• 제목/요약/키워드: Differential expression analysis

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Analysis of pile load distribution and ground behaviour depending on vertical offset between pile tip and tunnel crown in sand through laboratory model test (실내모형시험을 통한 사질토 지반에서 군말뚝과 터널의 수직 이격거리에 따른 하중분포 및 지반거동 분석)

  • Oh, Dong-Wook;Lee, Yong-Joo
    • Journal of Korean Tunnelling and Underground Space Association
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    • v.19 no.3
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    • pp.355-373
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    • 2017
  • Tunnelling in urban areas, it is essential to understand existing structure-tunnel interactive behavior. Serviced structures in the city are supported by pile foundation, since they are certainly effected due to tunnelling. In this research, thus, pile load distribution and ground behavior due to tunnelling below grouped pile were investigated using laboratory model test. Grouped pile foundations were considered as 2, 3 row pile and offsets (between pile tip and tunnel crown: 0.5D, 1.0D and 1.5D for generalization to tunnel diameter, D means tunnel diameter). Soil in the tank for laboratory model test was formed by loose sand (relative density: Dr = 30%) and strain gauges were attached to the pile inner shaft to estimate distribution of axial force. Also, settlements of grouped pile and adjacent ground surface depending on the offsets were measured by LVDT and dial gauge, respectively. Tunnelling-induced deformation of underground was measured by close range photogrammetric technique. Numerical analysis was conducted to analyze and compare with results from laboratory model test and close range photogrammetry. For expression of tunnel excavation, the concept of volume loss was applied in this study, it was 1.5%. As a result from this study, far offset, the smaller reduction of pile axial load and was appeared trend of settlement was similar among them. Particulary, ratio of pile load and settlement reduction were larger when the offset is from 0.5D to 1.0D than from 1.0D to 1.5D.

Feeding Effect of an Anabolic Steroid, Nandrolone, on the Male Rat Testis

  • Lee, Dong-Mok;Min, Tae-Sun;Choi, In-Ho;Cheon, Yong-Pil;Chun, Tae-Hoon;Park, Chang-Sik;Lee, Ki-Ho
    • Asian-Australasian Journal of Animal Sciences
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    • v.23 no.12
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    • pp.1566-1577
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    • 2010
  • Nandrolone, 19-nortestosterone, is a synthetic androgenic-anabolic steroid promoting muscle growth. Nandrolone is also present in pig meat and sera at non-negligible levels. A number of scientific reports have suggested a positive relationship between incidence of infertility and increased meat consumption in humans. The present study was designed to determine out the effect of feeding nandrolone on the testis of the male reproductive tract. Mixtures of food and nandrolone at different concentrations (0.005 ppm and 0.5 ppm) were supplied to pubertal male rats for 6 weeks. Body weight was recorded every week during the entire experimental period. At the end of the treatment, the testis, epididymis, and epididymal fat were collected and weighted. Sperm numbers in the caudal epididymis were counted. Differential gene or protein expression of steroidogenic enzymes in the testes among experimental groups was determined by semi-quantitative real-time PCR or western blotting analysis, respectively. Histological changes of the testis induced by nandrolone treatment were examined by hematoxylin and eosin staining. Immunohistochemical analysis was employed to detect changes in the localization of steroidogenic enzymes in the testes among experimental animals. There were no significant changes on body, testis, epididymis, and epididymal fat weights among experimental groups. A significant increase of caudal sperm number was found in the 0.5 ppm nandrolone-treated group. Histological examination of the testes noted a high frequency of germ cell sloughing in seminiferous tubules of 0.5 ppm nandrolone-treated rats. Even though transcript levels of $3{\beta}$-hydroxysteroid dehydrogenase (HSD) I, $17{\beta}$-HSD4, and $17{\alpha}$-hydroxylase were influenced by nandrolone treatments, protein levels of all molecules examined in the present study were not significantly affected. Immunohistochemical analysis showed no visible changes in the localization of steroidogenic enzymes in the testes among experimental groups. The current study showed that oral intake of nandrolone in male rats for 6 weeks did not cause significant damage to the testis. It is considered that a feeding effect of nandrolone on male fertility would not be remarkable.

