• ALGAE
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• v.38 no.2
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• pp.93-110
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• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.

• Animal Bioscience
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• v.34 no.2
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• pp.172-184
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• 2021

Objective: Vanin1 (VNN1) is a pantetheinase that can catalyze the hydrolysis of pantetheine to produce pantothenic acid and cysteamine. Our previous studies showed that VNN1 is specifically expressed in chicken liver. In this study, we aimed to investigate the roles of peroxisome proliferators activated receptor α (PPARα) and miRNA-181a-5p in regulating VNN1 gene expression in chicken liver. Methods: 5'-RACE was performed to identify the transcription start site of chicken VNN1. JASPAR and TFSEARCH were used to analyze the potential transcription factor binding sites in the promoter region of chicken VNN1 and miRanda was used to search miRNA binding sites in 3' untranslated region (3'UTR) of chicken VNN1. We used a knock-down strategy to manipulate PPARα (or miRNA-181a-5p) expression levels in vitro to further investigate its effect on VNN1 gene transcription. Luciferase reporter assays were used to explore the specific regions of VNN1 targeted by PPARα and miRNA-181a-5p. Results: Sequence analysis of the VNN1 promoter region revealed several transcription factor-binding sites, including hepatocyte nuclear factor 1α (HNF1α), PPARα, and CCAAT/enhancer binding protein α. GW7647 (a specific agonist of PPARα) increased the expression level of VNN1 mRNA in chicken primary hepatocytes, whereas knockdown of PPARα with siRNA increased VNN1 mRNA expression. Moreover, the predicted PPARα-binding site was confirmed to be necessary for PPARα regulation of VNN1 gene expression. In addition, the VNN1 3'UTR contains a sequence that is completely complementary to nucleotides 1 to 7 of miRNA-181a-5p. Overexpression of miR-181a-5p significantly decreased the expression level of VNN1 mRNA. Conclusion: This study demonstrates that PPARα is an important transcriptional activator of VNN1 gene expression and that miRNA-181a-5p acts as a negative regulator of VNN1 expression in chicken hepatocytes.

• Korean Journal of Organic Agriculture
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• v.23 no.4
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• pp.847-858
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• 2015

Bacillus amyloliquefaciens GR4-5 was isolated from the rhizosphere soil of Korean ginseng and displayed broad-spectrum suppression of ginseng root rot pathogens. The survivability of B. amyloliquefaciens GR4-5 in soil was investigated under three different conditions; indoor, outdoor - of which soil was put in 14 mL tube after treatment - and field environments. Soil samples were collected over a four-week period from three experimental designs, and assessed for 16S rRNA gene copy number by quantitative polymerase chain reaction (qPCR). In outdoor condition, the 16S rRNA gene copy number of Bacillus spp. was 8.35 log copies g $soil^{-1}$ immediately after the GR4-5 treatment. Two weeks later, the 16S rRNA gene copy number of Bacillus spp. (6.70 log copies g $soil^{-1}$) was similar to that of the control (6.38 log copies g $soil^{-1}$). In indoor condition, the 16S rRNA gene copy number of Bacillus spp. maintained in a certain level for a longer period than those in outdoor and field. The 16S rRNA gene copy number of Bacillus spp. in field experiment was reduced faster than that of outdoor condition. Our results show that B. amyloliquefaciens GR4-5 can survive in bulk soil for 1 week, indicating its potential use as a biocontrol agent following 7 day application intervals. This study presents that outdoor microcosm system design could be a useful method to assess easily the survivability of beneficial microorganisms.

• BMB Reports
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• v.48 no.7
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• pp.371-372
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• 2015

MicroRNAs (miRNAs) can regulate the expression of genes that are involved in multiple cellular pathways. However, their targets and mechanism of action associated with the autophagy pathway are not fully investigated yet. EWSR1 (EWS RNA-Binding Protein 1/Ewing Sarcoma Break Point Region 1) gene encodes a RNA/DNA binding protein that is ubiquitously expressed and plays roles in numerous cellular processes. Recently, our group has shown that EWSR1 deficiency leads to developmental failure and accelerated senescence via processing of miRNAs, but its role in the regulation of autophagy remains elusive. In this context, we further investigated and found that EWSR1 deficiency triggers the activation of the DROSHA-mediated microprocessor complex and increases the levels of miR125a and miR351, which directly target Uvrag. Interestingly, the miR125a- and miR351-targeted reduction of Uvrag led to the inhibition of autophagy in both ewsr1 knockout (KO) MEFs and ewsr1 KO mice. In summary, our study demonstrates that EWSR1 is associated with the posttranscriptional regulation of Uvrag via miRNA processing. The regulation of autophagy pathway in miRNAs-Uvrag-dependent manner provides a novel mechanism of EWSR1 deficiency-related cellular dysfunction. [BMB Reports 2015; 48(7): 371-372]

• Journal of Korean Neurosurgical Society
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• v.65 no.5
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• pp.697-709
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• 2022

Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.1-8
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• 2019

Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was characterized with particular transcription factors that bound exclusively with a different 16S rRNA-based secondary structure. In conclusion, the observed data of the present study provided in-depth insights into the mechanism of each Streptococcal species in its pathogenesis, which differ in each observed group, according to the differences in the 16S rRNA secondary structure it takes, and the consequent binding with its corresponding transcription factors. This study paves the way for further interventions of the in silico prediction, with the main conventional in vitro microbiota identification to present an interesting insight in terms of the gene expression pattern and the signaling pathway that each pathogenic species follows in the infected subgingival site.

