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Journal articles on the topic '2D-PAGE'

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Published: 4 June 2021

Last updated: 11 March 2023

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1

Matera, Robert, Katalin V. Horvath, Hari Nair, Ernst J. Schaefer, and Bela F. Asztalos. "HDL Particle Measurement: Comparison of 5 Methods." Clinical Chemistry 64, no. 3 (March 1, 2018): 492–500. http://dx.doi.org/10.1373/clinchem.2017.277632.

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Abstract BACKGROUND HDL cell cholesterol efflux capacity has been documented as superior to HDL cholesterol (HDL-C) in predicting cardiovascular disease risk. HDL functions relate to its composition. Compositional assays are easier to perform and standardize than functional tests and are more practical for routine testing. Our goal was to compare measurements of HDL particles by 5 different separation methods. METHODS HDL subfractions were measured in 98 samples using vertical auto profiling (VAP), ion mobility (IM), nuclear magnetic resonance (NMR), native 2-dimensional gel electrophoresis (2D-PAGE), and pre-β1-ELISA. VAP measured cholesterol in large HDL2 and small HDL3; IM measured particle number directly in large, intermediate, and small HDL particles; NMR measured lipid signals in large, medium, and small HDL; 2D-PAGE measured apolipoprotein (apo) A-I in large (α1), medium (α2), small (α3–4), and pre-β1 HDL particles; and ELISA measured apoA-I in pre-β1-HDL. The data were normalized and compared using Passing–Bablok, Lin concordance, and Bland–Altman plot analyses. RESULTS With decreasing HDL-C concentration, NMR measured a gradually lower percentage of large HDL, compared with IM, VAP, and 2D-PAGE. In the lowest HDL-C tertile, NMR measured 8% of large HDL, compared with IM, 22%; VAP, 20%; and 2D-PAGE, 18%. There was strong discordance between 2D-PAGE and NMR in measuring medium HDL (R2 = 0.356; rc = 0.042) and small HDL (R2 = 0.376; rc = 0.040). The 2D-PAGE assay measured a significantly higher apoA-I concentration in pre-β1-HDL than the pre-β1-ELISA (9.8 vs 1.6 mg/dL; R2 = 0.246; rc = 0.130). CONCLUSIONS NMR agreed poorly with the other methods in measuring large HDL, particularly in low HDL-C individuals. Similarly, there was strong discordance in pre-β1-HDL measurements between the ELISA and 2D-PAGE assays.

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2

Vijayendran, Chandran, Sebastian Burgemeister, Karl Friehs, Karsten Niehaus, and Erwin Flaschel. "2DBase: 2D-PAGE database of Escherichia coli." Biochemical and Biophysical Research Communications 363, no. 3 (November 2007): 822–27. http://dx.doi.org/10.1016/j.bbrc.2007.09.050.

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3

Hanneken, Marina, Doreen Ackermann, Simone König, and Günter Thesseling. "Koordinatenbestimmung von Proteinpunkten in 2D-PAGE-Gelen." BIOspektrum 20, no. 6 (September 30, 2014): 655–57. http://dx.doi.org/10.1007/s12268-014-0503-5.

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4

Chorney, M. J., J. S. Tung, Y. Bushkin, and F. W. Shen. "Structural characteristics of Tla products." Journal of Experimental Medicine 162, no. 3 (September 1, 1985): 781–89. http://dx.doi.org/10.1084/jem.162.3.781.

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Biochemical study of thymus leukemia antigen (TL) from thymocytes of various Tla genotypes and from leukemia cells revealed features that, given present evidence, are peculiar to TL among class I products of the H-2:Qa:Tla region of chromosome 17. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of TL from thymocytes of all TL+ mouse strains, precipitated by anti-TL antiserum or monoclonal antibodies, showed two closely migrating bands of equal intensity in the heavy (H) chain position (45-50,000 mol wt). Comparison of these two bands by two-dimensional isoelectric focusing (2D IEF)-SDS-PAGE and 2D chymotryptic peptide mapping showed no differences indicative of protein dissimilarity. Thus, the two components of the H chain doublet may differ only in a feature of glycosylation that does not affect charge. The two leukemias studied gave only a single band in the H chain position. On 2D peptide mapping and 2D IEF-SDS-PAGE, the patterns for TL of Tlaa and Tlae thymocytes, which are closely related serologically, were broadly similar, but clearly different from the pattern typical of Tlac and Tlad thymocytes. 2D peptide maps of TL from Tlaa thymocytes and Tlaa leukemia cells did not differ. Leukemia cells of Tlab origin (thymocytes TL-) gave 2D peptide and 2D IEF-SDS-PAGE patterns of a third type. With the exception of Tlaa, thymocytes of TL+ mice yielded additional TL products of higher molecular weight than the TL H chain.

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5

Pietrogrande, Maria Chiara, Nicola Marchetti, Francesco Dondi, and Pier Giorgio Righetti. "Decoding 2D-PAGE complex maps: Relevance to proteomics☆." Journal of Chromatography B 833, no. 1 (March 20, 2006): 51–62. http://dx.doi.org/10.1016/j.jchromb.2005.12.051.

