• Genomics & Informatics
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• v.21 no.2
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• pp.21.1-21.14
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• 2023

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

• Journal of Physiology & Pathology in Korean Medicine
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• v.17 no.2
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• pp.529-541
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• 2003

Yukmijihwang-tang has been widely used as an and-aging herbal medicine for hundred years in Asian countries. Numerous studies show that Yukmijihwangtang has anti-oxidative effect both in vivo and in vitro. It has been reported that Moutan Cortex Radicis extract (MCR) was the most effective herb in Yukmijihwang-tang on undifferentiated PC12 cells upon oxidative-stressed with hydrogen peroxide. The purpose of this study is to; 1) evaluate the recovery of neuronal damage by assessing the anti-oxidant effect of MCR on PC12 cells differentiated with nerve growth factor (NGF), 2) identify candidate genes responsible for anti-oxidative effect on differentiated PC12 cells by oligonucleotide chip microarray. PC12 cells, which were differentiated by treating with NGF, were treated without or with hydrogen peroxide in the presence or absence of various concentration of MCR. Cell survival was determined by using MTS assay. Measurement of intracellular reactive oxygen species (ROS) generation was determined using the H2DCFDA assay The viability of cells treated with MCR was significantly recovered from stressed PC12 cell. In addition, wide rage of concentrations of MCR shows dose-dependent inhibitory effect on ROS production in oxidative-stressed cells. Total RNAs of cells without treatment(Control group), only treated with H₂O₂ (stressed group) and treated with both H₂O₂ and of MCR (MCR group) were isolated, and cDNAs was synthesized using oligoT7(dT) primer. The fragmented cRNAs, synthesized from cDNAs, were applied to Affymetrix GeneChip Rat Neurobiology U34 Array. mRNA of Calcium/calmodulin-dependent protein kinase II delta subunit(CaMKII), neuron glucose transporter (GLUT3) and myelin/oligodendrocyte glycoprotein(MOG) were downregulated in Stressed group comparing to Control group. P2X2-5 receptor (P2X2R-5), P2X2-4 receptor (P2X2R-4), c-fos, 25 kDa synaptosomal attachment protein(SNAP-25a) and GLUT3 were downregulated, whereas A2 adenosine receptor (A2AR), cathechol-O-methyltransferase(COMT), glucose transporter 1 (GLUT1), EST223333, heme oxygenase (HO), VGF, UI-R-CO-ja-a-07-0-Ul.s1 and macrophage migration inhibitory factor (MIF) were upregulated in MCA group comparing to Control group. Expression of Putative potassium channel subunit protein (ACK4), P2X2A-5, P2X2A-4, Interferon-gamma inducing factor isoform alpha precursor (IL-18α), EST199031, P2XR, P2X2 purinoceptor isoform e (P2X2R-e), Precursor interleukin 18 (IL-18) were downregulated, whereas MOO, EST223333, GLUT-1, MIF, Neuronatin alpha, UI-R-C0-ja-a-07-0-Ul.s1, A2. adenosine receptor, COMT, neuron-specific enolase (NSE), HO, VGF, A rat novel protein which is expressed with nerve injury (E12625) were upregulated in MCR group comparing to Stressed group. The results suggest that decreased viability and AOS production of PC12 cell by H₂O₂ may be, at lease, mediated by impaired glucose transporter expression. It is implicated that the MCR treatment protect PC12 cell from oxidative stress via following mechanisms; improving glucose transport into the cell, enhancing expression of anti-oxidative genes and protecting from dopamine cytotoxicity by increment of COMT and MIF expression. The list of differentially expressed genes may implicate further insight on the action and mechanism behind the anti-oxidative effects of herbal extract Moutan Cortex Radicis.

• Journal of Life Science
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• v.27 no.10
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• pp.1111-1120
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• 2017

This study was conducted to select pepper lines that were tolerant to excessive water injury among the pepper germplasm and investigate the genetic characteristics of those lines to contribute to the breeding of pepper cultivars with stable productivity in abnormal weather. Each of the tolerant and susceptible lines went through immersion treatment, and differentially expressed genes between them were analyzed. The tolerant line showed increased expression of the CA02g26670 gene, which is involved in the CONSTANS protein pathway and regulation of flowering by day length, but it exhibited decreased expressions of CA01g21450, CA01g22480, CA01g34470, CA02g00370 and CA02g00380. The susceptible line showed increased gene expressions of CA02g09720, CA02g21290, CA03g16520, CA07g 02110, and CA12g17910, which are involved in the inhibition of proteolytic enzyme activity, DNA binding, inhibition of cell wall-degrading enzyme, and inhibition of nodulin, respectively. Meanwhile the expressions of CA02g02820, CA03g21390, CA06g17700 and CA07g18230 decreased in the susceptible line, in relation to calcium-ion binding, high temperature, synthesis of phosphocholine and cold stress, respectively. The expressions of genes related to apoptosis and peroxidase increased, while that of CA02g16990, which functions as a nucleoside transporter, decreased in both the tolerant and susceptible lines. Based on the different gene expressions between the tolerant and susceptible lines, further studies are needed on breeding abiotic stress-tolerant lines.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.56 no.3
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• pp.264-272
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• 2011