Improvement effect of cooked soybeans on HFD-deteriorated large intestinal health in rat model (쥐 모델에서 고지방사료로 악화된 대장 건강에 대한 콩의 개선 효과)

  • Choi, Jae Ho;Shin, Taekyun;Ryu, Myeong Seon;Yang, Hee-Jong;Jeong, Do-Youn;Unno, Tatsuya
    • Journal of Applied Biological Chemistry
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    • v.64 no.4
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    • pp.383-389
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    • 2021
  • Obesity is associated with impaired intestinal epithelial barrier function, which contribute to host systemic inflammation and metabolic dysfunction. Korean traditional foods, fiber-rich bean products, have been various biological activities in anti-inflammatory responses, but has not reported the large intestinal health. In this study, we investigated the intestinal health promoting effect of cooked soybeans (CSB) on high fat diet (HFD)-induced obesity model. SD rat were fed either a HFD or HFD supplemented with 10.6% CSB (HFD+CSB) for animal experimental period. CSB treatment significantly decreased the HFD-induced weights of body and fat. Also, CSB treatment improved HFD-reduced tight junction components (ZO-1, Claudin-1, and Occludin-1) mRNA expression in large intestine tissue. Additionally, histopathological evaluation showed that CSB treatment attenuated the HFD-increased inflammatory cells infiltration and epithelial damages in large intestine tissue. At the genus level, effects of CSB supplement not yet clear, while dietary effects showed differential abundance of several genera including Lactobacillus, Duncaniella, and Alloprevotella. NMDS analysis showed significant microbial shifts by HFD, while CSB did not shift gut microbiota. CSB increased the abundance of the genera Anaerotignum, Enterococcus, Clostridium sensu stricto, and Escherichia/Shigella by linear discriminant analysis effect size analysis, while reduced the abundance of Longicatena and Ligilactobacillus. These findings indicate that CSB supplement improves HFD-deteriorated large intestinal health by the amelioration of tight junction component, while CSB did not shift gut microbiotas.

Effect of Carthami Tinctorii Fructus Herbal-acupuncture Solution(CTF-HAS) on Gene Expression in HepG2 carcinomar cells (Oligonucleotide chip를 이용한 홍화자약침액(紅花子藥鍼液)이 간암세포주(肝癌細胞柱)의 유전자(遺傳子) 발현(發顯)에 미치는 영향(影響))

  • Lee, Kyung-min;Lim, Seong-chul;Jung, Tae-young;Seo, Jung-chul;Han, Sang-won
    • Journal of Acupuncture Research
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    • v.22 no.3
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    • pp.215-225
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    • 2005
  • Objective : It has long been known about the osteogenic effect of CTF-HAS on bone tissues. However, it has not been determined the effect of CTF-HAS on cancer cells. The purpose of this study is to screen the CTF-HAS mediated differentially expressed genes in cancer cells such as HepG2 hepatoma cells lines. Oligonucleotide microarray approach were employed to screen the differential expression genes. Methods : CTF-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of CTF-HAS(0.1, 0.5, 1.5, 10, $20mg/m{\ell}$) for 24 h. Cytotoxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with $1.5mg/m{\ell}$ of CTF-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide genechip (Human genome U133 Plus 2.0., Affimatrix Co.). ResuIts : It has no cytotoxic effects on HepG2 cells in all concentrations (0.1, 0.5, 1.5, 10, $20mg/m{\ell}$). More than twofold up-regulated genes were 19 genes. The number of more than twofold down-regulated genes was 13. Discussion : This study showed the screening of CTF-HAS mediated differentially regulated genes using combined approaches of oligonucleotide microarray. The screened genes will be used for the better understanding in therapeutic effect of CTF-HAS on cancer field.

