• BMB Reports
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• v.39 no.4
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• pp.441-447
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• 2006

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and non-redundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

• BMB Reports
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• v.44 no.9
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• pp.601-606
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• 2011

HMGB1 is associated with human cancers and is an activator of autophagy which mediates chemotherapy resistance. We here show that the mRNA levels of HMGB1 are high in leukemia cells and it is involved in the progression of childhood chronic myeloid leukemia (CML). HMGB1 decreases the sensitivity of human myeloid leukemia cells K562 to anti-cancer drug induced death through up-regulating the autophagy pathway, which is confirmed by the observation with an increase in fusion of autophagosomes and autophagolysosomes. When overexpressing HMGB1, both mRNA levels of Beclin-1, VSP34 and UVRAG which are key genes involved in mammalian autophagy and protein levels of p-Bcl-2 and LC3-II are increased. Luciferase assays document that over-expression of HMGB1 increases the transcriptional activity of JNK and ERK, which may be silenced by siRNA. The results suggest that HMGB1 regulates JNK and ERK required for autophagy, which provides a potential drug target for therapeutic interventions in childhood CML.

• BMB Reports
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• v.49 no.3
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• pp.179-184
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• 2016

Bone morphogenetic protein 9 (BMP9) is a potent inducer of osteogenic differentiation of mesenchymal stem cells. The Wnt antagonist Dickkopf-1 (Dkk1) is involved in skeletal development and bone remodeling. Here, we investigated the role of Dkk1 in BMP9-induced osteogenic differentiation of MSCs. We found that overexpression of BMP9 induced Dkk1 expression in a dose-dependent manner, which was reduced by the P38 inhibitor SB203580 but not the ERK inhibitor PD98059. Moreover, Dkk1 dramatically decreased not only BMP9-induced alkaline phosphatase (ALP) activity but also the expression of osteocalcin (OCN) and osteopontin (OPN) and matrix mineralization of C3H10T1/2 cells. Furthermore, exogenous Dkk1 expression inhibited Wnt/β-catenin signaling induced by BMP9. Our findings indicate that Dkk1 negatively regulates BMP9-induced osteogenic differentiation through inhibition of the Wnt/β-catenin pathway and it could be used to optimize the therapeutic use of BMP9 and for bone tissue engineering.

• BMB Reports
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• v.50 no.2
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• pp.60-70
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• 2017

Glaucoma is characterized by a slow and progressive degeneration of the optic nerve, including retinal ganglion cell (RGC) axons in the optic nerve head (ONH), leading to visual impairment. Despite its high prevalence, the biological basis of glaucoma pathogenesis still is not yet fully understood, and the factors contributing to its progression are currently not well characterized. Intraocular pressure (IOP) is the only modifiable risk factor, and reduction of IOP is the standard treatment for glaucoma. However, lowering IOP itself is not always effective for preserving visual function in patients with primary open-angle glaucoma. The second messenger cyclic adenosine 3',5'-monophosphate (cAMP) regulates numerous biological processes in the central nervous system including the retina and the optic nerve. Although recent studies revealed that cAMP generated by adenylyl cyclases (ACs) is important in regulating aqueous humor dynamics in ocular tissues, such as the ciliary body and trabecular meshwork, as well as cell death and growth in the retina and optic nerve, the functional role and significance of cAMP in glaucoma remain to be elucidated. In this review, we will discuss the functional role of cAMP in aqueous humor dynamics and IOP regulation, and review the current medications, which are related to the cAMP signaling pathway, for glaucoma treatment. Also, we will further focus on cAMP signaling in RGC growth and regeneration by soluble AC as well as ONH astrocytes by transmembrane ACs to understand its potential role in the pathogenesis of glaucoma neurodegeneration.

