• International Journal of Oral Biology
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• v.46 no.4
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• pp.155-159
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• 2021

This study aimed to develop strain-specific polymerase chain reaction (PCR) primers to detect Fusobacterium hwasookii KCOM 1249^T, F. hwasookii KCOM 1253, F. hwasookii KCOM 1256, F. hwasookii KCOM 1258, and F. hwasookii KCOM 1268 on the basis of nucleotide sequences of a gene specific to each strain. The unique genes for each F. hwasookii strain were determined on the basis of their genome sequences using Roary. The strain-specific PCR primers based on each strain-specific gene were designed using PrimerSelect. The specificity of each PCR primer was determined using the genomic DNA of the 5 F. hwasookii strains and 25 strains of oral bacterial species. The detection limit and sensitivity of each strain-specific PCR primer pair were determined using the genomic DNA of each target strain. The results showed that the strain-specific PCR primers correspond to F. hwasookii KCOM 1249^T, F. hwasookii KCOM 1253, F. hwasookii KCOM 1258, F. hwasookii KCOM 1256/F. nucleatum subsp. polymorphum KCOM 1260, or F. hwasookii KCOM 1268/Fusobacterium sp. oral taxon 203 were developed. The detection limits of these strain-specific PCR primers ranged from 0.2 to 2 ng of genomic DNA for each target strain. The results suggest that these strain-specific PCR primers are valuable in quality control for detecting specific F. hwasookii strains.

• Journal of Microbiology and Biotechnology
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• v.33 no.1
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• pp.28-34
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• 2023

Endoribonuclease YbeY is specific to the single-stranded RNA of ribosomal RNAs and small RNAs. This enzyme is essential for the maturation and quality control of ribosomal RNA in a wide range of bacteria and for virulence in some pathogenic bacteria. In this study, we determined the crystal structure of YbeY from Staphylococcus aureus at a resolution of 1.9 Å in the presence of zinc chloride. The structure showed a zinc ion at the active site and two molecules of tricarboxylic acid citrate, which were also derived from the crystallization conditions. Our structure showed the zinc ionbound local environment at the molecular level for the first time. Molecular comparisons were performed between the carboxylic moieties of citrate and the phosphate moiety of the RNA backbone, and a model of YbeY in complex with a single strand of RNA was subsequently constructed. Our findings provide molecular insights into how the YbeY enzyme recognizes singlestranded RNA in bacteria.

• Journal of Microbiology and Biotechnology
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• v.33 no.4
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• pp.511-518
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• 2023

The use of dietary protein products has increased with interests in health promotion, and demand for sports supplements. Among various protein sources, milk protein is one of the most widely employed, given its economic and nutritional advantages. However, recent studies have revealed that milk protein undergoes fecal excretion without complete hydrolysis in the intestines. To increase protein digestibility, heating and drying were implemented; however, these methods reduce protein quality by causing denaturation, aggregation, and chemical modification of amino acids. In the present study, we observed that Lacticaseibacillus rhamnosus IDCC 3201 actively secretes proteases that hydrolyze milk proteins. Furthermore, we showed that co-administration of milk proteins and L. rhamnosus IDCC 3201 increased the digestibility and plasma concentrations of amino acids in a high-protein diet mouse model. Thus, food supplementation of L. rhamnosus IDCC 3201 can be an alternative strategy to increase the digestibility of proteins.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.374-389
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• 2023

Organophosphorus (OP) pesticides, particularly malathion, parathion, diazinon, and chlorpyrifos, are widely used in both agricultural and residential contexts. This refractory quality is shared by certain organ phosphorus insecticides, and it may have unintended consequences for certain non-target soil species. Bioremediation cleans organic and inorganic contaminants using microbes and plants. Organophosphate-hydrolyzing enzymes can transform pesticide residues into non-hazardous byproducts and are increasingly being considered viable solutions to the problem of decontamination. When coupled with system analysis, the multi-omics technique produces important data for functional validation and genetic manipulation, both of which may be used to boost the efficiency of bioremediation systems. RNA-guided nucleases and RNA-guided base editors include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR), which are used to alter genes and edit genomes. The review sheds light on key knowledge gaps and suggests approaches to pesticide cleanup using a variety of microbe-assisted methods. Researches, ecologists, and decision-makers can all benefit from having a better understanding of the usefulness and application of systems biology and gene editing in bioremediation evaluations.

