Journal articles: '2D gel'

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Görg, Angelika. "Advances in 2D gel techniques." Trends in Biotechnology 18 (July 2000): 3–6. http://dx.doi.org/10.1016/s0167-7799(00)00011-1.

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Kaczmarek, K., B. Walczak, S. de Jong, and B. G. M. Vandeginste. "Matching 2D Gel Electrophoresis Images." Journal of Chemical Information and Computer Sciences 43, no. 3 (May 2003): 978–86. http://dx.doi.org/10.1021/ci0256337.

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RASHWAN, SHAMS, AMANY SARHAN, MUHAMMAD TALAAT FAHEEM, and BAYUMY A. YOUSSEF. "AUTOMATIC PROTEIN SPOTS QUANTIFICATION IN TWO-DIMENSIONAL GEL IMAGES." Advances in Adaptive Data Analysis 03, no. 03 (July 2011): 401–15. http://dx.doi.org/10.1142/s1793536911000726.

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Two-dimensional (2D) polyacrylamide gel electrophoresis of proteins is a robust and reproducible technique. It is the most widely used separation tool in proteomics. Current efforts in the field are directed at development of tools for expanding the range of proteins accessible with 2D gels. Proteomics was built around the 2D gel. The idea that multiple proteins can be analyzed in parallel grew from 2D gel maps. Proteomics researchers needed to identify interested protein spots by examining the gel. This is time-consuming, labor-extensive, and error-prone process. It is desired that the computer can analyze the proteins automatically by first detecting then quantifying the protein spots in the 2D gel images. In our previous work, we presented a new technique for segmentation of 2D gel images using the fuzzy c-means (FCM) algorithm using the notion of fuzzy relations. In this paper, we will describe the new relational FCM (RFCM) algorithm and use it for automatic protein spots quantification. We will also use two methods to evaluate its performance: the unsupervised evaluation method and comparison with the expert spots quantification.

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Winz, M. L., K. Rohr, and S. Wörz. "Geometric Alignment of 2D Gel Electrophoresis Images." Methods of Information in Medicine 48, no. 04 (2009): 320–23. http://dx.doi.org/10.3414/me9229.

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Summary Objectives: 2D gel electrophoresis (2-DE) is the method of choice for analyzing protein expression in the field of proteomics, for example, comparing a reference with a test population. However, due to complex physical and chemical processes the locations of proteins generally vary in different 2-DE images. To cope with these variations, accurate geometric alignment of 2-DE images is important. Methods: We introduce a new elastic registration approach for 2-DE images, which is based on an analytic solution of the Navier equation using Gaussian elastic body splines (GEBS). With this approach cross-effects in elastic deformations can be handled, which is important for the registration of 2-DE images. In addition, landmark correspondences can be included to aid the registration in regions which are difficult to register using intensity information alone. Results: We have successfully applied our approach to register 2-DE gel images of different levels of complexity. In each case, gel images from a reference group are compared with a test group. To analyze the performance of our approach, we have carried out a quantitative evaluation of the registration results. Moreover, we have performed an experimental comparison with a previous elastic registration scheme. Conclusions: From the results we found that our approach is well-suited for the registration of 2-DE gel images of different levels of complexity and it turned out that the approach is superior to a previous hybrid scheme. Moreover, our approach is well-suited in a fully automatic setting and the performance can further be improved when landmark correspondences are available.

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Bonchev, Danail, and Milan Randic. "Shannon’s entropy of proteomic 2D-gel maps." Chemical Physics Letters 372, no. 3-4 (April 2003): 548–52. http://dx.doi.org/10.1016/s0009-2614(03)00441-x.

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Johnson, D. Thor, Robert A. Harris, Stephanie French, Angel Aponte, and Robert S. Balaban. "Proteomic changes associated with diabetes in the BB-DP rat." American Journal of Physiology-Endocrinology and Metabolism 296, no. 3 (March 2009): E422—E432. http://dx.doi.org/10.1152/ajpendo.90352.2008.