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Griebel, Anja, Christian Obermaier, Reiner Westermeier, Martin Moche, and Knut Büttner. "Fluoreszenzmarkierung von Proteinen für 1D- und 2D-PAGE." BIOspektrum 19, no. 6 (October 2013): 653–55. http://dx.doi.org/10.1007/s12268-013-0375-0.

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7

Li, Feng, Françoise Seillier-Moiseiwitsch, and Valeriy R. Korostyshevskiy. "Region-based statistical analysis of 2D PAGE images." Computational Statistics & Data Analysis 55, no. 11 (November 2011): 3059–72. http://dx.doi.org/10.1016/j.csda.2011.05.013.

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8

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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Pavlicevic, Milica, Sladjana Stanojevic, and Biljana Vucelic-Radovic. "Influence of extraction method on protein profile of soybeans." Chemical Industry 67, no. 4 (2013): 687–94. http://dx.doi.org/10.2298/hemind120919115p.

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Comparison between protein profiles of soybean obtained by commonly used methods of extraction (Tris buffer and Tris-urea buffer) with methods used for extraction of plant proteins for 2D PAGE analysis (direct solubilization in IEF buffer, acetone extraction, phenol extraction, extraction with urea solubilization buffer and thiourea-urea extraction) was investigated. 2D profiles of samples extracted directly in IEF buffer, in urea solubilization buffer and in acetone were characterized with low number of spots. Analysis of 2D PAGE profiles of Tris buffer and Tris-urea buffer extracts showed high degree of horizontal and vertical streaking. Thiourea-urea extraction gave the highest number of less intense protein spots than phenol extraction. Method of choice, due to a large number of intense spots, would be phenol extraction.

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10

Tao, R., H. Yamane, H. Sassa, H. Mori, H. Murayama, T. M. Gradziel, A. M. Dandekar, and A. Sugiura. "Stylar Proteins Associated with Gametophytic Self-incompatibility in the Prunus." HortScience 32, no. 3 (June 1997): 514E—514. http://dx.doi.org/10.21273/hortsci.32.3.514e.

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Stylar proteins of four Prunus species, P. avium, P. dulcis, P. mume, and P. salicina, were surveyed by 2D-PAGE combined with immunoblot and N-terminal amino acid sequence analyses to identify S-proteins associated with gametophytic SI in the Prunus. All four S-allelic products tested for P. dulcis could be identified in the highly basic zone of the gel. These S-proteins had Mr of about 28–30 kDa and reacted with the anti-S4-serum prepared from Japanese pear (Pyrus serotina). Two of six S-allelic products tested for P. avium could be also identified in the 2D-PAGE profiles, with roughly the same pI and Mr as those of S-proteins of P. dulcis. Putative S-proteins for P. mume and P. salicina were found in the same area of 2D-PAGE as the area where S-proteins of P. avium and P. dulcis were located. N-terminal amino acid sequence analysis of these proteins revealed that they were similar to S-RNases reported previously.

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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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12

Bäck, Peter, Sofia Bengtsson, and Peter James. "Automated PreScan Function for Scanning Fluorescently Stained 2D-PAGE Gels." Journal of Proteome Research 4, no. 5 (October 2005): 1511–15. http://dx.doi.org/10.1021/pr0500408.

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MIKAMI, Satoshi, Tadashi KISHIMOTO, Hidetaka HORI, and Toshiaki MITSUI. "Technical Improvement to 2D-PAGE of Rice Organelle Membrane Proteins." Bioscience, Biotechnology, and Biochemistry 66, no. 5 (January 2002): 1170–73. http://dx.doi.org/10.1271/bbb.66.1170.

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14

Müller, D. R., P. Schindler, M. Coulot, H. Voshol, and J. van Oostrum. "Mass spectrometric characterization of stathmin isoforms separated by 2D PAGE." Journal of Mass Spectrometry 34, no. 4 (April 1999): 336–45. http://dx.doi.org/10.1002/(sici)1096-9888(199904)34:4<336::aid-jms765>3.0.co;2-u.

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15

Nowacka, Martyna, Paulina Jackowiak, Agnieszka Rybarczyk, Tomasz Magacz, Pawel M. Strozycki, Jan Barciszewski, and Marek Figlerowicz. "2D-PAGE as an effective method of RNA degradome analysis." Molecular Biology Reports 39, no. 1 (May 11, 2011): 139–46. http://dx.doi.org/10.1007/s11033-011-0718-1.

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Tiwari, Alka, W. Paul Williams, and Xueyan Shan. "MatGel: A MATLAB program for quantitative analysis of 2D polyacrylamide electrophoresis (2D-PAGE) protein gel images." MethodsX 9 (2022): 101930. http://dx.doi.org/10.1016/j.mex.2022.101930.

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17

Wang, Yong, Yi Ren Jiang, and Li Qin. "Using 2D-PAGE and Mass Spectrometry (LC-MS/MS) for Embryo Proteins Analysis in Antheraea pernyi." Advanced Materials Research 884-885 (January 2014): 556–59. http://dx.doi.org/10.4028/www.scientific.net/amr.884-885.556.