• Journal of Microbiology and Biotechnology
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• v.34 no.5
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• pp.1126-1134
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• 2024

The production of disulfide bond-containing recombinant proteins in Escherichia coli has traditionally been done by either refolding from inclusion bodies or by targeting the protein to the periplasm. However, both approaches have limitations. Two broad strategies were developed to allow the production of proteins with disulfide bonds in the cytoplasm of E. coli: i) engineered strains with deletions in the disulfide reduction pathways, e.g. SHuffle, and ii) the co-expression of oxidative folding catalysts, e.g. CyDisCo. However, to our knowledge, the relative effectiveness of these strategies has not been properly evaluated. Here, we systematically compare the purified yields of 14 different proteins of interest (POI) that contain disulfide bonds in their native state when expressed in both systems. We also compared the effects of different background strains, commonly used promoters, and two media types: defined and rich autoinduction. In rich autoinduction media, POI which can be produced in a soluble (non-native) state without a system for disulfide bond formation were produced in higher purified yields from SHuffle, whereas all other proteins were produced in higher purified yields using CyDisCo. In chemically defined media, purified yields were at least 10x higher in all cases using CyDisCo. In addition, the quality of the three POI tested was superior when produced using CyDisCo.

• The Korean Journal of Mycology
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• v.23 no.3 s.74
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• pp.226-231
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• 1995

Tile effects of addition of eggshell to sawdust substrate for the growth of F. velutipes were investigated. Eggshell used in this study contained 20.7% C, 0.81% N, 2530 ppm $P_2O_5$ and 44.37% Ca. The addition of eggshell resulted in the increase in bulk density and decrease of moisture content of the substrate. The addition of eggshell significantly increased the yield of the mushroom fruitbody. The addition rate of 15% (v/v), by 25% and at the rates of 5% and 10%, about 20%. Although the addition of eggshell to substrate did not improve the quality of mushroom, it increased the number of effective stipes as compared to control plot; approximately 13% more than in the control plot.

• Journal of Mushroom
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• v.5 no.1
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• pp.39-42
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• 2007

This study was carried out to characterize virus-like particles (VLPs) in Pleurotus ostreatus. The white and the dark gray mutants frequently observed in mushroom farms of Pleurotus ostreatus (Wonhyeong-neutari). A 5.8kb segments of dsRNA was detected only in the white mutants but not in the dark gray mutants. The VLPs were purified from the fruit bodies by Polyethylene Glycol (PEG) and ultracentrifugation. Electron microscopy analysis showed that VLPs were isometric about 14, 20~45nm in diameter. Further study is needed to reveal the morphological and yield variations of mushroom strains including VLPs observed in the mushroom farms. Also it is needed to maintain fundamental research for taxonomy, diagnosis, and physiology of VLPs in the mushroom strains.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.253-259
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• 2003

To assess microbiological indoor air quality in kindergartens, concentrations of viable airborne microorganisms were seasonally determined at three kindergartens in Ulsan from April, 2002 to January, 2003. Sampling was performed with an impaction-type air sampler and three different media. The numbers of bacteria grown on Staphylococcus medium were between 84 and 4,150 MPN/m3 with an average of 827 MPN/m3, and those on standard method agar ranged from 50 to 2,636 MPN/m3 with an average of 580 MPN/m3. The bacterial concentrations were highest in summer, followed by fall, spring, and winter, and were significantly correlated with indoor temperature. Among the colonies, 45.6~61.0% were observed as Gram-positive cocci and 8.5~20.6% were Gramnegative rods. Micrococcus species were the dominant organisms. The numbers of fungi ranged from 0 to 1,888 MPN/m3(661 MPN/m3 average) based on colony counts with dichloran rose bengal chloramphenicol agar. On average, the fungal concentrations were highest in summer and lowest in winter. Penicillium species and Aspergillus species were identified from the colonies. The obtained data can be utilized as a step to set a guideline for bioaerosols in indoor environment of schools.

