Relevant bibliographies by topics / Amplified Ribosomal DNA Restriction Analysis

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Academic literature on the topic 'Amplified Ribosomal DNA Restriction Analysis'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 February 2022

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Journal articles on the topic "Amplified Ribosomal DNA Restriction Analysis"

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Ramos, Sonny Cachero, Yeoung Min Hwang, Ji Hee Lee, Keun Sik Baik, and Chi Nam Seong. "Seasonal Variation of Bacterial Community in the Seawater of Gwangyang Bay Estimated by Amplified Ribosomal DNA Restriction Analysis." Journal of Life Science 23, no. 6 (2013): 770–78. http://dx.doi.org/10.5352/jls.2013.23.6.770.

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Ingianni, Angela, Sabrina Petruzzelli, Grazia Morandotti, and Raffaello Pompei. "Genotypic differentiation ofGardnerella vaginalisby amplified ribosomal DNA restriction analysis (ARDRA)." FEMS Immunology & Medical Microbiology 18, no. 1 (1997): 61–66. http://dx.doi.org/10.1111/j.1574-695x.1997.tb01028.x.

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Coton, M., J. M. Laplace, and E. Coton. "Zymomonas mobilis subspecies identification by amplified ribosomal DNA restriction analysis." Letters in Applied Microbiology 40, no. 2 (2005): 152–57. http://dx.doi.org/10.1111/j.1472-765x.2004.01652.x.

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Vaneechoutte, M., L. Dijkshoorn, I. Tjernberg, et al. "Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis." Journal of clinical microbiology 33, no. 1 (1995): 11–15. http://dx.doi.org/10.1128/jcm.33.1.11-15.1995.

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Mendoza-Espinoza, Alfredo, Ysabel Koga, and Amparo I. Zavaleta. "Amplified 16S Ribosomal DNA Restriction Analysis for Identification of Avibacterium paragallinarum." Avian Diseases 52, no. 1 (2008): 54–58. http://dx.doi.org/10.1637/8036-062507-reg.

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Mendoza-Espinoza, Alfredo, Ysabel Koga, and Amparo I. Zavaleta. "AMplified 16S Ribosomal DNA Restriction Analysis for Identification of Avibacterium paragallinarum." Avian Diseases Digest 3, no. 1 (2008): e19-e19. http://dx.doi.org/10.1637/1933-5334(2008)3[e19:asrdra]2.0.co;2.

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Jang, Jichan, Bongjoon Kim, Jongho Lee, Jeongho Kim, Gajin Jeong, and Hongui Han. "Identification ofWeissellaspecies by the genus-specific amplified ribosomal DNA restriction analysis." FEMS Microbiology Letters 212, no. 1 (2002): 29–34. http://dx.doi.org/10.1111/j.1574-6968.2002.tb11240.x.

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Vaneechoutte, M., H. De Beenhouwer, G. Claeys, et al. "Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis." Journal of Clinical Microbiology 31, no. 8 (1993): 2061–65. http://dx.doi.org/10.1128/jcm.31.8.2061-2065.1993.

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LEIRO, J., M. I. G. SISO, A. PARAMA, F. M. UBEIRA, and M. L. SANMARTIN. "RFLP analysis of PCR-amplified small subunit ribosomal DNA of three fish microsporidian species." Parasitology 120, no. 2 (2000): 113–19. http://dx.doi.org/10.1017/s0031182099005405.

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The phylogenetic relationships of the microsporidian species Microgemma caulleryi, Pleistophora finisterrensis and Tetramicra brevifilum were investigated on the basis of restriction fragment length polymorphism (RFLP) analysis of PCR-amplified small-subunit rDNA (SSUrDNA). Using PCR primers specific for microsporidian SSUrDNA, a single product was obtained from each species, and heteroduplex analysis indicated a high degree of sequence homology among the 3 products. In RFLP analysis of the PCR-amplified SSUrDNA, the enzymes AluI and DdeI gave restriction patterns that differed among all 3 species. Phylogenetic analysis using restriction patterns as differential characters indicated that Microgemma caulleryi and Tetramicra brevifilum are more closely related to each other than to Pleistophora finisterrensis.
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Guillemaut, Cécile, Véronique Edel-Hermann, Pierre Camporota, Claude Alabouvette, Marc Richard-Molard, and Christian Steinberg. "Typing of anastomosis groups ofRhizoctonia solaniby restriction analysis of ribosomal DNA." Canadian Journal of Microbiology 49, no. 9 (2003): 556–68. http://dx.doi.org/10.1139/w03-066.

