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Journal articles on the topic 'Denaturing gradient gel electrophoresis (DGGE)'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Cremonesi, Laura, Paola Carrera, Antonella Fumagalli, et al. "Validation of Double Gradient Denaturing Gradient Gel Electrophoresis through Multigenic Retrospective Analysis." Clinical Chemistry 45, no. 1 (1999): 35–40. http://dx.doi.org/10.1093/clinchem/45.1.35.

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Abstract Among established techniques for the identification of either known or new mutations, denaturing gradient gel electrophoresis (DGGE) is one of the most effective. However, conventional DGGE is affected by major drawbacks that limit its routine application: the different denaturant gradient ranges and migration times required for different DNA fragments. We developed a modified version of DGGE for high-throughput mutational analysis, double gradient DGGE (DG-DGGE), by superimposing a porous gradient over the denaturant gradient, which maintains the zone-sharpening effect even during le

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2

Fodde, Riccardo, and Monique Losekoot. "Mutation detection by denaturing gradient gel electrophoresis (DGGE)." Human Mutation 3, no. 2 (1994): 83–94. http://dx.doi.org/10.1002/humu.1380030202.

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3

Scarpellini, Paolo, Sergio Braglia, Paola Carrera, et al. "Detection of Rifampin Resistance in Mycobacterium tuberculosis by Double Gradient-Denaturing Gradient Gel Electrophoresis." Antimicrobial Agents and Chemotherapy 43, no. 10 (1999): 2550–54. http://dx.doi.org/10.1128/aac.43.10.2550.

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ABSTRACT We applied double gradient-denaturing gradient gel electrophoresis (DG-DGGE) for the rapid detection of rifampin (RMP) resistance fromrpoB PCR products of Mycobacterium tuberculosisisolates and clinical samples. The results of this method were fully concordant with those of DNA sequencing and susceptibility testing analyses. DG-DGGE is a valid alternative to the other methods of detecting mutations for predicting RMP resistance.

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Valášková, V., and P. Baldrian. "Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities." Plant, Soil and Environment 55, No. 10 (2009): 413–23. http://dx.doi.org/10.17221/132/2009-pse.

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In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denatu

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5

Blank, R. D., C. A. Sklar, and M. L. Martin. "Denaturing gradient gel electrophoresis to diagnose multiple endocrine neoplasia type 2." Clinical Chemistry 42, no. 4 (1996): 598–603. http://dx.doi.org/10.1093/clinchem/42.4.598.

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Abstract Multiple endocrine neoplasia type 2 (MEN 2) is an autosomal dominant cancer syndrome caused by mutations in the RET protooncogene. Others have already demonstrated the value of genetic testing in known MEN 2 kindreds. Previously described approaches to DNA-level diagnosis, particularly of index cases, are tedious. We developed appropriate denaturing gradient gel electrophoresis (DGGE) conditions for analysis of exons 10, 11, and 16 of this gene, where many of the pathogenic mutations map. We screened 16 members of a three-generation MEN 2 kindred by DGGE and found five affected but st

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Neufeld, Josh D., and William W. Mohn. "Fluorophore-Labeled Primers Improve the Sensitivity, Versatility, and Normalization of Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 71, no. 8 (2005): 4893–96. http://dx.doi.org/10.1128/aem.71.8.4893-4896.2005.

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ABSTRACT Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.

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Wood, Gary S., and Ahmet Z. Uluer. "Polymerase Chain Reaction/Denaturing Gradient Gel Electrophoresis (PCR/DGGE)." American Journal of Dermatopathology 21, no. 6 (1999): 547. http://dx.doi.org/10.1097/00000372-199912000-00008.

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8

Settanni, Luca, Sara Valmorri, Douwe van Sinderen, Giovanna Suzzi, Antonello Paparella, and Aldo Corsetti. "Combination of Multiplex PCR and PCR-Denaturing Gradient Gel Electrophoresis for Monitoring Common Sourdough-Associated Lactobacillus Species." Applied and Environmental Microbiology 72, no. 5 (2006): 3793–96. http://dx.doi.org/10.1128/aem.72.5.3793-3796.2006.

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ABSTRACT A combination of denaturing gradient gel electrophoresis (DGGE) and a previously described multiplex PCR approach was employed to detect sourdough lactobacilli. Primers specific for certain groups of Lactobacillus spp. were used to amplify fragments, which were analyzed by DGGE. DGGE profiles obtained from Lactobacillus type strains acted as standards to analyze lactobacilli from four regional Abruzzo (central Italy) sourdoughs.

