• Journal of Microbiology and Biotechnology
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• v.30 no.12
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• pp.1819-1826
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• 2020

Increasing evidence suggests a potential role of microbial colonization in the inception of chronic airway diseases. However, it is not clear whether the lung and gut microbiome dysbiosis is coincidental or a result of mutual interaction. In this study, we investigated the airway microbiome in interleukin 13 (IL-13)-rich lung environment and related alterations of the gut microbiome. IL-13-overexpressing transgenic (TG) mice presented enhanced eosinophilic inflammatory responses and mucus production, together with airway hyperresponsiveness and subepithelial fibrosis. While bronchoalveolar lavage fluid and cecum samples obtained from 10-week-old IL-13 TG mice and their C57BL/6 wild-type (WT) littermates showed no significant differences in alpha diversity of lung and gut microbiome, they presented altered beta diversity in both lung and gut microbiota in the IL-13 TG mice compared to the WT mice. Lung-specific IL-13 overexpression also altered the composition of the gut as well as the lung microbiome. In particular, IL-13 TG mice showed an increased proportion of Proteobacteria and Cyanobacteria and a decreased amount of Bacteroidetes in the lungs, and depletion of Firmicutes and Proteobacteria in the gut. The patterns of polymicrobial interaction within the lung microbiota were different between WT and IL-13 TG mice. For instance, in IL-13 TG mice, lung Mesorhizobium significantly affected the alpha diversity of both lung and gut microbiomes. In summary, chronic asthma-like pathologic changes can alter the lung microbiota and affect the gut microbiome. These findings suggest that the lung-gut microbial axis might actually work in asthma.

• The Plant Pathology Journal
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• v.23 no.2
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• pp.37-44
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• 2007

Colletotrichum contains many important pathogens which cause economically significant diseases of crops like pepper, strawberry, tomato and apple. Forty four isolates were collected to characterize the diversity of Colletotrichum causing apple anthracnose in various regions of Korea. They were analyzed by random amplified polymorphic DNA (RAPD), internal transcribed spacer (ITS) of rDNA and partial $\beta$-tubulin gene DNA sequence, and culture characteristics on PDA and PDA-Benomyl. From the results of molecular analyses, 31 strains belonged to Colletotrichum gloeosporioides, ribosomal DNA group (RG) 4 of Moriwaki et al. (2002), 8 strains belonged to C. acutatum, A2 group of Talhinhas et al. (2005) and 5 strains to C. acutatum, A3 group of Talhinhas et al. (2005). Most isolates of C. gloeosporioides RG4 grew faster on PDA than strains of C. acutatum, A2 and A3 groups and most RG4 strains were sensitive to Benomyl. However, a few strains of RG4 grew slower and were resistant to Benomyl. On the basis of molecular characteristics, apple isolates of C. acutatum were clearly differentiated from red pepper isolates of the species, but apple isolates of C. gloeosporioides were not.

• Journal of Applied Biological Chemistry
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• v.56 no.2
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• pp.61-67
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• 2013

Due to their diversity and abundancy, marine resources have emerged as important biological resources to compensate the limited sources of terrestrial biological materials. Phaeodactylum tricornutum (PT) is one of classical model diatoms most widely studied for its ecology, physiology, biochemistry and molecular biology. In this study, four different PT extracts on lipopolysaccharide (LPS)-stimulated macrophages were compared for anti-inflammatory effect and investigated for the underlying mechanisms. The extracts of PT inhibited nitric oxide production from LPS stimulated RAW 264.7 cells in a dose dependent manner. These extracts also inhibited the expression of mRNA and production of proteins of pro-inflammatory cytokines such as interleukin (IL)-$1{\beta}$, IL-6 and tumor necrosis factor-${\alpha}$. These inhibitory effects were found to be caused by blockage of nuclear factor-${\kappa}B$ activation and phosphorylation of p38 mitogen-activated protein kinases, extracellular signal-regulated kinases 1 and 2 and c-Jun N-terminal kinase.