• Biomedical Science Letters
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• v.25 no.1
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• pp.40-53
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• 2019

Of the Acinetobacter spp., A. baumannii (genospecies 2) is the most clinically significant in terms of hospital-acquired infections worldwide. It is difficult to perform Acinetobacter-related taxonomy using phenotypic characteristics and routine laboratory methods owing to clusters of closely related species. The ability to accurately identify Acinetobacter spp. is clinically important because antimicrobial susceptibility and clinical relevance differs significantly among the different genospecies. Based on the medical importance of pathogenic Acinetobacter spp., the distribution and characterization of Acinetobacter spp. isolates from 123 clinical samples was determined in the current study using four typically applied bacterial identification methods; partial rpoB gene sequencing, amplified rRNA gene restriction analysis (ARDRA) of the intergenic transcribed spacer (ITS) region of the 16~23S rRNA, the $VITEK^{(R)}$ 2 system (an automated microbial identification system) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). A. baumannii isolates (74.8%, 92/123) were the most common species, A. nosocomialis (10.6%, 13/123) and A. pittii isolates (7.5%, 9/123) were second and third most common strains of the A. calcoaceticus-A. baumannii (ACB) complex, respectively. A. soli (5.0%, 6/123) was the most common species of the non-ACB complex. RpoB gene sequencing and ARDRA of the ITS region were demonstrated to lead to more accurate species identification than the other methods of analysis used in this study. These results suggest that the use of rpoB genotyping and ARDRA of the ITS region is useful for the species-level identification of Acinetobacter isolates.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2002.10a
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• pp.170-170
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• 2002

College of Pharmacy, Ewha womans University, Seoul, 120-750, Korea 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is the most potent halogenated aromatic hydrocarbon congener that induces expression of several genes including CYP1A1. Exposure to TCDD results in many toxic actions such as carcinogenesis, hepatotoxicity, immune suppression, and reproductive and developmental toxicity. Dramatic differences in dioxin toxicity have been observed between the sexes of some animal species, suggesting hormonal modulation of dioxin action. Many studies have been reported and propose several mechanisms of anti-estrogenic effects of TCDD. In contrast, the effect of estrogen on the regulation of CYP1A1 are not clear at present. There are several reports showing conflicting results. It seems that induction/inhibition of CYP1A1 may be dependent on cell-type and concentration. The purpose of this study was to investigate the regulation of TCDD-induced CYP1A1 gene expression by estradiol and its metabolites. We examined whether estradiol and its metabolites altered TCDD-mediated induction of CYP1A1 enzyme activity. 17 ${\beta}$ estradiol and 16 ${\alpha}$ estriol at non cytotoxic concentrations caused a significant concentration dependent decline of TCDD-induced EROD activity To determine whether reduced EROD activity reflected altered CYP1A1 mRNA expression, we measured CYP1A1 mRNA level by RT-PCR. And to examine whether estradiol and its metabolites have effects on TCDD-induced CYP1A1 gene expression at the transcription level, we also peformed transient transfection with an AhR responsive reporter plasmid containing the 5' flanking region of the human CYP1A1 gene to examine whether estradiol and its metabolites have effects on TCDD-induced CYP1A1 gene expression at the transcription level.

• Clinical and Experimental Pediatrics
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• v.53 no.2
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• pp.178-183
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• 2010

Purpose : The aim of this study was to identify mutations associated with macrolide resistance in Mycoplasma pneumoniae (MP) and to establish a cultural method to determine antimicrobial susceptibility. Methods : Nasopharyngeal aspirates (NPAs) were collected from 62 children diagnosed with MP pneumonia by a serologic method or polymerase chain reaction. The 23S rRNA and L4 ribosomal protein genes of MP were amplified and sequenced. To identify mutations in these 2 genes, their nucleotide sequences were compared to those of the reference strain M129. MP cultivation was carried out for 32 (28 frozen and 5 refrigerated) NPAs and M129 strain using Chanock's glucose broth and agar plate in a 5% $CO_2$ incubator at $37^{\circ}C$ and examined at 2-3 day intervals for 6 weeks. Results : Among the 62 specimens, 17 had M144V mutations in ribosomal protein L4. The A2064G mutation was observed in 1 specimen; its 23S rRNA gene was successfully sequenced. Culture for MP was successful from the M129 strain and 2 of the 5 NPAs that were refrigerated for no longer than 3 days. However, MP did not grow from the 28 NPAs that were kept frozen at $-80^{\circ}C$ since 2003. Conclusion : We found the M144V mutation of L4 protein to be common and that of domain V of 23S rRNA gene was relatively rare among MP. Studies on the prevalence of macrolide-resistant MP and the relationship between the mutations of 23S rRNA gene and ribosomal protein L4 will aid in understanding the mechanism of macrolide resistance in MP.

• Korean Journal of Environmental Biology
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• v.32 no.4
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• pp.382-388
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• 2014

Shortfin eel (Anguilla bicolor pacifica) is a species of commercial importance and its production is greatly affected due to the infection by Heterosporis anguillarum. In this study, we evaluated the effect of H. anguillarum infection on the growth of Shortfin eel. A disease that trunk muscle of cultured shortfin eel, Anguilla bicolor pacifica, were irregular and resulted in death, breakout of the commercial eel culture farm. We observed that the trunk muscle of infected eels were irregular and represented white or yellowish externally. Histopathologically, a great numbers of large or small spores and sporophorocysts were also observed in degenerated muscle layer. The cloning of specific gene of H. anguillarum, encoding small subunit ribosomal RNA (SSU-rRNA) was amplified by the polymerase chain reaction(PCR) from the muscle lesion of diseased eel. The size of clone gene is well matched with the size of small subunit ribosomal RNA of H. anguillarum and thus confirming the infection by H. anguillarum.