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Journal articles on the topic '2D-Gel electrophoresis'

Author: Grafiati

Published: 4 June 2021

Last updated: 15 February 2022

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

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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12

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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13

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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14

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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15

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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16

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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17

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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18

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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19

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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20

Stochaj, W. R., T. Berkelman, and N. Laird. "Preparative 2D Gel Electrophoresis with Immobilized pH Gradients: IPG Strip Equilibration." Cold Spring Harbor Protocols 2006, no. 28 (October 1, 2006): pdb.prot4584. http://dx.doi.org/10.1101/pdb.prot4584.

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21

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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22

Hallajian, Mohammad. "Proteome Analysis of Mutant Drought Tolerant Iranian Rice Using 2D Gel Electrophoresis." Annual Research & Review in Biology 4, no. 14 (January 10, 2014): 2372–95. http://dx.doi.org/10.9734/arrb/2014/8159.

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23

Chardin, Hélène, and Gabriel Peltre. "Allergome: the characterization of allergens based on a 2D gel electrophoresis approach." Expert Review of Proteomics 2, no. 5 (October 2005): 757–65. http://dx.doi.org/10.1586/14789450.2.5.757.

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24

Singh, Puneetpal, Monica Singh, and Kanwaljit Kaur. "Genetic Evaluation of proteins with High Resolution Two Dimensional (2D) Gel Electrophoresis." Anthropologist 2, no. 2 (April 2000): 77–85. http://dx.doi.org/10.1080/09720073.2000.11890633.

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25

Øye, Ola, Katarina M. Jørgensen, Sigrun M. Hjelle, André Sulen, Dag Ulvang, and Bjørn Gjertsen. "Gel2DE - A software tool for correlation analysis of 2D gel electrophoresis data." BMC Bioinformatics 14, no. 1 (2013): 215. http://dx.doi.org/10.1186/1471-2105-14-215.

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26

Bergquist, Jonas, Johan Gobom, Anders Blomberg, Peter Roepstorff, and Rolf Ekman. "Identification of nuclei associated proteins by 2D-gel electrophoresis and mass spectrometry." Journal of Neuroscience Methods 109, no. 1 (August 2001): 3–11. http://dx.doi.org/10.1016/s0165-0270(01)00395-8.

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27

Posch, Anton, Thomas Franz, Sonja Hartwig, Birgit Knebel, Hadi Al-Hasani, Waltraud Passlack, Nancy Kunz, et al. "2D-ToGo workflow: increasing feasibility and reproducibility of 2-dimensional gel electrophoresis." Archives of Physiology and Biochemistry 119, no. 3 (May 17, 2013): 108–13. http://dx.doi.org/10.3109/13813455.2013.791699.

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28

Brown, Stuart, and Gillian Norris. "Improved consistency in 2D gel electrophoresis: Sheep plasma as a test case." ELECTROPHORESIS 38, no. 6 (January 16, 2017): 906–13. http://dx.doi.org/10.1002/elps.201600433.

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29

Reed, Patrick W., Allison Densmore, and Robert J. Bloch. "Optimization of large gel 2D electrophoresis for proteomic studies of skeletal muscle." ELECTROPHORESIS 33, no. 8 (April 2012): 1263–70. http://dx.doi.org/10.1002/elps.201100642.

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30

Kim, Helen, Mark B. Cope, Richie Herring, Gloria Robinson, Landon Wilson, Grier P. Page, and Stephen Barnes. "2D Difference Gel Electrophoresis of Prepubertal and Pubertal Rat Mammary Gland Proteomes." Journal of Proteome Research 7, no. 11 (November 7, 2008): 4638–50. http://dx.doi.org/10.1021/pr800121b.

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31

Valdés, Antonio, Belén Martínez-García, Joana Segura, Sílvia Dyson, Ofelia Díaz-Ingelmo, and Joaquim Roca. "Quantitative disclosure of DNA knot chirality by high-resolution 2D-gel electrophoresis." Nucleic Acids Research 47, no. 5 (January 15, 2019): e29-e29. http://dx.doi.org/10.1093/nar/gkz015.

