• Journal of Microbiology and Biotechnology
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• v.5 no.4
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• pp.194-199
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• 1995

A portion (7.4 kb) of ribosomal DNA tandem repeat unit from a genome of the mushroom T. matsutake has been cloned. A 1.75 kb EcoRI fragment was cloned first using S. cerevisiae 255 rRNA gene as a probe, and this was then used for further cloning. A chromosomal walking experiment was carried out and the upstream region of the 1.75 kb fragment was cloned using SmaI/BamHI enzyme, the size was estimated to be 5.2 kb in length. Part of the downstream region of the 1.75 kb fragment was also cloned using XbaI/BamHI enzymes. Restriction enzyme maps of three cloned DNA fragments were constructed. Northern hybridization, using total RNA of T. matsutake, and the restriction fragments of three cloned DNAs as probes, revealed that all four ribosomal RNA genes (large subunit[LSU], small subunit [SSU], 5.85 and 5S rRNA genes) are present in the cloned region. The gene organization of the rDNA are regarded as an intergenic spacer [IGS]2 (partial) - SSU rRNA - internal transcribed spacer [ITS]1 - 5.8S rRNA - ITS2 - LSU rRNA - IGS1 -5S rRNA - IG52 (partial).

• Journal of Veterinary Science
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• v.24 no.5
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• pp.73.1-73.16
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• 2023

Background: Highly pathogenic avian influenza virus (HPAIV) is considered a global threat to both human health and the poultry industry. MicroRNAs (miRNA) can modulate the immune system by affecting gene expression patterns in HPAIV-infected chickens. Objectives: To gain further insights into the role of miRNAs in immune responses against H5N1 infection, as well as the development of strategies for breeding disease-resistant chickens, we characterized miRNA expression patterns in tracheal tissues from H5N1-infected Ri chickens. Methods: miRNAs expression was analyzed from two H5N1-infected Ri chicken lines using small RNA sequencing. The target genes of differentially expressed (DE) miRNAs were predicted using miRDB. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were then conducted. Furthermore, using quantitative real-time polymerase chain reaction, we validated the expression levels of DE miRNAs (miR-22-3p, miR-146b-3p, miR27b-3p, miR-128-3p, miR-2188-5p, miR-451, miR-205a, miR-203a, miR-21-3p, and miR-200a3p) from all comparisons and their immune-related target genes. Results: A total of 53 miRNAs were significantly expressed in the infection samples of the resistant compared to the susceptible line. Network analyses between the DE miRNAs and target genes revealed that DE miRNAs may regulate the expression of target genes involved in the transforming growth factor-beta, mitogen-activated protein kinase, and Toll-like receptor signaling pathways, all of which are related to influenza A virus progression. Conclusions: Collectively, our results provided novel insights into the miRNA expression patterns of tracheal tissues from H5N1-infected Ri chickens. More importantly, our findings offer insights into the relationship between miRNA and immune-related target genes and the role of miRNA in HPAIV infections in chickens.

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.352-357
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• 1999

Enterobacter sp. B54 inhibited growth of the fungus Phytophthora capsici on potato dextrose agar (PDA). Three mutants with antifungal activities (denoted M54-47, M54-113, and M54-329) which were lost or increased, through Pl::Tn5 lac mutagenesis, were used to isolate genes responsible for fungal inhibition on PDA. Two clones were selected from the partially EcoR1-digested genomic library of the wild-type strain by probing with genomic flanking sequences of each mutant. We have isolated a 20-kb EcoR1 genomic DNA fragment from this strain that contains genes involved in hyphal growth inhibition of P. capsici on PDA. Subcloning and expression analysis of the above DNA fragment identified a 8-kb region which was necessary for antifungal activities. A 8-kb HindⅢDNA fragment covers three genomic loci inserted by Tn5 lac in each mutant. This suggested that all genes which are related to antifungal activities might be clustered in simple forms of at least 5-8 kb sizes.

