• Genomics & Informatics
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• 제21권3호
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• pp.35.1-35.12
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• 2023

The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.

• Journal of Korean Neurosurgical Society
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• 제66권6호
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• pp.642-651
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• 2023

Objective : Endothelial colony-forming cells (ECFCs) have been reported to play an important role in the pathogenesis of moyamoya disease (MMD). We have previously observed stagnant growth in MMD ECFCs with functional impairment of tubule formation. We aimed to verify the key regulators and related signaling pathways involved in the functional defects of MMD ECFCs. Methods : ECFCs were cultured from peripheral blood mononuclear cells of healthy volunteers (normal) and MMD patients. Low-density lipoproteins uptake, flow cytometry, high content screening, senescence-associated β-galactosidase, immunofluorescence, cell cycle, tubule formation, microarray, real-time quantitative polymerase chain reaction, small interfering RNA transfection, and western blot analyses were performed. Results : The acquisition of cells that can be cultured for a long time with the characteristics of late ECFCs was significantly lower in the MMD patients than the normal. Importantly, the MMD ECFCs showed decreased cellular proliferation with G1 cell cycle arrest and cellular senescence compared to the normal ECFCs. A pathway enrichment analysis demonstrated that the cell cycle pathway was the major enriched pathway, which is consistent with the results of the functional analysis of ECFCs. Among the genes associated with the cell cycle, cyclin-dependent kinase inhibitor 2A (CDKN2A) showed the highest expression in MMD ECFCs. Knockdown of CDKN2A in MMD ECFCs enhanced proliferation by reducing G1 cell cycle arrest and inhibiting senescence through the regulation of CDK4 and phospho retinoblastoma protein. Conclusion : Our study suggests that CDKN2A plays an important role in the growth retardation of MMD ECFCs by inducing cell cycle arrest and senescence.

• Mycobiology
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• 제51권5호
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• pp.360-371
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• 2023

Hispidin is an important styrylpyrone produced by Sanghuangporus sanghuang. To analyze hispidin biosynthesis in S. sanghuang, the transcriptomes of hispidin-producing and non-producing S. sanghuang were determined by Illumina sequencing. Five PKSs were identified using genome annotation. Comparative analysis with the reference transcriptome showed that two PKSs (ShPKS3 and ShPKS4) had low expression levels in four types of media. The gene expression pattern of only ShPKS1 was consistent with the yield variation of hispidin. The combined analyses of gene expression with qPCR and hispidin detection by liquid chromatography-mass spectrometry coupled with ion-trap and time-of-flight technologies (LCMS-IT-TOF) showed that ShPKS1 was involved in hispidin biosynthesis in S. sanghuang. ShPKS1 is a partially reducing PKS gene with extra AMP and ACP domains before the KS domain. The domain architecture of ShPKS1 was AMP-ACP-KS-AT-DH-KR-ACP-ACP. Phylogenetic analysis shows that ShPKS1 and other PKS genes from Hymenochaetaceae form a unique monophyletic clade closely related to the clade containing Agaricales hispidin synthase. Taken together, our data indicate that ShPKS1 is a novel PKS of S. sanghuang involved in hispidin biosynthesis.

• Parasites, Hosts and Diseases
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• 제61권4호
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• pp.455-462
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• 2023

Since 2015, countries in the Sahel region have implemented large-scale seasonal malaria chemoprevention (SMC). However, the mass use of sulfadoxine-pyrimethamine (SP) plus amodiaquine impacts the genetic diversity of malaria parasites and their sensitivity to antimalarials. This study aimed to describe and compare the genetic diversity and SP resistance of Plasmodium falciparum strains in Mali and Niger. We collected 400 blood samples in Mali and Niger from children aged 3-59 months suspected of malaria. Of them, 201 tested positive (Niger, 111, 55.2%; Mali, 90, 44.8%). Polymorphism of merozoite surface protein 1 (msp1) genetic marker showed 201 allotypes. The frequency of the RO33 allotype was significantly higher in Niger (63.6%) than in Mali (39.3%). There was no significant difference in the frequency of the K1 and MAD20 allotypes between the 2 countries. The multiplicity of infection was 2 allotypes per patient in Mali and one allotype per patient in Niger. The prevalence of strains with the triple mutants Pfdhfr51I/Pfdhfr59R/Pfdhps436A/F/H and Pfdhfr51I/Pfdhfr59R/Pfdhps437G was 18.1% and 30.2%, respectively, and 7.7% carried the quadruple mutant Pfdhfr51I/Pfdhfr59R/Pfdhps436A/F/H/Pfdhps437G. Despite the significant genetic diversity of parasite populations, the level of SP resistance was comparable between Mali and Niger. The frequency of mutations conferring resistance to SP still allows its effective use in intermittent preventive treatment in pregnant women and in SMC.