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Endophytic bacterium Pseudomonas fluorescens strain EP103 was effective against Phytophthora capsici causing blight in chili pepper (식물근권에서 분리한 Pseudomonas fluorescens strain EP103에 의한 고추역병억제)

  • Kim, Tack-Soo;Dutta, Swarnalee;Lee, Se Won;Park, Kyungseok
    • The Korean Journal of Pesticide Science
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    • v.18 no.4
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    • pp.422-428
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    • 2014
  • Endophytic bacterial strains from root tissue of strawberry were screened for their efficacy in growth improvement and control of Phytophthora blight disease of chili pepper plant under greenhouse condition. Plants treated with the strain EP103, identified as Pseudomonas fluorescens, showed growth improvement in terms of fresh weight and root length compared to the untreated control and other endophytic strains. When challenged with Phytophthora capsici, there was significant reduction of disease in EP103 treated plants with an efficacy of 78.7%. There was no direct inhibition of the target pathogen by EP103 when tested under in vitro antibiosis assay. Analysis of differential expression of selected marker genes for induced systemic resistance (ISR) in plants treated with EP103 and challenged with P. capsici showed up-regulation of PR1 and PR10 pathogenesis-related (PR) proteins. PCR analysis showed that EP103 produced secondary metabolites such as pyoluteorin, pyrrolnitrin, hydrogen cyanide and orfamide A. This study indicated the potential of endophytic P. fluorescens strain EP103 as an efficient biocontrol agent against P. capsici in chili pepper plant.

Differential Potential of Stem Cells Following Their Origin - Subacromial Bursa, Bone Marrow, Umbilical Cord Blood - (줄기세포의 분화능의 기원에 따른 비교 - 견봉하 점액낭, 골수, 탯줄 혈액 -)

  • Sim, Sung Woo;Moon, Young Lae;Kang, Jung Hun
    • Clinics in Shoulder and Elbow
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    • v.15 no.2
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    • pp.65-72
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    • 2012
  • Purpose: To evaluate the differentiation potential of stem cells and their immunophenotype from 3 different sources. Methods: Our study involved three stem cell sources-subacromial bursal tissue, bone marrow, and umbilical cord blood. We obtained the subacromial bursal tissue and bone marrow from the patients undergoing shoulder surgery. After collecting the sample, we applied specific induction media for neurogenic, adipogenic and osteogenic differentiation. Also, flow-cytometry analysis was done to reveal the cell surface antigens. Results: We obtained 100% (8 cases) neural and adipogenic differentiation, but 62.5% (5 of 8 cases) osseous differentiation among the subacromial bursal tissue group. Bone marrow derived cells showed 100% neural (6 cases) and adipogenic (5 cases) differentiation, but 80% (4 of 5 cases) osseous differentiation. Umbilical cord blood derived cells revealed 97% (65 of 67 cases) neural, 53.7% (29 of 54 cases) adipogenic and 68.4% (39 of 57 cases) osseous differentiation. Immunophenotype analysis revealed that surface markers of bone marrow, subacromial bursal cell and umbilical cord blood derived mesenchymal stem cells are different from each other. Conclusions: Mesenchymal stem cells are potential agents in regenerative medicine and are characterized by expression of surface markers and by their differentiation potential. Our study with stem cells from subacromial bursal tissue, bone marrow and umbilical cord discovered that each stem cell has unique differentiation potential and function based on its origin. Various stem cells show multi-lineage differentiations in vitro which can be correlated to in vivo conditions.

Real-Time PCR Analysis of Metabolic Pathway of PHB in Acidiphilium cryptum DX1-1

  • Xu, Ai-Ling;Xia, Jin-Lan;Liu, Ke-Ke;Li, Li;Yang, Yu;Nie, Zhen-Yuan;Qiu, Guan-Zhou
    • Journal of Microbiology and Biotechnology
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    • v.20 no.1
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    • pp.71-77
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    • 2010
  • The time, yield, and related genes expression of PHB accumulation of Acidiphilium cryptum DX1-1 were investigated under four different initial C/N ratios, 1.2, 2.4, 7.5, and 24. The results of time and yield of poly-$\beta$-hydroxybutyrate (PHB) accumulation show that the initial C/N ratio of 2.4 was optimum for strain DX1-1 to accumulate PHB, but both higher and lower initial C/N ratios did not favor that process. Based on the genome of Acidiphilium cryptum JF-5, 13 PHB accumulation related genes in strain JF-5 were chosen and successfully cloned from strain DX1-1. The differential expressions of the 13 functional genes, in different C/N ratios as cited above, were then studied by real-time PCR. The results show that all the 13 genes were most upregulated when the initial C/N ratio was 2.4, and among which the gene Acry_3030 encoding poly-$\beta$-hydroxybutyrate polymerase and Aery_0626 encoding acetyl-CoA synthetase were much more upregulated than the other genes, which proved that they play the most important role for PHB accumulation, and acetate is the main initial substance for PHB accumulation for strain DX1-1. Potential regulatory motifs analysis showed that the genes related to PHB accumulation are regulated by different promoters and that the motif had weak similarity to the model promoters, suggesting that PHB metabolism in Acidiphilium cryptum may be mediated by a different mechanism.