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Harris, K. A., and C. G. Teo. "Diversity of Hepatitis C Virus Quasispecies Evaluated by Denaturing Gradient Gel Electrophoresis." Clinical Diagnostic Laboratory Immunology 8, no. 1 (2001): 62–73. http://dx.doi.org/10.1128/cdli.8.1.62-73.2001.

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ABSTRACT Denaturing gradient gel electrophoresis (DGGE) was used to study the diversity of hepatitis C virus (HCV) quasispecies. Optimized DGGE running conditions were applied to screen for variations in sequences cloned from amplicons originating from the nonstructural 5b (NS5b) gene of HCV in blood of hemophilia patients, intravenous drug users, and blood donors (five specimens from each study group, ca. 40 clones studied per specimen). Clones identified by DGGE as unique were sequenced. NS5b sequence entropy and mean genetic distance in hemophiliacs did not differ significantly from those i

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Willame, Raphaël Boutte, Stana Grubisic, Pierre Balthasart, Annick Wilmotte, and Lucien Hoffmann. "Seasonal cyanobacterial dynamics in a mesoeutrophic reservoir: microscopic counts and DGGE (Denaturing Gradient Gel Electrophoresis)." Algological Studies 129 (September 1, 2009): 71–94. http://dx.doi.org/10.1127/1864-1318/2009/0129-0071.

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11

Wartiainen, Ingvild, Anne Grethe Hestnes, and Mette M. Svenning. "Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway) - denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures." Canadian Journal of Microbiology 49, no. 10 (2003): 602–12. http://dx.doi.org/10.1139/w03-080.

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The methanotrophic community in arctic soil from the islands of Svalbard, Norway (78°N) was analysed by combining group-specific PCR with PCR of the highly variable V3 region of the 16S rRNA gene and then by denaturing gradient gel electrophoresis (DGGE). Selected bands were sequenced for identification. The analyses were performed with DNA extracted directly from soil and from enrichment cultures at 10 and 20 °C. The two genera Methylobacter and Methylosinus were found in all localities studied. The DGGE band patterns were simple, and DNA fragments with single base differences were separated.

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Li, Y., C. Y. S. Ku, J. Xu, D. Saxena, and P. W. Caufield. "Survey of Oral Microbial Diversity using PCR-based Denaturing Gradient Gel Electrophoresis." Journal of Dental Research 84, no. 6 (2005): 559–64. http://dx.doi.org/10.1177/154405910508400614.

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Polymicrobial biofilms in the human oral cavity exhibit marked diversity. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) surveys microbial diversity by displaying PCR-generated 16S rDNA fragments that migrate at different distances, reflecting the differences in the base-pair ( i.e., % G+C) composition of the fragment. This study examined DGGE-generated diversity profiles of cultivable bacteria from individuals with different caries status. Initially, we developed a set of PCR-DGGE running conditions appropriate to oral bacteria. Next, we assessed migration standards from known o

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Hanh, Tran My, Cao Thi Dung, Tran Thi Thanh Huyen, and Pham The Hai. "Evaluating the qualities of probiotic products by a DGGE-based procedure." Vietnam Journal of Biotechnology 17, no. 3 (2020): 577–88. http://dx.doi.org/10.15625/1811-4989/17/3/13366.

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The quality of the probiotics is determined by the microbiological composition and can thus be verified by analyzing this characteristic. The use of the Denaturing Gradient Gel Electrophoresis (DGGE) allows the detection of each microorganism through the corresponding band on the gel, which can be considered as the "bar code" of that microorganism. This "bar code” principle demonstrates the potential for the application of DGGE technology to test microbial probiotics with or without a bacterium as registered to assess whether they are qualified. As such, in this study, we experiment the applic

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O'Callaghan, M., E. M. Gerard, G. H. J. Heilig, H. Zhang, T. A. Jackson, and T. R. Glare. "Denaturing gradient gel electrophoresis a tool for plant protection research." New Zealand Plant Protection 56 (August 1, 2003): 143–50. http://dx.doi.org/10.30843/nzpp.2003.56.6056.

