• Journal of Microbiology
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• v.45 no.2
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• pp.105-112
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• 2007

The objective of this study was to analyze the phylogenetic composition of bacterial community in the soil of an earth-cave (Niu Cave) using a culture-independent molecular approach. 16S rRNA genes were amplified directly from soil DNA with universally conserved and Bacteria-specific rRNA gene primers and cloned. The clone library was screened by restriction fragment length polymorphism (RFLP), and representative rRNA gene sequences were determined. A total of 115 bacterial sequence types were found in 190 analyzed clones. Phylogenetic sequence analyses revealed novel 16S rRNA gene sequence types and a high diversity of putative bacterial community. Members of these bacteria included Proteobacteria (42.6%), Acidobacteria (18.6%), Planctomycetes (9.0 %), Chloroflexi (Green nonsulfur bacteria, 7.5%), Bacteroidetes (2.1%), Gemmatimonadetes (2.7%), Nitrospirae (8.0%), Actinobacteria (High G+C Gram-positive bacteria, 6.4%) and candidate divisions (including the OP3, GN08, and SBR1093, 3.2%). Thirty-five clones were affiliated with bacteria that were related to nitrogen, sulfur, iron or manganese cycles. The comparison of the present data with the data obtained previously from caves based on 16S rRNA gene analysis revealed similarities in the bacterial community components, especially in the high abundance of Proteobacteria and Acidobacteria. Furthermore, this study provided the novel evidence for presence of Gemmatimonadetes, Nitrosomonadales, Oceanospirillales, and Rubrobacterales in a karstic hypogean environment.

• BMB Reports
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• v.32 no.4
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• pp.345-349
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• 1999

We fused the promoter region of an H3.2 chicken histone gene, whose expression is dependent on the cell cycle, to the 5' coding region of an H3.3 chicken histone gene, which is expressed constitutively at a low level throughout the cell cycle. This fusion gene showed a cell cycle-regulated pattern of expression, but in a different manner. The mRNA level of the fusion gene increase during the S phase of the cell cycle by about 3.7-fold at 6 h and 2.7-fold at 12 h after the serum stimulation. The mRNA level of the intact H3.2 gene, however, increased by an average of 3.6-fold at 6 h and 8.7-fold at 12 h. This different expression pattern might be due to the differences in their 3' end region that is responsible for mRNA stability. The 3' end of the H3.2 mRNA contains a stem-loop structure, instead of a poly(A) tail present in the H3.3 mRNA. We also constructed a similar fusion gene using a H3.3 histone gene whose introns had been eliminated to rule out the possibility of involvement of the introns in cell cycle-regulated expression. The expression of this fusion gene was almost identical to the fusion gene made previously. These results indicate that the promoter region of the H3.2 gene is only partially responsible for its expression during the S phase of the cell cycle.

• Tissue Engineering and Regenerative Medicine
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• v.15 no.6
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• pp.711-719
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• 2018

BACKGROUND: Collagen organization within tissues has a critical role in wound regeneration. Collagen fibril diameter, arrangements and maturity between connective tissue growth factor (CTGF) small interfering RNA (siRNA) and mismatch scrambled siRNA-treated wound were compared to evaluate the efficacy of CTGF siRNA as a future implement for scar preventive medicine. METHODS: Nanocomplexes of CTGF small interfering RNA (CTGF siRNA) with cell penetrating peptides (KALA and $MPG^{{\Delta}NLS}$) were formulated and their effects on CTGF downregulation, collagen fibril diameter and arrangement were investigated. Various ratios of CTGF siRNA and peptide complexes were prepared and down-regulation were evaluated by immunoblot analysis. Control and CTGF siRNA modified cells-populated collagen lattices were prepared and rates of contraction measured. Collagen organization in rabbit ear 8 mm biopsy punch wound at 1 day to 8 wks post injury time were investigated by transmission electron microscopy and histology was investigated with Olympus System and TS-Auto software. CONCLUSION: CTGF expression was down-regulated to 40% of control by CTGF siRNA/KALA (1:24) complexes (p<0.01) and collagen lattice contraction was inhibited. However, down-regulated of CTGF by CTGF $siRNA/MPG^{{\Delta}NLS}$ complexes was not statistically significant. CTGF KALA-treated wound appeared with well formed-basket weave pattern of collagen fibrils with mean diameter of $128{\pm}22nm$ (n = 821). Mismatch siRNA/KALA-treated wound showed a high frequency of parallel small diameter fibrils (mean $90{\pm}20nm$, n = 563). CONCLUSION: Controlling over-expression of CTGF by peptide-mediated siRNA delivery could improve the collagen orientation and tissue remodeling in full thickness rabbit ear wound.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.7 no.2
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• pp.137-142
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• 2004