• Journal of Microbiology and Biotechnology
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• v.24 no.12
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• pp.1606-1608
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• 2014

During an investigation of the fungal diversity of Korean soils, four Penicillium strains could not be assigned to any described species. The strains formed monoverticillate conidiophores with occasionally a divaricate branch. The conidia were smooth or finely rough-walled, globose to broadly ellipsoidal and $2.5-3.5{\times}2.0-3.0{\mu}m$ size. Their taxonomic novelty was determined using partial ${\beta}$-tubulin gene sequences and the ribosomal internal transcribed spacer region. The phylogenetic analysis showed that the isolates belonged to section Lanata-Divaricata and were most closely related to Penicillium raperi. Phenotypically, the strains differed from P. raperi in having longer and thicker stipes and thicker phialides. Strain KACC $47721^T$ from bamboo field soil was designated as the type strain of the new species, and the species was named Penicillium koreense sp. nov., as it was isolated from various regions in Korea.

• Genomics & Informatics
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• v.6 no.1
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• pp.44-49
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• 2008

Protein kinase C (PKC) is a family of kinases involved in the transduction of cellular signals that promote lipid hydrolysis. PKC plays a pivotal role in mediating cellular responses to extracellular stimuli involved in proliferation, differentiation and apoptosis. Comparative analysis of the PKC-${\alpha},{\beta},{\varepsilon}$ isozymes of 200 recently sequenced microbial genomes was carried out using variety of bioinformatics tools. Diversity and evolution of PKC was determined by sequence alignment. The ser/thr protein kinases of Streptomyces coelicolor A3 (2), is the only bacteria to show sequence alignment score greater than 30% with all the three PKC isotypes in the sequence alignment. S.coelicolor is the subject of our interest because it is notable for the production of pharmaceutically useful compounds including anti-tumor agents, immunosupressants and over two-thirds of all natural antibiotics currently available. The comparative analysis of three human isotypes of PKC and Serine/threonine protein kinase of S.coelicolor was carried out and possible mechanism of action of PKC was derived. Our analysis indicates that Serine/ threonine protein kinase from S. coelicolor can be a good candidate for potent anti-tumor agent. The presence of three representative isotypes of the PKC super family in this organism helps us to understand the mechanism of PKC from evolutionary perspective.

• Biomedical Science Letters
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• v.25 no.4
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• pp.321-330
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• 2019

Carbapenem is recently considered as the last resort of the therapeutics for gram negative bacterial infection. Increasing of organisms producing metallo-β-lactamase (MBL), we have difficulty in choosing the antimicrobial agents. Among 345 clinical isolates of Pseudomonas spp., 61 isolates (17.7%) were positive for the modified imipenem or meropenem-Hodge test and 55 isolates (15.9%) were positive for the imipenem-EDTA + SMA double disk synergy test (DDS). PCR and sequencing of bla_VIM-2-allele and bla_IMP-1-allele showed that 17 isolates of Pseudomonas aeruginosa, 9 isolates of Pseudomonas taiwnensis and 2 Pseudomonas plecoglossicida had bla_VIM-2, and 22 isolates of P. aeruginosa and one Pseudomonas otitidis had bla_IMP-6. These MBL genes were all in class 1 integron. The size of class 1 integron with bla_VIM-2 ranged from 3.5 kb to 5.5 kb in clinical isolates of Pseudomonas spp. including P. aeruginosa. bla_VIM-2 was most often located first in the class 1 integron, sometimes in the second or third position, and these integrons often had aacA4 or aadA1. Strict infection control measures are needed to more effectively prevent further spread of these MBL-producing Pseudomonas spp. In addition, MBL-producing Pseudomonas spp. is expected to continue to spread in various countries and regions.

• BMB Reports
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• v.51 no.3
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• pp.143-150
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• 2018

