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

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Published: 4 June 2021
Last updated: 7 February 2022

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1

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

WARD, E., M. J. ADAMS, E. S. MUTASA, C. R. COLLIER, and M. J. C. ASHER. "Characterization of Polymyxa species by restriction analysis of PCR-amplified ribosomal DNA." Plant Pathology 43, no. 5 (1994): 872–77. http://dx.doi.org/10.1111/j.1365-3059.1994.tb01631.x.

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12

Bunyard, Britt A., Michael S. Nicholson, and Daniel J. Royse. "Phylogeny of the GenusAgaricusInferred from Restriction Analysis of Enzymatically Amplified Ribosomal DNA." Fungal Genetics and Biology 20, no. 4 (1996): 243–53. http://dx.doi.org/10.1006/fgbi.1996.0039.

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13

Schlegel, L., F. Grimont, P. A. D. Grimont, and A. Bouvet. "Identification of Major Streptococcal Species by rrn-Amplified Ribosomal DNA Restriction Analysis." Journal of Clinical Microbiology 41, no. 2 (2003): 657–66. http://dx.doi.org/10.1128/jcm.41.2.657-666.2003.

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14

Miteva, V., I. Boudakov, G. Ivanova-Stoyancheva, B. Marinova, V. Mitev, and J. Mengaud. "Differentiation ofLactobacillus delbrueckiisubspecies by ribotyping and amplified ribosomal DNA restriction analysis (ARDRA)." Journal of Applied Microbiology 90, no. 6 (2001): 909–18. http://dx.doi.org/10.1046/j.1365-2672.2001.01320.x.

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15

Mei, Lee Chin, Sieo Chin Chin, Norhani Abdullah, and Ho Yin Wan. "Characterisations of Probiotic Lactobacillus Strains by Amplified Ribosomal DNA Restriction Analysis (ARDRA)." Materials Science Forum 981 (March 2020): 302–8. http://dx.doi.org/10.4028/www.scientific.net/msf.981.302.

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Twelve probiotic Lactobacillus strains for poultry were characterised by amplified ribosomal DNA restriction analysis (ARDRA) using Sau3AI, TaqI, HaeIII and AluI restriction endonucleases. Species-specific and strain-specific restriction patterns were observed from the bacterial strains. Numerical analysis of composite analysis of ARDRA exhibited D value of 0.8456. Whereas, the caculated D values of ARDRA patterns generated by Sau3AI, TaqI, HaeIII and AluI were 0.8309, 0.8382,0.8088 and 0.8088, repectively. Composite analysis of ARDRA was the most discriminative method when compared to the individual analysis. ARDRA could distinguished L. reuteri C 10 and L. panis C 17 into single strains. The 16S rRNA gene restriction patterns were also able to group L. gallinarum I 16 and I 26 into single strains. Lactobacillus brevis I 12, I 23, I 25, I 211 and I 218 seem to be multiple clones of the same bacterial strain as are L. reuteri C 1 and C 16. ARDRA is a valuable fingerprinting method to discriminate probiotic Lactobacillus strains.
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Kurabachew, Mekonnen, Øivind Enger, Ruth-Anne Sandaa, Eshetu Lemma, and Bjarne Bjorvatn. "Amplified ribosomal DNA restriction analysis in the differentiation of related species of mycobacteria." Journal of Microbiological Methods 55, no. 1 (2003): 83–90. http://dx.doi.org/10.1016/s0167-7012(03)00119-2.

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17

Dijkshoorn, Lenie, Barbara van Harsselaar, Ingela Tjernberg, Philippe J. M. Bouvet, and Mario Vaneechoutte. "Evaluation of Amplified Ribosomal DNA Restriction Analysis for Identification of Acinetobacter Genomic Species." Systematic and Applied Microbiology 21, no. 1 (1998): 33–39. http://dx.doi.org/10.1016/s0723-2020(98)80006-4.

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18

Wilson, M. J., W. G. Wade, and A. J. Welghtman. "Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA of humanCapnocytophaga." Journal of Applied Bacteriology 78, no. 4 (1995): 394–401. http://dx.doi.org/10.1111/j.1365-2672.1995.tb03424.x.