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To study the dynamic variation of protein components and contents inAntheraea pernyi, 2D-PAGE, in this job, was used to investigate embryo development. Some special protein spots expression profiles changed obviously were analyzed by mass spectrometry. 2D-PAGE results showed that the protein spots increased from 370 at the development stage of 12 h to 422 at 300 h. Eighteen special protein spots were identified byLC-MS/MS, and 8 kinds of proteins are found to include heat shock proteins families, Vitellogenin, KK-42-binding protein, actin-depolymerizing factor 1, etc., which are mainly involved in some important processes. Analyze the function of those proteins, so as to accumulate basic information on embryonic development inA. pernyi.

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18

Krause, Ingolf, Ursula M�ller, and Hans-Dieter Belitz. "Charakterisierung von Weizensorten durch SDS-Polyacrylamidgel-Elektrophorese (SDS-PAGE) und zweidimensionale Elektrophorese (2D-PAGE) der Glutenine." Zeitschrift f�r Lebensmittel-Untersuchung und -Forschung 186, no. 5 (May 1988): 398–406. http://dx.doi.org/10.1007/bf01127299.

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19

Nguyen, Thien An, and Jaejin Lee. "Simplified Two-Dimensional Generalized Partial Response Target of Holographic Data Storage Channel." Applied Sciences 12, no. 8 (April 18, 2022): 4070. http://dx.doi.org/10.3390/app12084070.

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With a high capacity and fast data access rate, holographic data storage (HDS) is a potential candidate for future storage systems. However, for page-oriented data processing, two-dimensional (2D) interference appears intensely in the HDS systems. Therefore, the new 2D generalized partial response (GPR) target is introduced to estimate the 2D interference. In addition, we also propose a method to analyze the 2D GPR target into two serial one-dimensional (1D) GPR targets. It makes us design a simple detection scheme composed of two serial 1D detectors instead of a complicated 2D detector. In simulations, the results show that our proposed scheme can improve the BER performance compared to the conventional 1D GPR target model.

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20

Nishioka, Keiji, Yusuke Kato, Shin-ichiro Ozawa, Yuichiro Takahashi, and Wataru Sakamoto. "Phos-tag-based approach to study protein phosphorylation in the thylakoid membrane." Photosynthesis Research 147, no. 1 (December 2, 2020): 107–24. http://dx.doi.org/10.1007/s11120-020-00803-1.

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AbstractProtein phosphorylation is a fundamental post-translational modification in all organisms. In photoautotrophic organisms, protein phosphorylation is essential for the fine-tuning of photosynthesis. The reversible phosphorylation of the photosystem II (PSII) core and the light-harvesting complex of PSII (LHCII) contribute to the regulation of photosynthetic activities. Besides the phosphorylation of these major proteins, recent phosphoproteomic analyses have revealed that several proteins are phosphorylated in the thylakoid membrane. In this study, we utilized the Phos-tag technology for a comprehensive assessment of protein phosphorylation in the thylakoid membrane of Arabidopsis. Phos-tag SDS-PAGE enables the mobility shift of phosphorylated proteins compared with their non-phosphorylated isoform, thus differentiating phosphorylated proteins from their non-phosphorylated isoforms. We extrapolated this technique to two-dimensional (2D) SDS-PAGE for detecting protein phosphorylation in the thylakoid membrane. Thylakoid proteins were separated in the first dimension by conventional SDS-PAGE and in the second dimension by Phos-tag SDS-PAGE. In addition to the isolation of major phosphorylated photosynthesis-related proteins, 2D Phos-tag SDS-PAGE enabled the detection of several minor phosphorylated proteins in the thylakoid membrane. The analysis of the thylakoid kinase mutants demonstrated that light-dependent protein phosphorylation was mainly restricted to the phosphorylation of the PSII core and LHCII proteins. Furthermore, we assessed the phosphorylation states of the structural domains of the thylakoid membrane, grana core, grana margin, and stroma lamella. Overall, these results demonstrated that Phos-tag SDS-PAGE is a useful biochemical tool for studying in vivo protein phosphorylation in the thylakoid membrane protein.

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21

Huber, Sylvia, Sabine Minnebusch, Stefan Wuertz, Peter A. Wilderer, and Brigitte Helmreich. "Impact of different substrates on biomass protein composition during wastewater treatment investigated by two-dimensional electrophoresis." Water Science and Technology 37, no. 4-5 (February 1, 1998): 363–66. http://dx.doi.org/10.2166/wst.1998.0667.

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The influence of different influent substrates on biomass protein composition was examined by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Activated sludge from six sequencing batch reactors (SBRs) was investigated; four reactors were fed with model substrates and two received effluents from a wood milling process and a paper production process, respectively. Our investigations showed that in 2D-PAGE complex substrates caused a less diverse protein pattern than model wastewater composed of simple and low molecular weight compounds. This may be caused by complex formation by high molecular weight compounds of substrate with proteins. A more likely explanation is the presence of a more diversified microbial population resulting in a lower concentration of individual proteins, so that detection limits after staining were too high to observe discrete spots.

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22

ÁLVAREZ-GARCÍA, G., A. PITARCH, A. ZABALLOS, A. FERNÁNDEZ-GARCÍA, C. GIL, M. GÓMEZ-BAUTISTA, A. AGUADO-MARTÍNEZ, and L. M. ORTEGA-MORA. "The NcGRA7gene encodes the immunodominant 17 kDa antigen ofNeospora caninum." Parasitology 134, no. 1 (October 11, 2006): 41–50. http://dx.doi.org/10.1017/s0031182006001284.