• Toxicological Research
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• v.21 no.3
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• pp.209-218
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• 2005

We investigated effects of recombinant human erythropoietin (rHuEPO) on profiles of mRNA transcripts in 6 male cynomolgus (M. fascicularis) monkey's spleen for 4 weeks. Six monkeys, composed of control and treatment group (Control : M1, M2, M3: Treatment : M4, M5, M6) were intravenously administered 3 times per week without or with a dose of rHuEPO 2730 IU/0.1 ml/kg. After 4 weeks rHuEPO treatment, spleen was removed for RNA isolation. Splenic gene expression was assessed using Affymetrix U133A 2.0 arrays containing 18,400 transcripts and variants, including 14,500 well-characterized human genes. Gene expression pattern was very different between individuals even in same treatment. In rHuEPO treated groups showed number of genes were up- or down-regulated (M4: 79: M5: 48; M6: 73 genes). Six genes (epidermal growth factor receptor, calgranulin A, estrogen receptor binding site associated antigen, matrix metalloproteinase 19, zinc finger and BTB domain containing 16, progestin and adipoQ receptor) were commonly expressed in rHuEPO treated group. The different individual response could be major considering factor in monkey experiment. Further study is needed to clarify the different individual response to rHuEPO in molecular level. This study will be valuable in the fundamental understanding and validation of molecular toxicology for bio-generic drugs including rHuEPO in cynomolgus monkey.

• KSBB Journal
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• v.28 no.1
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• pp.54-59
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• 2013

Three isolates, E. faecium P1, P2 and P3, from intestinal drugs of three phamaceutical companies, four clinical vancomycin resistant isolates, E. faecium V1, V2, V3 and E. faecalis V4, and three isolates, E. faecalis DW01, DW07 and DW14, from infant feces were tested for the presence of virulence genes, ace, agg, esp, efaA, gelE, sprE, vanA and vanB as well as fsrABC, regulatory genes of gelE and sprE, cylMBA, cytolysin activation genes and cpd, cob and ccf, pheromone genes by PCR and for their phenotype activities such as protease, biofilm formation, cell clumping and hemolysis. The genes encoding cell surface adherence proteins, ace, agg, esp and efaA, were predominantly amplified from the vancomycin resistant strain V4 and the fecal isolates DW01, DW07 and DW14. Both protease and biofilm formation activity were detected only from E. faecalis V4 from which the PCR products of gelE and spreE as well as fsrABC were amplified. The pheromone genes were amplified from the V4, DW01, DW07 and DW14 strains and these strains showed clumping activity. Biofilm formation was observed from the strains DW01, DW07 and DW14, all of which produced PCR products of pheromone, and V4 as well. Whole cytolysin regulator genes were amplified from DW01, DW07 and DW14 and ${\beta}$-hemolysis activity was detected from these strains. Any virulence genes or activities except the pheomone gene ccf were not detected from the pharmaceutical isolates, E. faecium P1, P2 and P3.

• Korean Journal of Oriental Medicine
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• v.8 no.2 s.9
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• pp.75-84
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• 2002

Obesity can be defined as a metabolic disease due to a increased state of fat tissue caused by an imbalance of calorie intake and use. To define genes that affected by different nutrient, we study gene expression from mice which were fed different nutrient. Epididymal and retro-peritineal adipose tissue were increase in high fat diet feeding mice compared with control, but liver and spleen were not. In serum, total cholesterol were differently increase in high fat diet feeding mice but total triglyceride and free fatty acid were not. That was maybe result of energy balance regulation in vivo system. aP2, PPART2 and FAS genes that were increased during adipogenesis were inclosed in high fat diet fed mice compared with control. In microarray assay, 1.4% of total genes were affected in epididymal adipose tissue by different nutrient. 1.1% of total genes were decreased down 0.5 fold and 0.3% were increased over 2 fold. These results indicated that many genes are affected in adipose tissue by nutrient.

• Microbiology and Biotechnology Letters
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• v.49 no.3
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• pp.449-457
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• 2021

The aim of the present study was to survey the frequency of inducible and constitutive phenotypes and inducible cross-resistant genes by regulating the methylation of 23S rRNA (ermA, ermB, and ermC) and macrolide efflux-related msrA gene in Staphylococcus aureus and S. epidermidis strains. A total of 172 bacterial isolates (identified based on standard tests), were examined in this study. Antibiotic susceptibility was determined by the disk diffusion method, and all isolates were evaluated with respect to inducible and constitutive phenotypes. The presence of ermA, ermB, ermC, and msrA genes was investigated by a PCR assay. The constitutive resistance phenotypes showed a higher distribution among the isolates. R phenotype was detected more among S. epidermidis isolates (46.25%). ermB, ermC, and msrA genes were detected more in methicillin-resistant S. aureus (MRSA) and methicillin-resistant S. epidermidis (MRSE) isolates that had R and HD phenotypes (>77% strains). The ermA gene had the lowest frequency among MRSA, MRSE, MSSA, and MSSE strains (<14% isolates). Distribution of inducible resistance genes in MRSA and MRSE strains, and possibly other species, leads to increased constitutive resistance to erythromycin, clindamycin, and other similar antibiotics. Therefore, it can be challenging to treat infections caused by these resistant strains.

