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Journal articles on the topic 'ITS-RFLP'

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Published: 4 June 2021
Last updated: 20 February 2023

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1

Lanoot, Benjamin, Marc Vancanneyt, Bart Hoste, Katrien Vandemeulebroecke, Margo C. Cnockaert, Peter Dawyndt, Zhiheng Liu, Ying Huang, and Jean Swings. "Grouping of streptomycetes using 16S-ITS RFLP fingerprinting." Research in Microbiology 156, no. 5-6 (June 2005): 755–62. http://dx.doi.org/10.1016/j.resmic.2005.01.017.

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2

KOFFI, YAO FULGENCE, CAMELIA DIGUTA, MIREILLE ALLOUE-BORAUD, LOUIS BAN KOFFI, MARCELLIN DJE, EVELINA GHERGHINA, and FLORENTINA MATEI. "PCR-ITS-RFLP identification of pineapple spoilage fungi." Romanian Biotechnological Letters 24, no. 3 (June 20, 2019): 418–24. http://dx.doi.org/10.25083/rbl/24.3/418.424.

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3

Midgley, David J., Susan M. Chambers, and John W. G. Cairney. "Spatial distribution of fungal endophyte genotypes in a Woollsia pungens (Ericaceae) root system." Australian Journal of Botany 50, no. 5 (2002): 559. http://dx.doi.org/10.1071/bt02020.

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Fungal endophytes were isolated from hair roots of Woollsia pungens Cav. (Muell.) and mapped according to the root portions from which they were isolated. A total of 119 isolates was obtained and restriction fragment length polymorphism (RFLP) analysis of the internal transcribed spacer (ITS) region indicated that the isolate assemblage comprised five RFLP types. ITS sequence comparison revealed that RFLP Types I and II had 99.6–99.8% sequence identity with known ericoid mycorrhizal endophytes from Australian epacrids. The remaining three RFLP types were most similar to non-mycorrhizal ascomycetes. Eighty-five per cent of isolates obtained were of RFLP Type I and these were widespread within the root system. Inter-simple sequence repeat PCR suggested that 94% of RFLP Type I isolates were of a single genotype that was widely distributed within the root system, with the remaining five isolates each representing a different genotype. Apparent spatial dominance of the root system by a single fungal genotype may indicate limited functional diversity in the mycorrhizal endophyte assemblage.
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4

Duttweiler, K. B., G. Y. Sun, J. C. Batzer, T. C. Harrington, and M. L. Gleason. "An RFLP-Based Technique for Identifying Fungi in the Sooty Blotch and Flyspeck Complex on Apple." Plant Disease 92, no. 5 (May 2008): 794–99. http://dx.doi.org/10.1094/pdis-92-5-0794.

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A restriction fragment length polymorphism (RFLP)-based technique was developed to identify members of the sooty blotch and flyspeck (SBFS) disease complex on apple because these fungi are difficult to identify using agar-plate isolation and morphological description. The method includes polymerase chain reaction (PCR) amplification of the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA) using a fungal-specific forward primer (ITS1-F) and an SBFS-specific reverse primer (Myc1-R), followed by digestion of the PCR product by the HaeIII restriction enzyme. When applied to previously identified isolates of 24 SBFS-causing species in nine genera, the PCR-RFLP assay produced 14 unique banding patterns. Different genera never shared the same RFLP pattern. To evaluate performance in vivo, the technique was applied to DNA extracted directly from SBFS colonies on apple fruit from three Iowa orchards. The primers amplified the rDNA of only SBFS fungi, with the exception of a Cladosporium sp.; however, its RFLP banding pattern was distinct from those of SBFS fungi. The majority (60%) of SBFS colonies in the in vivo trial were identified to genus by RFLP analysis. The PCR-RFLP assay greatly streamlined the identification process by minimizing the need for culturing, indicating its value as a tool for field studies of the SBFS complex.
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5

Hazlianda, Cut, Kamaliah Muis, and Isma Lubis. "A Comparative Study of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism and Fungal Culture for the Evaluation of Fungal Species in Patients with Tinea Cruris." Open Access Macedonian Journal of Medical Sciences 5, no. 7 (November 21, 2017): 844–47. http://dx.doi.org/10.3889/oamjms.2017.197.

