• Korean Journal of Microbiology
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• v.33 no.4
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• pp.257-261
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• 1997

To scrutinize the bacterial community composition of Lake Soyang in winter, bacterial numbers belonging to Eubacteria, Proteobacteria and Cytophaga-Flavobacterium group were estimated by using 16S and 23S rRNA targeted oligonucleotide probes. Total bacterial numbers ranged from $0.7{\times}10^6$ to $1.1{\times}10^6cells{\cdot}ml^{-1}$, and vertical profile of total bacteria showed a peak at 5 m depth. The ratio of eubacteria to total bacteria were 34~90% and at 5 m and 10 m depths those were low exhibiting, 39 and 34%, respectively. The percentage of proteobacteria ${\alpha}$-group ranged 10.8~28.7%, ${\beta}$-group 4.5~53.5%, ${\gamma}$-group 4.9~35.5% and Cytophaga-Flavobacterium group 6.1~21.1%. The dominant groups were ${\beta}$-group at 0, 2 and 5 m, ${\gamma}$-group at 10 m, ${\alpha}$-group at 30 m and Cytophaga-Flavobacterium group at 50 m depth. In winter season, Lake Soyang can be divided into three layer, 0~2 m, 5~10 m and 30~50 m, by the bacteria community composition. By this method, new informations about aquatic ecosystem were developed.

• Experimental and Molecular Medicine
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• v.50 no.12
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• pp.13.1-13.12
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• 2018

We aimed to explore whether changes in circulating levels of miRNAs according to type 2 diabetes mellitus (T2DM) or prediabetes status could be used as biomarkers to evaluate the risk of developing the disease. The study included 462 patients without T2DM at baseline from the CORDIOPREV trial. After a median follow-up of 60 months, 107 of the subjects developed T2DM, 30 developed prediabetes, 223 maintained prediabetes and 78 remained disease-free. Plasma levels of four miRNAs related to insulin signaling and beta-cell function were measured by RT-PCR. We analyzed the relationship between miRNAs levels and insulin signaling and release indexes at baseline and after the follow-up period. The risk of developing disease based on tertiles (T1-T2-T3) of baseline miRNAs levels was evaluated by COX analysis. Thus, we observed higher miR-150 and miR-30a-5p and lower miR-15a and miR-375 baseline levels in subjects with T2DM than in disease-free subjects. Patients with high miR-150 and miR-30a-5p baseline levels had lower disposition index (p = 0.047 and p = 0.007, respectively). The higher risk of disease was associated with high levels (T3) of miR-150 and miR-30a-5p ($HR_{T3-T1}=4.218$ and $HR_{T3-T1}=2.527$, respectively) and low levels (T1) of miR-15a and miR-375 ($HR_{T1-T3}=3.269$ and $HR_{T1-T3}=1.604$, respectively). In conclusion, our study showed that deregulated plasma levels of miR-150, miR-30a-5p, miR-15a, and miR-375 were observed years before the onset of T2DM and pre-DM and could be used to evaluate the risk of developing the disease, which may improve prediction and prevention among individuals at high risk for T2DM.

• Parasites, Hosts and Diseases
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• v.57 no.4
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• pp.341-357
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• 2019

Acanthamoeba, one of free-living amoebae (FLA), remains a high risk of direct contact with this protozoan parasite which is ubiquitous in nature and man-made environment. This pathogenic FLA can cause sight-threatening amoebic keratitis (AK) and fatal granulomatous amoebic encephalitis (GAE) though these cases may not commonly be reported in our clinical settings. Acanthamoeba has been detected from different environmental sources namely; soil, water, hotspring, swimming pool, air-conditioner, or contact lens storage cases. The identification of Acanthamoeba is based on morphological appearance and molecular techniques using PCR and DNA sequencing for clinico-epidemiological purposes. Recent treatments have long been ineffective against Acanthamoeba cyst, novel anti-Acanthamoeba agents have therefore been extensively investigated. There are efforts to utilize synthetic chemicals, lead compounds from medicinal plant extracts, and animal products to combat Acanthamoeba infection. Applied nanotechnology, an advanced technology, has shown to enhance the anti-Acanthamoeba activity in the encapsulated nanoparticles leading to new therapeutic options. This review attempts to provide an overview of the available data and studies on the occurrence of pathogenic Acanthamoeba among the Association of Southeast Asian Nations (ASEAN) members with the aim of identifying some potential contributing factors such as distribution, demographic profile of the patients, possible source of the parasite, mode of transmission and treatment. Further, this review attempts to provide future direction for prevention and control of the Acanthamoeba infection.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1409-1419
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• 2021