Purpose: The resistance of H. pylori to clarithromycin is one of the major causes of eradication failure. In H. pylori, clarithromycin resistance is due to point mutation in 23S rRNA. The aims of this study were to investigate the mutation of 23S rRNA and to examine the association of cagA, vacA genotype and clarithromycin resistant genes. Methods: H. pylori DNA was extracted from antral biopsy specimens from 27 children with H. pylori infection. Specific polymerase chain reaction (PCR) assays were used for cagA and vacA. Mutations associated with clarithromycin resistance were detected by using PCR restriction fragment length polymorphism (RFLP) analysis of 23S rRNA gene. Results: A2143G mutation was detected in one case and A2144G in 4, indicating 18.5% were clarithromycin resistant. Among the total of 27, cagA was present in 25 (93%), vacA s1a/m1 in 6 (22%), s1a/m2 in 3 (11%), s1c/m1 in 16 (59%), and s1c/m2 in 1 (4%). All of the 5 clarithromycin resistant strains were cagA (+), among which 2 were s1a/m1 and 2 were s1c/m1. There was no relation between genotypes and clarithromycin resistant genes. Conclusion: Detection of H. pylori resistance to clarithromycin using PCR RFLP from biopsy specimens might be useful for the selection of antibiotics. Clarithromycin resistant genes are not associated with genotypes of cagA and vacA.

• Proceedings of the KSAR Conference
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• 2001.03a
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• pp.79-79
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• 2001

This study was conducted to measure the total protein, DNA, and RNA contents of corpus luteum(CL) in various stages of estrous cycle and pregnancy. CLs were collected from a local slaughterhouse and stages of the estrous cycle of CL were classified as CL1~2, days 1 to 10; CL3(with/without central cavity), days 11 to 17; CL4, days 18 to 20 by method of Ireland et. al(1980) and stages of the pregnancy of CL were classified as P1~3, months 11~3: P4~6, months 4~6; P7~9, months 7~9 of pregnancy. CL3 with/without central cavity(CC) was identified as described by Kastelic et. al.(1990)-CL with CC, more than 2mm in diameter; CL without CC, less than 2mm in diameter. In total protein content, CL3 with CC was significantly lower than P7~9(p<.05). The total DNA content was lower in CL3 with CC than CL3 without CC and CL4(p<.05). In protein : DNA ratio, CL3 with CC was significantly lower than CL4(p<.05), CL3 without CC was significantly lower than P7~9(p<.05), CL4 was significantly lower than CL3 with CC, P1~3 and P7~9(p<.05). No differences were observed in RNA content, protein:RNA ratio, RNA/DNA of CLs in stages of estrous cycle and pregnancy.

• Reproductive and Developmental Biology
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• v.35 no.1
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• pp.99-103
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• 2011

Transducin-like enhancer protein 1(TLE-1) is protein associated with cell proliferation. This study analyzed change of TLE-1 mRNA expression during in vivo and in vitro maturation in porcine oocytes. Oocytes and granulose cells were collected from follicles of <2 mm, 2~6 mm and >6 mm in diameter in slaughtered pig's ovaries. Oocytes collected from follicles of 2~6 mm in diameter were used after in vitro maturation for 0, 10, 20 and 44 h. Cumulus cells and granulose cells were collected after treatment with hyaluronidase. In results, TLE-1 mRNA expression in oocytes collected from follicle >6 mm in diameter is increased, TLE-1 RNA expression in cumulus cells and granulosa cells from follicles <2 mm, 2 mm 6 mm and >6 mm in diameter. However, there is no significant difference. On the other hand, TLE-1 mRNA expression from oocytes cultured for 10 hand 44 h is increased, TLE-1 mRNA in cumulus cells cultured for 10 h is significant increased(p<0.05) than other culture periods. In conclusion, these results show that TLE-1 is expressed in all cell types of oocytes, cumulus cells and granulose cells, and associated with oocyte maturation.

