• Korean Journal of Microbiology
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• v.37 no.2
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• pp.114-119
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• 2001

Many isolates from different forest soil layers did not show appreciable growth on full strength of the conventional nutrient broth (NB medium) but grow on its 100-fold dilution (DNB medium). These isolates were divided into four types according to organic nutrient concentration in the growth medium from $1^{-1}\;to\;10^{-4}$dilution of normal NB medium. Oligotrophic bacteria were type II and type IV which grew in $10^{-4}$ dilution of NB (1 mg C/l) medium. Sixty strains were isolated for obligate oligotrophic bacteria. Chemotaxonomic and phylogenetic characteristics of eleven isolates of acetylene-reducing (nitrogen-fixing) oligotrophic bacteria from forest soil were investigated. They showed similar characteristics: the cellular fatty acid mainly consisted of straight-chain unsaturated $C_{18:1}$ (60-84% of total fatty acids). Ubiquinone Q-10 and a high guanine plus-cytosine content(61-64 mol%) were found. Eleven isolates of nitrogen-fixing oligotrophic bacteria were found to be closely related by full 16S rDNA sequence simility and many common taxonomic traits. Analysis of full 16S rDNA sequences of eleven isolates indicated that they were more closely related to Bradyrhizobium (similarity values: 98.1-98.8%), Agromonas, Nitrobacter, and Afipia.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1232-1236
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• 2013

The Cu cation binding sites of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex have been investigated to explain the $[Cu{\cdot}DNA]$ biological activity caused by the Cu association to DNA. The structure of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex was investigated by electrospray ionization mass spectrometry (ESI-MS). The fragmentation patterns of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex were analyzed by MS/MS spectra. In the MS/MS spectra of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex, three fragment ions were observed with the loss of d(CpG), {d(CpG) + Cyt}, and {d(CpG) + Cyt + dR}. The Cu cation binds to d(CpG) mainly by substituting the $H^+$ of phosphate group. Simultaneously, the Cu cation prefers to bind to a guanine base rather than a cytosine base. Five possible geometries were considered in the attempt to optimize the $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex structure. The ab initio calculations were performed at B3LYP/6-31G(d) level.

• Journal of Life Science
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• v.14 no.4
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• pp.608-613
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• 2004

Pyrimidine nucleotide N-ribosidase (pyrimidine 5'-nucleotide phosphoribo (deoxyribo) hydrolase/pyrimidine 5'-nucleoude nucleosidase, EC 3.2.2.10) directly catalyzes pyrimidine 5'-nucleotide to pyrimidine base and ribose (deoxyribo) 5-phosphate. In order to clarify the best nutritional conditions for the growth and the pyrimidine nucleotide N-ribosidase production of Pseudomonas oleovorans ATCC 8062 the effects of various nutrients such as different carbon and nitrogen sources were studied. For the both the growth and the enzyme production, 2% fumarate, 1.5% peptone, 5% corn steep liquor (CSL) and 1% ammonium chloride were excellent carbon and nitrogen sources, respectively. Optimum pH, temperature, and cultivation time for the enzyme production were 7.0, $28^{\circ}C$, and 48 h, respectively. The pyrimidine nucleotide N-ribosidase of P. oleovorans ATCC 8062 was not induced by UMP and its derivatives, and was constitutive enzyme.

• Korean Journal of Microbiology
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• v.27 no.1
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• pp.63-69
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• 1989

A pink-pigmented facultative methylotrophic bacterium, Methylobacterium sp. strain SY1, was isolated from soil through methanol-enrichment culture technique. The isolate was gram-negative, slightly curved rod, and motile by a single polarly inserted flagellum. The colony was smooth, bright pink, and slimy. The guanine plus cytosine content of the KNA was 66%. The cell was obigately aerobic and exhibited both catalase and oxidase activities. Carotenoid pigment and poly-$\beta$-hydroxybutyrate were present. It was found to have three kinds of plasmid with molecular weights 45,000, 38,500 and 23,000. Growth with methanol(0.5%) was fast ($t_{d}$=6.5h) and was optimal at $30^{\circ}C$ and at pH 7.0. The isolate could grow on several sugars, organic acids, amino acids, amines, and alcohols in addition to the methanol. Methanol was found to be assimilated through the serine pathway.