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BACKGROUND: Tinea cruris is the second most common dermatophytosis in the world and the most common in Indonesia. The conventional laboratory tests for dermatophyte infection are slow and less specific. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) is a PCR method with the addition of enzyme after amplification, therefore enabling for more specific results.AIM: This study aimed to find whether the PCR-RFLP test could yield the same fungal species result as a fungal culture.METHODS: The specimens were skin scrapings from thirty-one patients suspected tinea cruris. The tools and materials that were used were Sabaroud’s dextrose agar media, primer ITS 1 and ITS 4 and MvaI.RESULTS: The equation percentage of the test result species between PCR-RFLP and fungal culture was 50% of 12 subjects whose the test results were both positive from the fungal culture and PCR-RFLP. The percentage of the test result with fungal culture the fungal species were found, but in the PCR-RFLP test which the fungal species was not found, the percentage was 50% of 12 subjects which the test results were both positive as fungi from the culture and PCR-RFLP test.CONCLUSIONS: The species from PCR-RFLP examination was the same with the fungal culture.
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6

Burgermeister, Wolfgang, Helen Braasch, Kai Metge, Jianfeng Gu, Thomas Schröder, and Elvira Woldt. "ITS-RFLP analysis, an efficient tool for differentiation of Bursaphelenchus species." Nematology 11, no. 5 (2009): 649–68. http://dx.doi.org/10.1163/156854108/399182.

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Abstract Restriction analysis of amplified ribosomal ITS sequences has provided species-specific fragment patterns for nematodes of several genera, including Bursaphelenchus. We used restriction enzymes RsaI, HaeIII, MspI, HinfI and AluI to produce ITS-RFLP reference profiles of 44 Bursaphelenchus species, including two intraspecific types in each of B. mucronatus and B. leoni. In addition, reference profiles of Aphelenchoides stammeri and Ruehmaphelenchus asiaticus were produced. Reference profiles of six species are shown here for the first time. Identical ITS-RFLP patterns were usually obtained from different isolates and from individual specimens of the same species. However, in the case of B. 'corneolus', B. lini, B. singaporensis and B. sexdentati, additional bands in the patterns of certain isolates or individual nematodes were observed which may be explained by ITS sequence microheterogeneity, i.e., the presence of ITS sequence variants within the number of rDNA tandem repeats. Since these 'extra' bands appeared only with one out of the five restriction enzymes employed, they did not seriously impair identification of species based on the overall reference patterns. ITS-RFLP analysis has proved valuable for differentiation of the pathogenic pine wood nematode, B. xylophilus, from related species. In many recent descriptions of new Bursaphelenchus species, ITS-RFLP profiles have been used as additional species identification criteria. Comparison of profiles from isolates of many different origins has provided new information on intraspecific types or genetically distinct provenances of several Bursaphelenchus species.
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7

Wang, Qin, and Liang-Dong Guo. "Ectomycorrhizal community composition of Pinus tabulaeformis assessed by ITS-RFLP and ITS sequences." Botany 88, no. 6 (June 2010): 590–95. http://dx.doi.org/10.1139/b10-023.

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Ectomycorrhizal (ECM) fungal composition was examined in a Pinus tabulaeformis Carr. forest. A total of 28 root samples of P. tabulaeformis were collected in June and September. Thirty-five ECM morphotypes were identified according to ECM morphological characters, and 26 ECM fungi were identified based on the analyses of ITS-RFLP and ITS sequences. Tomentella , Sebacina , and Tuber were common genera, and Atheliaceae sp., Lactarius deliciosus , Tomentella ferruginea , and Tomentella sp. 3 were dominant species. Of these ECM fungi, 13 were found in June, 19 in September, and 6 during both sampling times. Atheliaceae sp. and T. ferruginea were the dominant fungi both in June and September. Lactarius deliciosus was dominant in June, but rare in September. Tomentella sp. 3 was dominant in September but rare in June.
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8

Wurzburger, Nina, Martin I. Bidartondo, and Caroline S. Bledsoe. "Characterization of Pinus ectomycorrhizas from mixed conifer and pygmy forests using morphotyping and molecular methods." Canadian Journal of Botany 79, no. 10 (October 1, 2001): 1211–16. http://dx.doi.org/10.1139/b01-079.