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ANeospora caninum17–19 kDa antigenic protein fraction (p17) in one-dimensional polyacrylamide gel electrophoresis (SDS-PAGE) is the immunodominant antigen recognized by sera from bovines naturally infected byN. caninum. To identify the proteins making up the p17 fraction, we screened a newN. caninumtachyzoite cDNA library with an affinity-purified antibody against p17 (APA17). We isolated several cDNA clones with 100% sequence identity to the NcGRA7gene. This previously described gene encodes a dense granule protein with an apparent molecular mass of 33 kDa. A second line of evidence emerged through a combined proteomic approach associating two-dimensional PAGE (2D-PAGE) to Western blotting and to mass spectrometry to characterize the p17 fraction. Two acidic immunodominant but minority protein spots were recognized by APA17 and by bovine sera. These antigens of 17 and 33 kDa are respectively composed of 4 and 2 isoforms. Furthermore, p17 isolation by 2D-PAGE and peptide sequencing by tandem mass spectrometry yielded a partial sequence of 17 amino acids, which allowed the putative amino terminal region of the NcGRA7 protein to be identified unambiguously.The NcGRA7 protein, without the putative signal peptide at the NH2-terminus, was cloned and expressed inEscherichia coliand when the purified recombinant protein (rNcGRA7) was analysed by SDS-PAGE and mass spectrometry, 2 bands of 24 and 33 kDa were resolved and identified as NcGRA7. These results demonstrate that the immunodominant 17 kDa antigen ofN. caninumis encoded by the NcGRA7gene.

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23

Manabe, Takashi. "The technique of 2D-PAGE for the analysis of native proteins." SEIBUTSU BUTSURI KAGAKU 34, no. 6 (1990): 317–20. http://dx.doi.org/10.2198/sbk.34.317.

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24

Skvortsov, V. S., N. N. Alekseychuk, and A. V. Rybina. "Correction of the electrophoretic shift in virtual 2D SDS-PAGE electrophoresis." Biomeditsinskaya Khimiya 63, no. 3 (2017): 278–83. http://dx.doi.org/10.18097/pbmc20176303278.

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Virtual electrophoresis in proteomics can be used to search localization of proteins and their proteoforms (especially those existing in low concentrations), to identify proteoforms found in experiments etc. Although the problem of predicting the isoelectric point is well studied, the need of electrophoretic shift correction is usually ignored. Researchers simply use the brutto molecular weight of the protein. In this study four data sets taken from the literature sources and the SWISS-2DPAGE database have been used to build correction equations for prediction of the electrophoretic shift (123, 72, 118 and 470 points, respectively). Two groups of models were built. The first model was based on the amino acid composition of proteins, the second one, on analysis of parameters calculated by amino acid sequences (theoretical molecular weight, hydrophobicity, charge distribution, ability to form helix structures). The coefficient of determination ranged from 0.35 to 0.75 in each single set, but cross-prediction between samples did not gave satisfactory results. At the same time, the direction of correction was predicted correctly in 74% of cases. After combining of the samples and dividing pooled data into 2 representative sets, the coefficient of determination during in the process of learning ranged from 0.44 to 0.51, and R2 of predictions were not less than 0.39. The direction of correction was predicted correctly in 80% of cases. This prediction models have been integrated into the program pIPredict v.2, freely available at http://www.ibmc.msk.ru/LPCIT/pIPredict.

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Cadoni, Mariano, and Andrea P. Sanna. "Unitarity and Page Curve for Evaporation of 2D AdS Black Holes." Entropy 24, no. 1 (January 8, 2022): 101. http://dx.doi.org/10.3390/e24010101.

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We explore the Hawking evaporation of two-dimensional anti-de Sitter (AdS2), dilatonic black hole coupled with conformal matter, and derive the Page curve for the entanglement entropy of radiation. We first work in a semiclassical approximation with backreaction. We show that the end-point of the evaporation process is AdS2 with a vanishing dilaton, i.e., a regular, singularity-free, zero-entropy state. We explicitly compute the entanglement entropies of the black hole and the radiation as functions of the horizon radius, using the conformal field theory (CFT) dual to AdS2 gravity. We use a simplified toy model, in which evaporation is described by the forming and growing of a negative mass configuration in the positive-mass black hole interior. This is similar to the “islands” proposal, recently put forward to explain the Page curve for evaporating black holes. The resulting Page curve for AdS2 black holes is in agreement with unitary evolution. The entanglement entropy of the radiation initially grows, closely following a thermal behavior, reaches a maximum at half-way of the evaporation process, and then goes down to zero, following the Bekenstein–Hawking entropy of the black hole. Consistency of our simplified model requires a non-trivial identification of the central charge of the CFT describing AdS2 gravity with the number of species of fields describing Hawking radiation.

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Hagen-Ansert, Sandra. "Beyond the Page: Creating a 3D Understanding of a 2D Image." Journal of Diagnostic Medical Sonography 20, no. 2 (March 2004): 147–49. http://dx.doi.org/10.1177/8756479304263207.

