different from the common mosaic symptom caused by AIMV-KR1 and KR2. Electron microscope observation of purified virus showed bacilliform virions containing a single-stranded plus-strand RNAs of 3.6, 2.6, 2.0 and 0.9 kbp in length, respectively, similar in size and appearance to those of Alfamovirus. In SDS-PAGE, the coat protein of the two viruses formed a consistent band that estimated to be about 24kDa. The CP genes of the AIMV strains, KR1, KR2, and Az have been amplified by RT-PCR using the specific primers designed to amplify CP gene from viral RNA-3, cloned and sequenced. Computer aided analysis of the amplified cDNA fragment sequence revealed the presence of a single open reading frame capable of encoding 221 amino acids. The nucleotide and peptide sequence of viral CP gene showed that strain KR1, KR2, and Az shared highest nucleotide sequence identities with AIMV strain 425-M at 97.7%, 98.2%, and 97.2%, respectively. CP gene sequences of two strains were almost identical compared with each other. Altogether, physical, serological, biological and molecular properties of the purified virus.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.4
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• pp.471-482
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• 2009

Nutrient availability may control muscle growth directly and indirectly through its influence on regulatory factors. We analyzed the effects of nutrient availability on the breast muscle insulin-like growth factor system. Real time RT-PCR was used to quantify the level of transcription in breast muscle from Langshan (LS) layer and Arbor Acres (AA) broiler chickens subjected to different feeding regimens during embryonic and postnatal development. The AA chickens were fed AA diet (AA, control group) while the LS chickens were either fed LS diet (LL) or AA diet (LA). According to our results, insulin-like growth factor (IGF)-II (embryonic day 16 (E16) - postnatal day 42 (P42)), IGF-I receptor (IGF-IR, E18-P42), and IGF binding protein (IGFBP)-2 (E18-P42), -5 (E16-P14), -7 (E12-P0), and -3 (E12-P0) were positively correlated with IGF-I, while IGFBP-3 (P0-P28) was negatively correlated with IGF-I. In comparison, IGF-IR (E18-P42), IGFBP-2 (E18-P42), IGFBP-5 (E14-P0), and IGFBP-3 (E16-P0) were positively correlated with IGF-II, while IGF-IR (E10-E16) and IGFBP-3 (P0-P28) were negatively correlated with IGF-II. Moreover, IGFBP-2 (E16-P42), -7 (E10-E16), and -3 (E10-E16) were positively correlated with IGF-IR, while IGFBP-3 (P0-P28) was negatively correlated with IGF-IR. Finally, IGFBP-7 (E12-P0) was positively correlated with IGFBP-3, while IGFBP-2 (P0-P28) and -7 (P0-P42) were negatively correlated with IGFBP-3. Overall, the AA chickens exhibited higher levels of IGF-I, IGF-IR, and IGFBP-2 mRNA expression than the LL chickens, while the opposite was true for IGFBP-7. No strain differences in IGF-I, IGF-IR, and IGFBP-7 mRNA expression were detected between LA and AA chickens; however, a strain difference was observed for IGFBP-2. LA chickens exhibited higher levels of IGFBP-2 than LL chickens, while the opposite was true for IGFBP-7. Our data show the first evidence that certain genes may be correlated during specific developmental periods and that strain differences in the expression of those genes in LS and AA chickens are due to differential responses to the same diet.

• The Journal of Pediatrics of Korean Medicine
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• v.25 no.1
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• pp.1-27
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• 2011

Objectives: The purpose of this study is to investigate the effects of Yijungtang(YJT) on atopic dermatitis in an in-vitro and in-vivo experiment using a RBL-2H3 mast cells and a NC/Nga atopic dermatitis mouse. Methods: In-vitro experiment, IL-4, IL-13 mRNA expression were evaluated by a real-time PCR, IL-4, IL-13 production by ELISA and transcription factor as GATA-1, GATA-2, NF-AT1, NF-AT2, AP-1 and NF-kB by western blotting. In-vivo experiment, clinical skin score we evaluated by, hematology and Serum total IgE and IgG1 of NC/Nga atopic dermatitis mouse, cytokine level, total number of cell, Immunohistochemical staining and Histological features of auxiliary lymph node(ALN), draining lymph node(DLN), peripheral blood mononuclear cells(PBMCs) and dorsal skin tissue in NC/Nga mouse. Results: YJT decreased IL-4, IL-13 mRNA expression, IL-4, IL-13 production and prominently decreased the expression of mast cell specific transcription factors including GATA-2, NF-AT2, c-Fos and NF-kB. YJT oral administration reduced the levels of skin severity scores. It also decreased the level of inflammatory cytokines such as IL-5, IL-13, histamine and IgE in the serum. It elevated IFN-gamma level in the spleenocyte culture supernatant but decreased. $CD3e^+$, $CD19^+$, $CD4^+$, $CD8^+$, $CD3e^+CD69^+$, $CD11b^+Gr-1^+$, $CCR3^+$ in the PBMCs, $CD4^+$, $CD8^+$, $CD3e^+CD69^+$, $B220^+CD23^+$ in the ALN, $CD4^+$, $CD3e^+CD69^+$ in the ALN and $CD4^+$, $CD11b^+Gr-1^+$ in the dorsal skin. Histological examination showed that infiltration levels of immune cells in the skin of AD-induced NC/Nga mice were much improved by YJT oral administration. Conclusions: The anti-allergic activities of YJT may be mediated by down-regulation of Th2 cytokines, such as IL-4 and IL-13, through the regulation GATA-2, NF-AT2 and NF-kB transcription factors in mast cells. YJT would be regulate molecular mediators and immune cells which are functionally associated with atopic dermatitis induced in NC/Nga mice, and may play an important role in recovering AD symptoms.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.98-108
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• 2015

Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.

