DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J 64 , 1382–1388 (2000). Øvreas L Soil community analysis using DGGE of 16S rDNA polymerase chain reaction
., Vajna, B., Hajdú, C., Márialigeti, K.: DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence- aided T-RFLP profile of mature compost. Microb Ecol 57, 522–533 (2009
Kowalchuk, G. A., Bodelier, P. L. E., Heilig, G. H. J., Stephen, J. R., Laanbroek, H. J.: Community analysis of ammonia-oxidizing bacteria, in relation to oxygen availability in soils and root oxygenated sediments, using PCR, DGGE and oligonucleotide probe
electrophoresis (DGGE) and 16S rRNA gene sequencing The DGGE was performed using an Ingeny PhorU system (Ingeny International, Goes, The Netherlands). PCR products were loaded onto 7% polyacrylamide gel, which contained 40%–60% denaturing gradient of
Bacterial communities from the sulfide containing curative well waters of Harkány Spa (Hungary) were investigated by cultivation independent molecular cloning and Denaturing Gradient Gel Electrophoresis (DGGE) methods between 2006 and 2008. The DGGE profiles of the bacterial communities originated from the wells of lukewarm waters showed seasonal similarities and were highly different from the thermal well. From the four clone libraries 22 different eubacterial species or genera were identified by sequence analysis. The majority of the clones of the lukewarm waters belonged to unidentified Epsilon-proteobacteria, Desulfocapsa sp. and Thiothrix spp., while the dominant clones of the thermal water were affiliated with the genus Denitratisoma sp. Most of the identified species and genera were related to bacteria with obligate or facultative chemolithotrophic sulfur metabolism, so the microbes of the curative waters may participate in the sulfur-cycle of the wells.
This study was conducted to investigate the presence of single nucleotide polymorphisms (SNPs) in the coding region of the bovine prion protein (PrP) gene among healthy and bovine spongiform encephalopathy (BSE-) affected cattle in Slovakia. Denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP) followed by DNA sequencing were used to identify SNPs and variations in octapeptide repeats. Altogether three single nucleotide polymorphisms (g234a, c339t and c576t) and variations in the number of octapeptide repeat units (5 or 6) were found in the analysed part of the prion protein gene. All single nucleotide polymorphisms were silent, causing no amino acid changes. Significant differences (P < 0.05) in the genotype distribution of g234a polymorphism were observed when the homozygous genotype with a mutated allele (caa/caa) was compared to the heterozygous genotype -/cag among healthy and BSE-affected cattle. The homozygous genotype caa/caa was characteristic of the group of BSE-affected cattle. Additionally, the homozygous genotype caa/caa was significant for the group of Simmental crossbreeds among healthy cattle. The allele and genotype distribution of the other polymorphisms was not significantly different among groups of healthy and BSE-affected cattle. The possible influence of a silent mutation on expression of the gene is not clearly determined and needs further investigations.
electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73, 127–141 (1998). Smalla K Application of denaturing gradient gel
Lyautey, E., B. Lacoste, L. Ten-Hage, J. L. Rols and F. Garabetian. 2005. Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: Methodological settings and fingerprints interpretation. Water Res. 39: 380
Geothermal wells characterized by thermal waters warmer than 30°C can be found in more than 65% of the area of Hungary. The examined thermal wells located nearby Szarvas are used for heating industrial and agricultural facilities because of their relatively high hydrocarbon content. The aim of this study was to reveal the prokaryotic community structure of the water of SZR18, K87 and SZR21 geothermal wells using molecular cloning methods and Denaturing Gradient Gel Electrophoresis (DGGE). Water samples from the outflow pipes were collected in 2012 and 2013. The phylogenetic distribution of archaeal molecular clones was very similar in each sample, the most abundant groups belonged to the genera Methanosaeta, Methanothermobacter and Thermofilum. In contrast, the distribution of bacterial molecular clones was very diverse. Many of them showed the closest sequence similarities to uncultured clone sequences from similar thermal environments. From the water of the SZR18 well, phylotypes closely related to genera Fictibacillus and Alicyclobacillus (Firmicutes) were only revealed, while the bacterial diversity of the K87 well water was much higher. Here, the members of the phyla Thermodesulfobacteria, Proteobacteria, Nitrospira, Chlorobi, OP1 and OPB7 were also detected besides Firmicutes.
rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE)— Lett. Appl. Microbiol. vol. 28 137–141 pp. Manfio G.P. Discrimination of Rh. tropici and Rh