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Arrigoni, Giorgio, Celine Fernandez, Cecilia Holm, Michaela Scigelova, and Peter James. "Comparison of MS/MS Methods for Protein Identification from 2D-PAGE." Journal of Proteome Research 5, no. 9 (September 2006): 2294–300. http://dx.doi.org/10.1021/pr0601281.

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Moerman, P. P., K. Sergeant, G. Debyser, I. Timperman, B. Devreese, and B. Samyn. "Automation of C-terminal sequence analysis of 2D-PAGE separated proteins." EuPA Open Proteomics 3 (June 2014): 250–61. http://dx.doi.org/10.1016/j.euprot.2014.03.004.

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Reisinger, Veronika, and Lutz Andreas Eichacker. "How to Analyze Protein Complexes by 2D Blue Native SDS-PAGE." PROTEOMICS 7, S1 (September 2007): 6–16. http://dx.doi.org/10.1002/pmic.200700205.

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Katsani, K. R., P. Tsiboli, K. Anagnostopoulos, H. Urlaub, and T. Choli-Papadopoulou. "Identification of the 50S Ribosomal Proteins from the Eubacterium Thermus thermophilus." Biological Chemistry 381, no. 11 (November 15, 2000): 1079–87. http://dx.doi.org/10.1515/bc.2000.133.

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Abstract The total protein mixture from the 50S subunit (TP-50) of the eubacterium Thermus thermophilus was characterized after blotting onto PVDF membranes from two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and sequencing. The proteins were numbered according to their primary structure similarity with their counterparts from other species. One of them has been marked with an asterisk, namely L*23, because unlike the other known ribosomal proteins it shows a very low degree of homology. A highly acidic 5S rRNA binding protein, TL5, was characterized and compared with the available primary structure information. Proteins L1 and L4 migrate similarly on 2D-PAGE. Protein L4, essential for protein biosynthesis, is N-terminally blocked and shows a strikingly low homology to other L4 proteins. In addition to L4, two other proteins, namely L10 and L11, were found to be N-terminally blocked. In conclusion, 33 proteins from the large subunit were identified, including TL5. Homologs to rpL25 and rpL26 were not found.

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Centlow, Magnus, Stefan R. Hansson, and Charlotte Welinder. "Differential Proteome Analysis of the Preeclamptic Placenta Using Optimized Protein Extraction." Journal of Biomedicine and Biotechnology 2010 (2010): 1–9. http://dx.doi.org/10.1155/2010/458748.

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The human placenta is a difficult tissue to work with using proteomic technology since it contains large amounts of lipids and glycogen. Both lipids and glycogen are known to interfere with the first step in the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the isoelectric focusing. In order to gain the best possible protein separation on 2D-PAGE, an optimized sample preparation protocol for placental proteins was developed. Two different buffers, urea/CHAPS and Hepes, were used for solubilization in combination with six different precipitation methods. The removal of glycogen from the samples by centrifugation was crucial for the final proteome maps. Solubilization with urea/CHAPS in combination with dichloromethane/methanol or acidified acetone proved to be the best precipitation procedures. When applied to clinical placenta samples apolipoprotein A1 was found to be accumulated in the preeclamptic placenta, where it may either have a nutritional effect or act as a modifier of signal transduction.

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Perrin, Clarisse, Chantal Poirson, Patrice Bracquart, Jean-Luc Gaillard, and Christiane Guimont. "Etablissement de l'empreinte protéique de base de Streptococcus thermophilus par 2D-PAGE." Sciences des Aliments 20, no. 1 (February 28, 2000): 97–104. http://dx.doi.org/10.3166/sda.20.97-104.

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Saledekh, H., F. Shekari, B. Jordan, and H. Baharvand. "Proteome Analysis of Mouse Liver Microsomal Fraction Using 2D BN/SDS-PAGE." Journal of Proteomics & Bioinformatics S2, no. 01 (July 2008): 118. http://dx.doi.org/10.4172/jpb.s1000093.

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Wu, Steven H., Michael A. Black, Robyn A. North, Kelly R. Atkinson, and Allen G. Rodrigo. "A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels." PLoS Computational Biology 5, no. 9 (September 18, 2009): e1000509. http://dx.doi.org/10.1371/journal.pcbi.1000509.

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Xia, K., M. Manning, H. Hesham, Q. Lin, C. Bystroff, and W. Colon. "Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE." Proceedings of the National Academy of Sciences 104, no. 44 (October 23, 2007): 17329–34. http://dx.doi.org/10.1073/pnas.0705417104.

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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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37

Lister, Adrian M. "Correction for Lister, The impact of Quaternary Ice Ages on mammalian evolution." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1452 (December 29, 2004): 1953–54. http://dx.doi.org/10.1098/rstb.2004.2000.

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Correction for ‘The impact of Quaternary Ice Ages on mammalian evolution’ by A. M. Lister (Phil. Trans. R. Soc. Lond. B 357 , 1643–1667. (doi: 10.1098/rstb.2003.1436 )). On page 230, the stippling in figure 2d,e was missing. The corrected figure and its caption appear below.