The Hippo signaling pathway plays an essential role in adult tissue homeostasis and organ size control. Abnormal regulation of Hippo signaling can be a cause for multiple types of human cancers. Since the awareness of the importance of the Hippo signaling in a wide range of biological fields has been continually grown, it is also understood that a thorough and well-rounded comprehension of the precise dynamics could provide fundamental insights for therapeutic applications. Several components in the Hippo signaling pathway are known to be targeted for proteasomal degradation via ubiquitination by E3 ligases. ${\beta}-TrCP$ is a well-known E3 ligase of YAP/TAZ, which leads to the reduction of YAP/TAZ levels. The Hippo signaling pathway can also be inhibited by the E3 ligases (such as ITCH) which target LATS1/2 for degradation. Regulation via ubiquitination involves not only complex network of E3 ligases but also deubiquitinating enzymes (DUBs), which remove ubiquitin from its targets. Interestingly, non-degradative ubiquitin modifications are also known to play important roles in the regulation of Hippo signaling. Although there has been much advanced progress in the investigation of ubiquitin modifications acting as regulators of the Hippo signaling pathway, research done to date still remains inadequate due to the sheer complexity and diversity of the subject. Herein, we review and discuss recent developments that implicate ubiquitin-mediated regulatory mechanisms at multiple steps of the Hippo signaling pathway.

• Journal of Environmental Science International
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• v.11 no.3
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• pp.149-154
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• 2002

This study was conducted to find the structure of phytoplankton community in the Hoeya river(Ulsan) from March 2000 to February 2001. The taxa of phytoplankton identified included 135 species, 5 divisions, 33 families and 82 genera. Among them, chrysophyta(diatoms) were 63 species(46.7%), chlorophyta(green algae) 47 species(34.8%), pyrrophyta(dinoflagellates) 13 species(9.6%), cyanophyta (cyanobacteria) 8 species(5.9%) and euglenophyta(euglenoids) 4 species(3.0%) respectively. Ecological important species is called frequently appearing species, red tide causative species, seawater species and pollution indicator. 22 species including Aulacoseira granulate were recorded frequently appearing species. 19 species including Ceratium furca were recorded as red tide causing species. And the pollution indicators were 33 species including Actinastrum hantzschii var. fluviatile. The highest standing crops were 3,103,441 cells/$\ell$ in August at the RW-1 and the lowest 1,245 cells/ $\ell$ in January at the RW-5. In the community analysis, the dominanance indices ranged from 0.34(October, RW-2) to 0.94(January, RW-1) and the diversity indices from 0.50(May, RW-2) to 2.57(September, RW-2). The saprobic indices were 2.43 in RW-1, 2.41 in RW-2, 2.375 in RW-3, 2.40 in RW-4, 2.43, in RW-5. Therefore, these areas were investigated "$\beta$-mesosaprobic". According to the similarity index among the stations, these areas were defined as residential district areas(RW-2 and RW-3), lower part of the dam (RW-1) and seawater areas(RW-4 and RW-5).

• Journal of Communications and Networks
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• v.11 no.3
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• pp.240-247
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• 2009

The results of performance analysis by adopting the channel scenarios characterized as Weibull fading for an multicarrierdirect sequence-coded division multiple access (MC-DS-CDMA) system are proposed in this investigation. On the other hand, an approximate simple expression with the criterion of bit error rate (BER) versus signal-to-noise ratio (SNR) method is derived for an MC-DS-CDMA system combining with maximal ratio combining (MRC) diversity based on the moment generating function (MGF) formula of Weibull statistics, and it associates with an alternative expression of Gaussian Q-function. Besides, the other point of view on the BER performance evaluation of an MC-DS-CDMA system is not only the assumption of both single-user and multi-user cases applied, but the phenomena of partial band interference (PBI) is also included. Moreover, in order to validate the accuracy in the derived formulas, some of the system parameters, such as Weibull fading parameter (${\beta}$), user number (K), spreading chip number (N), branch number (L), and the PBI (JSR) values, etc., are compared with each other in the numerical results. To the best of author's knowledge, it is a brand new idea which proposes the evaluation of the system performance for an MC-DS-CDMA system over the point of view with Weibull fading channel.

• Journal of Ecology and Environment
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• v.41 no.9
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• pp.271-280
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• 2017

Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, ${\beta}$-1,4-glucosidase, cellobiohydrolase, ${\beta}$-1,4-xylosidase, ${\beta}$-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was $125.9({\pm}5.7({\pm}1SE))$, $30.9({\pm}0.9)$, $15.7({\pm}0.6)$, $6.7({\pm}0.9)$, and $3.3({\pm}0.3)nmol\;g^{-1}\;h^{-1}$ at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1, and 17.5% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3, and 0.4% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.