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19

Bockelmann, Wilhelm, Michael Heller, and Knut J. Heller. "Identification of yeasts of dairy origin by amplified ribosomal DNA restriction analysis (ARDRA)." International Dairy Journal 18, no. 10-11 (2008): 1066–71. http://dx.doi.org/10.1016/j.idairyj.2008.05.008.

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20

Martin-Laurent, F., L. Philippot, S. Hallet, et al. "DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods." Applied and Environmental Microbiology 67, no. 5 (2001): 2354–59. http://dx.doi.org/10.1128/aem.67.5.2354-2359.2001.

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ABSTRACT The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure or sewage sludge onto a monoculture of maize for 15 years.
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21

O’Farrell, Katrina A., and Peter H. Janssen. "Detection of Verrucomicrobia in a Pasture Soil by PCR-Mediated Amplification of 16S rRNA Genes." Applied and Environmental Microbiology 65, no. 9 (1999): 4280–84. http://dx.doi.org/10.1128/aem.65.9.4280-4284.1999.

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ABSTRACT Oligonucleotide primers were designed and used to amplify, by PCR, partial 16S rRNA genes of members of the bacterial divisionVerrucomicrobia in DNA extracted from a pasture soil. By applying most-probable-number theory to the assay, verrucomicrobia appeared to contribute some 0.2% of the soil DNA. Amplified ribosomal DNA restriction analysis of 53 cloned PCR-amplified partial 16S rRNA gene fragments and comparative sequence analysis of 21 nonchimeric partial 16S rRNA genes showed that these primers amplified only 16S rRNA genes of members of the Verrucomicrobia in DNA extracted from the soil.
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22

Koeleman, Johannes G. M., Jeroen Stoof, Dennis J. Biesmans, Paul H. M. Savelkoul, and Christina M. J. E. Vandenbroucke-Grauls. "Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment Length Polymorphism Fingerprinting for Identification ofAcinetobacter Genomic Species and Typing ofAcinetobacter baumannii." Journal of Clinical Microbiology 36, no. 9 (1998): 2522–29. http://dx.doi.org/10.1128/jcm.36.9.2522-2529.1998.

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Thirty-one strains of Acinetobacter species, including type strains of the 18 genomic species and 13 clinical isolates, were compared by amplified ribosomal DNA restriction analysis (ARDRA), random amplified polymorphic DNA analysis (RAPD), and amplified fragment length polymorphism (AFLP) fingerprinting. ARDRA, performed with five different enzymes, showed low discriminatory power for differentiating Acinetobacter at the species and strain level. The standardized commercially available RAPD kit clearly enabled the discrimination of all Acinetobacter genomic species but showed great polymorphism between isolates ofAcinetobacter baumannii. AFLP fingerprinting with radioactively as well as fluorescently labelled primers showed high discriminatory power for the identification of 18Acinetobacter genomic species and typing of 13 clinical Acinetobacter isolates. Compared to radioactive AFLP, fluorescent AFLP was technically fast and simple to perform, and it permitted analysis with an automated DNA sequencer. Fluorescent AFLP seems particularly well suited for studying the epidemiology of nosocomial infections and outbreaks caused by Acinetobacterspecies.
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23

Mazinani, Z., and A. Asgharzadeh. "Genetic diversity of Azotobacter strains isolated from soils by amplified ribosomal DNA restriction analysis." Cytology and Genetics 48, no. 5 (2014): 293–301. http://dx.doi.org/10.3103/s0095452714050041.

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24

Rafin, Catherine, Yves Brygoo, and Yves Tirilly. "Restriction analysis of amplified ribosomal DNA of Pythium spp. isolated from soilless culture systems." Mycological Research 99, no. 3 (1995): 277–81. http://dx.doi.org/10.1016/s0953-7562(09)80898-8.

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25

Hall, V., P. R. Talbot, S. L. Stubbs, and B. I. Duerden. "Identification of Clinical Isolates of Actinomyces Species by Amplified 16S Ribosomal DNA Restriction Analysis." Journal of Clinical Microbiology 39, no. 10 (2001): 3555–62. http://dx.doi.org/10.1128/jcm.39.10.3555-3562.2001.