• Journal of Veterinary Science
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• 제24권5호
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• pp.69.1-69.11
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• 2023

Background: Kalkitoxin (KT) is an active lipopeptide isolated from the cyanobacterium Lyngbya majuscula found in the bed of the coral reef. Although KT suppresses cell division and inflammation, KT's mechanism of action in vascular smooth muscle cells (VSMCs) is unidentified. Therefore, our main aim was to investigate the impact of KT on vascular calcification for the treatment of cardiovascular disease. Objectives: Using diverse calcification media, we studied the effect of KT on VSMC calcification and the underlying mechanism of this effect. Methods: VSMC was isolated from the 6 weeks ICR mice. Then VSMCs were treated with different concentrations of KT to check the cell viability. Alizarin red and von Kossa staining were carried out to examine the calcium deposition on VSMC. Thoracic aorta of 6 weeks mice were taken and treated with different concentrations of KT, and H and E staining was performed. Real-time polymerase chain reaction and western blot were performed to examine KT's effect on VSMC mineralization. Calcium deposition on VSMC was examined with a calcium deposition quantification kit. Results: Calcium deposition, Alizarin red, and von Kossa staining revealed that KT reduced inorganic phosphate-induced calcification phenotypes. KT also reduced Ca⁺⁺-induced calcification by inhibiting genes that regulate osteoblast differentiation, such as runtrelated transcription factor 2 (RUNX-2), SMAD family member 4, osterix, collagen 1α, and osteopontin. Also, KT repressed Ca²⁺-induced bone morphogenetic protein 2, RUNX-2, collagen 1α, osteoprotegerin, and smooth muscle actin protein expression. Likewise, Alizarin red and von Kossa staining showed that KT markedly decreased the calcification of ex vivo ring formation in the mouse thoracic aorta. Conclusions: This experiment demonstrated that KT decreases vascular calcification and may be developed as a new therapeutic treatment for vascular calcification and arteriosclerosis.

• Nutrition Research and Practice
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• 제17권5호
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• pp.827-843
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• 2023

BACKGROUND/OBJECTIVES: Mitochondrial DNA leakage leads to inflammatory responses via endosome activation. This study aims to evaluate whether the perennial grass water extract (Pogonatherum panicum) ameliorate mitochondrial DNA (mtDNA) leakage. MATERIALS/METHODS: The major bioactive constituents of P. paniceum (PPW) were investigated by high-performance liquid chromatography, after which their antioxidant activities were assessed. In addition, RAW 264.7 macrophages were stimulated with lipopolysaccharide, resulting in mitochondrial damage. Quantitative polymerase chain reaction and enzyme-linked immunosorbent assay were used to examine the gene expression and cytokines. RESULTS: Our results showed that PPW extract-treated activated cells significantly decrease reactive oxygen species and nitric oxide levels by reducing the p2^phox and iNOS expression and lowering cytokine-encoding genes, including IL-6, TNF-α, IL-1β, PG-E2 and IFN-γ relative to the lipopolysaccharide (LPS)-activated macrophages. Furthermore, we observed that LPS enhanced the mtDNA leaked into the cytoplasm, increasing the transcription of Tlr9 and signaling both MyD88/Irf7-dependent interferon and MyD88/NF-κb p65-dependent inflammatory cytokine mRNA expression but which was alleviated in the presence of PPW extract. CONCLUSIONS: Our data show that PPW extract has antioxidant and anti-inflammatory activities by facilitating mtDNA leakage and lowering the Tlr9 expression and signaling activation.

• 한국동물생명공학회지
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• 제38권3호
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• pp.158-166
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• 2023

Background: Copy number variation (CNV) can be identified using next-generation sequencing and microarray technologies, the research on the analysis of its association with meat traits in livestock breeding has significantly increased in recent years. Hanwoo is an inherent species raised in the Republic of Korea. It is now considered one of the most economically important species and a major food source mainly used for meat (Hanwoo beef). Methods: In this study, CNVs and the relationship between the obtained CNV regions (CNVRs) can be identified in the Hanwoo steer samples (n = 473) using Illumina Hanwoo SNP 50K bead chip and bioinformatic tools, which were used to locate the required data and meat traits were investigated. The PennCNV software was used for the identification of CNVs, followed by the use of the CNV Ruler software for locating the different CNVRs. Furthermore, bioinformatics analysis was performed. Results: We found a total of 2,575 autosomal CNVs (933 losses, 1,642 gains) and 416 CNVRs (289 gains, 111 losses, and 16 mixed), which were established with ranged in size from 2,183 bp to 983,333 bp and 10,004 bp to 381,836 bp, respectively. Upon analyzing the restriction of minor alleles frequency > 0.05 for meat traits association, 6 CNVRs in the carcass weight, 2 CNVRs in the marbling score, 3 CNVRs in the backfat thickness, and 2 CNVRs in the longissimus muscle area were related to the meat traits. In addition, we identified an overlap of 347 CNVRs. Moreover, 3 CNVRs were determined to have a gene that affects meat quality. Conclusions: Our results confirmed the relationship between Hanwoo CNVR and meat traits, and the possibility of overlapping candidate genes, annotations, and quantitative trait loci that results depended on to contribute to the greater understanding of CNVs in Hanwoo and its role in genetic variation among cattle livestock.