A growing number of healthy dietary ingredients in fruits and vegetables have been shown to exhibit diverse biological activities. Phloretin, a dihydrochalcone flavonoid that is abundant in apples and pears, has anti-inflammatory effects on ulcerative colitis (UC) mice. The gut microbiota and metabolism are closely related to each other due to the existence of the food-gut axis in the human colon. To investigate the interplay of faecal metabolites and the microbiota in UC mice after phloretin treatment, phloretin (60 mg/kg) was administered by gavage to ameliorate dextran sulfate sodium (DSS)-induced UC in mice. Gut microbes and faecal metabolite profiles were detected by high-throughput sequencing and liquid chromatography mass spectrometry (LC-MS) analysis, respectively. The correlations between gut microbes and their metabolites were evaluated by Spearman correlation coefficients. The results indicated that phloretin reshaped the disturbed faecal metabolite profile in UC mice and improved the metabolic pathways by balancing the composition of faecal metabolites such as norepinephrine, mesalazine, tyrosine, 5-acetyl-2,4-dimethyloxazole, and 6-acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone. Correlation analysis identified the relations between the gut microbes and their metabolites. Proteus was negatively related to many faecal metabolites, such as norepinephrine, L-tyrosine, laccarin, dopamine glucuronide, and 5-acetyl-2,4-dimethyloxazole. The abundance of unidentified Bacteriodales_S24-7_group was positively related to ecgonine, 15-KETE and 6-acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone. The abundance of Christensenellaceae_R-7_group was negatively related to the levels of 15-KETE and netilmicin. Stenotrophomonas and 15-KETE were negatively related, while Intestinimonas and alanyl-serine were positively related. In conclusion, phloretin treatment had positive impacts on faecal metabolites in UC mice, and the changes in faecal metabolites were closely related to the gut microbiota.

• BMB Reports
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• v.55 no.9
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• pp.465-471
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• 2022

Understanding and monitoring virus-mediated infections has gained importance since the global outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Studies of high-throughput omics-based immune profiling of COVID-19 patients can help manage the current pandemic and future virus-mediated pandemics. Although COVID-19 is being studied since past 2 years, detailed mechanisms of the initial induction of dynamic immune responses or the molecular mechanisms that characterize disease progression remains unclear. This study involved comprehensively collected biospecimens and longitudinal multi-omics data of 300 COVID-19 patients and 120 healthy controls, including whole genome sequencing (WGS), single-cell RNA sequencing combined with T cell receptor (TCR) and B cell receptor (BCR) sequencing (scRNA(+scTCR/BCR)-seq), bulk BCR and TCR sequencing (bulk TCR/BCR-seq), and cytokine profiling. Clinical data were also collected from hospitalized COVID-19 patients, and HLA typing, laboratory characteristics, and COVID-19 viral genome sequencing were performed during the initial diagnosis. The entire set of biospecimens and multi-omics data generated in this project can be accessed by researchers from the National Biobank of Korea with prior approval. This distribution of large-scale multi-omics data of COVID-19 patients can facilitate the understanding of biological crosstalk involved in COVID-19 infection and contribute to the development of potential methodologies for its diagnosis and treatment.

• Molecules and Cells
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• v.24 no.3
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• pp.343-350
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• 2007

Mesenchymal stem/progenitor cells (MPCs) were isolated from porcine umbilical cord blood (UCB) and their morphology, proliferation, cell cycle status, cell-surface antigen profile and expression of hematopoietic cytokines were characterized. Their capacity to differentiate in vitro into osteocytes, adipocytes and chondrocytes was also evaluated. Primary cultures of adherent porcine MPCs (pMPCs) exhibited a typical fibroblast-like morphology with significant renewal capacity and proliferative ability. Subsequent robust cell growth was indicated by the high percentage of quiescent (G0/G1) cells. The cells expressed the mesenchymal surface markers, CD29, CD49b and CD105, but not the hematopoietic markers, CD45 and CD133 and synthesized hematopoietic cytokines. Over 21 days of induction, the cells differentiated into osteocytes adipocytes and chondrocytes. The expression of lineage specific genes was gradually upregulated during osteogenesis, adipogenesis and chondrogenesis. We conclude that porcine umbilical cord blood contains a population of MPCs capable of self-renewal and of differentiating in vitro into three classical mesenchymal lineages.