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We used morphotyping and molecular methods to characterize ectomycorrhizas of bishop pine (Pinus muricata D. Don) and Bolander pine (Pinus contorta ssp. bolanderi (Parl.) Critchf.) from mixed conifer and hydric pygmy forests on the northern California coast. Sixteen ectomycorrhizal morphotypes were described, producing 15 internal transcribed spacer restriction fragment length polymorphism (ITS-RFLP) types, and 12 were identified via ITS sequencing. From a given site, all root tips of a specific morphotype produced identical ITS-RFLP patterns. However, sometimes two morphotypes produced the same ITS-RFLP type, and sometimes samples of the same morphotype from two different sites produced two different ITS-RFLP types. These results indicate that surveys of ectomycorrhizal fungi based on morphology alone are not sufficient, and that grouping morphotypes prior to molecular analysis can expedite the process. Ectomycorrhizas from mixed conifer included Russuloid sp., Tomentella sublilacina (Ellis & Holw.) Wakef., Tuber sp., and two Thelephoroid species. Ectomycorrhizas from hydric pygmy included two Dermocybe spp., a Cortinarius sp., two Thelephoroid spp., and Suillus tomentosus (Kauffman) Singer. Both plant communities contained Cenococcum geophilum Fr.:Fr. The hydric pygmy sites were more similar to each other than to the mixed conifer site (Jaccard similarity). The presence of ectomycorrhizal taxa in one plant community type may reflect biotic (host specificity) or abiotic (soil fertility or hydrology) adaptation.Key words: ectomycorrhiza, bishop pine, Pinus muricata, Bolander pine, Pinus contorta ssp. bolanderi, morphotyping, ITS-RFLP.
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9

Diao, Ying, Xian-Ming Lin, Chao-Lin Liao, Chun-Zi Tang, Zhong-Jian Chen, and Zhong-Li Hu. "Authentication ofPanax ginsengfrom its Adulterants by PCR-RFLP and ARMS." Planta Medica 75, no. 05 (February 2, 2009): 557–60. http://dx.doi.org/10.1055/s-0029-1185321.

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10

Viaud, Muriel, Aymeric Pasquier, and Yves Brygoo. "Diversity of soil fungi studied by PCR-RFLP of ITS." Mycological Research 104, no. 9 (September 2000): 1027–32. http://dx.doi.org/10.1017/s0953756200002835.

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11

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 (September 1, 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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12

Burgermeister, Wolfgang, and Kai Metge. "Multiple displacement amplification of DNA for ITS-RFLP analysis of individual juveniles of Bursaphelenchus." Nematology 7, no. 2 (2005): 253–57. http://dx.doi.org/10.1163/1568541054879511.

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AbstractDifferentiation of the plant-pathogenic pinewood nematode, Bursaphelenchus xylophilus, from non-pathogenic Bursaphelenchus species is difficult because of high morphological similarities among closely related species. In recent years, ITS-RFLP analysis has become a useful tool for Bursaphelenchus species identification. Analysis of individual nematodes is hampered by the fact that sufficient template DNA for ITS-PCR cannot be extracted reliably. We have employed a whole genome amplification method, termed multiple displacement amplification (MDA), to 26 DNA extracts from individual juveniles to increase the amount of template DNA. Preamplification of the whole genomic DNA by MDA provided sufficient amounts of PCR product for ITS-RFLP analysis with 12 out of 20 B. xylophilus, two B. mucronatus, two B. fraudulentus and two B. eggersi samples tested. The introduction of MDA to ITS-RFLP analysis of nematodes may improve the reliability of diagnostic testing for limited samples and permit verification of analytical results.
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13

Said, Halima M., Keshav Krishnamani, Shaheed V. Omar, Andries W. Dreyer, Bianca Sansom, Dorothy Fallows, and Nazir A. Ismail. "Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting." Journal of Clinical Microbiology 54, no. 10 (August 3, 2016): 2547–52. http://dx.doi.org/10.1128/jcm.00408-16.

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The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing ofMycobacterium tuberculosisusing the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing ofM. tuberculosisisolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor.
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14

Maafi, Zahra Tanha, Sergei Subbotin, and Maurice Moens. "Molecular identification of cyst-forming nematodes (Heteroderidae) from Iran and a phylogeny based on ITS-rDNA sequences." Nematology 5, no. 1 (2003): 99–111. http://dx.doi.org/10.1163/156854102765216731.