• Journal of Life Science
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• v.25 no.6
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• pp.638-645
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• 2015

This study analyzed the physiological quality of Mesembryanthemum crystallinum (ice plant) extract. M. crystallinum is a succulent plant found in Africa, southern Europe, North America, South America, and Australia. It has known antidiabetic, antioxidant, and activation of lipid metabolism effects. Extracts from M. crystallinum were prepared with methanol (MCM), ethanol (MCE), hot water (MCHW), and methanol after hot water (MCHM) extractions. The yields of MCM, MCE, MCHW, and MCHM were 0.37, 0.33, 0.50, and 0.07%, respectively. To determine the biological activities of the extracts, mushroom tyrosinase, pancreatic lipase, 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical scavenging, nitric oxide (NO) production, and α-glucosidase assays were conducted. The DPPH radical scavenging activity of the MCHW extract was 62.9% at a concentration of 400 μg/ml, which was the highest of all the extracts. The MCM extract showed the highest inhibition activity of α-glucosidase and NO production (56.6 and 57.2%, respectively). The pancreatic lipase inhibition of the MCE extract was similar to that of the MCM extract, with significant inhibition of 90%. The mushroom tyrosinase inhibition of all the extracts was very low (approximately 30%). These results suggest that extracts from M. crystallinum have antioxidant, anti-inflammatory, antiobesity, and antidiabetic activities. Thus, it may have potential as a functional food product and therapeutic potential as an antidiabetic or antiobesity agent.

• Journal of Environmental Science International
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• v.14 no.8
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• pp.793-800
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• 2005

We isolated and identified microorganisms from the aerial environment of domestic museums. The fungi, Penicillium spp., Alternaria spp., and Cladosporium spp. were isolated in many museums. It seems that these fungi are related to biological degradation of textile remains. A total of 14 kinds of bacterial strains were isolated: Acinetobacter spp., Pseudomonas spp., Neisseria spp., Alcaligenes spp., Shigella spp., Klebsiella spp., Corynebacterium spp., Aerococcus spp., Bacillus spp., Micrococcus spp., Citrobacter spp., Erwinia spp., Salmonella spp., and Providencia spp. Acinetobacter spp., Pseudomonas spp., Neisseria spp., and Alcaligenes spp. were the predominate bacteria found in samples with a variety of bacteria. This suggests that there is a relationship between bacteria and the damage of textile remains. In the museum, we isolated Alternaria spp, Geotrichum spp., Penicillium spp. Acinetobacter spp., Pseudomonas spp., Alcaligenes spp. from the entrance, exhibit hall and storage, but they were found in smaller number and species in the exhibit cases and paulownia cases. We concluded that paulownia cases were not influenced by the microorganisms because of quality of care provided by the museum staff. Corynebacterium spp., and Bacillus spp. were not detected at the entrance and exhibit hall but were detected in paulownia cases. It is presumed that those bacteria did not flow in from outside, but resulted from contaminants in paulownia cases. In the distribution of microorganisms associated with textile remains, more fungi were detected than bacteria. Acinetobacter spp., Pseudomonas spp., and Neisseria spp., were isolated from silk items. Penicillium spp. and Cladosporium spp. were isolated in the silk and hump items. Aspergillus spp. and Penicillium spp. were isolated from the cotton items. On the other hands, there were no fungi strains in the wool items. Most of the isolated strains from textile remains were aerial microorganisms from the museum environment. These results suggest that textile remains were apt to contaminated by contact with the air.