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26

Vaneechoutte, Mario, Rudi Rossau, Paul Vos, et al. "Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA)." FEMS Microbiology Letters 93, no. 3 (1992): 227–33. http://dx.doi.org/10.1111/j.1574-6968.1992.tb05102.x.

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27

Lestari, Puji, Dwi Ningsih Susilowati, I. Made Samudera, et al. "Keragaman Genetik Rizobakteri Penghasil Asam Indol Asetat Berdasarkan 16S rRNA dan Amplified Ribosomal DNA Restriction Analysis." Jurnal AgroBiogen 13, no. 1 (2018): 25. http://dx.doi.org/10.21082/jbio.v13n1.2017.p25-34.

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<p>Asam indol asetat (AIA) dapat dihasilkan oleh bakteri rizosfer/rizobakteri pemacu pertumbuhan tanaman (PPT). Keragaman genetik isolat bakteri PPT indigenous Indonesia perlu diinvestigasi untuk mencari sumber potensial agen PPT dengan informasi kekerabatan intra dan interspesies yang jelas. Karena itu penelitian ini bertujuan mengetahui keragaman genetik rizobakteri penghasil AIA <em>indigenous</em> Indonesia dengan gen 16S rRNA, dilengkapi dengan ARDRA. Koleksi isolat bakteri BB Biogen diidentifikasi kandungan AIA-nya, morfologi secara makroskopis dan sekuensing pada sekuen 16S rRNA dan ARDRA. Total empat belas isolat rizobakteri memiliki kandungan AIA dalam kisaran 5,24-37,69 µg/ml dan tertinggi pada SM1. Karakteristik morfologi koloni rizobakteri mendukung variasi strain bakteri penghasil AIA. Delapan isolat terpilih diidentifikasi sebagai spesies Bacillus dengan homologi 96-99%. Lima isolat (SM1, JP4, KP3, MB2, dan CP3) diidentifikasikan sebagai <em>B. subtilis</em>, SC2 sebagai <em>B. amyloliquefaciens</em>, BL2 dekat dengan <em>B. velezensis, </em>dan JP3 memiliki homologi tinggi dengan <em>Brevundimonas olei. </em>Delapan isolat rizobakteri tersebut berkerabat dekat dengan strain bakteri referensi yang memiliki kesamaan spesies. Analisis ARDRA-<em>Rsa</em>I menghasilkan lima filotipe dengan keunikan pola sidik jari. Isolat CP3, MB 2, dan KP 3 berada dalam satu filotipe. Kedekatan isolat dalam <em>Bacillus</em> sp. digambarkan oleh filotipe 5 (<em>B. subtilis</em> SM1 dan <em>B. velezensis</em> BL2) yang diduga jauh dari <em>B. amyloliquefaciens</em> SC2 (filotipe 4) dan JP 3 pada genus <em>Brevundimonas </em>(filotipe 3). Keragaman genetik isolat rizobakteri penghasil AIA terhitung rendah berdasarkan 16S-rRNA dan ARDRA-<em>Rsa</em>I.</p>
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Schmidt, Olaf, and Ute Moreth. "Identification of the Dry Rot Fungus, Serpula lacrymans, and the Wild Merulius, S. himantioides, by Amplified Ribosomal DNA Restriction Analysis (ARDRA)." Holzforschung 53, no. 2 (1999): 123–28. http://dx.doi.org/10.1515/hf.1999.020.

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SummaryIsolates of the dry rot fungus,Serpula lacrymans, and of the morphologically similar wild merulius,S. himantioides, were investigated by amplified ribosomal DNA restriction analysis (ARDRA) of the internal transcribed spacer (ITS) region to prove this method as diagnosis tool for the economically important indoor rot fungi. The technique uses the polymerase chain reaction (PCR) to amplify the relatively variable sequences of the ITS region arranged between the highly conserved portions of the 18S and 28S RNA genes of the nuclear ribosomal DNA (rDNA) repeat unit. Subsequent digestion of the amplicon with restriction endonucleases may exhibit differences at species and subspecies level. Using the universal ITS 1/ITS 4 primer combination, the ITS region of all isolates ofS. lacrymansandS. himantioideswas amplified. The size of the amplified products was about 630bp in both species, as estimated from agarose gel electrophoresis. Digestion of the amplicon with the endonuclease pairsAluI/HhaI andAvaII/MboII, respectively, revealed identical rDNA-ITS fragments for the isolates of both species, indicating their genetic relationship. On the other hand, digestion withBglI/HinfI andHaeIII/TaqI, respectively, separated the fungi by means of different fragment patterns. Thus, ARDRA-ITS proved to be suited for the identification of both fungi.
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29

