Polymorphism analysis

Degradation of contaminants may occur with bacteria that have been isolated from pristine environments without established exposure to the contaminants, and exhibit no dependence on substrate concentration. For example, organisms from a previously unexposed forest soil were able to degrade 2,4,6-trichlorophenol at concentrations up to 5000 ppm, and terminal restriction fragment length polymorphism analysis revealed that at concentrations up to 500 ppm, the bacterial community was unaltered (Sanchez et al. 2004). 

Progress in molecular biology has provided a new perspective. Techniques such as the polymerase chain reaction and single-strand conformation polymorphism analysis have greatly facilitated the molecular analysis of erythroenzymopathies. These studies have clarified the correlation between the functional and structural abnormalities of the variant enzymes. In general, the mutations that induce an alteration of substrate binding site and/or enzyme instability might result in markedly altered enzyme properties and severe clinical symptoms. 

M6. Maekawa, M., Sudo, K., Kitajima, M., Matsuura, Y Li, S. S.-L., and Kanno, T., Detection and characterization of new genetic mutations in individuals heterozygous for lactate dehydroge-nase-B (H) deficiency using DNA conformation polymorphism analysis and silver staining. Hum. Genet. 91, 163-168 (1993). 

Sato, T. Hu, J. P Ohki, K. Yamaura, M. Washio, J. Matsuyama, J. Takahashi, N. Identification of mutans streptococci by restriction fragment length polymorphism analysis of polymerase chain reaction-amplified 16S ribosomal RNA genes. Oral Microbiol. Immunol. 2003,18, 323-326. 

Kain, K.C., Craig, A.A. and Ohrt, C. (1996) Single-strand conformational polymorphism analysis differentiates Plasmodium falciparum treatment failures from re-infections. Molecular and Biochemical Parasitology 79, 167—175. 

Saperstein, D. and Nickerson, J.M. (1991) Restriction fragment length polymorphism analysis using PCR coupled to restriction digests. BioTechniques 10, 488-489. 

Sheffield, V.C., Beck, J.S., Kwitek, A.E., Sandstrom, D.W. and Stone, E.M. (1993) The sensitivity of single strand conformation polymorphism analysis for the detection of single base substitutions. Genomics 16, 325-332. 

Beier DR, Dushkin H, Sussman DJ. Mapping genes in the mouse using single-strand conformation polymorphism analysis of recombinant inbred strains and interspecific crosses. Proc Natl Acad Sci USA 1992 89 9102-9106. 

Spire-Vayron de la Moureyre C, Debuysere H, Sabbagh N, Marez D, Vinner E, Chevalier ED et al. Detection of known and new mutations in the thiopurine S-methyltransferase gene by single-strand conformation polymorphism analysis. Hum Mutat 1998 12 177— 185. 

FISH, terminal restriction-fragment length polymorphism analysis (rRNA-based molecular techniques) and comparative 16S rDNA analysis... 

Snyder TM, McGown LB (2005) Multiplex single strand conformation polymorphism analysis by capillary electrophoresis with on-the-fly fluorescence lifetime detection. Appl Spectrosc 59 335-339... 

Maesawa, C Tamura, G Suzuki, Y., Ishida, K., Saito, K., and Satodate, R. (1992) Sensitive detection of p53 gene mutations in esophageal endoscopic biopsy specimens by cell sorting combined with polymerase chain reaction single-strand conformation polymorphism analysis. Jpn. J. Cancer Res. 83, 1253-1256. 

In another study, samples for polymorphic analysis were processed using gentle grinding after mixing [17]. Here, a combination of FTIR and Raman spectroscopy with multivariate analysis was utilized to quantify Form-II in mixtures with Form-I. Multivariate analysis using the PLS... 

Footz, T., Somerville, M.J., Tomaszewski, R., Elyas, B., Backhouse, C.J., Integration of combined heteroduplex/restriction fragment length polymorphism analysis on an electrophoresis microchip for the detection of hereditary haemochromatosis. Analyst 2004, 129, 25-31. 

Racky J, Schmitz HJ, Kauffmann HM, Schrenk D. Single nucleotide polymorphism analysis and functional characterization of the human Ah receptor (AhR) gene promoter. Arch Biochem Biophys 2004 421 91-98. 

Chen J, Iannone MA, Li MS, Taylor JD, Rivers P, Nelsen AJ, Slentz-Kesler KA, Roses A, Weiner MP. A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension. Genome Res 2000 10 549-557. 

Ross P, Hall L, Haff LA. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 2000 29 620-626, 628-629. 

Landegren U, Nilsson M, Kwok PY. Reading bits of genetic information methods for single-nucleotide polymorphism analysis. Genome Res 1998 8(8) 769-776. 

Several rapid and sensitive methods have been developed to detect mutations in cDNA and genomic DNA. These include ribonuclease (RNase) protection analysis, denaturing gradient gel electrophoresis, and single-strand conformation polymorphism analysis. These methods can be used in conjunction with the PCR technique to detect small deletions or insertions and single base substitutions. 

Single-strand conformation polymorphism analysis is the more popular method because of its simplicity and wide applicability to many different genes. This method makes use of... 

Tian H, Jaquins-Gerstl A, Munro N, Trucco M, Brody LC, Landers JP. Singlestrand conformation polymorphism analysis by capillary and microchip electrophoresis a fast, simple method for detection of common mutations in BRCA1 and BRCA2. Genomics 2000 63 25-34. 

Ulfelder KJ, Schwartz HE, Hall JM, Sunzeri FJ (1992) Restriction fragment length polymorphism analysis of ERBB2 oncogene by capillary electrophoresis. Anal Bio-chem 200 260-267. 

Leuders, T., and Friedrich, M. W. (2003). Evaluation of PGR amplification bias by terminal restriction fragment length polymorphism analysis of smaU-subunit rma and mcra genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol. 69, 320-326. 

Braker, G., Ayala-del-Pao, H. L., Devol, A. H., Fesefeldt, A., and Tiedje, J. M. (2001). Community structure of denitrifiers, bacteria, and archaea along redox gradients in pacific northwest marine sediments by terminal restriction firagment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67, 1893—1901. 

Moeseneder, M. M., Arrieta, J. M., Muyzer, G., Winter, C., andHemdl, G.J. (1999). Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65, 3518-3525. 

Scala, D. J., and Kerkhof, L. J. (2000). Horizontal heterogeneity of denitrifying hacterial communities in marine sediments hy terminal restriction fragment length polymorphism analysis. Appl. Environ. Microbiol. 66, 1980—1986. 

Polarized analysis There is useful spectral information arising from the analysis of polarization of Raman scattered light. This, typically called as polarized analysis, provides an insight into molecular orientation, molecular shape, and vibrational symmetry. One can also calculate the depolarization ratio. Overall, this technique enables correlation between group theory, symmetry, Raman activity, and peaks in the corresponding Raman spectra. It has been applied successful for solving problems in synthetic chemistry understanding macromolecular orientation in crystal lattices, liquid crystals or polymer samples and in polymorph analysis. 

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