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These studies were structured with the aim of utilizing emerging technologies in two-dimensional (2D) gel electrophoresis and mass spectrometry to evaluate protein expression changes associated with type 1 diabetes. We reasoned that a broad examination of diabetic tissues at the protein level might open up novel avenues of investigation of the metabolic and signaling pathways that are adversely affected in type 1 diabetes. This study compared the protein expression of the liver, heart, and skeletal muscle of diabetes-prone rats and matched control rats by semiquantitative liquid chromatography-mass spectrometry and differential in-gel 2D gel electrophoresis. Differential expression of 341 proteins in liver, 43 in heart, and 9 (2D gel only) in skeletal muscle was detected. These data were assembled into the relevant metabolic pathways affected primarily in liver. Multiple covalent modifications were also apparent in 2D gel analysis. Several new hypotheses were generated by these data, including mechanisms of net cytosolic protein oxidation, formaldehyde generation by the methionine cycle, and inhibition of carbon substrate oxidation via reduction in citrate synthase and short-chain acyl-CoA dehydrogenase.

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Ji, H. "Preparation of Eukaryotic Lysates for 2D Gel Electrophoresis." Cold Spring Harbor Protocols 2006, no. 28 (October 1, 2006): pdb.prot4571. http://dx.doi.org/10.1101/pdb.prot4571.

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Liang, C., and S. A. Gerbi. "Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method." Molecular and Cellular Biology 14, no. 2 (February 1994): 1520–29. http://dx.doi.org/10.1128/mcb.14.2.1520.

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The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

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Liang, C., and S. A. Gerbi. "Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method." Molecular and Cellular Biology 14, no. 2 (February 1994): 1520–29. http://dx.doi.org/10.1128/mcb.14.2.1520-1529.1994.

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The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

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Natale, Massimo, Bernardetta Maresca, Paolo Abrescia, and Enrico M. Bucci. "Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ." Proteomics Insights 4 (January 2011): PRI.S7971. http://dx.doi.org/10.4137/pri.s7971.

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A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performances.

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Papoutsaki, M.-V., E. Pappas, A. E. Papadakis, C. Varveris, J. Damilakis, and T. G. Maris. "Polymer gel dosimetry utilizing a 2D (SE) and a 2D (HASTE) multiple echo sequences." Journal of Physics: Conference Series 444 (June 26, 2013): 012088. http://dx.doi.org/10.1088/1742-6596/444/1/012088.

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Garrels, James I., B. Robert Franza, Scott D. Patterson, Keith Latham, Davor Solter, Cecile Chang, and Gerald Latter. "Protein databases constructed by quantitative 2D gel analysis and protein identification from 2D gels." Journal of Protein Chemistry 11, no. 4 (August 1992): 394–95. http://dx.doi.org/10.1007/bf01673752.

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Komatsu, Setsuko, Myeong W. Oh, Hee Y. Jang, Soo J. Kwon, Hye R. Kim, Jung H. Ko, Sun H. Woo, and Yohei Nanjo. "Proteomic Analyses of Soybean Root Tips During Germination." Protein & Peptide Letters 21, no. 12 (November 5, 2014): 1308–19. http://dx.doi.org/10.2174/0929866521666140526152426.

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Plant root systems form complex networks with the surrounding soil environment and are controlled by both internal and external factors. To better understand the function of root tips of soybean during germination, three proteomic techniques were used to analyze the protein profiles of root tip cells. Proteins were extracted from the root tips of 4-dayold soybean seedlings and analyzed using two-dimensional (2D) gel electrophoresis-based proteomics, SDS-gel based proteomics, and gel-free proteomics techniques. A total of 121, 862, and 341 proteins were identified in root tips using the 2D gel-based, SDS gel-based, and gel-free proteomic techniques, respectively. The proteins identified by 2D gel-based proteomic analysis were predominantly localized in the cytoplasm, whereas nuclear-localized proteins were most commonly identified by the SDS gel-based and gel-free proteomics techniques. Of the 862 proteins identified in the SDS gelbased proteomic analysis, 190 were protein synthesis-related proteins. Furthermore, 24 proteins identified using the 2Dgel based proteomic technique shifted between acidic and basic isoelectric points, and 2 proteins, heat shock protein 70.2 and AAA-type ATPase, displayed two different molecular weights at the same isoelectric point. Taken together, these results suggest that a number of proteins related to protein synthesis and modification are activated in the root tips of soybean seedlings during germination.

