• Food Science and Preservation
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• v.18 no.4
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• pp.604-611
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• 2011

Several wild yeasts were isolated from Korean grape varieties before and during spontaneous fermentation. Among them, four strains were isolated based on the alcohol content and flavor production in wine after fermentation of apple juice. In this study, the four yeast strains were identified and characterized. PCR-restriction fragment length polymorphism analysis of ITS I-5.8S-ITS II region with restriction endonuclease Hae III and Hinf I resulted in that all the strains showed a typical pattern of Saccharomyces cerevisiae. Pulse field gel electrophoresis showed three different chromosome patterns with a same band between strains SS89 and SS812. When ITS I-5.8S-ITS II sequences of the four strains were compared with one another, they were similar to those of Saccharomyces cerevisiae CBS 4054 type strain. Identity of the sequences was higher than 97% with those of the type strain. Phylogenetic analysis showed based on the sequences showed they were genetically closed to the type strain. The four identified strains were tested in a medium containing 200 ppm potassium metabisulfite, and the MM10 and WW108 inhibition rates resulted at up to 24 h. The four strains were tested at an incubation temperature of $30^{\circ}C$. The 30% sugar concentration in the medium (w/v) showed the highest growth in 36 h, especially in the case of SS89, which was close to growth 40. The four strains were tested in an 8% ethanol medium (v/v). Alcohol tolerance was initially kept in the incubation process. The strains began to adapt, however, to the exceeded resistance. The four strains showed the lowest inhibition rate at 24 h.

• BMB Reports
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• v.43 no.11
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• pp.732-737
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• 2010

RNA interference is a post-transcriptional silencing mechanism triggered by the bioavailability and/or exogenous introduction of double-stranded RNA (dsRNA) into cells. Here we describe a novel method for the synthesis of siRNA in a single vessel. The method employs in vitro transcription and a single-stranded DNA (ssDNA) template and design, which incorporates upon self-annealing, two promoters, two templates, and three loop regions. Using this method of synthesis we generated efficacious siRNAs designed to silence both exogenous and endogenous genes in mammalian cells. Due to its unique design the single-stranded template is easily amenable to adaptation for attachment to surface platforms for synthesis of siRNAs. A siRNA synthesis platform was generated using a 3' end-biotinylated ssDNA template tethered to a streptavidin coated surface that generates stable siRNAs under multiple cycles of production. Together these data demonstrate a unique and robust method for scalable siRNA synthesis with potential application in RNAi-based array systems.

• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.753-759
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• 2023

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4^T (KCTC 43402^T = GDMCC 1.3498^T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4^T. 16S rRNA sequence analysis showed that strain SS4^T most closely resembled Paenibacillus marchantiophytorum DSM 29850^T (98.22%), Paenibacillus nebraskensis JJ-59^T (98.19%), and Paenibacillus aceris KCTC 13870^T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4^T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4^T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850^T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4^T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

• Journal of Sensor Science and Technology
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• v.23 no.5
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• pp.310-313
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• 2014

We report a way to improve the ability of graphene to operate as a gas sensor by applying single stranded deoxyribonucleic acid (DNA). The sensitivity and recovery of the DNA-graphene sensor depending on the different DNA sequences are analyzed. The different sensor responses to reactive chemical vapors are demonstrated in the time domain. Because of the chemical gating effect of the deposited DNA, the resulting devices show complete and rapid recovery to baseline unlike the bare graphene at room temperature. The application of the pattern recognition technique can increase the potential of DNA-graphene sensors as a chemical vapor classifier.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1168-1169
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• 2005

• Journal of Life Science
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• v.18 no.11
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• pp.1499-1506
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• 2008

To examine antitumor activity of the edible plant Zanthoxylum schinifolium, the cytotoxic effect of various organic solvent extracts of its stems on human acute leukemia Jurkat T cells was investigated. Among these extracts such as methanol extract (SS-7), methylene chloride extract (SS-8), ethyl acetate extract (SS-9), n-butanol extract (SS-10), and residual fraction (SL-11), SS-8 exhibited the most cytotoxic activity against Jurkat T cells. The methylene chloride extract (SS-8) possessed the apoptogenic activity capable of inducing sub-G1 peak along with apoptotic DNA fragmentation in Jurkat T cells. Western blot analysis revealed that SS-8 induced apoptosis via mitochondrial cytochrome c release into cytoplasm, subsequent activation of caspase-9 and caspase-3, and cleavage of PARP, which could be blocked by overexpression of Bcl-xL. Jurkat T cell clone I2.1 $FADD^{-/-}$) and Jurkat T cell clone I9.2 (caspase-$8^{-/-}$ were as sensitive as was the wild-type Jurkat T cell clone A3 to the cytotoxic effect of SS-8, suggesting no contribution of Fas/FasL system to the SS-8-mediated apoptosis. The GC-MS analysis of SS-8 showed that it was composed of 16 ingredients including 9,12-octadecanoic acid (18.62%), 2,4-dihydro-5-methyl-4- (1-methylethylidene)- 2-(4-nitrophenyl)-3H- pyrazol-3-one (14.97%), hexadecanoic acid (14.23%), (z,z)-6,9-pentadecadien- 1-ol (13.73%), 5,6-dimethoxy-2-methyl benzofuran (10.95%), and 4-methoxy-2-methylcinnamic acid (5.38%). These results demonstrate that the methylene chloride extract of the stems of Z. schinifolium can induce apoptotic cell death in Jurkat T cells via intrinsic mitochondria-dependent caspase cascade regulated by Bcl-xL without involvement of the Fas/FasL system.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.3
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• pp.302-310
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• 2017

