• Biomedical Science Letters
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• v.8 no.3
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• pp.195-202
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• 2002

Osteoarthritis (OA), the most common form of arthritis, involves the destabilization of the normal balance between the degradation and the synthesis of articular cartilage and subchondral bone within a joint. As articular cartilage degrades over time, its smooth surface roughens and bone-against-bone contact ensues, producing the inflammation response symptomatic of this 'wear and tear' disease. Although a variety of genetic, developmental, metabolic, and traumatic factors may initiate the development of osteoarthritis, its symptoms (joint pain, stiffness, and curtailed function) typically evolve slowly, and patients experience periods of relative calm alternation with episodes of inflammation and pain. Rheumatoid arthritis (RA), an autoimmune disease of unknown etiology characterized by chronic synovitis and cartilage destruction, affect 1% of the total population. Cartilage is a specialized connective tissue in which the chondrocytes occupy only 5% of the volume. Cartilage is particularly rich in extracellular matrix, with matrix making up 90% of the dry weight of the tissue chondrocytes have cell processes that extend a short distance into the matrix, but do not touch other cells thus in cartilage, cell-matrix interactions are essential for the maintenance of the extracellular matrix. In this study, subtractive hybridization method was utilized to detect genes differentially expressed in chondrocytes treated with methylprednisolone. We have isolated 57 genes that expressed differentially in the chondreocytes by methylprednisolone. 13 clones of them were analyzed with sequencing and their homologies were searched. 8 cDNAS included KIAA 0368, upregulated during skeletal muscle growth 5 (usmg 5), ribosomal protein S 18 (RPS 18), skeletal muscle ryanodine receptor, radial spoke protein 3 (RSP 3), ribosomal protein QM, ribosomal protein L37a (RPL37A), cytochrome coxidase subunit VIII (COX8).

• Korean Journal Plant Pathology
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• v.10 no.3
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• pp.228-234
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• 1994

Genomic RNA was extracted from Cy strain of odontoglossum ringspot tobamovirus (ORSV-Cy) isolated from infected leaves of tobacco cv. Samsun. Size of the genomic RNA was about 6.6 kb in length. The genomic RNA was fractionated using Sephadex G-50 column chromatography into 2 fractions. They were polyadenylated at their 3'-end using E. coli poly(A) polymerase. Polyadenylated viral RNA was recovered by oligo (dT) primer adapter containing NotI restriction site and Moloney murine leukemia virus SuperScript reverse transcriptase (RNase H-). Second-strand cDNA was synthesized by using E. coli DNA ligase, E. coli DNA polymerase I and E. coli RNase H. Recombinant plasmids containing cDNAs for ORSV-Cy RNA ranged from about 800 bp to 3,000 bp. Among the selected 238 recombinants, pORCY-124 clone was the largest one covering 3'-terminal half of the viral RNA. This clone contained two restriction sites for EcoRI and XbaI and one site for AccI, AvaI, BglII, BstXI, HindIII, PstI, and TthIII 1. respectively. The clone contained partial viral replicase, a full-length movement protein and a complete coat protein genes followed by a 3' untranslated region of 414 nucleotides based on restriction mapping and nucleotide sequencing analyses. Clones pORCY-028, -068, -072, -187 and -224 were overlapped with the pORCY-124. Clones pORCY-014 and -095 covered 5' half upstream from the middle region of the viral RNA, which was estimated based on restriction mapping and partial sequence analysis. Constructed cDNA library covered more than 90% of the viral genome.

• Journal of Microbiology and Biotechnology
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• v.31 no.11
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• pp.1591-1600
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• 2021

Streptomyces coelicolor is a filamentous soil bacterium producing several kinds of antibiotics. S. coelicolor abs8752 is an abs (antibiotic synthesis deficient)-type mutation at the absR locus; it is characterized by an incapacity to produce any of the four antibiotics synthesized by its parental strain J1501. A chromosomal DNA fragment from S. coelicolor J1501, capable of complementing the abs- phenotype of the abs8752 mutant, was cloned and analyzed. DNA sequencing revealed that two complete ORFs (SCO6992 and SCO6993) were present in opposite directions in the clone. Introduction of SCO6992 in the mutant strain resulted in a remarkable increase in the production of two pigmented antibiotics, actinorhodin and undecylprodigiosin, in S. coelicolor J1501 and abs8752. However, introduction of SCO6993 did not show any significant difference compared to the control, suggesting that SCO6992 is primarily involved in stimulating the biosynthesis of antibiotics in S. coelicolor. In silico analysis of SCO6992 (359 aa, 39.5 kDa) revealed that sequences homologous to SCO6992 were all annotated as hypothetical proteins. Although a metalloprotease domain with a conserved metal-binding motif was found in SCO6992, the recombinant rSCO6992 did not show any protease activity. Instead, it showed very strong β-glucuronidase activity in an API ZYM assay and toward two artificial substrates, p-nitrophenyl-β-D-glucuronide and AS-BI-β-D-glucuronide. The binding between rSCO6992 and Zn²⁺ was confirmed by circular dichroism spectroscopy. We report for the first time that SCO6992 is a novel protein with β-glucuronidase activity, that has a distinct primary structure and physiological role from those of previously reported β-glucuronidases.