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Dlaska, Margit, Conrad Anderl, Wolfgang Eisterer, and Oliver E. Bechter. "Detection of Circular Telomeric DNA without 2D Gel Electrophoresis." DNA and Cell Biology 27, no. 9 (September 2008): 489–96. http://dx.doi.org/10.1089/dna.2008.0741.

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Horgan, Graham W. "Sample Size and Replication in 2D Gel Electrophoresis Studies." Journal of Proteome Research 6, no. 7 (July 2007): 2884–87. http://dx.doi.org/10.1021/pr070114a.

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Kaczmarek, K., B. Walczak, S. de Jong, and B. G. M. Vandeginste. "Feature Based Fuzzy Matching of 2D Gel Electrophoresis Images." Journal of Chemical Information and Computer Sciences 42, no. 6 (November 2002): 1431–42. http://dx.doi.org/10.1021/ci020266k.

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Chan, Yung-Kuan, Duan-Li Liau, Yung-Fu Chen, Hsien-Chu Wu, and Yen-Ping Chu. "A minute lossy method for 2D-gel images compression." International Journal of Imaging Systems and Technology 16, no. 1 (2006): 1–8. http://dx.doi.org/10.1002/ima.20062.

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Saitoh, Eiichi, Shinya Yamamoto, Eishiro Okamoto, Yoshimi Hayakawa, Takashi Hoshino, Ritsuko Sato, Satoko Isemura, Sadami Ohtsubo, and Masayuki Taniguchi. "Identification of Cysteine Proteases and Screening of Cysteine Protease Inhibitors in Biological Samples by a Two-Dimensional Gel System of Zymography and Reverse Zymography." Analytical Chemistry Insights 2 (January 2007): 117739010700200. http://dx.doi.org/10.4137/117739010700200011.

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We have developed a two-dimensional (2D-) gel system of zymography and reverse zymography for the detection and characterization of proteases and protease inhibitors. Isoelectric focusing (IEF) agarose gels with pH gradients were employed for separation in the first-dimension and sodium dodecyl sulfate (SDS)-polyacrylamide gel copolymerized with gelatin used for the second dimension. Proteases and protease inhibitors separated by IEF gel were applied on the second gel without trichloroacetic acid (TCA) fixation. Protease activity in the 2D-gel was visualized as transparent spots where gelatin substrate was digested after commassie brilliant blue (CBB) staining. Some of the transparent spots from the skin mucus extract of rainbow trout were determined to be a cysteine protease through use of E-64 or CA-074. In the reverse zymography technique, the gel was incubated with papain solution at 37°C for 18 h. Cysteine protease inhibitors from broad bean seeds were detected as clear blue spots after CBB staining. The amino (N-) terminal sequences of four papain inhibitor spots thus detected were demonstrated to be identical to that of favin β chain, a broad bean lectin. Taken together, our system can be considered to be an efficient technique for discovering and characterizing new proteases and protease inhibitors in biological samples. This is the first report describing a 2D-gel system of zymography and reverse zymography.

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Xiao, Yulong, Xiaoping Tan, Wei Xing, Kai Zhao, Bei Zhang, and Xiaohong Cheng. "Coumarin-based emissive hexacatenars: synthesis, 2D and 3D self-assembly and photodimerization." Journal of Materials Chemistry C 6, no. 40 (2018): 10782–92. http://dx.doi.org/10.1039/c8tc04040k.

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Various 2D columnar LC phases and gels with abnormal morphologies as well as reversible LC–LC and gel–gel phase transitions caused by photodimerization were observed in novel unsymmetric coumarin polycatenars.

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Shinomiya, T., and S. Ina. "Mapping an initiation region of DNA replication at a single-copy chromosomal locus in Drosophila melanogaster cells by two-dimensional gel methods and PCR-mediated nascent-strand analysis: multiple replication origins in a broad zone." Molecular and Cellular Biology 14, no. 11 (November 1994): 7394–403. http://dx.doi.org/10.1128/mcb.14.11.7394.