• Korean Journal of Food Science and Technology
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• v.36 no.6
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• pp.986-990
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• 2004

The immunomodulatory effect of Codonopsis lanceolata based on the production of cytokines and the activation of macrophage was studied. The mRNA expression of nitric oxide synthase (iNOS) was gradually induced after 24 hr treatment of Codonopsis lanceolata, and NO production was a maximum after 24 hr treatment with 1 mg/mL. RAW 264.7 cell on in vitro treatment with Codonopsis lanceolata induced mRNA of cytokines such as interleukin-1(IL-1)${\beta}$, interleukin-6(IL-6), tumor necrosis $factor(TNF)-{\alpha}\;and\;interferon(IFN)-{\gamma}$; $IL-1{\beta}$ and IL-6 mRNA were gradually induced up to 24 hr, $TNF-{\alpha}\;mRNA$ was regularly induced up to 24 hr, and $IFN-{\gamma}\;mRNA$ level was a maximum within 1 hr. These results suggest that Codonopsis lanceolata exerts as an effective immunomodulator and enhances antitumor activity of macrophages.

• Journal of Food Hygiene and Safety
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• v.35 no.6
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• pp.535-543
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• 2020

In addition to the ubiquitous roles of cellular RNA in genetic regulations, gene expression and phenotypic variations in response to environmental cues and chemotactic signals, the regulatory roles of a new type of RNA called extracellular RNAs (exRNAs) are an up-and-coming area of research interest. exRNA is transported outside the cell through membrane blebs known as membrane vesicles or extracellular vesicles (EVs). EV formation is predominant and conserved among all microbial forms, including prokaryotes, eukaryotes, and archaea. This review will focus on the three major topics concerning bacterially derived exRNAs, i.e., 1) the discovery of exRNA and influence of extraneous RNA over bacterial gene regulations, 2) the known secretion mechanism for the release of exRNA, and 3) the possible applications that can be devised with these exRNA secreted by different gram-negative and gram-positive bacteria. Further, this review will also provide an opinion on exRNA- and EV-derived applications such as the species-specific exRNA markers for diagnostics and the possible roles of exRNA in probiotics and the epigenetic regulations of the gut microbiome.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.11
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• pp.1644-1650
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• 2013

Ribosomal protein (rp) S6 is the substrate of ribosomal protein S6K (S6 kinase) and is involved in protein synthesis by mTOR/S6K/S6 signaling pathway. Some S6 cDNA have been cloned in mammals in recent years but has not been identified in the goat. To facilitate such studies, we cloned the cDNA encoding Cashmere goat (Capra hircus) S6 (GenBank accession GU131122) and then detected mRNA expression in seven tissues by real time PCR and protein expression in testis tissue by immunohistochemisty. Sequence analysis indicated that the obtained goat S6 was a 808 bp product, including a 3' untranslated region of 58 bp and an open reading frame of 750 bp which predicted a protein of 249 amino acids. The predicted amino acid sequence was highly homologous to cattle, human, mouse and rat S6. Expression analysis indicated S6 mRNA was expressed extensively in detected tissues and S6 protein was expressed in testis tissue.

• Journal of Life Science
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• v.21 no.6
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• pp.788-795
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• 2011

Accurate identification for pathogenic bacterium is an essential element in the clinical microbiology laboratory. We studied molecular analysis involving the identification of Chyseobacterium indologenes and evaluated the seventeen isolates in Korea with the 16S rRNA gene of the ribosome to estimate phylogenetic relationships within the genus Chyseobacterium in GenBank. The aligned data sets for C. indologenes were 1,176 nucleotides. Sequence variation within the C. indologenes was mostly due to nucleotide substitutions. Korean C. indologenes isolates were not strikingly different from the same species found in the other countries. However, the rates of base substitution in Korean C. indologenes isolates were higher than those of other C. indologenes isolates in GenBank. C. indologenes was placed as a sister species to C. isbiliense, C. hominis, C. hispanicum, C. molle, C. hungaricum, and C. pallidum.