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Analysis of microbial communities associated with plants insects and soil has been a significant challenge for plant protection researchers because of the lack of techniques with which to access these populations A new molecular community profiling technique 16S rRNA genebased PCR followed by denaturing gradient gel electrophoresis (DGGE) has been used to analyse microbial communities in a number of environments and has many potential uses in plant protection research The technique is currently being used for the analysis of insect gut microflora characterisation of phylloplane and rhizosphere

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15

Yu, Zhongtang, Rubén García-González, Floyd L. Schanbacher, and Mark Morrison. "Evaluations of Different Hypervariable Regions of Archaeal 16S rRNA Genes in Profiling of Methanogens by Archaea-Specific PCR and Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 74, no. 3 (2007): 889–93. http://dx.doi.org/10.1128/aem.00684-07.

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ABSTRACT Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobre

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16

Kotásková, Iva, Barbora Mališová, Hana Obručová, et al. "Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis." Journal of Molecular Microbiology and Biotechnology 27, no. 6 (2017): 350–55. http://dx.doi.org/10.1159/000484524.

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Complex samples are a challenge for sequencing-based broad-range diagnostics. We analysed 19 urinary catheter, ureteral Double-J catheter, and urine samples using 3 methodological approaches. Out of the total 84 operational taxonomic units, 37, 61, and 88% were identified by culture, PCR-DGGE-SS (PCR denaturing gradient gel electrophoresis followed by Sanger sequencing), and PCR-DGGE-RM (PCR- DGGE combined with software chromatogram separation by RipSeq Mixed tool), respectively. The latter approach was shown to be an efficient tool to complement culture in complex sample assessment.

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MIDDLETON, SIMON A., GUSTL ANZENBERGER, and LESLIE A. KNAPP. "Denaturing gradient gel electrophoresis (DGGE) screening of clones prior to sequencing." Molecular Ecology Notes 4, no. 4 (2004): 776–78. http://dx.doi.org/10.1111/j.1471-8286.2004.00799.x.

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Janse, Ingmar, Marion Meima, W. Edwin A. Kardinaal, and Gabriel Zwart. "High-Resolution Differentiation of Cyanobacteria by Using rRNA-Internal Transcribed Spacer Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 69, no. 11 (2003): 6634–43. http://dx.doi.org/10.1128/aem.69.11.6634-6643.2003.

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ABSTRACT For many ecological studies of cyanobacteria, it is essential that closely related species or strains can be discriminated. Since this is often not possible by using morphological features, cyanobacteria are frequently studied by using DNA-based methods. A powerful method for analysis of the diversity and dynamics of microbial populations and for checking the purity and affiliation of cultivated strains is denaturing gradient gel electrophoresis (DGGE). We realized high-resolution discrimination of a variety of cyanobacteria by means of DGGE analysis of sections of the internal transc

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Huang, Yue, Wenming Zong, Xing Yan, et al. "Succession of the Bacterial Community and Dynamics of Hydrogen Producers in a Hydrogen-Producing Bioreactor." Applied and Environmental Microbiology 76, no. 10 (2010): 3387–90. http://dx.doi.org/10.1128/aem.02444-09.

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ABSTRACT Variation in the hydrogen production rate was consistent with the succession of dominant bacteria during the batch fermentation process. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes and quantitative analysis of the hyd A genes at both the DNA and mRNA levels confirmed that C lostridium perfringens was the most dominant hydrogen producer in the bioreactor.

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Sánchez, Olga, Josep M. Gasol, Ramon Massana, Jordi Mas, and Carlos Pedrós-Alió. "Comparison of Different Denaturing Gradient Gel Electrophoresis Primer Sets for the Study of Marine Bacterioplankton Communities." Applied and Environmental Microbiology 73, no. 18 (2007): 5962–67. http://dx.doi.org/10.1128/aem.00817-07.

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ABSTRACT An annual seasonal cycle of composition of a bacterioplankton community in an oligotrophic coastal system was studied by denaturing gradient gel electrophoresis (DGGE) using five different primer sets. Analysis of DGGE fingerprints showed that primer set 357fGC-907rM grouped samples according to seasons. Additionally, we used the set of 16S rRNA genes archived in the RDPII database to check the percentage of perfect matches of each primer for the most abundant bacterial groups inhabiting coastal plankton communities. Overall, primer set 357fGC-907rM was the most suitable for the routi

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Panosyan, H. H. "BACTERIAL PROFILES OF KARVACHAR HOT SPRING IDENTIFIED BY COMBINATION OF DIFFERENT MOLECULAR APPROACHES." Proceedings of the YSU B: Chemical and Biological Sciences 54, no. 2 (252) (2020): 147–53. http://dx.doi.org/10.46991/pysu:b/2020.54.2.147.