Interferon regulatory factor 8 (IRF8) is essential for the development of B and T cells, as well as for the activity of dendritic cells and macrophages. We performed molecular characterization of IRF8 from rock fish, Sebastes schlegelii (Ss), and investigated the spatial and temporal profile of mRNA expression after challenge with lipopolysaccharide (LPS), polyinosinic:polycytidylic acid (poly I:C), or Streptococcus iniae. The full-length cDNA sequence of SsIRF8 was 1,657 bp, containing an ORF of 1,266 bp. The gene had a predicted molecular mass of 47.7 kDa and an isoelectric point of 5.99. The amino acid sequence coded by this gene showed the highest degree of identity (90.8%) and similarity (96.2%) with IRF8 from Oplegnathus fasciatus. The SsIRF8 mRNA was expressed ubiquitously, at varying levels, with the highest level of expression observed in the spleen. To confirm the role of SsIRF8 in mediating the immune response, we measured SsIRF8 mRNA expression in the splenic tissue at different time points after injection with LPS, poly I:C, or S. iniae. The qRT-PCR results showed that SsIRF8 mRNA expression in the poly I:C-injected group was highly upregulated 6 hr after exposure (P<0.05). Expression of SsIRF8 mRNA in the S. iniae-injected group peaked at 24 hr. These results suggest that SsIRF8 might be important in regulating the strength of the rockfish immune response to immunostimulatory agents.

• Clinical and Experimental Pediatrics
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• v.50 no.12
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• pp.1180-1187
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• 2007

Systemic lupus erythematosus (SLE) is an episodic, multi-system, autoimmune disease characterized by widespread inflammation of blood vessels and connective tissues and by the presence of antinuclear antibodies (ANAs), especially antibodies to native (double-stranded) DNA (dsDNA). Its clinical manifestations are extremely variable, and its natural history is unpredictable. Untreated, SLE is often progressive and has a significant fatality rate. The most widely used criteria for the classification of SLE are those of the American College of Rheumatology (ACR), which were revised in 1982 and modified in 1997. The presence of four criteria have been diagnosed as a SLE. Rashes are common at onset and during active disease. The oral mucosa is the site of ulceration with SLE. Arthralgia and arthritis affect most children and these symptoms are short in duration and can be migratory. Lupus nephritis may be more frequent and of greater severity in children than in adults. The initial manifestation of nephritis is microscopic hematuria, followed by proteinuria. The most common neuropsychiatric symptoms are depression, psychosis(hallucination and paranoia) and headache. CNS disease is a major cause of morbidity and mortality. Pericarditis is the most common cardiac manifestation. Libman-Sacks endocarditis is less common in children. The most frequently described pleuropulmonary manifestations are pleural effusions, pleuritis, pneunonitis and pulmonary hemorrhage. During the active phase ESR, CRP, gamma globulin, ferritin and anti-dsDNA are elevated. Antibodies to dsDNA occur in children with active nephritis. Antibodies to the extractable nuclear antigens (Sm, Ro/SS-A, La/SS-B) are strongly associated with SLE. Specific treatment should be individualized and based on the severity of the disease. Sepsis has replaced renal failure as the most common cause of death.

• Journal of Microbiology and Biotechnology
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• v.23 no.1
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• pp.22-28
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• 2013

Xo2276 is a putative transcription activator-like effector (TALE) in Xanthomonas oryzae pv. oryzae (Xoo). Xo2276 was expressed with a TAP-tag at the C-terminus in Xoo cells to enable quantitative analysis of protein expression and secretion. Nearly all TAP-tagged Xo2276 existed in an insoluble form; addition of rice leaf extracts from a Xoosusceptible rice cultivar, Milyang23, significantly stimulated secretion of TAP-tagged Xo2276 into the medium. In a T3SS-defective Xoo mutant strain, secretion of TAPtagged Xo2276 was blocked. Xo2276 is a Xoo ortholog of Xanthomonas campestris pv. vesicatoria (Xcv) AvrBs3 and contains a conserved DNA-binding domain (DBD), which includes 19.5 tandem repeats of 34 amino acids. Xo2276- DBD was expressed in E. coli and purified. Direct in vitro recognition of Xo2276-DBD on a putative target DNA sequence was confirmed using an electrophoretic mobility shift assay. This is the first study measuring the homologous expression and secretion of Xo2276 in vitro using rice leaf extract and its direct in vitro binding to the specific target DNA sequence.

• Molecules and Cells
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• v.40 no.2
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• pp.143-150
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• 2017

Homologous recombination (HR) is necessary for maintenance of genomic integrity and prevention of various mutations in tumor suppressor genes and proto-oncogenes. Rad51 and Rad54 are key HR factors that cope with replication stress and DNA breaks in eukaryotes. Rad51 binds to single-stranded DNA (ssDNA) to form the presynaptic filament that promotes a homology search and DNA strand exchange, and Rad54 stimulates the strand-pairing function of Rad51. Here, we studied the molecular dynamics of Rad51 and Rad54 during the cell cycle of HeLa cells. These cells constitutively express Rad51 and Rad54 throughout the entire cell cycle, and the formation of foci immediately increased in response to various types of DNA damage and replication stress, except for caffeine, which suppressed the Rad51-dependent HR pathway. Depletion of Rad51 caused severe defects in response to postreplicative stress. Accordingly, HeLa cells were arrested at the G2-M transition although a small amount of Rad51 was steadily maintained in HeLa cells. Our results suggest that cell cycle progression and proliferation of HeLa cells can be tightly controlled by the abundance of HR proteins, which are essential for the rapid response to postreplicative stress and DNA damage stress.