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32

Stochaj, W. R., T. Berkelman, and N. Laird. "Preparative 2D Gel Electrophoresis with Immobilized pH Gradients: SDS-PAGE of Proteins." Cold Spring Harbor Protocols 2006, no. 28 (October 1, 2006): pdb.prot4559. http://dx.doi.org/10.1101/pdb.prot4559.

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33

Bautsch, Wilfried. "Bacterial genome mapping by two-dimensional pulsed-field gel electrophoresis (2D-PFGE)." Molecular Biotechnology 2, no. 1 (August 1994): 29–44. http://dx.doi.org/10.1007/bf02789288.

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34

Natale, Massimo, Alfonso Caiazzo, Enrico M. Bucci, and Elisa Ficarra. "A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots." Genomics, Proteomics & Bioinformatics 10, no. 6 (December 2012): 336–44. http://dx.doi.org/10.1016/j.gpb.2012.06.005.

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35

Sutton, C. A., M. W. Shirley, and M. H. Wisher. "Characterization of coccidial proteins by two-dimensional sodium dodecyl sulphate–polyacrylamide gel electrophoresis." Parasitology 99, no. 2 (October 1989): 175–87. http://dx.doi.org/10.1017/s0031182000058613.

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SummaryTwo dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (2D SDS–PAGE) has been used to produce ‘fingerprint’ maps of the proteins from each of the 7 species of Eimeria which infect the chicken. All 7 species could be identified from their array of polypeptides but few differences were detected between strains of the same species. Alterations to the polypeptide array associated with the stage of sporulation of the oocysts were observed. lodination of sporozoites, 2D SDS–PAGE, autoradiography and immunoblotting techniques were combined to identify polypeptides with a surface moiety and those which were antigenic.

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36

Stochaj, W. R., T. Berkelman, and N. Laird. "Preparative 2D Gel Electrophoresis with Immobilized pH Gradients: IEF of Proteins in an IEF-Dedicated Electrophoresis Unit." Cold Spring Harbor Protocols 2006, no. 28 (October 1, 2006): pdb.prot4576. http://dx.doi.org/10.1101/pdb.prot4576.

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37

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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38

Lázaro, Beatriz, Jose Cárcamo, Ana Audícana, Ildefonso Perales, and Aurora Fernández-Astorga. "Viability and DNA Maintenance in Nonculturable Spiral Campylobacter jejuni Cells after Long-Term Exposure to Low Temperatures." Applied and Environmental Microbiology 65, no. 10 (October 1, 1999): 4677–81. http://dx.doi.org/10.1128/aem.65.10.4677-4681.1999.

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ABSTRACT Survival of Campylobacter jejuni at 4 and 20°C was investigated by using cellular integrity, respiratory activity, two-dimensional (2D) protein profile, and intact DNA content as indicators of potential viability of nonculturable cells. Intact DNA content after 116 days, along with cellular integrity and respiring cells, was detected for up to 7 months at 4°C by pulsed-field gel electrophoresis. Most changes in 2D protein profiles involved up- or down-regulation.

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39

Krogh, Morten, Céline Fernandez, Maria Teilum, Sofia Bengtsson, and Peter James. "A Probabilistic Treatment of the Missing Spot Problem in 2D Gel Electrophoresis Experiments." Journal of Proteome Research 6, no. 8 (August 2007): 3335–43. http://dx.doi.org/10.1021/pr070137p.

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40

Rashwan, Shaheera, Amany Sarhan, Muhamed Talaat Faheem, and Bayumy A. Youssef. "Fuzzy watershed segmentation algorithm: an enhanced algorithm for 2D gel electrophoresis image segmentation." International Journal of Data Mining and Bioinformatics 12, no. 3 (2015): 275. http://dx.doi.org/10.1504/ijdmb.2015.069659.