• BMB Reports
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• v.51 no.7
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• pp.356-361
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• 2018

Actin-binding LIM protein 1 (ABLIM1), a member of the LIM-domain protein family, mediates interactions between actin filaments and cytoplasmic targets. However, the role of ABLIM1 in osteoclast and bone metabolism has not been reported. In the present study, we investigated the role of ABLIM1 in the receptor activator of $NF-{\kappa}B$ ligand (RANKL)-mediated osteoclastogenesis. ABLIM1 expression was induced by RANKL treatment and knockdown of ABLIM1 by retrovirus infection containing Ablim1-specific short hairpin RNA (shAblim1) decreased mature osteoclast formation and bone resorption activity in a RANKL-dose dependent manner. Coincident with the downregulated expression of osteoclast differentiation marker genes, the expression levels of c-Fos and the nuclear factor of activated T-cells cytoplasmic 1 (NFATc1), critical transcription factors of osteoclastogenesis, were also decreased in shAblim1-infected osteoclasts during RANKL-mediated osteoclast differentiation. In addition, the motility of preosteoclast was reduced by ABLIM1 knockdown via modulation of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/Akt/Rac1 signaling pathway, suggesting another regulatory mechanism of ABLIM1 in osteoclast formation. These data demonstrated that ABLIM1 is a positive regulator of RANKL-mediated osteoclast formation via the modulation of the differentiation and PI3K/Akt/Rac1-dependent motility.

• Development and Reproduction
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• v.15 no.3
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• pp.205-213
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• 2011

Ethanol treatment during the brain growth spurt period has been known to induce the death of Purkinje cells. The underlying molecular mechanisms and the role of reactive oxygen species (ROS) in triggering ethanol-induced Purkinje cell death are, however, largely unresolved. We undertook TUNEL staining, western blotting assay and immunohistochemistry for the cleaved forms of caspase-3 and -9, with calbindin D28K double immunostaining to identify apoptotic Purkinje cells. The possibility of ROS-induced Purkinje cell death was immunohistochemically determined by using anti-8-hydroxy-2'deoxyguanosine (8-OHdG), a specific cellular marker for oxidative damage. The results show that Purkinje cell death of PD 5 rat cerebellum following ethanol administration is mediated by the activation of caspase-3 and -9. However, unexpectedly, TUNEL staining did not reveal any positive Purkinje cells while there were some TUNEL-positive cells in the internal and external granular layer. 8-OHdG was detected in the Purkinje cell layers at 8 h, peaked at 12-24 h, but not at 30 h post-ethanol treatment. No 8-0HdG immunoreactive cells were detected in the internal and external granular layer. The lobule specific 8-OHdG staining patterns following ethanol exposure are consistent with that of ethanol-induced Purkinje cell loss. Thus, we suggest that ethanol-induced Purkinje cell death may not occur by the classical apoptotic pathway and oxidative damage is involved in ethanol-induced Purkinje cell death in the developing cerebellum.

• Journal of Microbiology and Biotechnology
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• v.19 no.5
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• pp.439-446
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• 2009

The biosynthesis study of antibiotics saframycin (SFM) in Streptomyces lavendulae and safracin (SAC) in Pseudomonas fluorescens demonstrated that 3-hydroxy-S-methyl-O-methyltyrosine (3hSmOmTyr), a nonproteinogenic amino acid, is the precursor of the tetrahydroisoquinoline molecular core. In the biosynthetic gene cluster of SAC/SFM, sacD/sfmD encodes a protein with high homology to each other but no sequence similarity to other known enzymes; sacF/sfmM2 and sacG/sfmM3 encode methyltransferases for C-methylation and O-methylation; and sacE/sfinF encodes a small protein with significant sequence similarity to the MbtH-like proteins, which are frequently found in the biosynthetic pathways of non ribosomal peptide antibiotics and siderophores. To address their function, the biosynthetic cassette of 3h5mOmTyr was heterologously expressed in S. coelicolor and P. putida, and an in-frame deletion and complementation in trans were carried out. The results revealed that (i) SfmD catalyzes the hydroxylation of aromatic rings; (ii) sacD/sacF/sacG in the SAC gene cluster and sfmD/sfmM2/sfmM3 in the SFM cluster are sufficient for the biosynthesis of 3h5mOmTyr; and (iii) the mbtH-like gene is not required for the biosynthesis of the 3h5mOmTyr precursor.

