• Title, Summary, Keyword: 2DGE

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Crop proteomics: Practical method for high resolution of two-dimensional electrophoresis (작물 단백질체 분석을 위한 이차원 전기영동 사용법)

  • Kim, U.G.;Jung, Hwa-Jin;Lee, Su-Ji;Kim, Sun-Tae
    • Journal of Plant Biotechnology
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    • v.39 no.1
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    • pp.81-92
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    • 2012
  • Two-dimensional gel electrophoresis (2-DGE) is one of the most important technologies for high-resolution separation of proteins for proteomics. In this study, we present a detail 2-DGE protocol which allows detection and quantification of total plant proteins separated on gels to improve matching in image analysis. This protocol highlighted here may be useful for researchers, who like to first study for the development of protein biomarkers involved in development, biotic and abiotic stresses in plant.

Using DGE for Enhancing SMK and PCK of Pre-service Elementary Teachers for the Figure Problem (예비 초등교사들의 도형 문제에 대한 SMK와 PCK 강화를 위한 DGE 활용)

  • Kang, Jeong Gi;Kim, Min Jeong;Jeong, Sang Tae;Roh, Eun Hwan
    • Journal of the Korean School Mathematics Society
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    • v.17 no.2
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    • pp.139-166
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    • 2014
  • The purpose of the study is to enhance the teaching competence for pre-service elementary teacher by using DGE in order to enhance SMK and PCK for them. To do this, we investigated the initial SMK and PCK for 23 pre-service elementary teachers, the reality of implementation activity of DGE and the change of SMK and PCK after quest activity by DGE. As results, 3 pre-service elementary teachers made errors which are misunderstanding a general angle as special angle, an excessive jump of logic and a circulation logic in the aspect of an initial SMK. In the aspect of contents of PCK, most of pre-service elementary teachers proposed teaching focused on the character using in the problem solving. And most of pre-service elementary teachers proposed teaching methods which are based on explanation, measurement and material manipulation. The reality of implementation activity of DGE was classified 4 cases which are a difficulty in understanding the concept of dynamics and embodying in DGE, an obsession about construction of $75^{\circ}$ and generalization, a difficulty in interpreting 'folding activity' mathematically and a good implementation activity. After quest activity by DGE, the case which is misunderstanding a general angle as special angle could be improved, but the others are not. And after quest activity by DGE, most of pre-service elementary teachers still proposed teaching focused on the character using in the problem solving in the aspect of contents of PCK, and some of pre-service elementary teachers added only teaching methods which are involving visual confirmation by GSP. From these results, we could extract some pedagogical implications helping pre-service teachers to reinforce SMK and PCK by DGE.

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A Study on Antibacterial Activity of Daehwanggeonwoo-san(Dahwangqianniu-san) Ethanol Extract against Methicillin-Resistant Staphylococcus Aureus (대황견우산(大黃牽牛散) 에탄올 추출물의 Methicillin 내성 Staphylococcus aureus에 대한 항균활성 연구)

  • Park, Ju-yeong;Na, Yong-su;Oh, Gong-cheon;Lee, Sang-mi;Choi, Byeong-kwon;Lee, Yoon-seung;Song, Yung-sun
    • Journal of Korean Medicine Rehabilitation
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    • v.28 no.2
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    • pp.21-35
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    • 2018
  • Objectives The objective of this study is to determine the antimicrobial effect of Daehwanggyeonu-san(Dahwangqianniu-san,DGE) and synergistic effects with antibiotics oxacillin, ampicillin, and gentamicin against Methicillin-Resistant Staphylococcus aureus(MRSA). Methods The antibacterial activity of DGE extract was evaluated againest MRSA strains by using the Disc diffusion method, broth microdilution method(minimal inhibitory concentration; MIC), checkerboard dilution test. The checkerboard dilution test was used to examined synergetic effect of oxacillin, ampicillin, gentamicin, ciprofloxacin with DGE extract. Results DGE showed antimicrobial activity against MRSA with an MIC value of $125{\sim}250{\mu}g/mL$. In the checkerboard test, the interation of DGE with all tested antibiotics produced almost synergy or partial synergy against MRSA. Conclusions This study shows that DGE reduced the MICs of several antibiotics tested, and a remarkable antibacterial effect of DGE, with membrane permeability enhancers and ATP synthase inhibitors. This study can be a valuable source for the development of a new drug with low MRSA resistance.