• ALGAE
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• 제38권4호
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• pp.283-294
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• 2023

Previous research indicated that free-living sporangial filament keep hollow morph under high-culture density and form bipartite cells under low-culture density, while the following conchospore release was inhibited by high light. Here, we further explored the molecular bases of these affects caused by light and culture density using a transcriptome analysis. Many differentially expressed genes (DEGs) related to carbon dioxide concentration and fixation, photosynthesis, chlorophyll synthesis and nitrogen absorption were upregulated under high-light conditions compared with low-light conditions, indicating the molecular basis of rapid vegetative growth under the former. The stress response- and ion transport-related DEGs, as well as the gene encoding the vacuole formation-brefeldin A-inhibited guanine nucleotide exchange protein (BIG, py05721), were highly expressed under high-density conditions, indicating the molecular basis of the hollow morph of free-living sporangial filaments under high-culture density conditions. Additionally, the brefeldin A treatment indicated that the hollow morph was directly influenced by vacuole formation-related vesicle traffic. Others DEGs related to cell wall components, zinc-finger proteins, ASPO1527, cell cycle and cytoskeleton were highly expressed in the low density with low-light group, which might be related to the formation and release of conchospores. These results provide a deeper understanding of sporangial filaments in Neopyropia yezoensis and related species.

• 한국환경농학회지
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• 제42권4호
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• pp.269-278
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• 2023

Antibiotics either kill or inhibit the growth of bacteria. However, antibiotic-resistant bacteria are difficult to treat with antibiotics. Infections caused by such bacteria often lead to severe diseases. Antibiotic resistance genes (ARG) can be horizontally transmitted across different bacterial species, necessitating a comprehensive understanding of how ARGs spread across various environments. In this study, we analyzed the plasmid sequences of 33 extended-spectrum beta-lactamases (ESBL) producing Escherichia coli isolated from pigs, farms, and their owners. We conducted an antibiotic susceptibility test (AST) with aztreonam and seven other antibiotics, as well as whole genome sequencing (WGS) of the strains using MinION. Our results demonstrated that the plasmids that did not harbor ARGs were mostly non-conjugative, whereas the plasmids that harbored ARGs were conjugative. The arrangement of these ARGs exhibited a pattern of organization featuring a series of ARG cassettes, some of which were identical across the isolates collected from different sources. Therefore, this study suggests that the sets of ARG cassettes on plasmids were mostly shared between pigs and their owners. Hence, enhanced surveillance of ARG should be implemented in farm environments to proactively mitigate the risk of antibiotic-resistant bacterial infections.

• 대한약침학회지
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• 제26권4호
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• pp.307-318
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• 2023

Objectives: Bacterial biofilm is regarded as a significant threat to the production of safe food and the arise of antibiotic-resistant bacteria. The objective of this investigation is to evaluate the quorum sensing inhibitory effect of Nepeta curviflora methanolic extract. Methods: The effectiveness of the leaves at sub-inhibitory concentrations of 2.5, 1.25, and 0.6 mg/mL on the virulence factors and biofilm formation of P. aeruginosa was evaluated. The effect of N. curviflora methanolic extract on the virulence factors of P. aeruginosa, including pyocyanin, rhamnolipid, protease, and chitinase, was evaluated. Other tests including the crystal violet assay, scanning electron microscopy (SEM), swarming motility, aggregation ability, hydrophobicity and exopolysaccharide production were conducted to assess the effect of the extract on the formation of biofilm. Insight into the mode of antiquorum sensing action was evaluated by examining the effect of the extract on the activity of N-Acyl homoserine lactone (AHL) and the expression of pslA and pelA genes. Results: The results showed a significant attenuation in the production of pyocyanin and rhamnolipid and in the activities of protease and chitinase enzymes at 2.5 and 1.25 mg/mL. In addition, N. curviflora methanolic extract significantly inhibited the formation of P. aeruginosa biofilm by decreasing aggregation, hydrophobicity, and swarming motility as well as the production of exopolysaccharide (EPS). A significant reduction in AHL secretion and pslA gene expression was observed, indicating that the extract inhibited quorum sensing by disrupting the quorum-sensing systems. The quorum-sensing inhibitory effect of N. curviflora extract appears to be attributed to the presence of kaempferol, quercetin, salicylic acid, rutin, and rosmarinic acid, as indicated by LCMS analysis. Conclusion: The results of the present study provide insight into the potential of developing anti-quorum sensing agents using the extract and the identified compounds to treat infections resulting from quorum sensing-mediated bacterial pathogenesis.