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41

Dowsey, Andrew W., Michael J. Dunn, and Guang-Zhong Yang. "Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline." Bioinformatics 24, no. 7 (February 28, 2008): 950–57. http://dx.doi.org/10.1093/bioinformatics/btn059.

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42

Spandidos, Athanasia, and Terence H. Rabbitts. "Sub-proteome Differential Display: Single Gel Comparison by 2D Electrophoresis and Mass Spectrometry." Journal of Molecular Biology 318, no. 1 (April 2002): 21–31. http://dx.doi.org/10.1016/s0022-2836(02)00052-9.

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43

Riess, D., and I. Lavrik. "2D-gel Electrophoresis As a Tool to Investigate the Composition of CD95 DISC." Acta Naturae 2, no. 2 (June 15, 2010): 96–101. http://dx.doi.org/10.32607/20758251-2010-2-2-96-101.

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44

Kamashev, D. E., T. V. Rakitina, D. S. Matyushkina, D. V. Evsyutina, A. A. Vanyushkina, Yu K. Agapova, V. E. Anisimova, et al. "Proteome of HU-Lacking E. coli Studied by Means of 2D Gel Electrophoresis." Russian Journal of Bioorganic Chemistry 45, no. 5 (September 2019): 366–73. http://dx.doi.org/10.1134/s1068162019050029.

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45

Yerlekar, Ashwini, and Priyanka Dudhe. "A Review on Study and Comparison between 2D Gel Electrophoresis and Mass Spectrometry." IOSR Journal of Computer Engineering 16, no. 2 (2014): 97–104. http://dx.doi.org/10.9790/0661-162597104.

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46

Michieletto, Davide, Davide Marenduzzo, and Enzo Orlandini. "Topological patterns in two-dimensional gel electrophoresis of DNA knots." Proceedings of the National Academy of Sciences 112, no. 40 (September 8, 2015): E5471—E5477. http://dx.doi.org/10.1073/pnas.1506907112.

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Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an “entanglement number” and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.

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47

Stochaj, W. R., T. Berkelman, and N. Laird. "Preparative 2D Gel Electrophoresis with Immobilized pH Gradients: Isoelectric Focusing of Proteins in a Multipurpose Flatbed Electrophoresis Unit." Cold Spring Harbor Protocols 2006, no. 28 (October 1, 2006): pdb.prot4575. http://dx.doi.org/10.1101/pdb.prot4575.

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48

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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49

van den Heuvel, L. P., M. H. Farhoud, R. A. Wevers, B. G. M. van Engelen, and J. A. M. Smeitink. "Proteomics and neuromuscular diseases: theoretical concept and first results." Annals of Clinical Biochemistry: International Journal of Laboratory Medicine 40, no. 1 (January 1, 2003): 9–15. http://dx.doi.org/10.1258/000456303321016123.

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Abstract:

Although many patients suspected of suffering disturbances of the mitochondrial energy metabolism have been investigated, only a fraction of these patients have been diagnosed at the molecular level. Introduction of new techniques like proteomics will be necessary to understand the various clinical and biochemical aberrations in the field of mitochondrial disorders. Two-dimensional electrophoresis is the first, important step in the proteomics strategy. Separation of soluble proteins is performed on the basis of isoelectric point (net charge) in one direction and on molecular mass in the other. The technique provides an overview of the majority of proteins expressed in a sample (e.g. muscle biopsy, muscle cell or mitochondrial fraction). Once an abnormal spot is observed in the gel the responsible protein can be identified by analysing a limited part of its amino acid sequence by mass spectrometry. We optimized two-dimensional (2D) gel electrophoresis to obtain high resolution 2D-maps and tested the reproducibility of the technique. Potentially, this new technique is capable of identifying novel mitochondrial diseases and defining their molecular basis.

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Lohnes, Karen, Neil R. Quebbemann, Kate Liu, Fred Kobzeff, Joseph A. Loo, and Rachel R. Ogorzalek Loo. "Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics." Methods 104 (July 2016): 163–69. http://dx.doi.org/10.1016/j.ymeth.2016.01.013.

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