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We have mapped an initiation region of DNA replication at a single-copy chromosomal locus in exponentially proliferating Drosophila tissue culture cells, using two-dimensional (2D) gel replicon mapping methods and PCR-mediated analysis of nascent strands. The initiation region was first localized downstream of the DNA polymerase alpha gene by determining direction of replication forks with the neutral/alkaline 2D gel method. Distribution of replication origins in the initiation region was further analyzed by using two types of 2D gel methods (neutral/neutral and neutral/alkaline) and PCR-mediated nascent-strand analysis. Results obtained by three independent methods were essentially consistent with each other and indicated that multiple replication origins are distributed in a broad zone of approximately 10 kb. The nucleotide sequence of an approximately 20-kb region that encompasses the initiation region was determined and searched for sequence elements potentially related to function of replication origins.

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Shinomiya, T., and S. Ina. "Mapping an initiation region of DNA replication at a single-copy chromosomal locus in Drosophila melanogaster cells by two-dimensional gel methods and PCR-mediated nascent-strand analysis: multiple replication origins in a broad zone." Molecular and Cellular Biology 14, no. 11 (November 1994): 7394–403. http://dx.doi.org/10.1128/mcb.14.11.7394-7403.1994.

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We have mapped an initiation region of DNA replication at a single-copy chromosomal locus in exponentially proliferating Drosophila tissue culture cells, using two-dimensional (2D) gel replicon mapping methods and PCR-mediated analysis of nascent strands. The initiation region was first localized downstream of the DNA polymerase alpha gene by determining direction of replication forks with the neutral/alkaline 2D gel method. Distribution of replication origins in the initiation region was further analyzed by using two types of 2D gel methods (neutral/neutral and neutral/alkaline) and PCR-mediated nascent-strand analysis. Results obtained by three independent methods were essentially consistent with each other and indicated that multiple replication origins are distributed in a broad zone of approximately 10 kb. The nucleotide sequence of an approximately 20-kb region that encompasses the initiation region was determined and searched for sequence elements potentially related to function of replication origins.

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Issaq, Haleem J., and Timothy D. Veenstra. "Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives." BioTechniques 44, no. 5 (April 2008): 697–700. http://dx.doi.org/10.2144/000112823.

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Savelonas, Michalis A., Eleftheria A. Mylona, and Dimitris Maroulis. "Unsupervised 2D gel electrophoresis image segmentation based on active contours." Pattern Recognition 45, no. 2 (February 2012): 720–31. http://dx.doi.org/10.1016/j.patcog.2011.08.003.

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Pallen, Catherine, Claire Friry-Santini, Corinne Herouet-Guicheney, and Annabelle Capt. "Technical variability of 2D gel electrophoresis – Application to soybean allergens." Toxicology Reports 1 (2014): 734–42. http://dx.doi.org/10.1016/j.toxrep.2014.09.002.

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Patel, K., and H. M. Cartwright. "Analysis of 2D Gel Series Data Using Advanced Statistical Tools." Biochemical Society Transactions 28, no. 5 (October 1, 2000): A147. http://dx.doi.org/10.1042/bst028a147c.

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Linskens, Maarten H. K., and Joel A. Huberman. "Ambiguities in results obtained with 2D gel replicon mapping techniques." Nucleic Acids Research 18, no. 3 (1990): 647–52. http://dx.doi.org/10.1093/nar/18.3.647.

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Di Vona, Maria Luisa, Silvia Licoccia, Laura Montanaro, and Enrico Traversa. "Sol−Gel Synthesis of NASICON: 1D and 2D NMR Investigation." Chemistry of Materials 11, no. 5 (May 1999): 1336–41. http://dx.doi.org/10.1021/cm9807788.

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Krivoruchko, O. P., T. V. Larina, A. V. Ishchenko, E. V. Pestryakov, and M. A. Merzliakov. "Sol–gel synthesis of 2D and 3D nanostructured YSZ:Yb3+ ceramics." Inorganic Materials 53, no. 5 (April 23, 2017): 540–47. http://dx.doi.org/10.1134/s0020168517050144.