• Journal of Microbiology and Biotechnology
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• v.24 no.2
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• pp.270-279
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• 2014

Microbial community shifts, associated with performance data, were investigated in an anaerobic batch digester treating high-solid food waste under mesophilic conditions using, a combination of molecular techniques and chemical analysis methods. The batch process was successfully operated with an organic removal efficiency of 44.5% associated with a biogas yield of 0.82 L/g $VS_{removal}$. Microbial community structures were examined by denaturing gel gradient electrophoresis. Clostridium and Symbiobacterium organisms were suggested to be mainly responsible for the organic matter catabolism in hydrolysis and acidogenesis reactions. The dynamics of archaeal and methanogenic populations were monitored using real-time PCR targeting 16S rRNA genes. Methanosarcina was the predominant methanogen, suggesting that the methanogenesis took place mainly via an aceticlastic pathway. Hydrogenotrophic methanogens were also supported in high-solid anaerobic digestion of food waste through syntrophism with syntrophic bacterium. Microbial community shifts showed good agreement with the performance parameters in anaerobic digestion, implying the possibility of diagnosing a high-solid anaerobic digestion process by monitoring microbial community shifts. On the other hand, the batch results could be relevant to the start-up period of a continuous system and could also provide useful information to set up a continuous operation.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1081-1089
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• 2008

A novel ginsenoside-hydrolyzing ${\beta}$-glucosidase was purified from Paecilomyces Bainier sp. 229 by a combination of Q-Sepharose FF, phenyl-Sepharose CL-4B, and CHT ceramic hydroxyapatite column chromatography. The purified enzyme was a monomeric protein with a molecular mass estimated to be 115 kDa. The optimal enzyme activity was observed at pH 3.5 and $60^{\circ}C$. It was highly stable within pH 3-9 and at temperatures lower than $55^{\circ}C$. The enzyme was specific to ${\beta}$-glucoside. The order of enzyme activities against different types of ${\beta}$-glucosidic linkages was ${\beta}$-(1-6)>${\beta}$-(1-2)>${\beta}$-(1-4). The enzyme converted ginsenoside Rb1 to CK specifically and efficiently. An 84.3% amount of ginsenoside Rb1, with an initial concentration of 2 mM, was converted into CK in 24 h by the enzyme at $45^{\circ}C$ and pH 3.5. The hydrolysis pathway of ginsenoside Rb1 by the enzyme was $Rb1{\to}Rd{\to}F2{\to}CK$. Five tryptic peptide fragments of the enzyme were identified by a newly developed de novo sequencing method of post-source decay (PSD) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. By comparing the five identified peptide sequences with the NCBI database, this purified ${\beta}$-glucosidase proves to be a new protein that has not been reported before.

• Applied Biological Chemistry
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• v.45 no.4
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• pp.203-206
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• 2002

${\gamma}-Tocopherol$ methyltransferase (TMT) is an enzyme catalyzing ${\gamma}-tocopherol$ into ${\alpha}-tocopherol$ at the final step of ${\alpha}-tocopherol$ synthesis pathway. Putative TMT cDNA clone specific to Perilla frutescens immature seeds was isolated from cDNA library. The cDNA clone consisted of 1369 bp open reading frame encoding 369 amino acids with a relative Mw of 42 kDa. Results revealed the CDNA has 60% homology to Arabidopsis thaliana TMT, and possesses methyltransferase and S-adenosyl methionine-binding domains, suggesting that cDNA encodes a ${\gamma}-tocopherol$ methyltransferase To characterize the properties of the TMT gene, the cDNA sequences coding for mature TMT were expressed in E. coli and assayed to determine the enzyme activity in vitro.