It needs to develop high phosphate-available rice that is able to minimize environmental pollution caused by phosphate fertilizer. Then we have transformed 4 rice transporter genes, OsPT(Oryza sativa Phosphate Transporter)1, OsPT4, OsPT7 or OsPT8, to rice (Oryza sativa cv. Dongjin) via Agrobacterium-mediated transformation. We tested adaptation in the P-deficient condition of Dongjin (parental) and each transgenic line in the pot and the field conditions. Definite physiological changes have been observed in OsPTs transgenic lines including culm length, root formation and heading date. Phosphate uptake at harvesting stage was about three times higher in OsPT1-OX (overexpression) and OsPT4-OX than in Dongjin (wt) without P application. There are no variations in total phosphate-content of brown rice of OsPT1-OX in spite of high phosphate uptake. Practically the expression of OsPT1 has contributed to stabilize grain production without P fertilization in rice cultivation than Dongjin.

• Journal of Physiology & Pathology in Korean Medicine
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• v.18 no.4
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• pp.1041-1054
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• 2004

Electroacupuncture (EA) has been reported to increase pain threshold, and to enhance the NK cell activity by up-regulation of IFN-γ and endogenous β-endolphin. For the purpose of understanding the molecular mechanism of EA stimulation, we analyzed the gene expression profile of rat hypothalamus, treated on Zusanli (ST36) with EA, in comparison with control group by oligonucleotide chip microarray (Affymetrix GeneChip Rat Neurobiology U34 Array) and real-time RT-PCR. Sprague-Dawley (S-D) male rats were stimulated at the Zusanli (ST36) acupoint in restriction holder. Simultaneously the control group was given only holder stress without EA stimulation. In order to prove the appropriateness of EA treatment, we measured spleen NK cell activity with standard 51Cr release assay. NK cell activity of EA group was significantly increased comparing to control group. The microarray and PCR results show that EA treatment up-regulates expression of genes associated with 1) nerve growth such as NGF induced factor A and VGF, 2) signal transduction such as 5HT3 receptor subunit, AMPA receptor binding protein and Na-dependent neurotransmitter transporter, and 3) anti-oxidation such as superoxide dismutase and glutathione S-transferase. In addition, the activity of the anti-oxidative enzyme, SOD of hypothalamus, liver and RBC was enhanced compared to that of control. The list of differentially expressed genes may implicate further insight on the mechanism of acupuncture effects.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.534-539
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• 2010

'Hongro' is early-mid maturing cultivar with good quality like 'Tsugaru' and it has not preharvest drop. The CAX1 gene was introduced into Korean apple cultivar 'Hongro' by Agrobacterium tumefaciens LBA4404 harboring pBI121 to obtain transgenic apple with enhanced Ca level. The CAX1 gene playing the role of $H^+/Ca^{2+}$ transporter from Arabidopsis thaliana increases Ca concentration in several plants. Regenerated transgenic lines were confirmed by polymerase chain reaction (PCR) analysis and Southern blot analysis of genomic DNA for the existence of CAX1 gene. Southern blot analysis of 'Hongro' transformants showed that two putative transgenic lines were integrated with CAX1 gene in genomic DNA. The CAX1 comparative expression levels of two transgenic lines were higher than that of non-transformant evaluated by comparative quantification analysis using a real-time PCR. These two lines were multiplied in vitro, and micro-grafted on apple rootstocks 'M.9' in the isolated greenhouse. Since two years after micro-grafting, the fruits came into bearing. Compared to Ca level of the non-transgenic 'Hongro', that of the CAX1 transgenic 'Hongro' in the flesh and leaves was higher.

• Journal of Korean Medicine for Obesity Research
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• v.22 no.2
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• pp.93-101
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• 2022

Objectives: This study aimed to observe the anti-diabetic effect and underlying mechanisms of Galgunhwanggumhwangryun-tang (GHH; Gegen-Qinlian-decoction) in the C2C12 myotubes. Methods: GHH (1.0 mg/ml) or metformin (0.75 mM) or insulin (100 nM) were treated in C2C12 myotubes after 4 days differentiation. The glucose uptake was assessed by 2-[N-(7-160 nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-d-glucose uptake by C2C12 cells. The expression of adenosine monophosphate-activated protein kinase (AMPK) and phosphorylation AMPK (pAMPK) were measured by western blot. We also evaluated gene expression of glucose transporter type 4 (Slc2a4, formerly known as GLUT4), glucokinase (Gk), carnitine palmitoyltransferase IA (Cpt1a), nuclear respiratory factors 1 (Nrf1), mitochondrial transcription factor A (Tfam), and peroxisome proliferator-activated receptor γ coactivator 1α (Ppargc1a) by quantitative real-time polymerase chain reaction. Results: GHH promoted glucose uptake in C2C12 myotubes. The expression of AMPK protein, which plays an essential role in glucose metabolism, was increased by treatment with GHH. GHH treatment tended to increase gene expression of Slc2a4, Gk, and Nrf1 but was not statistically significant. However, GHH significantly improved Tfam and Ppargc1a gene expression in C2C12 myotubes. Conclusions: In summary, GHH treatment promoted glucose uptake in C2C12 myotubes. We suggest that these effects are associated with increased gene expression involved in mitochondrial biosynthesis and oxidative phosphorylation, such as Tfam and Ppargc1a, and increased expression of AMPK protein.