Molina, Francis I., Peng Shen, Shung-Chang Jong, and Kazuhiko Orikono. "Molecular evidence supports the separation of Lentinula edodes from Lentinus and related genera." Canadian Journal of Botany 70, no. 12 (1992): 2446–52. http://dx.doi.org/10.1139/b92-302.

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Restriction polymorphisms in two regions of the ribosomal DNA (rDNA) repeat unit were examined in 18 strains of Lentinus, Neolentinus, Pleurotus, and the shiitake mushroom Lentinula edodes. The polymerase chain reaction was used to separately amplify the 18S rDNA and the region spanning the two internal transcribed spacers and the 5.8S ribosomal RNA gene. Amplified products were digested with a battery of 10 restriction endonucleases and the two data sets were subjected to cluster analysis. All strains of Lentinula edodes consistently exhibited identical restriction profiles that were distinct from those of the genera Lentinus, Neolentinus, and Pleurotus. The internal transcribed spacer region exhibited more variability than the 18S rDNA, giving distinctive profiles for two strains of Lentinus tigrinus and for one strain of Neolentinus lepideus. Similarity coefficients were clustered with the unweighted pair group method with arithmetic average, single-linkage method, and complete-linkage method. Results from cluster analysis of the two data sets were highly congruent and tree topologies were consistent irrespective of the clustering method used. The distinctiveness of the groups was further confirmed by computing for consensus trees and cophenetic correlation coefficients. Ribosomal DNA restriction polymorphisms support the placement of the strains examined in separate taxa. Key words: Lentinula, Lentinus, Neolentinus, Pleurotus, ribosomal DNA.
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de Moura Nascimento, Ernandes Joel, and Sueli Teresinha Van Der Sand. "Restriction analysis of the amplified ribosomal DNA spacers ITS1 and ITS2 of Bipolaris sorokiniana isolates." World Journal of Microbiology and Biotechnology 24, no. 5 (2007): 647–52. http://dx.doi.org/10.1007/s11274-007-9517-1.

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31

Heyndrickx, M., L. Vauterin, P. Vandamme, K. Kersters, and P. De Vos. "Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy." Journal of Microbiological Methods 26, no. 3 (1996): 247–59. http://dx.doi.org/10.1016/0167-7012(96)00916-5.

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32

Magalhães Cruz, Leonardo, Emanuel Maltempi de Souza, Olmar Baler Weber, José Ivo Baldani, Johanna Döbereiner, and Fábio de Oliveira Pedrosa. "16S Ribosomal DNA Characterization of Nitrogen-Fixing Bacteria Isolated from Banana (Musa spp.) and Pineapple (Ananas comosus (L.) Merril)." Applied and Environmental Microbiology 67, no. 5 (2001): 2375–79. http://dx.doi.org/10.1128/aem.67.5.2375-2379.2001.

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ABSTRACT Nitrogen-fixing bacteria isolated from banana (Musaspp.) and pineapple (Ananas comosus (L.) Merril) were characterized by amplified 16S ribosomal DNA restriction analysis and 16S rRNA sequence analysis. Herbaspirillum seropedicae, Herbaspirillum rubrisubalbicans,Burkholderia brasilensis, and Burkholderia tropicalis were identified. Eight other types were placed in close proximity to these genera and other alpha and betaProteobacteria.
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Jackson, Colin J., Richard C. Barton, and E. Glyn V. Evans. "Species Identification and Strain Differentiation of Dermatophyte Fungi by Analysis of Ribosomal-DNA Intergenic Spacer Regions." Journal of Clinical Microbiology 37, no. 4 (1999): 931–36. http://dx.doi.org/10.1128/jcm.37.4.931-936.1999.