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A method based on restriction analysis of polymerase chain reaction (PCR)-amplified ribosomal DNA was developed for the rapid characterization of large populations of Rhizoctonia solani at the anastomosis group (AG) level. The restriction maps of the internal transcribed spacers (ITS) sequences were compared for 219 isolates of R. solani belonging to AG-1 to AG-12 and AG-BI, representing diverse geographic and host range origins. Four discriminant restriction enzymes (MseI, AvaII, HincII, and MunI) resolved 40 restriction fragment length polymorphism (RFLP) types among the 219 ITS sequences of R. solani. Each RFLP type could be assigned to a single AG except for two RFLP types, which were common to two AG. A fifth enzyme allowed the discrimination of AG-6 and AG-12. In addition, the combination of four enzymes allowed the discrimination of subsets within AG-1, AG-2, AG-3, and AG-4. The efficiency of the typing method was confirmed by analyzing PCR-amplified ITS sequences of 30 reference strains. Furthermore, the PCR–RFLP method was used to characterize at the AG level 307 isolates of R. solani originating from ten sugar beet fields exhibiting patches of diseased plants in France. The PCR-based procedure described in this paper provides a rapid method for AG typing in R. solani.Key words: Rhizoctonia solani, anastomosis group, PCR–RFLP, ITS, identification, sugar beet.
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Dissertations / Theses on the topic "Amplified Ribosomal DNA Restriction Analysis"

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Dulanto, Gomez Jimmy Ronald. "Identificación rápida de especies del género Vibrio asociados con el cultivo de "langostino blanco" Litopenaeus vannamei por amplified ribosomal DNA restriction analysis (ARDRA)." Bachelor's thesis, Universidad Nacional Mayor de San Marcos, 2013. https://hdl.handle.net/20.500.12672/3432.

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La investigación tuvo como objetivo incorporar una metodología de identificación rápida conocida como ARDRA (Amplified Ribosomal DNA Restriction Analysis) para identificar especies del género Vibrio. Se estandarizó la técnica con cepas referenciales. Luego, se aislaron cepas bacterianas asociadas con el cultivo de Litopenaeus vannamei. Posteriormente, se realizaron pruebas bioquímicas para encontrar cepas candidatas de pertenecer al género Vibrio. Al finalizar esta primera etapa, la técnica ARDRA estandarizada, fue aplicada en las cepas candidatas, confirmando de esta manera la factibilidad de la metodología bajo las condiciones estudiadas. En una segunda etapa, se secuenció la región 16S rDNA para confirmar e identificar las cepas candidatas por análisis filogenético. Se reportaron tres especies diferentes con alta similitud pertenecientes al Vibrio core group (Vibrio communis, Vibrio harveyi y Vibrio parahaemolyticus). Con estos resultados, fue posible diseñar una identificación rápida por ARDRA para identificar el Vibrio core group y la especie Vibrio communis. La metodología de diseño del ARDRA fue soportado por una valoración diagnóstica bioinformática, obteniendo de esta evaluación, una sensibilidad y una especificidad de 97,1 y 76,9%, respectivamente para la identificación del Vibrio core group, mientras que para identificar la especie Vibrio communis, se obtuvo una sensibilidad y una especificidad de 100 y 97,4%, respectivamente. Finalmente, se ha demostrado que es posible identificar ciertas especies del genero Vibrio asociados con la acuicultura de Litopenaeus vannamei, por ARDRA y esta metodología de identificación, tiene la ventaja de ser mucho más rápido y económico en comparación con la identificación por análisis filogenético, teniendo a su vez la desventaja de ser dependiente del uso del secuenciamiento en un primer momento para el diseño del ARDRA. Palabras clave: Litopenaeus vannamei, ARDRA, Vibrio communis, Vibrio harveyi, Vibrio parahaemolyticus, Vibrio core group, evaluación diagnóstica bioinformática.<br>Tesis
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Du, Plessis Gerda. "Actinobacterial diversity of the Ethiopian Rift Valley lakes." University of the Western Cape, 2011. http://hdl.handle.net/11394/5385.