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Abstract RFLP and sequences of ITS-rDNA of 45 populations of cyst-forming nematodes collected from different parts of Iran were analysed and identified as representatives of 21 species. Eight enzymes generated RFLP for all studied populations. Comparison of RFLP profiles and sequences of the ITS regions with published data confirmed the presence of Heterodera avenae, H. filipjevi, H. glycines, H. hordecalis, H. latipons, H. schachtii and H. trifolii in Iran. RFLP patterns and ITS sequences for H. elachista, H. turcomanica, H. mothi and C. cacti were obtained for the first time in this study. Heterodera humuli, H. goettingiana, H. fici, H. elachista, H. turcomanica and Cactodera cacti are recorded for the first time in Iran. These results correspond with morphological and morphometric identification of the populations. Several populations were not identified at the species level and are attributed to Heterodera sp.; some of these may correspond to new species. Twenty-one new sequences from Iranian cyst-forming nematodes and 36 known sequences were used for the phylogenetic analyses. The cyst-forming nematodes formed several clades corresponding to their morphological features. Heterodera mothi and H. elachista clustered with high support with other Cyperi group species and H. turcomanica formed a moderately to highly supported clade with the Humuli group.
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15

Hsiang, Tom, and Chundren Wu. "Genetic relationships of pathogenic Typhula species assessed by RAPD, ITS-RFLP and ITS sequencing." Mycological Research 104, no. 1 (January 2000): 16–22. http://dx.doi.org/10.1017/s0953756299001033.

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16

Montoro, Ernesto, José Valdivia, and Sylvia Cardoso Leão. "Molecular Fingerprinting of Mycobacterium tuberculosisIsolates Obtained in Havana, Cuba, by IS6110 Restriction Fragment Length Polymorphism Analysis and by the Double-Repetitive-Element PCR Method." Journal of Clinical Microbiology 36, no. 10 (1998): 3099–102. http://dx.doi.org/10.1128/jcm.36.10.3099-3102.1998.

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Mycobacterium tuberculosis sputum isolates from 38 patients, obtained in the first 6 months of 1997 in Havana, Cuba, were characterized by IS6110 restriction fragment length polymorphism (RFLP) analysis and the double-repetitive-element PCR (DRE-PCR) method. Among 41 strains from 38 patients, 24 and 25 unique patterns, and 5 and 4 cluster patterns, were found by the RFLP and DRE-PCR methods, respectively. Patients within two of these clusters were found to be epidemiologically related, while no relation was observed in patients in the other clusters. The DRE-PCR method is rapid, and it was as discriminating as IS6110 RFLP analysis in identifying an epidemiological association. Its simplicity makes the technique accessible for subtyping of M. tuberculosisstrains in laboratories not equipped to perform RFLP analysis.
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17

Maciel, Danielli Barreto, Lílian Vieira de Medeiros, Vivian Vieira de Medeiros, Mariele Porto Carneiro Leão, Luis Eduardo Aranha Camargo, and Neiva Tinti de Oliveira. "[NO TITLE AVAILABLE]." Brazilian Archives of Biology and Technology 53, no. 6 (December 2010): 1255–66. http://dx.doi.org/10.1590/s1516-89132010000600001.

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Studies were performed to analyze the genetic characterization using RFLP-ITS and Intron (primer EI1) markers and the amplification of the cap20 pathogenicity gene by PCR in Colletotrichum gloeosporioides isolates of different hosts plant. The genetic variability was accessed using RFLP-ITS and Intron markers and grouping by UPGMA method. Primers to cap20 gene were constructed using selected sequences of the GenBank (National Center of Biotechnology Information, http://www.ncbi.nlm.nih.gov) with the Primer 3 program. The dendrograms analysis showed that the RFLP-ITS marker was more informative to separate the Colletotrichum sp, and that primer EI1 demonstrated greater genetic diversity. The amplification of the DNA of the Colletotrichum isolates to the cap20 gene with primers P1 and P2 indicated that this gene could present variations into C. gloeosporioides related with the host, and also that it was present in other Colletotrichum sp.
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18

Savage, PD, CA Hanson, and JH Kersey. "Identification of a restriction fragment length polymorphism involving the oncogene ETS-1 on chromosome 11q23." Blood 70, no. 1 (July 1, 1987): 327–29. http://dx.doi.org/10.1182/blood.v70.1.327.327.

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Abstract Twenty four samples of DNA from 23 unrelated individuals were analyzed for the presence of a novel restriction fragment length polymorphism (RFLP) involving the proto-oncogene ETS-1 at an Xba I site. Four samples from unrelated individuals lacked an Xba I site, giving rise to a longer restriction fragment detectable by Southern analysis; two samples were from normal tissue, and two were from acute myelogenous leukemic blasts. Thus, no association could be found between the RFLP and disease among the individuals studied. Pedigree analysis of another cohort demonstrated Mendelian inheritance consistent with a somatic polymorphism. The practical applications of RFLP analysis in clinical and research settings, and the usefulness of this Xba I RFLP in the study of hematologic malignancies because of its location in 11q23, are discussed.
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19

Savage, PD, CA Hanson, and JH Kersey. "Identification of a restriction fragment length polymorphism involving the oncogene ETS-1 on chromosome 11q23." Blood 70, no. 1 (July 1, 1987): 327–29. http://dx.doi.org/10.1182/blood.v70.1.327.bloodjournal701327.