• Archives of Pharmacal Research
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• v.25 no.1
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• pp.11-24
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• 2002

The antitumor antibiotic (+)-CC-1065 can alkylate N3 of guanine in certain sequences. A previous high-field $^1H$ NMR study on the$(+)-CC-1065d[GCGCAATTG*CGC]_2$ adduct ($^*$ indicates the drug alkylation site) showed that drag modification on N3 of guanine results in protonation of the cross-strand cytosine [Park, H-J.; Hurley, L. H. J. Am. Chem. Soc.1997, 119,629]. In this contribution we describe a further analysis of the NMR data sets together with restrained molecular dynamics. This study provides not only a solution structure of the (+)-CC-1065(N3- guanine) DNA duplex adduct but also new insight into the molecular basis for the sequence- specific interaction between (+)-CC-1065 and N3-guanine in the DNA duplex. On the basis of NOESY data, we propose that the narrow minor groove at the 7T8T step and conformational kinks at the junctions of 16C17A and 18A19T are both related to DNA bending in the drugDNA adduct. Analysis of the one-dimensional $^1H$ NMR (in $H_2O$) data and rMD trajectories strongly suggests that hydrogen bonding linkages between the 8-OH group of the (+)-CC-1065 A-sub-unit and the 9G10C phosphate via a water molecule are present. All the phenomena observed here in the (+)-CC-1065(N3-guanine) adduct at 5'$-AATTG^*$are reminiscent of those obtained from the studies on the (+)-CC-1065(N3-adenine) adduct at $5'-AGTTA^*$, suggesting that (+)-CC-1065 takes advantage of the conformational flexibility of the 5'-TPu step to entrap the bent structure required for the covalent bonding reaction. This study reveals a common molecular basis for (+)-CC-1065 alkylation at both $5'-TTG^*$ and $5'-TTA^*$, which involves a trapping out of sequence-dependent DNA conformational flexibility as well as sequence-dependent general acid and general base catalysis by duplex DNA.

• YAKHAK HOEJI
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• v.35 no.3
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• pp.203-215
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• 1991

Using the calorimetric [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] (MTT)assay, we evaluated the chemosensitivity of 8 anticancer drugs{vincristine(VCR), vinblastine(VBL), adriamycin(ADR), cisplatin(CPDD), etoposide(VP-16), cytosine arabinoside(ara-C), bleomycin (Bleo) and cyclophosphamide(CYC)} and the cytotoxicity-enhancing effects of ($\pm$)-ar-turmerone and the extracts of the crude drugs {Lithospermum eythrorhizon(LE) and Scutellaria baicalensis (SB)} on the above mentioned anticancer drugs against HL-60 and KG-1 cells among 8 anticancer drugs, VCR, VBL, ADR, and CPDD inhibited the growth of both cell lines by more than 50%, while VP-16, ara-C, Bleo, and CYC were less effective. ($\pm$)-ar-Turmerone had significant inhibitory effects against both cell lines, showing the ID$_{50}$ values of 11.730 $\mu\textrm{g}$/ml and 0.292 $\mu\textrm{g}$/ml for HL-60 and KG-1 cells. respectively. But the extracts of LE and SB roots showed no significant cytotoxic effects. According to ID$_{50}$ values, the cytotoxicities of VCR, VBL and ADR against HL-60 were enhanced two, eight and three times by mixing ($\pm$)-ar-turmerone, five, seven and three times by adding the extract of LE root, and twenty, six and three times by mixing the extract of SB root, respectively. The cytotoxicities of the above mentioned drugs against KG-1 cell were enhanced two, seven and three times by mixing ($\pm$)-ar-turmerone, two, three and three times by combining wilth the extract of LB root, and two, five and two times by adding the extract of SB root, respectively. The cytotoxicity-potentiating effects of ($\pm$)-ar-turmerone and the extracts of LE and SB roots against HL-60 cell were greater than KG-1 cell.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.170-175
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• 2019

Objective: Uncoupling protein 3 gene (UCP3) is a candidate gene associated with the meat quality of pigs. The aim of this study was to explore the regulation mechanism of UCP3 expression and provide a theoretical basis for the research of the function of porcine UCP3 gene in meat quality. Methods: Bisulfite sequencing polymerase chain reaction (PCR) and quantitative real-time PCR (Q-PCR) were used to analyze the methylation of UCP3 5′-flanking region and UCP3 mRNA expression in the adipose tissue or skeletal muscle of three pig breeds at different ages (1, 90, 210-day-old Putian Black pig; 90-day-old Duroc; and 90-day-old Dupu). Results: Results showed that two cytosine-guanine dinucleotide (CpG) islands are present in the promoter region of porcine UCP3 gene. The second CpG island located in the core promoter region contained 9 CpG sites. The methylation level of CpG island 2 was lower in the adipose tissue and skeletal muscle of 90-day-old Putian Black pigs compared with 1-day-old and 210-day-old Putian Black pigs, and the difference also existed in the skeletal muscle among the three 90-day-old pig breeds. Furthermore, the obvious changing difference of UCP3 mRNA expression was observed in the skeletal muscle of different groups. However, the difference of methylation status and expression level of UCP3 gene was not significant in the adipose tissue. Conclusion: Our data indicate that UCP3 mRNA expression level was associated with the methylation status of UCP3 promoter in the skeletal muscle of pigs.