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Wu, Jia-Rui, and David M. Gilbert. "Rapid DNA preparation for 2D gel analysis of replication intermediates." Nucleic Acids Research 23, no. 19 (1995): 3997–98. http://dx.doi.org/10.1093/nar/23.19.3997.

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Daszykowski, M., E. Mosleth Færgestad, H. Grove, H. Martens, and B. Walczak. "Matching 2D gel electrophoresis images with Matlab ‘Image Processing Toolbox’." Chemometrics and Intelligent Laboratory Systems 96, no. 2 (April 2009): 188–95. http://dx.doi.org/10.1016/j.chemolab.2009.01.011.

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Cheng, Hao-Tsai, Sen-Yung Hsieh, Chang-Mu Sung, Betty Chien-Jung Pai, Nai-Jen Liu, and Carl PC Chen. "Optimizing Human Bile Preparation for Two-Dimensional Gel Electrophoresis." BioMed Research International 2016 (2016): 1–6. http://dx.doi.org/10.1155/2016/5185317.

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Aims. Bile is an important body fluid which assists in the digestion of fat and excretion of endogenous and exogenous compounds. In the present study, an improved sample preparation for human bile was established.Methods and Material. The method involved acetone precipitation followed by protein extraction using commercially available 2D Clean-Up kit. The effectiveness was evaluated by 2-dimensional electrophoresis (2DE) profiling quality, including number of protein spots and spot distribution.Results. The total protein of bile fluid in benign biliary disorders was 0.797 ± 0.465 μg/μL. The sample preparation method using acetone precipitation first followed by 2D Clean-Up kit protein extraction resulted in better quality of 2DE gel images in terms of resolution as compared with other sample preparation methods. Using this protocol, we obtained approximately 558 protein spots on the gel images and with better protein spots presentation of haptoglobin, serum albumin, serotransferrin, and transthyretin.Conclusions. Protein samples of bile prepared using acetone precipitation followed by 2D Clean-Up kit exhibited high protein resolution and significant protein profile. This optimized protein preparation protocol can effectively concentrate bile proteins, remove abundant proteins and debris, and yield clear presentation of nonabundant proteins and its isoforms on 2-dimensional electrophoresis gel images.

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Singh, Pramod Kumar, Nidhi Shrivastava, Krishna Chaturvedi, Bechan Sharma, and Sameer S. Bhagyawant. "Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry." Biochemistry Research International 2016 (2016): 1–6. http://dx.doi.org/10.1155/2016/1049462.

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Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins withArabidopsis thaliana.

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WU, YUKUN, and LE ZHANG. "COMPARISON OF TWO ACADEMIC SOFTWARE PACKAGES FOR ANALYZING TWO-DIMENSIONAL GEL IMAGES." Journal of Bioinformatics and Computational Biology 09, no. 06 (December 2011): 775–94. http://dx.doi.org/10.1142/s0219720011005665.

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One of the key limitations for proteomic studies using two-dimensional (2D) gel is the lack of automatic, fast, robust, and reliable methods for detecting, matching, and quantifying protein spots. Although there are commercial software packages for 2D gel image analysis, extensive human intervention is still needed for spot detection and matching, which is time-consuming and error-prone. Moreover, the commercial software packages are usually expensive and non–open source. Thus, it is very beneficial for researchers to have free software that is fast, fully automatic, and robust. In this paper, we review and compare two recently developed and publicly available software packages, RegStatGel and Pinnacle, for analyzing 2D gel images. These two software packages share some common features and also have some fundamental difference in the aspects of spot detection and quantification. Based on our experience, RegStatGel is much better in terms of spot detection and matching. It also contains more advanced statistical tools and is more user-friendly. In contrast, Pinnacle is quite sensitive to background noise and relies on external statistical software packages for statistical analysis.

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Cohen, S., and S. Lavi. "Induction of circles of heterogeneous sizes in carcinogen-treated cells: two-dimensional gel analysis of circular DNA molecules." Molecular and Cellular Biology 16, no. 5 (May 1996): 2002–14. http://dx.doi.org/10.1128/mcb.16.5.2002.