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Molecular techniques, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA genes clone library construction and metagenomic analysis, were used to describe the bacterial composition of the Karvachar geothermal spring. It was shown the predominance of bacteria belonging to the phyla Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria in the studied spring. Representatives of phylum Firmicutes were not detected in the clone library, while DGGE profiling and metagenome analysis confirmed the presence of Firmicutes as one of the major components in the bacterial community.

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Temmerman, R., I. Scheirlinck, G. Huys, and J. Swings. "Culture-Independent Analysis of Probiotic Products by Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 69, no. 1 (2003): 220–26. http://dx.doi.org/10.1128/aem.69.1.220-226.2003.

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ABSTRACT In order to obtain functional and safe probiotic products for human consumption, fast and reliable quality control of these products is crucial. Currently, analysis of most probiotics is still based on culture-dependent methods involving the use of specific isolation media and identification of a limited number of isolates, which makes this approach relatively insensitive, laborious, and time-consuming. In this study, a collection of 10 probiotic products, including four dairy products, one fruit drink, and five freeze-dried products, were subjected to microbial analysis by using a cu

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McCammon, Mark T., John S. Gillette, Derek P. Thomas, et al. "Detection of rpoB Mutations Associated with Rifampin Resistance in Mycobacterium tuberculosis Using Denaturing Gradient Gel Electrophoresis." Antimicrobial Agents and Chemotherapy 49, no. 6 (2005): 2200–2209. http://dx.doi.org/10.1128/aac.49.6.2200-2209.2005.

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ABSTRACT Denaturing gradient gel electrophoresis (DGGE) was used to probe for mutations associated with rifampin (RIF) resistance in the rpoB gene of Mycobacterium tuberculosis. DGGE scans for mutations across large regions of DNA and is comparable to DNA sequencing in detecting DNA alterations. Specific mutations are often recognized by their characteristic denaturation pattern, which serves as a molecular fingerprint. Five DGGE primer sets that scanned for DNA alterations across 775 bp of rpoB were developed. These primer sets were used to scan rpoB for DNA alterations in 296 M. tuberculosis

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Si-Ping, Zheng, Chen Bin, Guan Xiong, and Zheng Wei-Wen. "Diversity analysis of endophytic bacteria withinAzolla microphyllausing PCR-DGGE and electron microscopy." Chinese Journal of Agricultural Biotechnology 5, no. 3 (2008): 269–76. http://dx.doi.org/10.1017/s1479236208002441.

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AbstractUsing 16S rDNA-polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE), electron microscopy and a conventional plating method, the genetic diversity and phenotype polymorphism of the endophytic bacteria withinAzolla microphyllawere explored. The 16S rDNA-PCR-DGGE profile showed a complex and divergent bacterial community, withBacillus cereusas the dominant species, within theAzolla–cyanobacteria association. This result was supported by the fact that endobacterial cells exhibited distinct ultrastructural characteristicsin vivoand,in vitro, bacteria displayed variou

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Satokari, Reetta M., Elaine E. Vaughan, Antoon D. L. Akkermans, Maria Saarela, and Willem M. de Vos. "Bifidobacterial Diversity in Human Feces Detected by Genus-Specific PCR and Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 67, no. 2 (2001): 504–13. http://dx.doi.org/10.1128/aem.67.2.504-513.2001.

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ABSTRACT We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bi

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Drees, Kevin P., Julia W. Neilson, Julio L. Betancourt, et al. "Bacterial Community Structure in the Hyperarid Core of the Atacama Desert, Chile." Applied and Environmental Microbiology 72, no. 12 (2006): 7902–8. http://dx.doi.org/10.1128/aem.01305-06.

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ABSTRACTSoils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70°S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populat

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Pérez-Ortega, Sergio, Ave Suija, and Asunción de los Ríos. "The connection betweenAbrothallusand its anamorph stateVouauxiomycesestablished by Denaturing Gradient Gel Electrophoresis (DGGE)." Lichenologist 43, no. 3 (2011): 277–79. http://dx.doi.org/10.1017/s0024282911000089.