• Clinical and Experimental Pediatrics
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• v.62 no.2
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• pp.55-61
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• 2019

Purpose: Myotonic dystrophy, also known as dystrophia myotonica (DM), is an autosomal dominant disorder with 2 genetically distinct forms. DM type 1 (DM1) is the more common form and is caused by abnormal expansion of cytosine/thymine/guanine (CTG) repeats in the DM protein kinase (DMPK ) gene. Our study aimed to determine whether the age of onset is correlated with CTG repeat length in a population of pediatric patients with DM1. Methods: We retrospectively identified 30 pediatric patients with DM1 that underwent DMPK testing, of which the clinical data of 17 was sufficient. The cohort was divided into 2 subgroups based on the clinical phenotype (congenital-onset vs. late-onset) and number of CTG repeats (<1,000 vs. ${\geq}1,000$). Results: We found no significant difference between the age of onset and CTG repeat length in our pediatric patient population. Based on clinical subgrouping, we found that the congenital-onset subgroup was statistically different with respect to several variables, including prematurity, rate of admission to neonatal intensive care unit, need for respiratory support at birth, hypotonia, dysphagia, ventilator dependence, and functional status on last visit, compared to the late-onset subgroup. Based on genetic subgrouping, we found a single variable (poor feeding in neonate) that was significantly different in the large CTG subgroup than that in the small CTG subgroup. Conclusion: Clinical variables exhibiting statistically significant differences between the subgroups should be focused on prognosis and designing tailored management approaches for the patients; our findings will contribute to achieve this important goal for treating patients with DM1.

• Tuberculosis and Respiratory Diseases
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• v.82 no.2
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• pp.126-132
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• 2019

Background: The development of lung cancer results from the interaction between genetic mutations and dynamic epigenetic alterations, although the exact mechanisms are not completely understood. Changes in DNA methylation may be a promising biomarker for early detection and prognosis of lung cancer. We evaluated the serial changes in genome-wide DNA methylation patterns in blood samples of lung cancer patients. Methods: Blood samples were obtained for three consecutive years from three patients (2 years before, 1 year before, and after lung cancer detection) and from three control subjects (without lung cancer). We used the MethylationEPIC BeadChip method, which covers the 850,000 bp cytosine-phosphate-guanine (CpG) site, to conduct an epigenome-wide analysis. Significant differentially methylated regions (DMRs) were identified using p-values <0.05 in a correlation test identifying serial methylation changes and serial increase or decrease in ${\beta}$ value above 0.1 for three consecutive years. Results: We found three significant CpG sites with differentially methylated ${\beta}$ values and 7,105 CpG sites with significant correlation from control patients without lung cancer. However, there were no significant DMRs. In contrast, we found 11 significant CpG sites with differentially methylated ${\beta}$ values and 10,562 CpG sites with significant correlation from patients with lung cancer. There were two significant DMRs: cg21126229 (RNF212) and cg27098574 (BCAR1). Conclusion: This study revealed DNA methylation changes that might be implicated in lung cancer development. The DNA methylation changes may be the possible candidate target regions for the early detection and prevention of lung cancer.

• BMB Reports
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• v.54 no.2
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• pp.98-105
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• 2021

The clustered regularly interspaced short palindromic repeats (CRISPR) system is a family of DNA sequences originally discovered as a type of acquired immunity in prokaryotes such as bacteria and archaea. In many CRISPR systems, the functional ribonucleoproteins (RNPs) are composed of CRISPR protein and guide RNAs. They selectively bind and cleave specific target DNAs or RNAs, based on sequences complementary to the guide RNA. The specific targeted cleavage of the nucleic acids by CRISPR has been broadly utilized in genome editing methods. In the process of genome editing of eukaryotic cells, CRISPR-mediated DNA double-strand breaks (DSB) at specific genomic loci activate the endogenous DNA repair systems and induce mutations at the target sites with high efficiencies. Two of the major endogenous DNA repair machineries are non-homologous end joining (NHEJ) and homology-directed repair (HDR). In case of DSB, the two repair pathways operate in competition, resulting in several possible outcomes including deletions, insertions, and substitutions. Due to the inherent stochasticity of DSB-based genome editing methods, it was difficult to achieve defined single-base changes without unanticipated random mutation patterns. In order to overcome the heterogeneity in DSB-mediated genome editing, novel methods have been developed to incorporate precise single-base level changes without inducing DSB. The approaches utilized catalytically compromised CRISPR in conjunction with base-modifying enzymes and DNA polymerases, to accomplish highly efficient and precise genome editing of single and multiple bases. In this review, we introduce some of the advances in single-base level CRISPR genome editing methods and their applications.