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Extrachromosomal circular DNA molecules are associated with genomic instability, and circles containing inverted repeats were suggested to be the early amplification products. Here we present for the first time the use of neutral-neutral two-dimensional (2D) gel electrophoresis as a technique for the identification, isolation, and characterization of heterogeneous populations of circular molecules. Using this technique, we demonstrated that in N-methyl-N'-nitro-N-nitrosoguanidine-treated simian virus 40-transformed Chinese hamster cells (CO60 cells), the viral sequences are amplified as circular molecules of various sizes. The supercoiled circular fraction was isolated and was shown to contain molecules with inverted repeats. 2D gel analysis of extrachromosomal DNA from CHO cells revealed circular molecules containing highly repetitive DNA which are similar in size to the simian virus 40-amplified molecules. Moreover, enhancement of the amount of circular DNA was observed upon N-methyl-N'-nitro-N-nitrosoguanidine treatment of CHO cells. The implications of these findings regarding the processes of gene amplification and genomic instability and the possible use of the 2D gel technique to study these phenomena are discussed.

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Fan, Guang, Yanping Zhong, Cristina Smith, James Huang, and Rita Braziel. "A Proteomic Approach to Discovery of Candidate Proteins Involved in the Transformation of Follicular Lymphoma." Blood 106, no. 11 (November 16, 2005): 984. http://dx.doi.org/10.1182/blood.v106.11.984.984.

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Abstract Background: Follicular lymphoma (FL) undergoes transformation to a high grade diffuse large B-cell lymphoma (tr-DLBCL) in about 50% of patients. During transformation, a more virulent subclone of tumor cells emerges, leading to a rapidly progressive clinical course and resistance to therapy. The identification of proteins involved in transformation is critical for understanding the mechanism of transformation and developing molecularly targeted therapy. In this study, we compared protein expression between grade 1- FL (G1-FL) and tr-DLBCL using 2D-gel electrophoresis and Western blot analysis. Design: Frozen tissue and frozen cells were obtained from the Department of Pathology, Oregon Health and Science University tumor bank. The protein expression profiles of 3 G1-FL and 3 tr-DLBCL were compared using 2D-gel electrophoresis. Protein identification was done using a MALDI mass spectrometer. Frozen cells of an additional 11 non-paired GI-FL and 11 non-paired tr-DLBCL, and 2 pairs of G1-FL and tr-DLBCL specimens were used for Western blot confirmation of the initial 2D-gel findings. Results: 2D-gel analysis and MALDI protein identification revealed 14 differentially expressed proteins between G1-FL and tr-DLBCL (figure 1), all of which are known to play important roles in cellular energy/metabolic pathways, signal transduction pathways, and protein and nuclear synthesis. The two most differentially expressed proteins on 2D-gel analysis were superoxide dismutase (MnSOD2) and growth factor receptor bound protein 2 (Grb2). Western blot analysis of MnSOD2 and Grb2 confirmed their relative over- or under-expression in frozen cells from multiple additional clinical lymphoma samples, including 2 paired- and 22 non-paired G1-FL and tr-DLBCL. Both 2D-gel analysis and Western Blot showed a significantly higher level of expression of MnSOD2 and a lower expression of Grb2 expression in tr-DLBCL (figure 2). Summary: Using proteomic profiling, confirmed by Western blot analysis of clinical G1-FL and tr-DLBCL samples, we have confirmed 2 proteins (MnSOD2 and Grb2) that are expressed at significantly different levels in G1-FL and DLBCL. MnSOD2 is capable of protecting cells from reactive oxygen species and regulating signal transduction pathways to influence cell growth and apoptosis. Inhibition of MnSOD2 has been shown in studies of several cancer cell lines to render cancer cells more susceptible to apoptosis. Grb2 is a member of a critical signaling pathway leading to Ras activation in hematopoietic cells. Both proteins may play a critical role in FL transformation. These proteins have the potential to be therapeutic drug targets, diagnostic and/or prognostic markers, or biomarkers for monitoring therapeutic response. Summary of Differentially Expressed Spots Summary of Differentially Expressed Spots Figure Figure

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Rashwan, Shaheera, Mohamed Talaat Faheem, Amany Sarhan, and Bayumy A. B. Youssef. "A Wavelet Relational FuzzyC-Means Algorithm for 2D Gel Image Segmentation." Computational and Mathematical Methods in Medicine 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/430516.