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Andringa, Kelly K., Adrienne L. King, Heather B. Eccleston, Sudheer K. Mantena, Aimee Landar, Nirag C. Jhala, Dale A. Dickinson, Giuseppe L. Squadrito, and Shannon M. Bailey. "Analysis of the liver mitochondrial proteome in response to ethanol and S-adenosylmethionine treatments: novel molecular targets of disease and hepatoprotection." American Journal of Physiology-Gastrointestinal and Liver Physiology 298, no. 5 (May 2010): G732—G745. http://dx.doi.org/10.1152/ajpgi.00332.2009.

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S-adenosylmethionine (SAM) minimizes alcohol hepatotoxicity; however, the molecular mechanisms responsible for SAM hepatoprotection remain unknown. Herein, we use proteomics to determine whether the hepatoprotective action of SAM against early-stage alcoholic liver disease is linked to alterations in the mitochondrial proteome. For this, male rats were fed control or ethanol-containing liquid diets ± SAM and liver mitochondria were prepared for proteomic analysis. Two-dimensional isoelectric focusing (2D IEF/SDS-PAGE) and blue native gel electrophoresis (BN-PAGE) were used to determine changes in matrix and oxidative phosphorylation (OxPhos) proteins, respectively. SAM coadministration minimized alcohol-dependent inflammation and preserved mitochondrial respiration. SAM supplementation preserved liver SAM levels in ethanol-fed rats; however, mitochondrial SAM levels were increased by ethanol and SAM treatments. With use of 2D IEF/SDS-PAGE, 30 proteins showed significant changes in abundance in response to ethanol, SAM, or both. Classes of proteins affected by ethanol and SAM treatments were chaperones, beta oxidation proteins, sulfur metabolism proteins, and dehydrogenase enzymes involved in methionine, glycine, and choline metabolism. BN-PAGE revealed novel changes in the levels of 19 OxPhos proteins in response to ethanol, SAM, or both. Ethanol- and SAM-dependent alterations in the proteome were not linked to corresponding changes in gene expression. In conclusion, ethanol and SAM treatment led to multiple changes in the liver mitochondrial proteome. The protective effects of SAM against alcohol toxicity are mediated, in part, through maintenance of proteins involved in key mitochondrial energy conserving and biosynthetic pathways. This study demonstrates that SAM may be a promising candidate for treatment of alcoholic liver disease.

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Weinkauf, Marc, Grit Hutter, Yvonne Zimmermann, Elena Hartmann, Andreas Rosenwald, Wolfgang Hiddemann, and Martin H. Dreyling. "RNA-Expression and Proteome Analysis Identify Complementary but Not Identical Molecular Targets in Enzastaurin-Treated Mantle Cell Lymphoma." Blood 114, no. 22 (November 20, 2009): 1915. http://dx.doi.org/10.1182/blood.v114.22.1915.1915.

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Abstract Abstract 1915 Poster Board I-938 Introduction: Protein kinase C beta (PKCbeta), a pivotal enzyme in B-cell signaling and survival, is over-expressed in most cases of mantle cell lymphoma (MCL) and results in activation of PI3K/AKT pathway. Enzastaurin, an oral serine/threonine kinase inhibitor, suppresses signaling through PKCbeta/PI3K/AKT pathways, induces apoptosis, reduces proliferation, and suppresses tumor-induced angiogenesis. Aim: To optimize the treatment options with this promising inhibitor the goal of this study was to elucidate the molecular pathways altered by Enzastaurin treatment in MCL. Methods: Four documented MCL cell lines (Granta 519, HBL-2, Jeko-1, Rec-1) were harvested after 2-8h Enzastaurin exposure at a previously defined dose of 10μM and analyzed by RNA-array and proteome analysis as previously described (2D-polyacrylamide-gel-electrophoresis (2D-PAGE); Weinkauf 2009). Regulated molecules were mapped in a functional interaction network and candidates representing different pathways were verified by Western blotting. Results: Enzastaurin exposure led to significant reduction of cell viability in all cell lines (15-20%). This was also reflected in distinct alterations of the observed protein patterns in 2D-PAGE after enzastaurin exposure. Of a total of 977 concurrent protein spots 115 (12%) spots exhibited significantly (>3fold) altered protein levels after 4h of enzastaurin exposure. Mass spectrometry of 62 protein spots (39 increase; 23 decreased) identified 108 different candidate proteins, which were used to create a protein interaction network identifying the affected functional pathways. The results of the 2D-PAGE analysis were verified by Western blot in selected candidate proteins of apoptosis (VIM, PLEC1), DNA-repair (RAD50, PCNA, RFC1) and gene expression (EEF1D, SMC1A) pathways. In parallel, RNA-expression array analysis identified 180 different genes regulated early after enzastaurin treatment. Again these genes were mapped to an interaction network, highlighting enzastaurin involvement in e.g. NFkB-, apoptosis and B-cell- and death receptor signaling pathways. Interestingly, the involved genes complemented the regulated proteins in the functional pathways. Network analysis of both screenings (2D-PAGE-based proteomics and RNA-expression array) classified the candidate molecules in functional groups, including DNA repair and replication (e.g. RAD50, PCNA), apoptosis (e.g.PSMC4, VIM), signal transduction (e.g. GRB2, EF1D) and gene expression/mRNA processing (e.g.EEF1D, SFRS7). Thus, combined analysis of both screening methods resulted in a more comprehensive network than each respective analysis. Conclusion: Enzastaurin-treatment affects three main cellular control mechanisms as highlighted by two independent screening approaches (proteomics and expression array analysis). Interestingly, these two layers of molecular response (protein and RNA respectively) resulted in minimal overlap of identified molecules at this early (4h) time, but indicated common pathways nonetheless. Ongoing experiments now incorporate this knowledge to select optimal combination partners of enzastaurin. Disclosures: Dreyling: Lilly Deutschland GmbH: Research Funding.

