Novel application of the MSSCP method in biodiversity studies

Journal of Basic Microbiology

Volumn 52, Issue 1, 2012, Pages 104-109

  Tomczyk Z ak, Karolina ^a   Kaczanowski, Szymon ^a   Górecka, Magdalena ^a   Zieenkiewicz, Urszula ^a  

^a INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

Biofilm; Diversity; LIBSHUFF; MSSCP

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; RNA 16S;

ARTICLE; BACTERIUM; BIODIVERSITY; BIOFILM; CLASSIFICATION; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; POLAND; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SINGLE STRAND CONFORMATION POLYMORPHISM;

BACTERIA; BIODIVERSITY; BIOFILMS; DNA, BACTERIAL; GENE LIBRARY; POLAND; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA;

BACTERIA (MICROORGANISMS);

EID: 84856845741     PISSN: 0233111X     EISSN: 15214028     Source Type: Journal    
DOI: 10.1002/jobm.201000117     Document Type: Article

References (19)

1. Schloss, P.D., Handelsman, J., 2008. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 34.
2. Wommack, K.E., Bhavsar, J., Ravel, J., 2008. Metagenomics: read length matters. Appl. Environ. Microbiol., 74, 1453-1463.
3. Brodie, E.L., DeSantis, T.Z., Joyner D.C., Baek, S.M. et al., 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol., 72, 6288-6298.
4. Case, R.J., Boucher, Y., Dahllöf, I., Holmström, C. et al., 2007. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol., 73, 278-288.
5. Gelsomino, A., Keijzer-Wolters, A.C., Cacco, G., van Elsas, J.D., 1999. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J. Microbiol. Methods, 38, 1-15.
6. Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K., Sekiya, T., 1989. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA, 86, 2766-2770.
7. Lee, D.H., Zo, Y.G., Kim, S.J., 1996. Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl. Environ. Microbiol., 62, 3112-3120.
8. Hong, H., Pruden, A., Reardon, K.F., 2007. Comparison of CE-SSCP and DGGE for monitoring a complex microbial community remediating mine drainage. J. Microbiol. Methods, 69, 52-64.
9. Kaczanowski, R., Trzeciak, L., Kucharczyk, K., 2001. Multitemperature single-strand conformation polymorphism. Electrophoresis, 22, 3539-3545.
10. Vallian, S., Nassiri, I., 2010. Development of a sensitive deaminated single-strand conformation polymorphism (DSSCP). Appl. Biochem. Biotechnol., 160, 927-931.
11. Bezak, A., Kaczanowski, R., Dossenbach-Glaninger, A., Kucharczyk, K. et al., 2005. Detection of single nucleotide polymorphisms in coagulation factor XI deficient patients by multitemperature single-strand conformation polymorphism analysis. J. Clin. Lab. Anal., 19, 233-240.
12. Ignacak, M., Turek-Plewa, J., Limon, J., Trzeciak, W.H., 2004. A novel c.C2754 > T transition in the androgen receptor gene introduces the premature termination codon Q798X and results in a truncated form of the receptor. Gynecol. Endocrinol., 19, 178-181.
13. Szewczyk, B., Barski, P., Sihler, W., Rabalski, L. et al., 2008. Detection and identification of baculovirus pesticides by multitemperature single strand conformational polymorphism. J. Environ. Sci. Health B, 43, 539-545.
14. Zhou, J., Bruns, M.A., Tiedje, J.M., 1996. DNA recovery from soils of diverse composition. Appl.. Environ. Microbiol., 62, 316-322.
15. Beijerinck, M.W., 1898. Notiz liber Pleurococcius vulgaris. Zent. Bakt. II, 4, 785-787.
16. Lane, D.J., 1991.16S/23S rRNA sequencing. In: Stackebrandt, E., Goodfellow, M., (eds.), Nucleic Acid Techniques in Bacterial Systematics. Wiley, Chichester 115-148.
17. Muyzer, G., de Waal, E.C., Uitterlinden, A.G., 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl. Environ. Microbiol., 59, 695-700.
18. Baker, G.C., Smith, J.J., Cowan, D.A., 2003. Review and re-analysis of domain-specific 16Sprimers. J. Microbiol. Methods, 55, 541-555.
19. Singleton, D.R., Furlong, M.A., Rathbun, S.L., Whitman, W.B., 2001. Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Appl. Environ. Microbiol., 67, 4373-4376.