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One of the most famous algorithms that appeared in the area of image segmentation is the FuzzyC-Means (FCM) algorithm. This algorithm has been used in many applications such as data analysis, pattern recognition, and image segmentation. It has the advantages of producing high quality segmentation compared to the other available algorithms. Many modifications have been made to the algorithm to improve its segmentation quality. The proposed segmentation algorithm in this paper is based on the FuzzyC-Means algorithm adding the relational fuzzy notion and the wavelet transform to it so as to enhance its performance especially in the area of 2D gel images. Both proposed modifications aim to minimize the oversegmentation error incurred by previous algorithms. The experimental results of comparing both the FuzzyC-Means (FCM) and the Wavelet FuzzyC-Means (WFCM) to the proposed algorithm on real 2D gel images acquired from human leukemias, HL-60 cell lines, and fetal alcohol syndrome (FAS) demonstrate the improvement achieved by the proposed algorithm in overcoming the segmentation error. In addition, we investigate the effect of denoising on the three algorithms. This investigation proves that denoising the 2D gel image before segmentation can improve (in most of the cases) the quality of the segmentation.

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Yoshdia, Yutaka, and Tadashi Yamamoto. "Proteomic analysis of human kidney glomerulus with fluoresent 2D difference gel electrophoresis (2D DIGE) using saturation labeling." SEIBUTSU BUTSURI KAGAKU 50, no. 3Special (2006): 211–15. http://dx.doi.org/10.2198/sbk.50.3special_211.

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Izawa, Kenichi, Toshiaki Ogasawara, Hideki Masuda, Hirofumi Okabayashi, Charmian J. O'Connor, and Isao Noda. "2D gel permeation chromatography (2D GPC) correlation studies of the growth process for perfluoro-octyltriethoxysilane polymer aggregates." Physical Chemistry Chemical Physics 4, no. 6 (February 13, 2002): 1053–61. http://dx.doi.org/10.1039/b107556j.

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Sarkar, Saswati, Shyamal Kumar Bhadra, and Sunirmal Jana. "Fabrication, characterization and water wetting behavior of mesoscale 1D/2D periodic structured silica-zirconia sol–gel thin films." RSC Advances 6, no. 52 (2016): 46048–59. http://dx.doi.org/10.1039/c6ra00380j.

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Xavier, Ilungo J., and George G. Khachatourians. "Heat-shock response of the entomopathogenic fungus Beauveria brongniartii." Canadian Journal of Microbiology 42, no. 6 (June 1, 1996): 577–85. http://dx.doi.org/10.1139/m96-078.

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The heat-shock response of five strains of the entomopathogenic fungus Beauveria brongniartii was studied using two-dimensional (2D) gel electrophoresis. The fungal cells were heat shocked at 45 °C for 1 h and the total cellular protein was subjected to 2D gel electrophoresis. Proteins were separated in the first dimension using isoelectric focusing (pH range of 3.0–10) and in the second dimension by sodium dodecyl sulphate – polyacrylamide gel electrophoresis. More than 150 polypeptides for each strain were visualized by silver staining and have been assigned individual numbers as polypeptide coordinates. Analysis of the polypeptide map obtained by 2D gels indicated three patterns; several unique heat-shock proteins (HSPs) were (i) induced, (ii) enhanced, or (iii) repressed. Some of the HSPs induced by 45 °C were unique for each of the strains tested. Identification of heat-inducible protein synthesis or repression has ramifications for field survival and performance of entomopathogenic fungi. As well, the HSPs can be used as "signature proteins" for identification pruposes and this raises the possibility of using HSPs as a diagnostic tool applicable to other pest control fungi.Key words: heat-shock proteins, heat-shock response, two-dimensional electrophoresis, entomopathogenic fungi, Beauveria brongniartii.