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Ljujic, Mila, Aleksandra Nikolic, Aleksandra Divac, Valentina Djordjevic, and Dragica Radojkovic. "Screening of alpha-1-antitrypsin gene by denaturing gradient gel electrophoresis (DGGE)." Journal of Biochemical and Biophysical Methods 68, no. 3 (2006): 167–73. http://dx.doi.org/10.1016/j.jbbm.2006.05.005.

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Iacumin, Lucilla, Francesca Cecchini, Marco Vendrame, and Giuseppe Comi. "Emulsion PCR (ePCR) as a Tool to Improve the Power of DGGE Analysis for Microbial Population Studies." Microorganisms 8, no. 8 (2020): 1099. http://dx.doi.org/10.3390/microorganisms8081099.

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To the authors’ knowledge, this is the first report of the use of emulsion-Polymerase chain reaction (e-PCR) coupled with denaturing gradient gel electrophoresis (DGGE) analysis. In the present work the effectiveness of ePCR in improving the power of the DGGE technique for microbial population studies was tested. Our results indicated that ePCR results in uniform amplification of several DNA molecules, overcoming the major limitations of conventional PCR, such as preferential amplification and DNA concentration dependence. Moreover, ePCR-DGGE resulted in higher sensitivity when compared to con

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Quéméneur, Marianne, Aurélie Cébron, Patrick Billard, et al. "Population Structure and Abundance of Arsenite-Oxidizing Bacteria along an Arsenic Pollution Gradient in Waters of the Upper Isle River Basin, France." Applied and Environmental Microbiology 76, no. 13 (2010): 4566–70. http://dx.doi.org/10.1128/aem.03104-09.

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ABSTRACT Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional aoxB genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the aoxB-carrying bacterial population, composed of members of the Alpha-, Beta- and Gammaproteobacteria, depending on arsenic (As) and Eh levels in Upper Isle River Basin waters. The highest aoxB gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers

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Li, Chao, Xian Li Li, Min Ji, and Yu Kun Ma. "Performance and Microbial Characteristics of a Hybrid Biological Reactor Treating Industrial Wastewater." Advanced Materials Research 485 (February 2012): 438–41. http://dx.doi.org/10.4028/www.scientific.net/amr.485.438.

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To reveal the succession procedure of microbial community in hybrid biological reactor (HBR), the molecular biological techniques of polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE), cloning and sequencing and ﬂuorescence in situ hybridization (FISH) were applied. PCR-DGGE results showed that the microbial community accumulated in both suspended-growth and attached-growth biomasses. Proteobacteria was found to be the dominant genera of bacteria in the sludge. Denitrifying bacteria was found accumulated in the biofilms. FISH results showed that there were more nitrif

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Nielsen, D. S., P. L. Møller, V. Rosenfeldt, A. Pærregaard, K. F. Michaelsen, and M. Jakobsen. "Case Study of the Distribution of Mucosa-Associated Bifidobacterium Species, Lactobacillus Species, and Other Lactic Acid Bacteria in the Human Colon." Applied and Environmental Microbiology 69, no. 12 (2003): 7545–48. http://dx.doi.org/10.1128/aem.69.12.7545-7548.2003.

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ABSTRACT The distribution of mucosa-associated bacteria, bifidobacteria and lactobacilli and closely related lactic acid bacteria, in biopsy samples from the ascending, transverse, and descending parts of the colon from four individuals was investigated by denaturing gradient gel electrophoresis (DGGE). Bifidobacterial genus-specific, Lactobacillus group-specific, and universal bacterial primers were used in a nested PCR approach to amplify a fragment of the 16S rRNA gene. DGGE profiles of the bifidobacterial community were relatively simple, with one or two amplicons detected at most sampling

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D’Elia, Thomas V., Chester R. Cooper, and Carl G. Johnston. "Source tracking ofEscherichia coliby 16S–23S intergenic spacer region denaturing gradient gel electrophoresis (DGGE) of therrnBribosomal operon." Canadian Journal of Microbiology 53, no. 10 (2007): 1174–84. http://dx.doi.org/10.1139/w07-083.