• Journal of Microbiology and Biotechnology
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• v.23 no.5
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• pp.637-643
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• 2013

We have demonstrated that 1-deoxynojirimycin (DNJ) isolated from Bacillus subtilis MORI could enhance the levels of adiponectin and its receptors in differentiated 3T3-L1 adipocytes, which has been shown to be effective in lowering blood glucose levels and enhancing insulin sensitivity. DNJ was not toxic to differentiated 3T3-L1 adipocytes for up to a concentration of $5{\mu}M$. In terms of expression levels of adiponectin and its receptors (AdipoR1 and AdipoR2), DNJ in concentrations as low as $0.5{\mu}M$ elevated both mRNA and protein levels of adiponectin and transcript levels of AdipoR1 and AdipoR2. In addition, DNJ increased phosphorylation of 5' adenosine monophosphate-activated protein kinase (AMPK) in a statistically significant manner. Finally, treatment with DNJ resulted in increased mRNA expression of glucose transporter 4 (GLUT4), which encodes for a glucose transporter, along with a significant increase in glucose uptake into the adipocytes based on results of a 2-deoxy-D-[$^3H$] glucose uptake assay. Our findings indicate that DNJ may greatly facilitate glucose uptake into adipose tissues by increasing the action of adiponectin via its up-regulated expression as well as its receptor genes. In addition, the glucose-lowering effects of DNJ may be achieved by an increased abundance of GLUT4 protein in the plasma membrane, as a consequence of the increased transcript levels of the GLUT4 gene and the activation of AMPK.

• Journal of Life Science
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• v.26 no.9
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• pp.1027-1032
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• 2016

Antigen is substance causing disease derived from pathogen. Living organism has the immune system in terms of defense mechanism against antigen. Antigen is processed through several pathways such as phagocytosis, antibody action, complement activation, and cytotoxins by NK or cytotoxic T lymphocyte via MHC molecule. Lymph node (LN) is comprised of the complicated 3 dimensional network and several stromal cells. Fibroblastic reticular cells (FRC) are distributed in T zone for interaction with T cells. FRC produces the extra cellular matrix (ECM) into LN for ECM reorganization against pathogen infections and secretes homing chemokines. However, it has not so much been known about the involvement of the antigen process of FRC. The present report is for the function of FRC on antigen process. For this, FRC was positioned with several infected situations such as co-culture with macrophage, T cell, lipopolysaccharide (LPS) and TNFα stimulation. When co-culture between FRC with macrophage and T cells was performed, morphological change of FRC was observed and empty space between FRCs was made by morphological change. The matrix metallo-proteinase (MMP) activity was up-regulated by Y27632 and T cells onto FRC. Furthermore, inflammatory cytokine, TNFα regulated the expression of adhesion molecules and MHC I antigen transporter in FRC by gene chip assay. NO production was elevated by FRC monolayer co-cultured with macrophage stimulated by LPS. GFP antigen was up-taken by macrophage co-cultured with FRC. Collectively, it suggests that FRC assists of the facilitation of antigen process and LN stroma is implicated into antigen process pathway.

• Ecology and Resilient Infrastructure
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• v.8 no.3
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• pp.135-142
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• 2021

Biopolymers have been known as eco-friendly soil strengthening materials and studied to apply levees. However, the effect of biopolymer on vegetation is not fully understood. In this study, we analyzed the root growth of Camelina sativa L. (Camelina) when the xanthan gum was amended to soil in Aluminum (Al) stress conditions. Amendment of 0.05% xanthan gum increased root growth of Camelina under Al stress conditions. Under the Al stress condition, expression of aluminum activate malate transporter 1 (ALMT1) gene of Camelina root was induced but showed a lower level of expression in xanthan gum amended soil than non-amended soil. Additionally, the binding capacity of xanthan gum with Al ions in the solution was confirmed. Using morin staining and ICP-OES analysis, the Al content of the roots in the xanthan gum soil was lower than in the non-xanthan gum soil. These results suggest that xanthan gum amended soils may reduce the detrimental effects of Al on the roots and positively affect the growth of plants. Therefore, xanthan gum is not only an eco-friendly construction material but also can protect the roots in the disadvantageous environment of the plant.