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41

Januskevicius, Justinas, Zivile Stankeviciute, Dalis Baltrunas, Kęstutis Mažeika, Aldona Beganskiene, and Aivaras Kareiva. "Aqueous Sol-Gel Synthesis of Different Iron Ferrites: From 3D to 2D." Materials 14, no. 6 (March 22, 2021): 1554. http://dx.doi.org/10.3390/ma14061554.

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In this study, an aqueous sol-gel synthesis method and subsequent dip-coating technique were applied for the preparation of yttrium iron garnet (YIG), yttrium iron perovskite (YIP), and terbium iron perovskite (TIP) bulk and thin films. The monophasic highly crystalline different iron ferrite powders have been synthesized using this simple aqueous sol-gel process displaying the suitability of the method. In the next step, the same sol-gel solution was used for the fabrication of coatings on monocrystalline silicon (100) using a dip-coating procedure. This resulted, likely due to substrate surface influence, in all coatings having mixed phases of both garnet and perovskite. Thermogravimetric (TG) analysis of the precursor gels was carried out. All the samples were investigated by X-ray powder diffraction (XRD) analysis. The coatings were also investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM) and Mössbauer spectroscopy. Magnetic measurements were also carried out.

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Hashemi, M., M. Pooladi, and SKR Abad. "Proteomics analysis of human brain glial cell proteome by 2D gel." Indian Journal of Cancer 51, no. 2 (2014): 159. http://dx.doi.org/10.4103/0019-509x.138271.

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Lilley, Kathryn S., and David B. Friedman. "All about DIGE: quantification technology for differential-display 2D-gel proteomics." Expert Review of Proteomics 1, no. 4 (December 2004): 401–9. http://dx.doi.org/10.1586/14789450.1.4.401.

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Kondo, Tadashi. "Cancer biomarker development and two-dimensional difference gel electrophoresis (2D-DIGE)." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1867, no. 1 (January 2019): 2–8. http://dx.doi.org/10.1016/j.bbapap.2018.07.002.

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Vedelago, J., D. Chacón Obando, F. Malano, R. Conejeros, R. Figueroa, D. Garcia, G. González, et al. "Fricke and polymer gel 2D dosimetry validation using Monte Carlo simulation." Radiation Measurements 91 (August 2016): 54–64. http://dx.doi.org/10.1016/j.radmeas.2016.05.003.

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Molina-Mora, Jose Arturo, Diana Chinchilla-Montero, Carolina Castro-Peña, and Fernando García. "Two-dimensional gel electrophoresis (2D-GE) image analysis based on CellProfiler." Medicine 99, no. 49 (December 4, 2020): e23373. http://dx.doi.org/10.1097/md.0000000000023373.

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Patel, Bhavinkumar B., Xin-Ming Li, Maketa P. Dixon, Elena L. Blagoi, Steven H. Seeholzer, Yibai Chen, C. Glenn Miller, et al. "Searchable High-Resolution 2D Gel Proteome of the Human Colon Crypt." Journal of Proteome Research 6, no. 6 (June 2007): 2232–38. http://dx.doi.org/10.1021/pr060641e.

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Tan, Niu J., Leona D. J. Daim, Amilia A. M. Jamil, Norhafizah Mohtarrudin, and Karuppiah Thilakavathy. "An effective placental cotyledons proteins extraction method for 2D gel electrophoresis." ELECTROPHORESIS 38, no. 5 (February 1, 2017): 633–44. http://dx.doi.org/10.1002/elps.201600377.

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Pasquali, Matias, Tommaso Serchi, Jenny Renaut, Lucien Hoffmann, and Torsten Bohn. "2D difference gel electrophoresis reference map of aFusarium graminearumnivalenol producing strain." ELECTROPHORESIS 34, no. 4 (January 22, 2013): 505–9. http://dx.doi.org/10.1002/elps.201200256.

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Mahon, Piers, and Paul Dupree. "Quantitative and reproducible two-dimensional gel analysis using Phoretix 2D Full." ELECTROPHORESIS 22, no. 10 (June 2001): 2075–85. http://dx.doi.org/10.1002/1522-2683(200106)22:10<2075::aid-elps2075>3.0.co;2-c.

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Journal articles on the topic '2D gel'

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