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This research validates a novel approach for source tracking based on denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from Escherichia coli isolates. Escherichia coli from different animal sources and from river samples upstream from, at, and downstream of a combined sewer overflow were subjected to DGGE to determine sequence variations within the 16S–23S intergenic spacer region (ISR) of the rrnB ribosomal operon. The ISR was analyzed to determine if E. coli isolates from various animal sources could be differentiated from each other. DNA isolated from the E. coli ani

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Shrivastava, Umesh Prasad. "Molecular Diversity Assessment of Plant Growth Promoting Rhizobacteria Using Denaturing Gradient Gel Electrophoresis (DGGE) of 16s rRNA Gene." International Journal of Applied Sciences and Biotechnology 5, no. 1 (2017): 72–80. http://dx.doi.org/10.3126/ijasbt.v5i1.17029.

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The rhizobacteria were isolated from rhizosphere of rice plant of different fields of 4 districts of Nepal and 5 districts of Bihar and Uttar Pradesh, adjoining states of India with Nepal. The DGGE analysis was performed for diversity analysis. For the construction of dendrogram, 16S rRNA gene was amplified by two different sets of primers. The DGGE ladder consisting of PCR amplified products of nine pure bacterial cultures were obtained. The first DGGE ladder was prepared by 400 bp fragment of 16S rDNA with GC clamp and the second DGGE ladder was prepared with 200 bp fragment of 16S rDNA with

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Nissen, H., P. S. Hansen, O. Faergeman, and M. Hørder. "Mutation screening of the codon 3500 region of the apolipoprotein B gene by denaturing gradient-gel electrophoresis." Clinical Chemistry 41, no. 3 (1995): 419–23. http://dx.doi.org/10.1093/clinchem/41.3.419.

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Abstract Familial defective apolipoprotein B (FDB) is a clinical condition resembling familial hypercholesterolemia. The underlying genetic defects are mutations in the apolipoprotein B-100 (apo B-100) gene. Two mutations (Arg3500 --&gt; Gln and Arg3531 --&gt; Cys) are known to date. We designed a denaturing gradient-gel electrophoresis (DGGE) technique to detect sequence variations in codons 3456-3553 of the apo B-100 gene. In 46 heterozygous FDB patients with the predominant codon 3500 mutation, a uniform four-band DGGE pattern was seen, whereas 57 non-FDB patients showed the uniform

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Bergsma-Vlami, M., M. E. Prins, M. Staats, and J. M. Raaijmakers. "Assessment of Genotypic Diversity of Antibiotic-Producing Pseudomonas Species in the Rhizosphere by Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 71, no. 2 (2005): 993–1003. http://dx.doi.org/10.1128/aem.71.2.993-1003.2005.

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ABSTRACT The genotypic diversity of antibiotic-producing Pseudomonas spp. provides an enormous resource for identifying strains that are highly rhizosphere competent and superior for biological control of plant diseases. In this study, a simple and rapid method was developed to determine the presence and genotypic diversity of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas strains in rhizosphere samples. Denaturing gradient gel electrophoresis (DGGE) of 350-bp fragments of phlD, a key gene involved in DAPG biosynthesis, allowed discrimination between genotypically different phlD + ref

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Yu, Zhongtang, and Mark Morrison. "Comparisons of Different Hypervariable Regions of rrs Genes for Use in Fingerprinting of Microbial Communities by PCR-Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 70, no. 8 (2004): 4800–4806. http://dx.doi.org/10.1128/aem.70.8.4800-4806.2004.

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ABSTRACT Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial diversity and community structure, but no systematic comparison has been made of the DGGE profiles obtained when different hypervariable (V) regions are amplified from the same community DNA samples. We report here a study to make such comparisons and establish a preferred choice of V region(s) to examine by DGGE, when community DNA extracted from samples of digesta is used. When the members of the phylogenetically representative set of 218 rrs genes archived in the RDP II database were c

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Wu, Ri Na, Xiao Meng Pang, Xi Yan Wang, and Jun Rui Wu. "PCR-DGGE Analysis of Bacterial Diversity of Intestinal System in Hyperlipidemia Rats." Advanced Materials Research 726-731 (August 2013): 898–901. http://dx.doi.org/10.4028/www.scientific.net/amr.726-731.898.

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Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene has been regarded as one of powerful tools for gaining insight into the bacterial diversity of intestinal system. In the present study, hyperlipidemia model was constructed in rat according to the tests of blood lipids. Fecal samples of rats were collected after 60d feeding, and DGGE was used to investigate the diversities of intestinal bacteria in the artificially-induced hyperlipidemia rats and normal rats. The results showed that two patterns had similarities, but there were also some different bacteria communities. Mo

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Li-Yan, Chang, Wang Qi, and Mei Ru-Hong. "Effect of nanoparticles on the bacterial community of the cucumber phyllosphere." Chinese Journal of Agricultural Biotechnology 6, no. 2 (2009): 141–45. http://dx.doi.org/10.1017/s1479236209990179.

