Gradient gels

Figure 9.3 Schematic illustration of the electrophoretic transfer of proteins in the chromatophoresis process. After being eluted from the HPLC column, the proteins were reduced with /3-mercaptoethanol in the protein reaction system (PRS), and then deposited onto the polyacrylamide gradient gel. (PRC, protein reaction cocktail). Reprinted from Journal of Chromatography, 443, W. G. Button et al., Separation of proteins by reversed-phase Mgh-performance liquid cliromatography , pp 363-379, copyright 1988, with permission from Elsevier Science.

Rothe, GM, Determination of Molecular Mass, Stoke radius. Frictional Coefficient and Isomer-Type of Non-denatured Proteins by Time-Dependent Pore Gradient Gel Electrophoresis, Electrophoresis 9, 307, 1988. 

The purity of the AE fraction was investigated by SDS-PAGE using Pharmacia PhastSystem with 10 - 15% SDS-gradient gels. Electrophoresis and silver staining of the proteins were performed as described by the manuals from Pharmacia. For determination of pi lEF 3-9 PhastSystem gels were used. 

Reciprocally, the growth on single C source significantly decreases the bacterial diversity. For example, in the rhizosphere soil of potato, a dramatic reduction in the number of ribotypes was found by temperature gradient gel electrophoresis (TGGE) after 48 h of incubation with single C source substrate in Biolog microplate wells (I46). 

A. Denaturing Gradient Gel Electrophoretic Fingerprints of Microbial Communities... 

G. Muyzer and K. Smalla, Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73 127 (1998). 

T. Vallaeys, E. Topp, G. Muyzer, V. Macheret, G. Laguerre, A. Rigaud, and G. Soulas, Evaluation of denaturing gradient gel electrophoresis in the detection of I6S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24 279 (1997). 

G. Muyzer, E. C. de Waal, and A. G. Uitterlinden, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for I6S rRNA. Appl. Environ. Microbiol. 59 695 (1993). 

G. A. Kowalchuk, J. R. Stephen, W. DeBoer, J. 1. Prosser, T. M. Embley, and J. W. Woldendorp, Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified I6S ribosomal DNA fragments. Appl. Environ. Microbiol. 6.1 1489 (1997). 

Abrams, E.S. and Stanton, V.P. Jr (1992) Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids. Methods inEnzymology 212, 71-104. 

Myers, R.M., Fischer, S.G., Lerman, L.S. and Maniatis, T. (1985a) Nearly all base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Research 13, 3131-3145. 

Sheffield, V.C., Beck, J.S., Nichols, B., Cousineau, A, Lidral, A. and Stone, E.M. (1992) Detection of multiallele polymorphisms within gene sequences by GC-clamped denaturing gradient gel electrophoresis. American Journal of Human Genetics 50, 567—575. 

Stothard, J.R., Frame, IA. and Miles, MA. (1997) Use of polymerase chain reaction-based single strand conformational polymorphism and denaturing gradient gel electrophoresis methods for detection of sequence variation of ribosomal DNA of Trypanosoma cruzi. International Journal for Parasitology 27, 339-343. 

Denaturing gradient gel electrophoresis (DGGE), real-time PCR, and FISH... 

Zhao XQ, Yang LY, Yu ZY et al (2008) Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments. J Env Sci 20 224-230... 

Gelsomino A, Cacco G (2006) Compositional shifts of bacterial groups in a solarized and amended soil as determined by denaturing gradient gel electrophoresis. Soil Biol Biochem 38 91-102. doi 10.1016/j.soilbio.2005.04.021... 

Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of Bacterial Communities in the Rhizosphere of Chrysanthemum via Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA as Well as DNA Fragments Coding for 16S rRNA. Appl Environ Micrbiol 67 172-178... 

Sekiguchi H, Kushida A, Takenaka S (2007) Effects of cattle manure and green manure on the microbial community structure in upland soil determined by denaturing gradient gel electro-horesis. Microbes Environ 22 327-335... 

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