• Journal of Microbiology and Biotechnology
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• v.31 no.4
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• pp.510-519
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• 2021

The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. Artemisia argyi, a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of Nocardia, Paracoccus, Marmoricola and Knoelia from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in A. argyi were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.

• Journal of Practical Agriculture & Fisheries Research
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• v.23 no.1
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• pp.117-128
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• 2021

The skeletal muscle development of Hanwoo steer has been processed in the prenatal and postnatal periods. Bovine satellite cell located in perimysium of muscle tissues has differentially distributed in peripheral tissues. The study of postnatal development of satellite cells can help understand the genetic and functional regulation of meat characteristics. Factors affecting muscle size increase are related to the accumulation of DNA or synthesis of RNA proteins. In this study, we observed muscle development and differentiation after culturing bovine satellite cells derived from longissimus dorsi and semimembranosus regions of Hanwoo muscle tissue. In addition, RNA sequencing data were analyzed for differentially expressed genes (DEG) involved in intracellular muscle development and growth. The DEG of the two muscle tissues were compared according to 1day, 2day, 4day, and 7day. The overall gene expression level was confirmed by the heat map. Gene Ontology (GO) classification method was used to compare the expression level of gene groups affecting LD and SM development. The histology of GO was consistent with the time-cause change of LD and SM cell morphology. SM showed more active skeletal muscle development than LD. Even within the same time, SM expressed more genes than LD, thus synthesizing more muscle fibers

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.116-116
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• 2018

Bioconversion, the enzymatic process by microorganism on organic precursor to desired products. The natural extract is converted into a form that can be easily absorbed into the skin, while scaling up of to higher quantity is possible. Selection of naturally processed raw material rather than chemically processed is preferred. Therefore, fermentation was carried out by mixing Rubus coreanus Miquel, soybean, Zanthoxylum schinifolium as bioconverting materials, the possibility of inflammation, whitening material were checked. In this study, useful microorganisms were isolated from various salted fish, and 16S rDNA sequence was analyzed to confirm their genetic characteristics. Combining the three natural materials using bioconversion technology to study their activity before and after fermentation. To evaluate the antioxidant activity and the active ingredient content the DPPH radical scavenging activity and the total polyphenol content were examined. Raw 264.7 cells were used to evaluate MTT assay, NO and $TNF-{\alpha}$ production inhibitory activity. Also, to evaluate the whitening activity, tyrosinase inhibitory activity and melanin formation inhibitory activity were measured using B16F10 cells. In total 34 strains were obtained from various salted fish. The effective strains useful for the bioconversion process, showed that DPPH radical scavenging ability and polyphenol content were increased in the two kinds of microbial treatment groups compared to the untreated group. 16S rDNA sequencing analysis of the strains showed excellent in Pediococcus pentosaceus B1 in comparison. An increase of up-to 156% in anti-oxidative activity and 141% in polyphenol content was observed after bioconversion. In addition, after mixed fermentation the toxidty of Raw 264.7 and B16F10 cells tended to decrease and a significant increase was observed in anti-inflammatory activity as well. Also, tyrosinase activity and melanin significantly. synthesis decreased significantly.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3507-3511
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• 2014

Background: The prostaglandin-endoperoxide synthase 2 [PTGS2, commonly known as cyclooxygenase-2 (COX-2)] is an enzyme induced by proinflammatory stimuli that is often overexpressed in malignant tissue and involved in the synthesis of prostaglandins and thromboxanes, regulators of processes such as inflammation, cell proliferation, and angiogenesis, all relevant for cancer development. We investigated whether a functional genetic polymorphism, rs5277, in COX-2 may have a risk-modifying effect on sporadic colorectal cancer in an Iranian population. Materials and Methods: We conducted a case-control study on 167 patients with colorectal cancer and 197 cancer-free controls in Taleghani Hospital in Tehran, Iran, between 2007 and 2011. Peripheral blood samples of both groups were processed for DNA extraction and genotyping of the COX-2 gene polymorphism (rs5277) using PCR-RFLP. RFLP results were confirmed by direct sequencing. Logistic regression analysis was performed to calculate the adjusted odds ratio (OR) and 95% confidence interval (95% CI). Results: There was no significant difference in the distribution of COX-2 gene rs5277 polymorphism genotype and the allelic form, among CRC patients compared with the healthy control group (p: 0.867). Conclusions: Our results suggest that rs5277 polymorphism in COX2 could not be a good prognostic indicator for patients with CRC.