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Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus Trichophyton rubrum. The polymorphisms were detected by hybridization ofEcoRI-digested T. rubrum genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates ofT. rubrum. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonucleaseMvaI produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as T. rubrum-T. soudanense andT. quinkeanum-T. schoenlenii could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of T. rubrum and for species identification of common dermatophyte fungi.
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Bekal, S., J. P. Gauthier, and R. Rivoal. "Genetic diversity among a complex of cereal cyst nematodes inferred from RFLP analysis of the ribosomal internal transcribed spacer region." Genome 40, no. 4 (1997): 479–86. http://dx.doi.org/10.1139/g97-064.

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This study examined the restriction polymorphism (RFLP) of the nuclear ribosomal DNA in Heterodera avenae, H. filipjevi, H. mani, H. latipons, and the taxonomically unclear Gotland strain in order to establish a molecular characterization and phylogenetic relationships in the complex of cereal cyst nematodes (CCN). The internal transcribed spacer (ITS) and 5.8S rDNA were amplified by PCR from a single female or a cyst of 27 different geographic isolates of the CCN complex and one population of H. schachtii, used as outgroup. The amplified product was 1.2 kb long and 14 of 15 enzymes produced restriction fragments for each isolate. Relationships between populations were determined from UPGMA analysis based on distance values calculated from RFLP data. Digestions with TaqI clearly differentiated H. avenae, H. latipons, and a group composed of H. filipjevi and the Gotland strain. Six endonucleases (HaeIII, HinfI, ItaI, PstI, TaqI, and Tru9I) produced the same restriction pattern with H. filipjevi and the Gotland strain, and both were clearly separated from H. avenae with PstI. Restriction sites have revealed a mixture of the species H. latipons and H. avenae, and possible infraspecific variation in H. avenae. The inferred phylogenetic relationships of species in the CCN complex are in agreement with their morphological characterization.Key words: cereal cyst nematodes, Heterodera avenae, PCR, RFLP, ribosomal diversity.
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Grundmann, G. L., and P. Normand. "Microscale Diversity of the GenusNitrobacter in Soil on the Basis of Analysis of Genes Encoding rRNA." Applied and Environmental Microbiology 66, no. 10 (2000): 4543–46. http://dx.doi.org/10.1128/aem.66.10.4543-4546.2000.

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ABSTRACT We looked at the diversity of NO2 −oxidizers at field scale by examining isolates at clump scale and in microsamples of soil (diameter, 50 μm). The genetic distances (as determined by amplified ribosomal DNA restriction analysis performed with Nitrobacter-specific primers) in a small clump of soil were as large as those between reference strains from large geographical areas. Diversity in individual microsamples was shown by serotyping.
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36

Whisson, SC, BJ Howlett, ECY Liew, DJ Maclean, JM Manners, and JAG Irwin. "An Assessment of Genetic Relationships between Members of the Phytophthora megasperma Complex and Phytophthora vignae using Molecular Markers." Australian Systematic Botany 6, no. 4 (1993): 295. http://dx.doi.org/10.1071/sb9930295.

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Genetic relationships between Phytophora megasperma f. sp. glycinea (Pmg) and morphologically similar taxa, P. megasperma f. sp. medicaginis (Pmm), P. megasperma f. sp. trifolii (Pmt), P. megasperma from Douglas Fir (PmDF) and asparagus (PmAS) and Phytophthora vignae, were explored by restriction fragment length polymorphism (RFLP) analysis of nuclear DNA using random genomic multi-copy, cDNA, and ribosomal DNA probes as well as random amplified polymorphic DNA (RAPDs) and RFLP analysis of ribosomal intergenic spacer regions amplified by the polymerase chain reaction (PCR). Each method detected large differences between these taxa and P. megasperma f. sp. glycinea. P. vignae was more closely related to P. megasperma f. sp. glycinea than the other taxa on the basis of the cDNA RFLPs and RFLPs of PCR amplified rDNA intergenic spacer regions. We conclude that each of the taxa examined represent separate species. This supports the most recent reclassification based on mitochondrial RFLPs and electrophoretic protein patterns of the host-specific taxa to P. sojae (Pmg), P. trifolii (Pmt) and P. medicaginis (Pmm).
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37

Momol, E. A., M. T. Momol, J. L. Norelli, S. V. Beer, T. J. Burr, and H. S. Aldwinckle. "RELATEDNESS OF ERWINIA AMYLOVORA STRAINS BASED ON AMPLIFIED 16S-23S RIBOSOMAL DNA RESTRICTION ENZYME ANALYSIS - ARDREA." Acta Horticulturae, no. 489 (July 1999): 55–60. http://dx.doi.org/10.17660/actahortic.1999.489.5.