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>Magister Scientiae - MSc<br>The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomics studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. The actinobacterial OTUs detected belonged to both the Rubrobacterales and Actinomycetales orders with members of the genus Arthrobacter being found in all three lakes. Geochemical properties were significantly different between the lakes, although more than one property attributed to the variance between community compositions. The diversity detected in the culture-based study differed significantly and all isolates belonged to the genus Streptomyces. Two novel strains were characterized by means of phylogenetic (16S rRNA gene sequence), physiological, morphological and biochemical analyses. Both novel isolates were capable of growing under "extreme" conditions- pH 12, 10% NaCl and 45°C. Partial enzyme characterization revealed that both strains produced xylanase enzymes that were active at pH 6.5 and 8.5 with an increase in activity up to 45°C. The results obtained revealed a previously undetected diversity of actinobacteria in the Ethiopian Rift Valley with a potentially novel subpopulation adapted to haloalkaline conditions. The low 16S rRNA sequence similarity of a substantial proportion of the libraries suggests that culture-based isolation may play a vital role in deciphering the community fingerprint.<br>The National Research Foundation and the Norwegian Research Council
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Zhang, Jianhua. "Restriction fragment length polymorphism analysis of chloroplast DNA, mitochondrial DNA, and ribosomal DNA in turfgrasses." Diss., This resource online, 1994. http://scholar.lib.vt.edu/theses/available/etd-06062008-170748/.

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Jung, Andreas. "Sequentielle Genotypisierung von Pseudomonas aeruginosa-Isolaten und Übereinstimmung von bakteriologischen Proben aus dem oberen und unteren Respirationstrakt von Patienten mit cystischer Fibrose." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2005. http://dx.doi.org/10.18452/15351.

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Die Frage nach adäquaten mikrobiologischen und molekulargenetischen Methoden, um die Kolonisation des Respirationstrakts von Mukoviszidose-Patienten mit Pseudomonas aeruginosa nachzuweisen und zu charakterisieren, wird kontrovers diskutiert. Von 38 klinisch stabilen Patienten mit cystischer Fibrose (CF) wurden sequentiell im Abstand von 18 Monaten Proben aus Rachenabstrich, Sputum und Bronchiallavage (BAL) entnommen und bezüglich Pseudomonas-Nachweis untersucht. Die Pseudomonas-Stämme wurden mittels Random Amplified Polymorphic DNA (RAPD)-Analyse und Pulsfeld-Gelelektrophorese (PFGE) von DNA-Makrorestriktionsfragmenten typisiert und bezüglich der Frage nach genetisch divergierenden Isolaten innerhalb des selben Individuums sowie nach möglichen longitudinalen genetischen Veränderungen evaluiert. Sensitivität, negative und positive prädiktive Werte und Spezifität, um eine P. aeruginosa-Besiedlung zu erkennen, waren 36%, 74%, 83% und 96% im Falle der Kulturen aus dem Oropharynx von nicht-expektorierenden Patienten und 92%, 94%, 100% und 100% für Sputumkulturen von expektorierenden Probanden. RAPD-Analyse und PFGE waren in der Lage, zwischen unterschiedlichen Pseudomonas-Stämmen zu diskriminieren, wobei nur die DNA-Makrorestriktion zwischen Subtypen unterscheiden konnte. Die Genotypen der Pseudomonas-Isolate aus Rachenabstrich und Sputum divergierten in 55% und 40% zu den Isolaten der BAL. Longitudinale Variationen des Genotyps wurden in 62% der Fälle beobachtet, die Hälfte davon war nur mittels bronchoskopisch gewonnener Proben erkennbar. Zusammengefasst besitzen Sputumproben bezüglich des Pseudomonas-Nachweises dieselbe Wertigkeit wie Kulturen aus der BAL, während Rachenabstriche in einer frühen Krankheitsphase für die Charakterisierung der bakteriellen Flora des unteren Respirationstrakts wenig geeignet sind. Die Methode der DNA-Makrorestriktion kann als zuverlässige Technik für epidemiologische Untersuchungen empfohlen werden. Unterschiedliche Genotypen innerhalb desselben Individuums und longitudinale genetische Alterationen sind häufig, jedoch unter Umständen nur bronchoskopisch nachweisbar.<br>There is controversy about adequate specimen to detect and characterise colonisation of cystic fibrosis (CF) airways by Pseudomonas aeruginosa. Oropharyngeal, sputum and bronchoalveolar lavage (BAL) samples were evaluated sequentially from 38 stable CF patients for the detection of P. aeruginosa. Pseudomonas strains were typed by random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. The occurrence of genetically different isolates within the same host and longitudinal variations in the genotype during repeated examinations was assessed. Sensitivity, negative and positive predictive values and specificity to detect P. aeruginosa were 36%, 74%, 83% and 96% for oropharyngeal cultures in non-expectorating patients and 92%, 94%, 100% and 100% for sputum cultures from expectorating patients, respectively. RAPD analysis and PFGE were suitable to characterize P. aeruginosa CF isolates, although only DNA macrorestriction was able to distinguish between identical and closely related strains. Genotypes of Pseudomonas isolates recovered from oropharyngeal swabs and sputum differed to the strains recovered by bronchoscopy in 55% and 40%, respectively. In 62% longitudinal variations in the genotype occurred. Half of these alterations were only detectable from bronchoscopically obtained samples. In conclusion, sputum samples have the same value as specimens from BAL to detect P. aeruginosa colonisation, whereas cultures from the oropharynx are not suitable for characterising the bacterial conditions in the CF lungs in an early disease state. DNA macrorestriction is recommended as an excellent tool for epidemiological investigations. Different genotypes within the same host and longitudinal genetic alterations are common and may be detectable in the BAL fluid exclusively.
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Books on the topic "Amplified Ribosomal DNA Restriction Analysis"