• Microbiology and Biotechnology Letters
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• v.32 no.4
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• pp.297-306
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• 2004

Heat shock proteins (HSPs) were induced in cells in the thermal stress, and the HSP90 family is one of the major classes of HSPs. Gene encoding HSPs have been characterized from various mammals and piscine. We have cloned and sequenced the HSP90 cDNA from a brain cDNA library constructed from flounder (Paralichthys oliThe result of sequence analysis shows it to be the HSP90~. The nucleotide sequence of the HSP90$\beta$ was composed of 2791 long, encoding 726 amino acid residues. The flounder hsp90$\beta$ gene showed very high sequence homology with hsp90f3 of European sea bass (96.6%), zebrafish (92.9%), Atlantic salmon (92.0%) and human (89.5%). We also constructed a phylogenetic tree based on HSP90 amino acid sequences from vertebrate species. Gene-specific primers were selected and used in RT-PCR reactions to measure the basal hsp90$\beta$ mRNA. The hsp90f3 gene is constitutively expressed at a fairly high level in all examined tissues (brain, liver, kidney, muscle, and spleen). In order to express protein of flounder hsp90$\beta$ in E. coli, we used the His-tagged pETvector. Then, the expression of flounder HSP90$\beta$ was confirmed by Western blot analysis.

• Korean Journal of Clinical Laboratory Science
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• v.49 no.4
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• pp.413-419
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• 2017

Four imipenem-resistant bacteria were isolated from the clinical specimens of a patient with pneumonia. To identify the isolates, we used the GN card of Vitek II system and performed a phylogenetic analysis based on 16S rRNA gene sequence. The isolates were identified as P. aeruginosa (2 strains), P. monteilii (1 strain), and P. putida (1 strain), and were tested for antibiotic resistance after determining the MIC of imipenem to be $${\geq_-}8{\mu}g/mL$$ using the AST-N225 card of Vitek II system. The imipenem-resistant genotypes were determined using PCR products amplified using specific ${\beta}-Lactamase$ gene primers. The MBL gene was identified in all four isolates. One strain of P. aeruginosa exhibited the VIM and SHV-1 type genes, while the other strain exhibited both VIM and OXA group II genes. According to the antimicrobial susceptibility test, the bacteria were more susceptible to amikacin than other antibiotics. DNA fingerprint analysis using ERIC-PCR to analyze the epidemiological relationship between strains estimated that both the P. aeruginosa isolates were similar, but exhibited different DNA band types. It is uncommon to find four strains of imipenem-resistant bacteria with different DNA band types in a single patient.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.269-277
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• 2016

Erm proteins methylate the specific adenine residue ($A_{2058}$, E. coli numbering) on 23S rRNA to confer the $MLS_B$ (macrolidelincosamide-streptogramin B) antibiotic resistance on a variety of microorganisms ranging from antibiotic producers to pathogens. When phylogenetic tree is constructed, two main clusters come out forming each cluster of Actinobacteria and Firmicutes. Two representative Erm proteins from each cluster were selected and their in vitro methylation activities were compared. ErmS and ErmE from Actinobacteria cluster exhibited much higher activities than ErmB and ErmC' from Firmicutes: 9 fold difference when ErmC' and ErmE were compared and 13 fold between ErmS and ErmB. Most of the difference was observed and presumed to be caused by N-terminal and C-terminal extra region from ErmS and ErmE, respectively because NT59TE in which N-terminal end 59 amino acids was truncated from wild type ErmS exhibited only 22.5% of wild type ErmS activity. Meanwhile, even NT59TE showed three and 2.2 times more activity when it was compared to ErmB and C, respectively, suggesting core region from antibiotic producers contains extra structure enabling higher activity. This is suggested to be possible through the extra region of 197RWS199 (from both ErmS and ErmE), 261GVGGSLY267 (from ErmS), and 261GVGGNIQ267 (from ErmE) and 291SVV293 (from ErmS) and 291GAV293 (from ErmE) by multiple sequence alignment.

• Journal of Life Science
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• v.26 no.1
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• pp.8-16
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• 2016

Reactive oxygen species (ROS), at appropriate concentrations, mediate various normal cellular functions, including defense against pathogens, signal transduction, cellular growth, and gene expression. A recent study demonstrated that ROS and ROS-generating NADPH oxidase (Nox) are important in self-renewal and neuronal differentiation of subventricular zone (SVZ) neural stem cells in adult mouse brains. In this study, we found that endogenous ROS were detected in SVZ neural stem cells cultured from postnatal mouse brains. Nox4 was predominantly expressed in cultured cells, while the levels of the Nox1 and Nox2 transcripts were very low. In addition, the Nox4 gene was highly upregulated (by up to 10-fold) during neuronal differentiation. Immunocytochemical analysis detected the Nox4 protein mainly in neurons positive for the neuronal specific tubulin Tuj1. After differentiation, endogenous ROS were detected exclusively in neuron-like cells with processes. In addition, perturbation of the cellular redox state with N-acetyl cysteine, a ROS scavenger, during neuronal differentiation greatly inhibited neurogenesis. Lastly, knockdown of Nox4 using short hairpin RNA decreased neurogenesis. These findings suggest that Nox4 may be a major ROS-generating enzyme in postnatal SVZ neural stem cells, and Nox4-mediated ROS generation may be important in their neuronal differentiation.