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38

Hibbett, David S., and Rytas Vilgalys. "Evolutionary Relationships of Lentinus to the Polyporaceae: Evidence from Restriction Analysis of Enzymatically Amplified Ribosomal DNA." Mycologia 83, no. 4 (1991): 425. http://dx.doi.org/10.2307/3760353.

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39

Lappayawichit, P., S. Rienthong, D. Rienthong, et al. "Differentiation of Mycobacterium species by restriction enzyme analysis of amplified 16S–23S ribosomal DNA spacer sequences." Tubercle and Lung Disease 77, no. 3 (1996): 257–63. http://dx.doi.org/10.1016/s0962-8479(96)90010-6.

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40

WATURANGI, DIANA ELIZABETH, IVANA FRANCISCA, and CINDY OKTAVIA SUSANTO. "Genetic Diversity of Methylotrophic Bacteria from Human Mouth Based on Amplified Ribosomal DNA Restriction Analysis (ARDRA)." HAYATI Journal of Biosciences 18, no. 2 (2011): 77–81. http://dx.doi.org/10.4308/hjb.18.2.77.

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41

Roy, Denis, and Stéphane Sirois. "Molecular differentiation ofBifidobacteriumspecies with amplified ribosomal DNA restriction analysis and alignment of short regions of theldhgene." FEMS Microbiology Letters 191, no. 1 (2000): 17–24. http://dx.doi.org/10.1111/j.1574-6968.2000.tb09313.x.

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42

Shehata, Afaf I., A. A. Al Aidan, B. Al Shahrani, N. A. Al-Harbi, and Sulamain Ali Alharbi. "Typing of Acinetobacter Baumannii Strains isolated from Hospital Patients by Amplified Ribosomal DNA Restriction Analysis (ARDRA)." Biosciences Biotechnology Research Asia 8, no. 2 (2011): 469–82. http://dx.doi.org/10.13005/bbra/889.

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43

Hibbett, David S., and Rytas Vilgalys. "Evolutionary Relationships of Lentinus to the Polyporaceae: Evidence from Restriction Analysis of Enzymatically Amplified Ribosomal Dna." Mycologia 83, no. 4 (1991): 425–39. http://dx.doi.org/10.1080/00275514.1991.12026032.

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44

Alves, Artur, Alan J. L. Phillips, Isabel Henriques, and António Correia. "Evaluation of amplified ribosomal DNA restriction analysis as a method for the identification of Botryosphaeria species." FEMS Microbiology Letters 245, no. 2 (2005): 221–29. http://dx.doi.org/10.1016/j.femsle.2005.03.005.

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45

Roy, Denis, Stéphane Sirois, and Daniel Vincent. "Molecular Discrimination of Lactobacilli Used as Starter and Probiotic Cultures by Amplified Ribosomal DNA Restriction Analysis." Current Microbiology 42, no. 4 (2001): 282–89. http://dx.doi.org/10.1007/s002840110218.

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46

Ponnusamy, K., S. Jose, I. Savarimuthu, G. P. Michael, and M. Redenbach. "Genetic diversity study of Chromobacterium violaceum isolated from Kolli hills by amplified ribosomal DNA restriction analysis (ARDRA) and random amplified polymorphic DNA (RAPD)." Letters in Applied Microbiology 53, no. 3 (2011): 341–49. http://dx.doi.org/10.1111/j.1472-765x.2011.03115.x.

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47

Silva, WPK, DS Multani, BJ Deverall, and BR Lyon. "RFLP and Rapd Analyses in the Identification and Differentiation of Isolates of the Leaf Spot Fungus Corynespora cassiicola." Australian Journal of Botany 43, no. 6 (1995): 609. http://dx.doi.org/10.1071/bt9950609.