• Journal of KIISE:Software and Applications
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• v.35 no.6
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• pp.347-356
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• 2008

High-throughput microarray is one of the most popular tools in molecular biology, and various computational methods have been developed for the microarray data analysis. While the computational methods easily extract significant features, it suffers from inferring modules of multiple co-regulated genes. Hypernetworhs are motivated by biological networks, which handle all elements based on their combinatorial processes. Hence, the hypernetworks can naturally analyze the biological effects of gene combinations. In this paper, we introduce a hypernetwork classifier for microRNA (miRNA) profile analysis based on microarray data. The hypernetwork classifier uses miRNA pairs as elements, and an evolutionary learning is performed to model the microarray profiles. miTNA modules are easily extracted from the hypernetworks, and users can directly evaluate if the miRNA modules are significant. For experimental results, the hypernetwork classifier showed 91.46% accuracy for miRNA expression profiles on multiple human canters, which outperformed other machine learning methods. The hypernetwork-based analysis showed that our approach could find biologically significant miRNA modules.

• Molecules and Cells
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• v.38 no.9
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• pp.765-772
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• 2015

Saussurea lappa has been reported to possess anti-atopic properties. In this study, we have confirmed the S. lappa's anti-atopic properties in Nc/Nga mice and investigated the candidate gene related with its properties using microarray. We determined the target gene using real time PCR in in vitro experiment. S. lappa showed the significant reduction in atoptic dermatitis (AD) score and immunoglobulin E compared with the AD induced Nc/Nga mice. In the results of microarray using back skin obtained from animals, we found that S. lappa's properties are closely associated with cytokine-cytokine receptor interaction and the JAK-STAT signaling pathway. Consistent with the microarray data, real-time RT-PCR confirmed these modulation at the mRNA level in skin tissues from S. lappa-treated mice. Among these genes, PI3Kca and $IL20R{\beta}$ were significantly downregulated by S. lappa treatment in Nc/Nga mouse model. In in vitro experiment using HaCaT cells, we found that the S. lappa components, including alantolactone, caryophyllene, costic acid, costunolide and dehydrocostus lactone significantly decreased the expression of PI3Kca but not $IL20R{\beta}$ in vitro. Therefore, our study suggests that PI3Kca-related signaling is closely related with the protective effects of S. lappa against the development of atopic-dermatitis.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.10
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• pp.1481-1492
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• 2012

The interaction of the genes involved in intestinal development is the molecular basis of the regulatory mechanisms of intestinal development. The objective of this study was to identify the significant pathways and key genes that regulate intestinal development in Landrace piglets, and elucidate their rules of operation. The differential expression of genes related to intestinal development during suckling time was investigated using a porcine genome array. Time sequence profiles were analyzed for the differentially expressed genes to obtain significant expression profiles. Subsequently, the most significant profiles were assayed using Gene Ontology categories, pathway analysis, network analysis, and analysis of gene co-expression to unveil the main biological processes, the significant pathways, and the effective genes, respectively. In addition, quantitative real-time PCR was carried out to verify the reliability of the results of the analysis of the array. The results showed that more than 8000 differential expression transcripts were identified using microarray technology. Among the 30 significant obtained model profiles, profiles 66 and 13 were the most significant. Analysis of profiles 66 and 13 indicated that they were mainly involved in immunity, metabolism, and cell division or proliferation. Among the most effective genes in these two profiles, CN161469, which is similar to methylcrotonoyl-Coenzyme A carboxylase 2 (beta), and U89949.1, which encodes a folate binding protein, had a crucial influence on the co-expression network.

• Journal of the Korean Crystal Growth and Crystal Technology
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• v.17 no.6
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• pp.256-263
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• 2007

For $P_B=50Torr,\;P_T=5401Torr,\;T_S=450^{\circ}C,\;{\Delta}T=20K$, Ar=5, Pr=3.34, Le=0.01, Pe=4.16, Cv=1.05, adiabatic and linear thermal profiles at walls, the intensity of solutal convection (solutal Grashof number $Grs=7.86{\times}10^6$) is greater than that of thermal convection (thermal Grashof number $Grt=4.83{\times}10^5$) by one order of magnitude, which is based on the solutally buoyancy-driven convection due to the disparity in the molecular weights of the component A ($Hg_2Cl_2$) and B (He). With increasing the partial pressure of component B from 20 up to 800 Torr, the rate is decreased exponentially. It is also interesting that as the partial pressure of component B is increased by a factor of 2, the rate is approximately reduced by a half. For systems under consideration, the rate increases linearly and directly with the dimensionless Peclet number which reflects the intensity of condensation and sublimation at the crystal and source region. The convective transport decreases with lower g level and is changed to the diffusive mode at $0.1g_0$. In other words, for regions in which the g level is $0.1g_0$ or less, the diffusion-driven convection results in a parabolic velocity profile and a recirculating cell is not likely to occur. Therefore a gravitational acceleration level of less than $0.1g_0$ can be adequate to ensure purely diffusive transport.