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AbstractWith the rapid development of nanotechnology, the security of nanomaterials has been an increasing cause for concern. In this study, the impact of titanium dioxide nanoparticles (nano-TiO2) on the phyllosphere bacterial community were analysed by both a culturable-dependent method and a polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) method. The quantity of culturable phyllosphere bacteria was significantly reduced with an increased concentration of nano-TiO2. With increasing concentrations from 0.002 to 20 mg/ml of nano-TiO2, the quantity of culturable phy

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Cook, AA, P. Bhadury, NJ Debenham, et al. "Denaturing gradient gel electrophoresis (DGGE) as a tool for identification of marine nematodes." Marine Ecology Progress Series 291 (2005): 103–13. http://dx.doi.org/10.3354/meps291103.

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Siqueira, José F., Isabela N. Rôças, and Alexandre S. Rosado. "Application of Denaturing Gradient Gel Electrophoresis (DGGE) to the Analysis of Endodontic Infections." Journal of Endodontics 31, no. 11 (2005): 775–82. http://dx.doi.org/10.1097/01.don.0000155221.33667.bb.

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Dar, Shabir A., J. Gijs Kuenen, and Gerard Muyzer. "Nested PCR-Denaturing Gradient Gel Electrophoresis Approach To Determine the Diversity of Sulfate-Reducing Bacteria in Complex Microbial Communities." Applied and Environmental Microbiology 71, no. 5 (2005): 2325–30. http://dx.doi.org/10.1128/aem.71.5.2325-2330.2005.

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ABSTRACT Here, we describe a three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors. In the first step, the nearly complete 16S rRNA gene was amplified using bacterial primers. Subsequently, this product was used as a template in a second PCR with group-specific SRB primers. A third round of amplification was conducted to obtain fragments suitable for DGGE. The largest number of bands was observed in DGGE patterns of products obtained with primers specific for the Desul

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Kawai, Mako, Eiichi Matsutera, Hisashi Kanda, Nobuyasu Yamaguchi, Katsuji Tani, and Masao Nasu. "16S Ribosomal DNA-Based Analysis of Bacterial Diversity in Purified Water Used in Pharmaceutical Manufacturing Processes by PCR and Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 68, no. 2 (2002): 699–704. http://dx.doi.org/10.1128/aem.68.2.699-704.2002.

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ABSTRACT The bacterial community in partially purified water, which is prepared by ion exchange from tap water and is used in pharmaceutical manufacturing processes, was analyzed by denaturing gradient gel electrophoresis (DGGE). 16S ribosomal DNA fragments, including V6, -7, and -8 regions, were amplified with universal primers and analyzed by DGGE. The bacterial diversity in purified water determined by PCR-DGGE banding patterns was significantly lower than that of other aquatic environments. The bacterial populations with esterase activity sorted by flow cytometry and isolated on soybean ca

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Gast, Rebecca J., Mark R. Dennett, and David A. Caron. "Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 70, no. 4 (2004): 2028–37. http://dx.doi.org/10.1128/aem.70.4.2028-2037.2004.

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ABSTRACT The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a culture-independent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different m

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Pandey, Pramod, Dhrubajyoti Chowdhury, and Yi Wang. "Denaturing Gradient Gel Electrophoresis Approach for Microbial Shift Analysis in Thermophilic and Mesophilic Anaerobic Digestions." Gels 10, no. 5 (2024): 339. http://dx.doi.org/10.3390/gels10050339.

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To determine the evolution of microbial community and microbial shift under anaerobic processes, this study investigates the use of denaturing gradient gel electrophoresis (DGGE). In the DGGE, short- and medium-sized DNA fragments are separated based on their melting characteristics, and this technique is used in this study to understand the dominant bacterial community in mesophilic and thermophilic anaerobic digestion processes. Dairy manure is known for emitting greenhouse gases (GHGs) such as methane, and GHG emissions from manure is a biological process that is largely dependent on the ma

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Esseili, M. A., I. I. Kassem, J. Lis, and V. Sigler. "Application of denaturing gradient gel electrophoresis (DGGE) for assessing fecal pollution sources at a recreational beach." Journal of Water and Health 12, no. 4 (2014): 846–57. http://dx.doi.org/10.2166/wh.2014.034.

