• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.189-193
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• 2008

A Gram-positive and endospore-forming strain, $JH8^T$, was isolated from deep-sea sediment and identified as a member of the genus Paenibacillus on the basis of 16S rRNA gene sequence and phenotypic analyses. According to a phylogenetic analysis, the most closely related species was Paenibacillus wynnii LMG $22176^T$ (96.9%). Strain $JH8^T$ was also facultatively anaerobic and grew optimally at $20-25^{\circ}C$. The major cellular fatty acid was anteiso-$C_{15:0}$, and the DNA G+C content was 53.1mol%. The DNA-DNA relatedness between the isolate and Paenibacillus wynnii LMG $22176^T$ was 7.6%, indicating that strain $JH8^T$ and P. wynnii belong to different species. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, strain $JH8^T$ would appear to belong to a novel species, for which the name Paenibacillus donghaensis sp. novo is proposed (type strain=KCTC $13049^T=LMG\;237S0^T$).

• Journal of Microbiology and Biotechnology
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• v.19 no.2
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• pp.113-120
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• 2009

Twenty-seven fenitrothion-degrading bacteria were isolated from different soils, and their genetic and phenotypic characteristics were investigated. Analysis of the 16S rDNA sequence showed that the isolates were related to members of the genera Burkholderia, Pseudomonas, Sphingomonas, Cupriavidus, Corynebacterium, and Arthrobacter. Among the 27 isolates, 12 different chromosomal DNA fingerprinting patterns were obtained by polymerase chain reaction(PCR) amplification of repetitive extra genic palindromic(REP) sequences. The isolates were able to utilize fenitrothion as a sole source of carbon and energy, producing 3-methyl-4-nitrophenol as the intermediate metabolite during the complete degradation of fenitrothion. Twenty-two of 27 isolates were able to degrade parathion, methyl-parathion, and p-nitrophenol but only strain BS2 could degrade EPN(O-ethyl-O-p-nitrophenyl phenylphosphorothioate) as a sole source of carbon and energy for growth. Eighteen of the 27 isolates had plasmids. When analyzed with PCR amplification and dot-blotting hybridization using various specific primers targeted to the organophosphorus pesticide hydrolase genes of the previously reported isolates, none of the isolates showed positive signals, suggesting that the corresponding genes of our isolates had no significant sequence homology with those of the previously isolated organophosphate pesticide-degrading bacteria.

• Microbiology and Biotechnology Letters
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• v.46 no.2
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• pp.162-170
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• 2018

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

• Journal of Microbiology and Biotechnology
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• v.29 no.11
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• pp.1806-1816
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• 2019

Candida albicans is an opportunistic fungus possessing multiple virulence factors controlling pathogenicity. Cell wall proteins are the most important among these factors, being the first elements contacting the host. Ddr48 is a cell wall protein consisting of 212 amino acids. A DDR48 haploinsufficient mutant strain was previously found necessary for proper oxidative stress response and drug resistance. In this study, we aimed to further elucidate the role of Ddr48 by performing additional phenotypic characterization assays. A combinatory proteomic and bioinformatics approach was also undertaken to determine differentially expressed cell wall proteins. Results showed that the mutant strain exhibited a 10% decrease in adhesion mirrored by a 20% decrease in biofilm formation, and slight sensitivity to menadione, diamide, and SDS. Both strains showed similar hyphae formation, virulence, temperature tolerance, and calcofluor white and Congo red sensitivities. Furthermore, a total of 8 and 10 proteins were identified exclusively in the wild-type strain grown under filamentous and non-filamentous conditions respectively. Results included proteins responsible for superoxide stress resistance (Sod4 and Sod6), adhesion (Als3, Hyr4, Pmt1, and Utr2), biofilm formation (Hsp90, Ece1, Rim9, Ipp1, and Pra1) and cell wall integrity (Utr2 and Pga4). The lack of detection of these proteins in the mutant strain correlates with the observed phenotypes.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.307.2-308
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• 2002

Acharan sulfate. a new glycosaminoglycan(GAG) isolated from the giant African snail Achatina fulica. was shown to have antitumor activity in vivo. To elucidate the mechanisms for the antitumor activity. we examined its impact on professional antigen presenting cells such as macrophages and dendritic cells (DCs). Acharan sulfate stimulated cytokine production (TNF-a and IL -1b). nitric oxide release. and morphological changes in a dose dependent manner on a macrophage cell Line Raw 264.7 cells. The differentiation-inducing activity of acharan sulfate was examined on immature DCs. Immature DCs were generated from mouse bone marrow (BM) cells by culturing with GM-CSF and IL-4, and then stimulated with acharan sulfate. The resultant DCs were then examined for funcional and phenotypic properties. It was found that acharan sulfate could induce functional maturation of immature DCs as determined by increased allogenic mixed lymphocyte reaction (MLR) and IL-12 production. Phenotypic. analysis for the expression of class II MHC molecules and major co-stimulatory molecules such as B7-1, B7-2 and CD40 also confirmed that acharan sulfate could induce maturation of immature DCs. These results suggest that that the antitumor activity of acharan sulfate is at least in part due to activation adn induction of differentiation of professinal antigen presenting cells. (omitted)

• Korean Journal of Poultry Science
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• v.39 no.4
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• pp.279-282
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• 2012

Clinical-chemical traits are commonly used biomarkers to examine the health status of individuals. There is an appreciable range of normal variation in most clinical-chemical traits and the determining factors of this variation have been relatively uninvestigated in chickens. The aim of this study was to estimate the genetic parameters (i.e., heritability, genetic correlation) for 8 clinical-chemical traits (glucose, total protein, creatinine, high-density lipoprotein cholesterol, total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase and amylase) in an $F_1$ intercross established by purebred breeding among the 5 lines of Korean native chickens. Phenotypic data were collected from approximately 600 $F_1$ animals. The genetic parameters for the clinical-chemical traits estimated by a mixed animal model using the restricted maximum likelihood method were presented. Estimated heritabilities ranged from 8.9% (glucose) to 39.6% (high-density lipoprotein cholesterol). Interestingly, both the sign and the size of the genetic and phenotypic correlations were largely different between the same several pair of clinical-chemical traits. The findings in this study will provide useful information to address issues in both quantitative trait locus study and genetic management in Korean native chickens.