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Genetic variabilty in isolates of the fungal plant pathogen Corynespora cassiicola cultured from pawpaw, mimosa and thyme hosts was assessed using restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) regions of ribosomal DNA and random amplified polymorphic DNA (RAPD) analysis of total fungal DNA. Strains of Corynespora could be distinguished from a member of the closely-related genus Helminthosporium on the basis of amplified ITS fragment size, but could not be typed individually as the ITS regions of all isolates exhibited identical size and restriction endonuclease digestion pattern. However, RAPD profiles generated by 14 decamer primers of arbitrary sequence did reveal significant differences between some of the C. cassiicola isolates and succeeded in differentiating all but two of the strains. Cluster analysis of 218 amplified DNA fragments showed that the five isolates could be placed into three groups that correspond with their host origin and morphological characteristics. The use of these molecular techniques will be extended to assess intra-specific variation in C. cassiicola isolates from rubber trees in Sri Lanka, where highly pathogenic strains present a serious threat to the natural rubber industry.
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48

Zeng, Yinxin, Wenqi Liu, Huirong Li, Yong Yu, and Bo Chen. "Effect of restriction endonucleases on assessment of biodiversity of cultivable polar marine planktonic bacteria by amplified ribosomal DNA restriction analysis." Extremophiles 11, no. 5 (2007): 685–92. http://dx.doi.org/10.1007/s00792-007-0086-x.

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49

Ahmed, Abdalla O. A., Moawia M. Mukhtar, Marly Kools-Sijmons, et al. "Development of a Species-Specific PCR-Restriction Fragment Length Polymorphism Analysis Procedure for Identification ofMadurella mycetomatis." Journal of Clinical Microbiology 37, no. 10 (1999): 3175–78. http://dx.doi.org/10.1128/jcm.37.10.3175-3178.1999.

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Madurella mycetomatis is the commonest cause of eumycetoma in Sudan and other countries in tropical Africa. Currently, the early diagnosis of mycetoma is difficult. In attempting to improve the identification of M. mycetomatis and, consequently, the diagnosis of mycetoma, we have developed specific oligonucleotide primers based on the sequence of the internal transcribed spacer (ITS) regions spacing the genes encoding the fungal ribosomal RNAs. The ITS regions were amplified with universal primers and sequenced, and then two sets of species-specific primers were designed which specifically amplify parts of the ITS and the 5.8S ribosomal DNA gene. The new primers were tested for specificity with DNA isolated from human mycetoma lesions and DNA extracted from cultures of M. mycetomatis reference strains and related fungi as well as human DNA. To study the genetic variability of the ITS regions of M. mycetomatis, ITS amplicons were obtained from 25 different clinical isolates and subjected to restriction fragment length polymorphism (RFLP) analysis with CfoI, HaeIII,MspI, Sau3AI, RsaI, andSpeI restriction enzymes. RFLP analysis of the ITS region did not reveal even a single difference, indicating the homogeneity of the isolates analyzed during the current study.
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50

Hellgren, M., and N. Högberg. "Ecotypic variation of Gremmeniella abietina in northern Europe: disease patterns reflected by DNA variation." Canadian Journal of Botany 73, no. 10 (1995): 1531–39. http://dx.doi.org/10.1139/b95-166.

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Genetic variation in Gremmeniella abietina isolated from Pinus sylvestris, Pinus contorta, and Picea abies in southern and northern Fennoscandia was studied with arbitrary primed polymerase chain reaction. Fennoscandian G. abietina isolates were clearly separated into two ecotypically distinct groups based on their amplified banding patterns. Analysis of variance based on amplified fragments, AMOVA, and principal component analysis confirmed the separation of the isolates into the two groups. One group contained isolates associated with a disease syndrome affecting young trees covered by deep snow during winter in northern Fennoscandia. The second group of isolates was found on trees between 15 and 40 years old, scattered throughout the crowns. It occurs throughout Fennoscandia but is most frequent in the southern parts. No size polymorphism was found in fragments resulting after restriction enzyme digestion of internal transcribed spacer and intergenic spacer regions of nuclear ribosomal DNA. An estimate of gene flow between populations calculated based on amplified band frequencies, FST, indicated that there was restricted genetic exchange between populations of the two groups of isolates. Key words: Gremmeniella abietina, arbitrary primed polymerase chain reaction, genetic variation, ecotypes, ribosomal DNA.
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