Identification of Differentially Expressed Radiation-induced Genes in Cervix Carcinoma Cells Using Suppression Subtractive Hybridization (자궁경부암세포에서 방사선조사시 차등 발현되는 유전자 동정)

  • Kim Jun-Sang;Lee Young-Sook;Lee Jeung Hoon;Lee Woong-Hee;Seo Eun Young;Cho Moon-June
    • Radiation Oncology Journal
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    • v.23 no.1
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    • pp.43-50
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    • 2005
  • Purpose : A number of genes and their products are Induced early or late following exposure of cells to ionizing radiation. These radiation-Induced genes have various effects on irradiated cells and tissues. Suppression subtractive hybridization (SSH) based on PCR was used to Identify the differentially expressed genes by radiation in cervix carcinoma cells. Materials and Methods : Total RNA and poly $(A)^+$ mRNA were Isolated from Irradiated and non-irradiated HeLa cells. Forward- and reverse-subtracted cDNA libraries were constructed using SSH. Eighty-eight clones of each were used to randomly select differentially expressed genes using reverse Northern blotting (dot blot analysis). Northern blotting was used to verify the screened genes. Results : Of the 17t clones, 10 genes in the forward-subtracted library and 9 genes In the reverse-subtracted library were identified as differentially expressed radiation-induced genes by PCR-select differential screening. Three clones from the forward-subtracted library were confirmed by Northern blotting, and showed increased expression in a dose-dependent manner, including a telomerase catalytic subunit and sodium channel-like protein gene, and an ESTs (expressed sequence tags) gene. Conclusion : We Identified differentially expressed radiation-induced genes with low-abundance genes with SSH, but further characterization of theses genes are necessary to clarify the biological functions of them.

A systematic exploration of ginsenoside Rg5 reveals anti-inflammatory functions in airway mucosa cells

  • Hyojin Heo;Yumin Kim;Byungsun Cha;Sofia Brito;Haneul Kim;Hyunjin Kim;Bassiratou M. Fatombi;So Young Jung;So Min Lee;Lei Lei;Sang Hun Lee;Geon-woo Park;Byeong-Mun Kwak;Bum-Ho Bin;Ji-Hwan Park;Mi-Gi Lee
    • Journal of Ginseng Research
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    • v.47 no.1
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    • pp.97-105
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    • 2023
  • Background: Hyperactivated airway mucosa cells overproduce mucin and cause severe breathing complications. Here, we aimed to identify the effects of saponins derived from Panax ginseng on inflammation and mucin overproduction. Methods: NCI-H292 cells were pre-incubated with 16 saponins derived from P. ginseng, and mucin overproduction was induced by treatment with phorbol 12-myristate 13-acetate (PMA). Mucin protein MUC5AC was quantified by enzyme-linked immunosorbent assay, and mRNA levels were analyzed using quantitative polymerase chain reaction (qPCR). Moreover, we performed a transcriptome analysis of PMA-treated NCI-H292 cells in the absence or presence of Rg5, and differential gene expression was confirmed using qPCR. Phosphorylation levels of signaling molecules, and the abundance of lipid droplets, were measured by western blotting, flow cytometry, and confocal microscopy. Results: Ginsenoside Rg5 effectively reduced MUC5AC secretion and decreased MUC5AC mRNA levels. A systematic functional network analysis revealed that Rg5 upregulated cholesterol and glycerolipid metabolism, resulting in the production of lipid droplets to clear reactive oxygen species (ROS), and modulated the mitogen-activated protein kinase and nuclear factor (NF)-kB signaling pathways to regulate inflammatory responses. Rg5 induced the accumulation of lipid droplets and decreased cellular ROS levels, and N-acetyl-ⳑ-cysteine, a ROS inhibitor, reduced MUC5AC secretion via Rg5. Furthermore, Rg5 hampered the phosphorylation of extracellular signal-regulated kinase and p38 proteins, affecting the NF-kB signaling pathway and pro-inflammatory responses. Conclusion: Rg5 alleviated inflammatory responses by reducing mucin secretion and promoting lipid droplet-mediated ROS clearance. Therefore, Rg5 may have potential as a therapeutic agent to alleviate respiratory disorders caused by hyperactivation of mucosa cells.

