• Journal of Life Science
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• v.12 no.5
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• pp.610-621
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• 2002

Conserved genes are importantly used to understand the major function in survival and replication of living organism. This study was focused on identification of conserved genes in microbial species and measuring the degree of conservation. For this purpose, in silico analysis was performed to search conserved genes based on the conservation level within microbial species. The ortholog list of COGs (Clusters of Orthologous Groups of proteins) in NCBI was used and whole genomes of 43 microbial species were included in that list. The distance value, derived from CLUSTALW multiple alignment program, was used as a descriptor of the conservation level of orthologs. It was revealed that 43 microbial genomes hold 72 conserved orthologs in common. The majority(72.2%) of the conserved genes was related to "translation, ribosomal structure and biogenesis" functional category. A GTPase-translation elogation factor(COG0050) was the best conserved gene from the distance value analysis. The 72 conserved genes, found in this research, would be useful not only to study minimal function genes but also new drug target among pathogens and to make a model of the virtual cell.tual cell.

• The Plant Pathology Journal
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• v.30 no.1
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• pp.33-42
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• 2014

Nivalenol (NIV) and deoxynivalenol (DON) are predominant Fusarium-producing mycotoxins found in grains, which are mainly produced by Fusarium asiaticum and F. graminearum. NIV is found in most of cereals grown in Korea, but the genetic basis for NIV production by F. asiaticum has not been extensively explored. In this study, 12 genes belonging to the trichothecene biosynthetic gene cluster were compared at the transcriptional level between two NIV-producing F. asiaticum and four DON-producing F. graminearum strains. Chemical analysis revealed that time-course toxin production patterns over 14 days did not differ between NIV and DON strains, excluding F. asiaticum R308, which was a low NIV producer. Both quantitative real-time polymerase chain reaction and Northern analysis revealed that the majority of TRI gene transcripts peaked at day 2 in both NIV and DON producers, which is 2 days earlier than trichothecene accumulation in liquid medium. Comparison of the gene expression profiles identified an NIV-specific pattern in two transcription factor-encoding TRI genes (TRI6 and TRI10) and TRI101, which showed two gene expression peaks during both the early and late incubation periods. In addition, the amount of trichothecenes produced by both DON and NIV producers were correlated with the expression levels of TRI genes, regardless of the trichothecene chemotypes. Therefore, the reduced production of NIV by R308 compared to NIV or DON by the other strains may be attributable to the significantly lower expression levels of the TRI genes, which showed early expression patterns.

• Journal of Microbiology and Biotechnology
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• v.17 no.4
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• pp.560-570
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• 2007

The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the l6S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.

• Journal of Biosystems Engineering
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• v.39 no.2
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• pp.142-149
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• 2014

Purpose: A multispectral algorithm for detection and differentiation of defective (defects on apple skin) and normal Red Delicious apples was developed from analysis of a series of hyperspectral line-scan images. Methods: A fast line-scan hyperspectral imaging system mounted on a conventional apple sorting machine was used to capture hyperspectral images of apples moving approximately 4 apples per second on a conveyor belt. The detection algorithm included an apple segmentation method and a threshold function, and was developed using three wavebands at 676 nm, 714 nm and 779 nm. The algorithm was executed on line-by-line image analysis, simulating online real-time line-scan imaging inspection during fruit processing. Results: The rapid multispectral algorithm detected over 95% of defective apples and 91% of normal apples investigated. Conclusions: The multispectral defect detection algorithm can potentially be used in commercial apple processing lines.

• Journal of Wetlands Research
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• v.20 no.2
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• pp.116-123
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• 2018

The objective of this study was to examine effects of stand age on soil $CO_2$ efflux in plantation Pinus koraiensis, and to elucidate what extent plant (fine) root and soil microbial biomass contribute to the whole soil $CO_2$ efflux. In three age classes (20-yr-old. 40-yr-old, 70-yr-old) of plantation Pinus koraiensis, in-situ soil respiration, plant fine root biomass and soil microbial biomass were measured from April to November in 2004. Regardless of stand age, soil temperature and soil $CO_2$ efflux increased until July then slowly decreased. Soil respiration was higher in 70-yr-old stand than in 20- and 40-yr stands. Fine root biomass and soil microbial biomass was also higher in 70-yr-old stand. Root exclusion decreased soil respiration in 40-yr stand, but not in 70-yr stand. Soil microbial biomass was higher in 70-yr stand, but there was no monthly variation between July and November. The results suggest that soil respiration may increase as plant stand ages and microbial contribution could play more roles in older stands.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1352-1359
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• 2018

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (${\text\tiny{L}}-arabinose$, ${\text\tiny{L}}-rhamnose$, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.