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We investigated the effectiveness of Escherichia coli community fingerprinting for identifying fecal pollution sources impacting a recreational beach. E. coli in water collected from the beach, nearby creek and storm sewer outfall were enumerated using membrane filtration, while E. coli communities were characterized following polymerase chain reaction analysis and denaturing gradient gel electrophoresis (DGGE) fingerprinting. Analysis of E. coli densities to determine the contributions of the creek and storm sewer during dry weather was inconclusive. However, DGGE fingerprinting indicated tha

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Piwat, S., and R. Teanpaisan. "16S rRNA PCR-Denaturing Gradient Gel Electrophoresis of Oral Lactobacillus casei Group and Their Phenotypic Appearances." ISRN Microbiology 2013 (September 23, 2013): 1–6. http://dx.doi.org/10.1155/2013/342082.

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This study aimed to develop a 16S rRNA PCR-denaturing gradient gel electrophoresis (DGGE) to identify the species level of Lactobacillus casei group and to investigate their characteristics of acid production and inhibitory effect. PCR-DGGE has been developed based on the 16S rRNA gene, and a set of HDA-1-GC and HDA-2, designed at V2-V3 region, and another set of CARP-1-GC and CARP-2, designed at V1 region, have been used. The bacterial strains included L. casei ATCC 393, L. paracasei CCUG 32212, L. rhamnosus ATCC 7469, L. zeae CCUG 35515, and 46 clinical strains of L. casei/paracasei/rhamnosu

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Blajman, J. E., M. V. Zbrun, M. L. Signorini, et al. "Development of cecal-predominant microbiota in broilers during a complete rearing using denaturing gradient gel electrophoresis." Animal Production Science 57, no. 3 (2017): 458. http://dx.doi.org/10.1071/an15475.

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Understanding of the intestinal microbiota is crucial to enhance intestinal health and performance parameters in animals. A more exhaustive research of the intestinal microbiota of broilers could be of interest to implement appropriate intervention measures. The aim of the present study was to investigate the development of the predominant cecal microbiota in broilers that were fed a Lactobacillus salivarius DSPV 001P strain during a complete rearing using denaturing gradient gel electrophoresis (DGGE). Bacterial DNA from cecal samples of 24 broilers at different ages were amplified by PCR and

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Nowak, E., R. Brousseau, J. Garrett, et al. "Characterization of formulated microbial products by denaturing gradient gel electrophoresis, total cellular fatty acid analysis, and DNA microarray analysis." Canadian Journal of Microbiology 54, no. 5 (2008): 380–90. http://dx.doi.org/10.1139/w08-015.

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Two commercial products, Biotize and Cycle, containing bacteria as an active ingredient were characterized for species identification and batch-to-batch variation by denaturing gradient gel electrophoresis (DGGE), total cellular fatty acid analysis (FAA), and a taxonomic DNA microarray. DGGE was useful at assessing the stability of consortia in different batches, and cluster analysis differentiated each batch even when only slight differences in species composition were observed. DGGE, FAA, and DNA microarray results indicated little batch-to-batch variation in Biotize and some batch variation

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Habibi, Moh. "Identifikasi Biodeteriogen Sebagai Langkah Awal Konservasi Benda Cagar Budaya." Jurnal Konservasi Cagar Budaya 10, no. 2 (2016): 23–30. http://dx.doi.org/10.33374/jurnalkonservasicagarbudaya.v10i2.151.

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Indonesia mempunyai Benda Cagar Budaya (BCB) yang berlimpah. BCB tersebut dapat mengalami degradasi disebabkan mikroorganisme. Penelitian ini bertujuan untuk memberikan pengetahuan mengenai teknik molecular yang digunakan untuk deteksi biodeteriogen pada benda cagar budaya. Teknik Molekuler yang dapat digunakan adalah Fingerprinting, meliputi DGGE (Denaturing Temperature Gradient Gel Electrophoresis), SSCP (Single Strand Conformation Polymorphism), ARDRA (Amplified Ribosomal DNA Restriction Analysis), dan Clone Library. Teknik ini mempunyai beberapa kelebihan, seperti tingkat presisi yang ting

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