• BMB Reports
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• v.28 no.5
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• pp.443-450
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• 1995

Cloned staphylococcal peptidoglycan hydrolase was used in determining the physiological characteristics of peptidoglycan hydrolase. This enzyme hydrolyzed the bacterial cell walls and released the N-terminal alanine, but not the reducing groups. This cloned gene product was localized in the cytoplasm of transformed Escherichia coli. Activity gels indicated the enzyme had an Mr of about 54,000, which was consistent with the deduced Mr from sequencing of the cloned gene. The activity bound to CM-cellulose but not DEAE-cellulose resin, indicating it as a basic protein. Enhanced enzyme activity in a low concentration of cations, and inhibited enzyme activity in a solution with dissolved phospholipids, suggested that the activity and the availability of this basic protein may be regulated between negatively charged and positively charged cellular molecules. The activity against boiled crude cell wall was much greater than against purifed cell wall, suggesting protein associated with crude cell wall may aid in the binding of the peptidoglycan hydrolase The cloned peptidoglycan hydrolase showed positive activity on whole cells of some lysostaphin-resistant coagulase-negative staphylococci. The cloned enzyme may be an alternative for lysostaphin for lysis of staphylococci.

• BMB Reports
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• v.37 no.3
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• pp.269-274
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• 2004

DNA polymerases without the 3' exonuclease function ($exo^-$ pol) have been widely used in sequencing and SNP genotyping. As a major player that expedited the coming of the postgenomic era, $exo^-$ polymerases worked remarkably well in the Human Genome Sequencing Project. However, it has become a challenge for this class of polymerases to efficiently screen the large number of SNPs that are found in the human genome. For more than three decades it has been recognized that polymerase fidelity varied according to the presence of proofreading activity that is mediated by its internal 3' exonuclease. Polymerases with proofreading function are famous for their high fidelity in DNA replication both in vivo and in vitro, but this well-known class of polymerases has been almost completely neglected in genetic analysis in the postgenomic era. We speculate that $exo^+$ polymerases may exhibit higher nucleotide identification ability when compared to $exo^-$ polymerases for an in vitro genetic analysis. With the application of $exo^+$ polymerases in SNP assays, a novel mechanism for the maintenance of DNA replication, the on/off switch, was discovered. Two new SNP assays have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of $exo^+$ polymerases. Furthermore, the on/off switch mechanism embodies a powerful nucleotide identification ability, which can be used to discriminate the bases that are upstream of the 3' terminus, and thus defines a new concept in de novo sequencing technology. Application of $exo^+$ polymerases to genetic analysis, and especially SNP assays, will greatly accelerate the pace to personalized medicine.

• Food Science of Animal Resources
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• v.37 no.4
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• pp.535-541
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• 2017

This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat. From the Illumina sequencing, a total of 187,671 reads were obtained from 12 chicken samples. Regardless of the type of chicken meat (i.e., whole meat and chicken breast) and storage temperatures ($4^{\circ}C$ and $10^{\circ}C$), Pseudomonas weihenstephanensis and Pseudomonas congelans were the most prominent bacterial species. Serratia spp. and Acinetobacter spp. were prominent in chicken breast and whole chicken meat, respectively. The 118 isolated strains of psychrotrophic bacteria comprised Pseudomonas spp. (58.48%), Serratia spp. (10.17%), and Morganella spp. (6.78%). All isolates grew well at $10^{\circ}C$ and they induced different proteolytic activities depending on the species and strains. Parallel analysis of the next generation sequencing and culture dependent approach provides in-depth information on the biodiversity of the spoilage microbiota in chicken meat. Further study is needed to develop better preservation methods against these spoilage bacteria.

• Mycobiology
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• v.33 no.4
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• pp.210-214
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• 2005

More than 120 isolates of lactic acid bacteria obtained from Kimchi was screened for antifungal activity against Aspergillus fumigatus. Approximately 10% of the isolates showed inhibitory activity and only 4.16% (five isolates) exhibited strong activity against the indicator fungus A. fumigatus. The five isolates showed a wide rang of antifungal activity against A. flavus, Fusarium moniliforme, Penicillium commune, and Rhizopus oryzae. They were identified by 16S rDNA sequencing as Lactobacillus cruvatus, L. lactis subsp. lactis, L. casei, L. pentosus, and L. sakei. The effect of Lactobacillus on mycelial growth and fungal biomass as well as its ability to produce toxic compounds were determined. The results indicate that the three species, Lactobacillus casei, L. lactis subsp. lactis, and L. pentosus, are active against A. fumigatus.

• Journal of Environmental Science International
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• v.1 no.2
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• pp.125-136
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• 1992

Digestion of a municipal wastewater sludge by the anaerobic sequencing batch reactor (ASBR) was investigated to evaluate the performance of the ASBR process at a critical condition of high-solids-content fined. The reactors were operated at an HRT of 10 days with an equivalent loading rate of 0.8-1.5 gVS/L/d at 35$^{\circ}C$ The main conclusions drawn from this study were as follows: 1. Digestion of a municipal wastewater sludge was possible using the ASBR in spite of high concentration of settleable solids in the sludge. The ASBRS with 3- and 4-day cycle period showed almost identical high digestion performances. 2. No adverse effect on digestion stability was observed In the ASBRS in spite of withdrawal and replenishment of 30% or 40% of liquid contents. A conventional anaerobic digester could be easily converted to the ASBR without any stability problem. 3. Flotation thickening occurred in thicken step of the ASBRS throughout steady state, and floating bed volume at the end of thicken period occupied about 70% of the working volume of the reactor Efficiency of flotation thickening in the ASBRS could be comparable to that of additional gravity thickening of a completely mixed digester. 4. Solids were accumulated rapidly in the ASBR during start-up period. Solids concentrations in the ASBRS were 2.6 times higher than that in the completely mixed control reactor at steady state. Dehydrogenase activity had a strong correlation with the solids concentration. Dehydrogenase activity of the digested flu형e in the ASBR was 2.9 times higher than that of the flu형e in the control reactor, and about 25 times higher than that of the subnatant in the ASBR. 5. Remarkable increase in equivalent gas production of 52% was observed at the ASBRS compared with the control reactor in spite of similar quality of clarified effluent from the ASBRS and control reactor. The increase in gas production from the ASBRS was believed to be combined results of accumulation of microorganisms, higher driving force applied, and additional long-term degradation of organics continuously accumulated.