An Iterative Spot Matching for 2-Dimensional Protein Separation Images (반복 점진적 방법에 의한 2차원 단백질 분리 영상의 반점 정합)

  • Kim, Jung-Ja;Hoang, Minh T.;Kim, Dong-Wook;Kim, Nam-Gyun;Won, Yong-Gwan
    • Journal of Biomedical Engineering Research
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    • v.28 no.5
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    • pp.601-608
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    • 2007
  • 2 Dimensional Gel Electrophoresis(2DGE) is an essentialmethodology for analysis on the expression of various proteins. For example, information for the location, mass, expression, size and shape of the proteins obtained by 2DGE can be used for diagnosis, prognosis and biological progress by comparison of patients with the normal persons. Protein spot matching for this purpose is comparative analysis of protein expression pattern for the 2DGE images generated under different conditions. However, visual analysis of protein spots which are more than several hundreds included in a 2DGE image requires long time and heavy effort. Furthermore, geometrical distortion makes the spot matching for the same protein harder. In this paper, an iterative algorithm is introduced for more efficient spot matching. Proposed method is first performing global matching step, which reduces the geometrical difference between the landmarks and the spot to be matched. Thus, movement for a spot is defined by a weighted sum of the movement of the landmark spots. Weight for the summation is defined by the inverse of the distance from the spots to the landmarks. This movement is iteratively performed until the total sum of the difference between the corresponding landmarks is larger than a pre-selected value. Due to local distortion generally occurred in 2DGE images, there are many regions in whichmany spot pairs are miss-matched. In the second stage, the same spot matching algorithm is applied to such local regions with the additional landmarks for those regions. In other words, the same method is applied with the expanded landmark set to which additional landmarks are added. Our proposed algorithm for spot matching empirically proved reliable analysis of protein separation image by producing higher accuracy.

Development of a Dynamic Geometry Environment to Collect Learning History Data

  • Mun, Kill-Sung;Han, Beom-Soo;Han, Kyung-Soo;Ahn, Jeong-Yong
    • Journal of the Korean Data and Information Science Society
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    • v.18 no.2
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    • pp.375-384
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    • 2007
  • As teachings that use the ICT are more popular, many studies on the dynamic geometry environment(DGE) are under way. An important factor emphasized in the studies is to practical use learning activities of learners. In this study, we first define the learning history data in DGE. Second we develop a prototype of the DGE that is able to collect and analyze the learning history data automatically. The environment enables not only to grasp leaning history but also to create and manage new learning objects.

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The Algorithm of Protein Spots Segmentation using Watersheds-based Hierarchical Threshold (Watersheds 기반 계층적 이진화를 이용한 단백질 반점 분할 알고리즘)

  • Kim Youngho;Kim JungJa;Kim Daehyun;Won Yonggwan
    • The KIPS Transactions:PartB
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    • v.12B no.3
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    • pp.239-246
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    • 2005
  • Biologist must have to do 2DGE biological experiment for Protein Search and Analysis. This experiment coming into being 2 dimensional image. 2DGE (2D Gel Electrophoresis : two dimensional gel electrophoresis) image is the most widely used method for isolating of the objective protein by comparative analysis of the protein spot pattern in the gel plane. The process of protein spot analysis, firstly segment protein spots that are spread in 2D gel plane by image processing and can find important protein spots through comparative analysis with protein pattern of contrast group. In the algorithm which detect protein spots, previous 2DGE image analysis is applies gaussian fitting, however recently Watersheds region based segmentation algorithm, which is based on morphological segmentation is applied. Watersheds has the benefit that segment rapidly needed field in big sized image, however has under-segmentation and over-segmentation of spot area when gray level is continuous. The drawback was somewhat solved by marker point institution, but needs the split and merge process. This paper introduces a novel marker search of protein spots by watersheds-based hierarchical threshold, which can resolve the problem of marker-driven watersheds.