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Raberg, Matthias, Frank Reinecke, Rudolf Reichelt, Ursula Malkus, Simone König, Markus Pötter, Wolfgang Florian Fricke, et al. "Ralstonia eutropha H16 Flagellation Changes According to Nutrient Supply and State of Poly(3-Hydroxybutyrate) Accumulation." Applied and Environmental Microbiology 74, no. 14 (May 23, 2008): 4477–90. http://dx.doi.org/10.1128/aem.00440-08.

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ABSTRACT Two-dimensional polyacrylamide gel electrophoresis (2D PAGE), in combination with matrix-assisted laser desorption ionization-time of flight analysis, and the recently revealed genome sequence of Ralstonia eutropha H16 were employed to detect and identify proteins that are differentially expressed during different phases of poly(3-hydroxybutyric acid) (PHB) metabolism. For this, a modified protein extraction protocol applicable to PHB-harboring cells was developed to enable 2D PAGE-based proteome analysis of such cells. Subsequently, samples from (i) the exponential growth phase, (ii) the stationary growth phase permissive for PHB biosynthesis, and (iii) a phase permissive for PHB mobilization were analyzed. Among several proteins exhibiting quantitative changes during the time course of a cultivation experiment, flagellin, which is the main protein of bacterial flagella, was identified. Initial investigations that report on changes of flagellation for R. eutropha were done, but 2D PAGE and electron microscopic examinations of cells revealed clear evidence that R. eutropha exhibited further significant changes in flagellation depending on the life cycle, nutritional supply, and, in particular, PHB metabolism. The results of our study suggest that R. eutropha is strongly flagellated in the exponential growth phase and loses a certain number of flagella in transition to the stationary phase. In the stationary phase under conditions permissive for PHB biosynthesis, flagellation of cells admittedly stagnated. However, under conditions permissive for intracellular PHB mobilization after a nitrogen source was added to cells that are carbon deprived but with full PHB accumulation, flagella are lost. This might be due to a degradation of flagella; at least, the cells stopped flagellin synthesis while normal degradation continued. In contrast, under nutrient limitation or the loss of phasins, cells retained their flagella.

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Fuchs, Dagmar, Isabel Winkelmann, Ian T. Johnson, Edwin Mariman, Uwe Wenzel, and Hannelore Daniel. "Proteomics in nutrition research: principles, technologies and applications." British Journal of Nutrition 94, no. 3 (September 2005): 302–14. http://dx.doi.org/10.1079/bjn20051458.

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The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.

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COLLINS, Richard F., Toby D. FLINT, Andreas HOLZENBURG, and Robert C. FORD. "Structural changes in photosystem II after treatment with the zero-length bifunctional cross-linker 1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide: an electron microscopic study." Biochemical Journal 319, no. 2 (October 15, 1996): 585–89. http://dx.doi.org/10.1042/bj3190585.

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Two-dimensional (2D) crystals of photosystem II (PS II) treated with various concentrations of the zero-length crosslinker 1-ethyl-3-(3-dimethylaminopropyl)carbodi-imide (EDC) were analysed by electron microscopy in conjunction with crystallographic image processing. The preparations were characterized by SDS/PAGE and oxygen-evolution measurements, and the effectiveness of cross-linking was monitored by measuring the level of protection afforded against high concentrations of NaCl and CaCl2, which normally remove extrinsic proteins from PS II. We found that low concentrations of EDC (0.25%) increase the order of 2D crystals of PS II. Treatments with EDC concentrations higher than 0.5% did not improve the order of 2D crystals but induced gross structural changes, which were correlated with a decrease in oxygen evolution activity. Structural changes due to cross-linking did not affect packing or symmetry of the 2D crystals, further supporting the conclusion that PS II has a monomeric nature in vivo.

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Innanen, V. T., N. Korogyi, E. Jobb, and J. McGarrity. "An additional protein in 2D-PAGE of plasma from the spontaneously hypertensive rat." Clinical Chemistry 34, no. 2 (February 1, 1988): 432–33. http://dx.doi.org/10.1093/clinchem/34.2.432a.

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Wilson, Nicole L., Benjamin L. Schulz, Niclas G. Karlsson, and Nicolle H. Packer. "Sequential Analysis of N- and O-Linked Glycosylation of 2D-PAGE Separated Glycoproteins." Journal of Proteome Research 1, no. 6 (December 2002): 521–29. http://dx.doi.org/10.1021/pr025538d.