• Advances in environmental research
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• v.9 no.3
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• pp.215-232
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• 2020

Crude oils are essential source of energy. It is majorly found in geographical locations beneath the earth's surface and crude oil is the main factor for the economic developments in the world. Natural crude oil contains unrefined petroleum composed of hydrocarbons of various molecular weights and it contains other organic materials like aromatic compounds, sulphur compounds, and many other organic compounds. These hydrocarbons are rapidly getting degraded by biosurfactant producing microorganisms. The present study deals with the isolation, purification, and characterization of biosurfactant producing microorganism from oil-contaminated soil. The ability of the microorganism producing biosurfactant was investigated by well diffusion method, drop collapse test, emulsification test, oil displacement activity, and blue agar plate method. The isolate obtained from the oil contaminated soil was identified as Bacillus subtilis. The identification was done by microscopic examinations and further characterization was done by Biochemical tests and 16SrRNA gene sequencing. Purification of the biosurfactant was performed by simple liquid-liquid extraction, and characterization of extracted biosurfactants was done using Fourier transform infrared spectroscopy (FTIR). The degradation of crude oil upon treatment with the partially purified biosurfactant was analyzed by FTIR spectroscopy and Gas-chromatography mass spectroscopy (GC-MS).

• Journal of Interdisciplinary Genomics
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• v.4 no.1
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• pp.15-18
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• 2022

Hemophilia A is a rare X-linked congenital deficiency of clotting factor VIII (FVIII) that is traditionally diagnosed by measuring FVIII activity. Various mutations of the FVIII gene have been reported and they influence on the FVIII protein structure. A deficiency of or reduction in FVIII protein manifests as spontaneous or induced bleeding depending on the disease severity. Mutations of the FVIII gene provide important information on the severity of disease and inhibitor development. FVIII mutations also affect the discrepant activities found using different FVIII assays. FVIII activity is affected differently depending on the mutation site. Long-range PCR is commonly used to detect intron 22 inversion, the most common mutation in severe hemophilia. However, point mutations are also common in patients with hemophilia, and direct Sanger sequencing and copy number variant analysis are being used to screen for full mutations in the FVIII gene. Advances in molecular genetic methods, such as next-generation sequencing, may enable accurate analysis of mutations in the factor VIII gene, which may be useful in the diagnosis of mild to moderate hemophilia. Genetic analysis is also useful in diagnosing carriers and managing bleeding control. This review discusses the current knowledge about mutations in hemophilia and focuses on the clinical aspects associated with these mutations and the importance of genetic analysis.

• Journal of Interdisciplinary Genomics
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• v.3 no.2
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• pp.41-46
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• 2021

Inherited platelet function disorders (IPFDs) are a disease group of heterogeneous bleeding disorders associated with congenital defects of platelet functions. Normal platelets essential role for primary hemostasis by adhesion, activation, secretion of granules, aggregation, and procoagulant activity of platelets. The accurate diagnosis of IPFDs is challenging due to unavailability of important testing methods, including light transmission aggregometry and flow cytometry, in several medical centers in Korea. Among several IPFDs, Glanzmann thrombasthenia (GT) is a most representative IPFD and is relatively frequently found compare to the other types of rarer IPFDs. GT is an autosomal recessive disorder caused by mutations of ITGA2B or ITGB3. There are quantitative or qualitative defects of the GPIIb/IIIa complex in platelet, which is the binding receptor for fibrinogen, von Willbrand factor, and fibronectin in GT patients. Therefore, patients with GT have normal platelet count and normal platelet morphology, but they have severely decreased platelet aggregation. Thus, GT patients have a very severe hemorrhagic phenotypes that begins at a very early age and persists throughout life. In this article, the general contents about platelet functions and respective IPFDs, the overall contents of GT, and the current status of genetic diagnosis of GT in Korea will be reviewed.

• Journal of Korean Society of Water and Wastewater
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• v.33 no.1
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• pp.55-62
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• 2019

The respirometric technique has been used to analyze the nitrification process in a sequencing batch reactor(SBR) treating municipal wastewater. Especially the profile of the respiration rate very well expressed the reaction characteristics of nitrification. As the nitrification process required a significant amount of oxygen for nitrogen oxidation, the respiration rate due to nitrification was high. The maximum nitrification respiration rate, which was about $50mg\;O_2/L{\cdot}h$ under the period of sufficient nitrification, was related directly to the nitrification reaction rate and showed the nitrifiers activity. The growth rate of nitrifiers is the most critical parameter in the design of the biological nutrient removal systems. On the basis of nitrification kinetics, the maximum specific growth rate of nitrifiers in the SBR was estimated as $0.91d^{-1}$ at $20^{\circ}C$, and the active biomass of nitrifiers was calculated as 23 mg VSS/L and it was about 2% of total biomass.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.