Red Ginseng Extract Improves Liver Fibrosis in Mice Treated with the Endocrine Disruptor Bisphenol A (내분비교란물질 비스페놀 A를 처리한 마우스에서 홍삼 추출물의 간 섬유화 개선)

  • Choi, Jehun;Park, Chun Geon;Seo, Kyoung Hee;Kim, Hyung Don;Yoon, Ji Hye;Ahn, Young Sup;Kim, Jin Seong
    • Korean Journal of Plant Resources
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    • v.30 no.2
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    • pp.125-132
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    • 2017
  • Bisphenol A (BPA), a known endocrine disruptor, induces toxicity in cells and in experimental animals. Ginseng extracts were evaluated to determine whether they can inhibit BPA-induced toxicity. The antioxidant activity of fresh ginseng extract (WGE), dried white ginseng extract (DGE), and dried red ginseng extract (RGE) was measured using the DPPH assay. WGE and RGE increased DPPH free radical scavenging activity. Cell viability was measured in HepG2 cells following treatment with BPA and ginseng extracts using the MTT assay. DGE and RGE increased HepG2 cell viability following treatment with $200{\mu}M$ BPA. RGE reduced levels of biochemical markers of liver damage, aspartate aminotransferase (AST) and alanine aminotransferase (ALT) that increased in mice following treatment with BPA. In addition, the regeneration and proliferation of damaged liver cells were significantly increased in RGE-treated mice. Moreover, RGE inhibited hepatic fibrosis in the surrounding area and in the central vein of the liver microstructure. RGE also significantly inhibited BPA-induced cytotoxicity. In addition, RGE protected liver damage and regenerated liver tissues in BPA-treated animals. These results show that RGE may represent a potential candidate drug for the treatment and prevention of liver damage caused by environmental toxins.

Physiological and Proteomics Analysis to Potassium Starvation in Rice

  • Kim, Sang-Gon;Wang, Yiming;Lee, Chang-Hoon;Chi, Yong-Hun;Kim, Keun-Ki;Choi, In-Soo;Kim, Yong-Chul;Kang, Kyu-Young;Kim, Sun-Tae
    • Korean Journal of Environmental Agriculture
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    • v.30 no.4
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    • pp.395-401
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    • 2011
  • BACKGROUND: Potassium (K) is one of the macronutrients which are essential for plant growth and development. Its deficiency in paddy soils is becoming one of the limiting factors for increasing rice yield in Asia. METHODS AND RESULTS: To investigate physiological symptoms under K-starvation (NP) compared with complete media (NPK) condition, we measured shoot/root length, weight, nutrients, and patterns of protein expression. The shoot growth was significantly reduced, but root growth was not affected by K-starvation. However, biomasses were decreased in both shoot and root. Uptake of K was reduced up to 85%, while total concentrations of P, Ca, Mg, Na were increased in root and shoot. To better understand the starved K mechanism of rice, comparative proteome analysis for proteins isolated from rice leaves was conducted using 2-DGE. Five spots of differentially expressed proteins were analyzed by MALDI-TOF MS. Analysis of these K-starvation response proteins suggested that they were involved in metabolism and defense. CONCLUSION(s): Physiological and 2-DGE based proteomics approach used in our study results in observation of morphology or nutrients change and identification of K-starvation responsive proteins in rice root. These results have important roles in maintaining nutrient homeostasis and would also be useful for further characterization of protein function in plant K nutrition.

Detection of Landmark Spots for Spot Matching in 2DGE (2차원 전기영동 영상의 스팟 정합을 위한 Landmark 스팟쌍의 검출)

  • Han, Chan-Myeong;Suk, Soo-Young;Yoon, Young-Woo
    • Journal of the Korean Society of Industry Convergence
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    • v.14 no.3
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    • pp.105-111
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    • 2011
  • Landmark Spots in 2D gel electrophoresis are used in many methods of 2DEG spot matching. Landmark Spots are obtained manually and it is a bottle neck in the entire protein analysis process. Automated landmark spots detection is a very crucial topic in processing a massive amount of 2DGE data. In this paper, Automated landmark spot detection is proposed using point pattern matching and graph theory. Neighbor spots are defined by a graph theory to use and only a centered spot and its neighbor spots are considered for spot matching. Normalized Hausdorff distance is introduced as a criterion for measuring degree of similarity. In the conclusion, the method proposed in this paper can get about 50% of the total spot pairs and the accuracy rate is almost 100%, which the requirements of landmark spots are fully satisfied.