• Journal of Ginseng Research
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• v.43 no.1
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• pp.116-124
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• 2019

Background: Ginsenosides are known as the principal pharmacological active constituents in Panax medicinal plants such as Asian ginseng, American ginseng, and Notoginseng. Some ginsenosides, especially the 20(R) isomers, are found in trace amounts in natural sources and are difficult to chemically synthesize. The present study provides an approach to produce such trace ginsenosides applying biotransformation through Escherichia coli modified with relevant genes. Methods: Seven uridine diphosphate glycosyltransferase (UGT) genes originating from Panax notoginseng, Medicago sativa, and Bacillus subtilis were synthesized or cloned and constructed into pETM6, an ePathBrick vector, which were then introduced into E. coli BL21star (DE3) separately. 20(R)-Protopanaxadiol (PPD), 20(R)-protopanaxatriol (PPT), and 20(R)-type ginsenosides were used as substrates for biotransformation with recombinant E. coli modified with those UGT genes. Results: E. coli engineered with $GT95^{syn}$ selectively transfers a glucose moiety to the C20 hydroxyl of 20(R)-PPD and 20(R)-PPT to produce 20(R)-CK and 20(R)-F1, respectively. GTK1- and GTC1-modified E. coli glycosylated the C3-OH of 20(R)-PPD to form 20(R)-Rh2. Moreover, E. coli containing $p2GT95^{syn}K1$, a recreated two-step glycosylation pathway via the ePathBrich, implemented the successive glycosylation at C20-OH and C3-OH of 20(R)-PPD and yielded 20(R)-F2 in the biotransformation broth. Conclusion: This study demonstrates that rare 20(R)-ginsenosides can be produced through E. coli engineered with UTG genes.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2004.06a
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• pp.236-241
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• 2004

In Escherichia coli, L-lysine biosynthetic pathway is composed of nine enzymatic reactions. It has been well established that most of the lysine biosynthetic genes are regulated by the lysine availability, even though they are all scattered around the chromosome without forming any multigenic operon structure. However, no transcriptional regulatory mechanism has been identified except for the activation of lysA gene by the LysR. In this study, changes in transcriptome profiles of wild type cells and lysR deletion mutant cells grown in the absence or presence of lysine were investigated by using DNA microarray technique. Microarray data analysis revealed three groups of genes whose expression varies depending on the availability of lysine or LysR or both. To further examine the regulatory patterns of lysine biosynthetic genes, lacZ operon fusions were constructed and their expression was measured under various conditions. Obtained results strongly suggest that there is an additional regulatory mechanism which senses the lysine availability and coordinates gene expression.

• Molecules and Cells
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• v.41 no.5
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• pp.390-400
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• 2018

Studies have revealed that miR-103a-3p contributes to tumor growth in several human cancers, and high miR-103a-3p expression is associated with poor prognosis in advanced gastric cancer (GC) patients. Moreover, bioinformatics analysis has shown that miR-103a-3p is upregulated in The Cancer Genome Atlas (TCGA) stomach cancer cohort. These results suggest that miR-103a-3p may function as an oncogene in GC. The present study aimed to investigate the role of miR-103a-3p in human GC. miR-103a-3p expression levels were increased in 33 clinical GC specimens compared with adjacent nontumor stomach tissues. Gain- and loss-of-function studies were performed to identify the correlation between miR-103a-3p and tumorigenesis in human GC. Inhibiting miR-103a-3p suppressed GC cell proliferation and blocked the S-G2/M transition in MKN-45/SGC-7901 cells, whereas miR-103a-3p overexpression improved GC cell proliferation and promoted the S-G2/M transition in vitro. Bioinformatics and dual-luciferase reporter assays confirmed that ATF7 is a direct target of miR-103a-3p. Analysis of the TCGA stomach cancer cohort further revealed that miR-103a-3p expression was inversely correlated with ATF7 expression. Notably, silencing ATF7 showed similar cellular and molecular effects as miR-103a-3p overexpression, namely, increased GC cell proliferation, improved CDK2 expression and decreased P27 expression. ATF7 overexpression eliminated the effects of miR-103a-3p expression. These findings indicate that miR-103a-3p promotes the proliferation of GC cell by targeting and suppressing ATF7 in vitro.