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He, Zhicong, Lina P. Aristoteli, Leonard Kritharides, and Brett Garner. "HPLC analysis of discrete haptoglobin isoform N-linked oligosaccharides following 2D-PAGE isolation." Biochemical and Biophysical Research Communications 343, no. 2 (May 2006): 496–503. http://dx.doi.org/10.1016/j.bbrc.2006.03.007.

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Pütz, Stephanie M., Fotini Vogiatzi, Thorsten Stiewe, and Albert Sickmann. "Malignant transformation in a defined genetic background: proteome changes displayed by 2D-PAGE." Molecular Cancer 9, no. 1 (2010): 254. http://dx.doi.org/10.1186/1476-4598-9-254.

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Májek, Pavel, Zuzana Riedelová-Reicheltová, Jiří Suttnar, and Jan E. Dyr. "Staining of proteins for 2D SDS-PAGE using Coomassie Blue-speed versus sensitivity?" ELECTROPHORESIS 34, no. 13 (July 2013): 1972–75. http://dx.doi.org/10.1002/elps.201300087.

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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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Ukolova, I. V., I. G. Kondratov, M. A. Kondakova, I. V. Lyubushkina, O. I. Grabelnykh, and G. B. Borovskii. "Mitochondrial сomplexome of etiolated pea shoots." Proceedings of Universities. Applied Chemistry and Biotechnology 11, no. 4 (January 8, 2022): 570–80. http://dx.doi.org/10.21285/2227-2925-2021-11-4-570-580.

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Studies into mitochondrial сomplexomes in various organisms provide an insight into the native organization of proteins and metabolic pathways in the organelles of the subject under study. “Complexome” is a relatively recent concept describing the proteome of protein complexes, supercomplexes, and oligomeric proteins. Complexome analysis is performed using current electrophoretic and mass spectrometric techniques, in particular, by two-dimensional electrophoresis (2D BN/SDS-PAGE) in combination with mass spectrometry (MS). Unlike 2D IEF/SDS-PAGE, this method enables analysis of not only hydrophilic proteins of the mitochondrial matrix, but also membrane proteins and their associations, thus expanding the possibilities of studying the organelle proteome. In the present work, the complexome of etiolated pea shoots was studied for the first time using 2D BN/SDS-PAGE followed by MALDI-TOF MS. To this end, 145 protein spots excised from the gel were analyzed; 110 polypeptides were identified and assigned to different functional groups. A densitometric analysis revealed that the major protein group comprised the enzymes of the mitochondrial energy system (1), accounting for an average of 43% of the total polypeptide content. The remaining 57% was primarily distributed among the following functional categories: pyruvate dehydrogenase complex and citric acid cycle (2); amino acid metabolism (3); nucleic acid processing (4); protein folding (5); antioxidant protection (6); carrier proteins (7); other proteins (8); proteins having unknown functions (9). The obtained data indicate the complex organization of the pea proteome. In addition to the enzymes of the OXPHOS system, the proteins of other functional categories are found to form supramolecular structures. It is suggested that the presence of proteins from other cellular compartments may indicate the interaction of mitochondria with the enzymes or structures of corresponding organelles. In general, the obtained data on the pea complexome represent a kind of a mitochondrial “passport” that reflects the native state of the proteome of organelles corresponding to their physiological status.

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Stelzer, Sacha, Suhelen Egan, Martin R. Larsen, Douglas H. Bartlett, and Staffan Kjelleberg. "Unravelling the role of the ToxR-like transcriptional regulator WmpR in the marine antifouling bacterium Pseudoalteromonas tunicata." Microbiology 152, no. 5 (May 1, 2006): 1385–94. http://dx.doi.org/10.1099/mic.0.28740-0.

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The dark-green-pigmented marine bacterium Pseudoalteromonas tunicata produces several target-specific compounds that act against a range of common fouling organisms, including bacteria, fungi, protozoa, invertebrate larvae and algal spores. The ToxR-like regulator WmpR has previously been shown to regulate expression of bioactive compounds, type IV pili and biofilm formation phenotypes which all appear at the onset of stationary phase. In this study a comparison of survival under starvation or stress between the wild-type P. tunicata strain and a wmpR mutant (D2W2) does not suggest a role for WmpR in regulating starvation- and stress-resistant phenotypes such as those that may be required in stationary phase. Both proteomic [2-dimensional PAGE (2D-PAGE)] and transcriptomic (RNA arbitrarily primed PCR) studies were used to discover members of the WmpR regulon. 2D-PAGE identified 11 proteins that were differentially expressed by WmpR. Peptide sequence data were obtained for six of these proteins and identified using the draft P. tunicata genome as being involved in protein synthesis, amino acid transamination and ubiquinone biosynthesis, as well as hypothetical proteins. The transcriptomic analysis identified three genes significantly up-regulated by WmpR, including a TonB-dependent outer-membrane protein, a non-ribosomal peptide synthetase and a hypothetical protein. Under iron-limitation the wild-type showed greater survival than D2W2, indicating the importance of WmpR under these conditions. Results from these studies show that WmpR controls the expression of genes encoding proteins involved in iron acquisition and uptake, amino acid metabolism and ubiquinone biosynthesis in addition to a number of proteins with as yet unknown functions.

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