• The Journal of Korean Obstetrics and Gynecology
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• v.23 no.2
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• pp.57-70
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• 2010

Purpose: In this study, we investigated the effects of GDB(Gidaebang) on the immune response to establish the treatment mechanism of vaginitis. Methods: We examined the effects of GDB on the DCs(Dendritic cells) phenotypic and functional maturation. iDCs were cultured in the presence of GM-CSF and the generated iDCs were respectively stimulated by GDB or LPS as the control group for 24 hours. To evaluate the DCs phenotypic and functional maturation, we used flow cytometric analysis, RT-PCR and ELISA. Results: 1. GDB upregulated the expression of class II MHC and CD40 on DCs. 2. GDB upregulated the expression of CD80 and CD86 on DCs. 3. GDB induced cytokine IL-12 production and mRNA expression in DCs. Conclusion: These results suggest that GDB is able to improve the antigen-presenting capacity of DCs through the upregulation of their maturation, and might induce proliferation of T cells. In conclusion, this immunomodulatory properties of GDB may be useful in the treatment of vaginitis.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.1
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• pp.69-72
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• 2004

Somaclonal variation, defined as phenotypic and genetic variations among regenerated plants from a parental plant, could be caused by changes in chromosome structure, single gene mutation, cytoplasm genetic mutation, insertion of transposable elements, and DNA methylation during plant regeneration. The objective of this study was to evaluate DNA variations among somaclonal variants from the cotyledonary node culture in soybean. A total of 61 soybean somaclones including seven $\textrm{R}_1$ lines and seven $\textrm{R}_2$ lines from Iksannamulkong as well as 27 $\textrm{R}_1$ lines and 20 $\textrm{R}_2$ lines from Jinju 1 were regenerated by organogenesis from the soybean cotyledonary node culture system. Field evaluation revealed no phenotypic difference in major agronomic traits between somaclonal variants and their wild types. AFLP and SSR analyses were performed to detect variations at the DNA level among somaclonal variants of two varieties. Based on AFLP analysis using 36 primer sets, 17 of 892 bands were polymorphic between Iksannamulkong and its somaclonal variants and 11 of 887 bands were polymorphic between Jinju 1 and its somaclonal variants, indicating the presence of DNA sequence change during plant regeneration. Using 36 SSR markers, two polymorphic SSR markers were detected between Iksannamulkong and its somaclonal variants. Sequence comparison amplified with the primers flanking Satt545 showed four additional stretches of ATT repeat in the variant. This suggests that variation at the DNA level between somaclonal variants and their wild types could provide basis for inducing mutation via plant regeneration and broadening crop genetic diversity.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.188-188
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• 2017

Rice (Oryza sativa L.) is one of the major crops that is seriously impacted by global soil salinization. Rice is among those crops where most of the high-yielding cultivars are highly sensitive to salinity. The key to a plant survival under NaCl salt stress is by maintaining a high $K^+/Na^+$ ratio in its cells. Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) were used to find out salt tolerant rice genotypes. In the current experiment phenotyping and genotyping studies were correlated to differentiate different rice accessions for salinity tolerance. Eight rice accessions along with check plant Dongjin were screened by physiological studies using Yoshida solution with 50mM NaCl stress condition. The physiology studies identified four tolerant and four susceptible accessions based on their potassium concentration, sodium concentration, $K^+/Na^+$ ratio and biomass. 17 SSR markers were used to evaluate these rice accessions for salt tolerance out of which five molecular markers were able to discriminate tolerant accessions from the susceptible accessions. Banding pattern of the accessions was scored comparing to the banding pattern of Dongjin. The study identifies accessions based on their association of $K^+/Na^+$ ratio with molecular markers which is very reliable. These markers identified can play a significant role in screening large set of rice accessions for salt tolerance; these markers can be utilized to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.

• The Plant Pathology Journal
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• v.29 no.4
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• pp.374-385
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• 2013

Environmental stresses induce several plant pathogenic bacteria into a viable but nonculturable (VBNC) state, but the basis for VBNC is largely uncharacterized. We investigated the physiology and morphology of the copper-induced VBNC state in the plant pathogen Ralstonia solanacearum in liquid microcosm. Supplementation of $200{\mu}M$ copper sulfate to the liquid microcosm completely suppressed bacterial colony formation on culture media; however, LIVE/DEAD BacLight bacterial viability staining showed that the bacterial cells maintained viability, and that the viable cells contain higher level of DNA. Based on electron microscopic observations, the bacterial cells in the VBNC state were unchanged in size, but heavily aggregated and surrounded by an unknown extracellular material. Cellular ribosome contents, however, were less, resulting in a reduction of the total RNA in VBNC cells. Proteome comparison and reverse transcription PCR analysis showed that the Dps protein production was up-regulated at the transcriptional level and that 2 catalases/peroxidases were present at lower level in VBNC cells. Cell aggregation and elevated levels of Dps protein are typical oxidative stress responses. $H_2O_2$ levels also increased in VBNC cells, which could result if catalase/peroxidase levels are reduced. Some of phenotypic changes in VBNC cells of R. solanacearum could be an oxidative stress response due to $H_2O_2$ accumulation. This report is the first of the distinct phenotypic changes in cells of R. solanacearum in the VBNC state.