• Animal Bioscience
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• v.35 no.11
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• pp.1771-1786
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• 2022

Objective: Inosine monophosphate (IMP) is a key factor that imparts of meat flavor. Differences in the IMP content in the muscles were evaluated to improve chicken meat quality. Methods: For this study, the IMP content was detected by high performance liquid chromatography. The gene expression profiles of Jingyuan chickens with different feeding patterns and different sexes were analyzed by RNA-sequencing (RNA-seq). Results: Breast muscle IMP content in free-range chickens was extremely significantly higher than that of caged chickens (p<0.01). Breast muscle IMP content in hens was also higher than that of cocks, but the difference was not significant. Correlation analysis showed that the breast muscle IMP content in caged hens and cocks was negatively correlated with the shear force, and the breast muscle IMP content in free-range hens was significantly negatively correlated with the shear force (p<0.05). The two key genes associated with IMP synthesis in chickens with different feeding patterns were glutamate-ammonia ligase (GLUL) and phosphodiesterase 10A (PDE10A). Bioinformatics analysis revealed that the GLUL and PDE10A genes are involved in glutamine biosynthesis and purine salvage pathways respectively. In addition, GLUL expression was positively correlated with the IMP content in caged and free-range chickens, and PDE10A expression was significantly positively correlated with the IMP content in caged and free-range chickens (p<0.05). Conclusion: These findings will facilitate the comprehension of the deposition of IMP in the muscles and thereby aid the process of selection and breeding of good quality local chickens.

• Molecules and Cells
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• v.46 no.6
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• pp.351-359
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• 2023

Deamination of adenine or cytosine in RNA, called RNA editing, is a constitutively active and common modification. The primary role of RNA editing is tagging RNA right after its synthesis so that the endogenous RNA is recognized as self and distinguished from exogenous RNA, such as viral RNA. In addition to this primary function, the direct or indirect effects on gene expression can be utilized in cancer where a high level of RNA editing activity persists. This report identified actin-related protein 2/3 complex inhibitor (ARPIN) as a target of ADAR1 in breast cancer cells. Our comparative RNA sequencing analysis in MCF7 cells revealed that the expression of ARPIN was decreased upon ADAR1 depletion with altered editing on its 3'UTR. However, the expression changes of ARPIN were not dependent on 3'UTR editing but relied on three microRNAs acting on ARPIN. As a result, we found that the migration and invasion of cancer cells were profoundly increased by ADAR1 depletion, and this cellular phenotype was reversed by the exogenous ARPIN expression. Altogether, our data suggest that ADAR1 suppresses breast cancer cell mobility via the upregulation of ARPIN.

• BMB Reports
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• v.38 no.1
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• pp.89-96
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• 2005

Earlier, we reported that the bacteriophage $\lambda$ P gene product is lethal to Escherichia coli, and the E. coli rpl mutants are resistant to this $\lambda$ P gene-mediated lethality. In this paper, we show that under the $\lambda$ P gene-mediated lethal condition, the host DNA synthesis is inhibited at the initiation step. The rpl8 mutation maps around the 83 min position in the E. coli chromosome and is 94% linked with the dnaA gene. The rpl8 mutant gene has been cloned in a plasmid. This plasmid clone can protect the wild-type E. coli from $\lambda$ P gene-mediated killing and complements E. coli dnaAts46 at $42^{\circ}C$. Also, starting with the wild-type dnaA gene in a plasmid, the rpl-like mutations have been isolated by in vitro mutagenesis. DNA sequencing data show that each of the rpl8, rpl12 and rpl14 mutations has changed a single base in the dnaA gene, which translates into the amino acid changes N313T, Y200N, and S246T respectively within the DnaA protein. These results have led us to conclude that the rpl mutations, which make E. coli resistant to $\lambda$ P gene-mediated host lethality, are located within the DNA initiator gene dnaA of the host.