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Kleinkauf, Phillip Scott. Bacterial community structure of hydrothermal vents at Guaymas Basin, Mexico as determined by amplified ribosomal DNA restriction analysis. 2000.

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Book chapters on the topic "Amplified Ribosomal DNA Restriction Analysis"

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Edel, V., C. Steinberg, N. Gautheron, and C. Alabouvette. "Differentiation of Fusarium Species by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Ribosomal DNA." In Developments in Plant Pathology. Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-009-0043-1_91.

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Massol-Deya, Arturo A., David A. Odelson, Robert F. Hickey, and James M. Tiedje. "Bacterial community fingerprinting of amplified 16S and 16–23S ribosomal DNA gene sequences and restriction endonuclease analysis(ARDRA)." In Molecular Microbial Ecology Manual. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0351-0_20.

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Uchiyama, K., T. Suzuki, H. Tatsumi, H. Kanetake, and S. Shioya. "Amplified 16S Ribosomal DNA Restriction Analysis of Microbial Community Structure During Rapid Degradation of a Biopolymer, PHA, by Composting." In Microbiology of Composting. Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-662-08724-4_7.

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Eden, Peter A., Thomas M. Schmidt, Richard P. Blakemore, and Norman R. Pace. "Phylogenetic Analysis of Aquaspirillum Magnetotacticum Using PCR-Amplified 16S Ribosomal RNA-Specific DNA." In Iron Biominerals. Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3810-3_9.

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Jacobson, D. R., and J. N. Buxbaum. "Detection of Variant Transthyretin Genes by Restriction Analysis of PCR-Amplified Genomic DNA." In Amyloid and Amyloidosis 1990. Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3284-8_160.

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Matsumoto, Masaru, and Nobukai Matsuyama. "Relp Analysis of the PCR-Amplified 28S Ribosomal DNA for Revision of Genetic Relationships in Rhizotonia Spp." In Major Fungal Diseases of Rice. Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-017-2157-8_15.

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"Probes, Allele Mutations, and Restriction Enzymes." In DNA Fingerprinting, edited by Lorne t. Kirby. Oxford University Press, 1993. http://dx.doi.org/10.1093/oso/9780716770015.003.0010.

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Positive identification is the ultimate objective of forensic analysis of blood and other tissue specimens. Nucleotide probes can be very effective tools for detecting genetic markers in this identification process. The genetic markers should be highly polymorphic; allelic variants should be easily and readily detectable; if amplification is required, the alleles should be efficiently amplified using PCR technology; and a statistically sound estimate of the population allele and genotype frequencies should be available. Probes are single-stranded fragments of DNA or RNA containing the complementary code for a specific sequence of genome bases. Probes available for DNA profile analysis will, no doubt, eventually number in the hundreds. Currently, the most valuable detect tandem repetitive sequence fragments either at a specific locus under high-stringency analysis conditions or at numerous loci under low-stringency conditions. Each locus consists of many possible alleles with frequencies that vary depending on the specific population. Other factors also enter into the selection of probes, including ease of amplification, stability, cross-reactivity, and general availability. Rate of allele mutation is also a prime consideration in probe selection. Mutation can be considered at two levels: as the basis for the large number of tandem repeat (VNTR) alleles formed during evolution and as a possible reason for spurious unassignable bands in typing analysis. Although highly unlikely, somatic mutations may be of concern in forensic testing if DNA from different tissues, such as blood and hair roots, are being matched. Germ line (gamete) mutations must be considered when parentage analyses are undertaken. These situations could give rise to false negative results and, therefore, false exclusions. Different considerations also apply for single versus multilocus probes. If a band that is not seen in the putative father is detected in an offspring, the man could incorrectly be excluded if the single-locus probe approach is used. This situation would necessitate testing with more than the usual four or five probes.
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