• Journal of Korean Biological Nursing Science
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• v.21 no.2
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• pp.133-140
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• 2019

Purpose: The purpose of this study was to check the degree of residual microbial contamination after disinfection of reusable suction containers, used in an intensive care unit (ICU) and present basic data for efficient use through cost analysis in comparison to disposable suction containers. Methods: This study was conducted on 32 reusable suction containers used in an ICU on a selected specific day. After disinfection and washing, specimens were collected from the used containers and cultured to check for microbial contamination. Additionally, a comparative narrative study analyzes the cost of using reusable suction containers and disposable suction containers. Data were analyzed with the SPSS WIN 20.0 program using real numbers and percentage ${\chi}^2$-test. Results: As a result of the study, microorganisms were found in all samples where in 30 were gram-positive (62.5%) while 13 were gram-negative (27.1%). Based on level of contamination, microorganisms were less than 10CFU/ml in 18 samples (56.3%); 11-99CFU/ml in six samples (18.8%); and more than 100CFU/ml in eight samples (25%). Cost per day for a reusable suction container was $10,655+{\alpha}$ while cost per day for a disposable suction container was 10,666 won. Conclusion: This study found that reusable suction containers, even after disinfection, accounted for factors of potential infection as well as microbial contamination. So, disposable suction containers are superior in cost-effectiveness and highly efficient for use with infected patients.

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1561-1572
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• 2022

Plastic pollution has been recognized as a serious environmental problem, and microbial degradation of plastics is a potential, environmentally friendly solution to this. Here, we analyzed and compared microbial communities on waste plastic films (WPFs) buried for long periods at four landfill sites with those in nearby soils to identify microbes with the potential to degrade plastics. Fourier-transform infrared spectroscopy spectra of these WPFs showed that most were polyethylene and had signs of oxidation, such as carbon-carbon double bonds, carbon-oxygen single bonds, or hydrogen-oxygen single bonds, but the presence of carbonyl groups was rare. The species richness and diversity of the bacterial and fungal communities on the films were generally lower than those in nearby soils. Principal coordinate analysis of the bacterial and fungal communities showed that their overall structures were determined by their geographical locations; however, the microbial communities on the films were generally different from those in the soils. For the pulled data from the four landfill sites, the relative abundances of Bradyrhizobiaceae, Pseudarthrobacter, Myxococcales, Sphingomonas, and Spartobacteria were higher on films than in soils at the bacterial genus level. At the species level, operational taxonomic units classified as Bradyrhizobiaceae and Pseudarthrobacter in bacteria and Mortierella in fungi were enriched on the films. PICRUSt analysis showed that the predicted functions related to amino acid and carbohydrate metabolism and xenobiotic degradation were more abundant on films than in soils. These results suggest that specific microbial groups were enriched on the WPFs and may be involved in plastic degradation.

• Journal of Microbiology and Biotechnology
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• v.34 no.9
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• pp.1890-1897
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• 2024

Fermentation has been identified as an effective strategy to alter the chemical makeup of tobacco, thereby enhancing its quality. The deliberate introduction of microorganisms can hasten the fermentation process. In this research, microbial consortia harvested from the tobacco surface were utilized to enhance the tobacco quality. This enhancement also elevated several sensory attributes of HnB cigarettes, such as aroma richness, moisture, strength, and reduced irritation, achieving a sensory quality rating of 84.5. This marks a notable improvement compared to the 82 rating of the original, unfermented cigarettes. Untargeted metabolomics analysis revealed a decrease in total polyphenols and unsaturated fatty acids, while the levels of polyacids, alcohols, ketones, furans, and other compounds increased in the fermented tobacco. Additionally, KEGG pathway enrichment analysis indicated that the enhancement in tobacco quality through microbial consortia fermentation is linked to various biological pathways, with pathways related to fatty acid and amino acid degradation playing pivotal roles. The findings of this study will serve as a reference for the commercial production of HnB cigarettes, and the elucidated mechanism offers a theoretical basis for exploring microbial fermentation as a means to improve tobacco quality.

• Journal of Dairy Science and Biotechnology
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• v.7 no.1
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• pp.6-19
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• 1989

Twenty-five commercial food grade and alalytical grade lipases were used to study the patterns of release of short-chain free fatty acids (FFA) from milk fat in cheese slurries. Principal component Analysis showed that there were four distinctive groups by the FFA ratios and five groups by the FFA concentrations. However, Average Linkage Cluster Analysis showed that the patterns of FFA released were dependent upon distance defined between groups of lipases. All the lipases tested with both statistical analysis had distinctive specificities in hydrolyzing short-chain FFA from milk fat. Lipases from ruminant-animal origins produced an extremely high ratio (>40%) of butyric acid and a low ratio (<26%) of capric acid to total short chain FFA. Lipases from porcinepancreas and some microbial origins showed balanced production in both bytyric and capric acid. However, most lipases from microbial origins released a high ratio of capric acid but similar ratios to other origin enzymes for short-chain free fatty acids. Ruminant-animal origin lipases produced short-chain FFA much higher in concentration than other lipases. Lipases from porcine pancreas as well as microbial origins showed different concentrations of the fatty acids. Ratios of short-chain FFA in each sample were not significantly changed during incubation periods (4 wk), whereas concentrations of the FFA increased considerably.