A Study of the Reactive Movement Synchronization for Analysis of Group Flow (그룹 몰입도 판단을 위한 움직임 동기화 연구)

  • Ryu, Joon Mo;Park, Seung-Bo;Kim, Jae Kyeong
    • Journal of Intelligence and Information Systems
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    • v.19 no.1
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    • pp.79-94
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    • 2013
  • Recently, the high value added business is steadily growing in the culture and art area. To generated high value from a performance, the satisfaction of audience is necessary. The flow in a critical factor for satisfaction, and it should be induced from audience and measures. To evaluate interest and emotion of audience on contents, producers or investors need a kind of index for the measurement of the flow. But it is neither easy to define the flow quantitatively, nor to collect audience's reaction immediately. The previous studies of the group flow were evaluated by the sum of the average value of each person's reaction. The flow or "good feeling" from each audience was extracted from his face, especially, the change of his (or her) expression and body movement. But it was not easy to handle the large amount of real-time data from each sensor signals. And also it was difficult to set experimental devices, in terms of economic and environmental problems. Because, all participants should have their own personal sensor to check their physical signal. Also each camera should be located in front of their head to catch their looks. Therefore we need more simple system to analyze group flow. This study provides the method for measurement of audiences flow with group synchronization at same time and place. To measure the synchronization, we made real-time processing system using the Differential Image and Group Emotion Analysis (GEA) system. Differential Image was obtained from camera and by the previous frame was subtracted from present frame. So the movement variation on audience's reaction was obtained. And then we developed a program, GEX(Group Emotion Analysis), for flow judgment model. After the measurement of the audience's reaction, the synchronization is divided as Dynamic State Synchronization and Static State Synchronization. The Dynamic State Synchronization accompanies audience's active reaction, while the Static State Synchronization means to movement of audience. The Dynamic State Synchronization can be caused by the audience's surprise action such as scary, creepy or reversal scene. And the Static State Synchronization was triggered by impressed or sad scene. Therefore we showed them several short movies containing various scenes mentioned previously. And these kind of scenes made them sad, clap, and creepy, etc. To check the movement of audience, we defined the critical point, ${\alpha}$and ${\beta}$. Dynamic State Synchronization was meaningful when the movement value was over critical point ${\beta}$, while Static State Synchronization was effective under critical point ${\alpha}$. ${\beta}$ is made by audience' clapping movement of 10 teams in stead of using average number of movement. After checking the reactive movement of audience, the percentage(%) ratio was calculated from the division of "people having reaction" by "total people". Total 37 teams were made in "2012 Seoul DMC Culture Open" and they involved the experiments. First, they followed induction to clap by staff. Second, basic scene for neutralize emotion of audience. Third, flow scene was displayed to audience. Forth, the reversal scene was introduced. And then 24 teams of them were provided with amuse and creepy scenes. And the other 10 teams were exposed with the sad scene. There were clapping and laughing action of audience on the amuse scene with shaking their head or hid with closing eyes. And also the sad or touching scene made them silent. If the results were over about 80%, the group could be judged as the synchronization and the flow were achieved. As a result, the audience showed similar reactions about similar stimulation at same time and place. Once we get an additional normalization and experiment, we can obtain find the flow factor through the synchronization on a much bigger group and this should be useful for planning contents.