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Twenty four samples of DNA from 23 unrelated individuals were analyzed for the presence of a novel restriction fragment length polymorphism (RFLP) involving the proto-oncogene ETS-1 at an Xba I site. Four samples from unrelated individuals lacked an Xba I site, giving rise to a longer restriction fragment detectable by Southern analysis; two samples were from normal tissue, and two were from acute myelogenous leukemic blasts. Thus, no association could be found between the RFLP and disease among the individuals studied. Pedigree analysis of another cohort demonstrated Mendelian inheritance consistent with a somatic polymorphism. The practical applications of RFLP analysis in clinical and research settings, and the usefulness of this Xba I RFLP in the study of hematologic malignancies because of its location in 11q23, are discussed.
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20

HUA, Guo-Hua. "HaeⅡ RFLP of INHA and its relationship to goat litter size." HEREDITAS 29, no. 08 (2007): 972. http://dx.doi.org/10.1360/yc-007-0972.

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21

Matsumoto, Tadashi, Shigeru Aoki, Tomoko Sawai, and Yoshiro Tsuji. "A novelH19/HhaI RFLP and its allele frequency in the Japanese." Japanese Journal of Human Genetics 39, no. 1 (March 1994): 205–6. http://dx.doi.org/10.1007/bf01915958.

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22

Villanueva da Fonseca, Luisa Andrea, Maria Anilda Santos Araújo, Denise Maria Wanderlei Silva, and Fernanda Cristina De Albuquerque Maranhão. "ITS-RFLP optimization for dermatophyte identification from clinical sources in Alagoas (Brazil) versus phenotypic methods." Journal of Infection in Developing Countries 16, no. 11 (November 29, 2022): 1773–77. http://dx.doi.org/10.3855/jidc.17077.

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Introduction: Dermatophytoses are superficial mycoses, and the identification of their etiological agents is routinely performed by culture and microscopic features, which is time-consuming and relies on personnel expertise. Molecular approaches have been developed to provide faster and reliable results; therefore, this study aimed to identify dermatophytes isolated from Alagoas state patients, employing phenotypical and molecular methods. Methodology: Clinical samples for morphological identification were collected from private and public laboratories and cultivated on Sabouraud dextrose agar. DNA extraction was followed by ITS amplicon analysis after restriction enzyme digestion DdeI (ITS-RFLP). Results: Out of fourteen representative strains, ITS-RFLP with DdeI efficiently identified Microsporum canis, Nannizzia gypsea, and Trichophyton rubrum, while species of the complex T. tonsurans/T. mentagrophytes presented the same restriction pattern. After genotyping, 2 T. tonsurans and 1 Microsporum sp. strain were reclassified as T. rubrum. Conclusions: RFLP of ITS-region followed by DdeI digestion produced faster and relatively reliable results than classic methods; however, this method has not been as efficient for closely related dermatophytes cryptic species.
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23

Graf, Joerg. "Diverse Restriction Fragment Length Polymorphism Patterns of the PCR-Amplified 16S rRNA Genes in Aeromonas veronii Strains and Possible Misidentification ofAeromonas Species." Journal of Clinical Microbiology 37, no. 10 (1999): 3194–97. http://dx.doi.org/10.1128/jcm.37.10.3194-3197.1999.

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Restriction fragment length polymorphism analysis after PCR amplification (RFLP-PCR) of the 16S rRNA gene has been previously proposed as a rapid method to identify Aeromonas species. In the present study, the precision of RFLP-PCR was evaluated with 62Aeromonas reference strains. The analysis revealed thatAeromonas veronii biovar sobria strains produce various patterns, possibly leading to its misidentification as an environmental species. For most other Aeromonas species little variation was noted. This study supports the usefulness of RFLP-PCR analysis to separate three clinically important species but also reveals possible misidentifications that necessitate further biochemical tests to validate the preliminary identification.
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24

Morgan, JM, and MK Tan. "Chromosomal Location of a Wheat Osmoregulation Gene Using RFLP Analysis." Functional Plant Biology 23, no. 6 (1996): 803. http://dx.doi.org/10.1071/pp9960803.

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The chromosomal location of an osmoregulation gene locus (or) was examined by exploring genetic linkage to restriction fragment length polymorphism (RFLP) loci which have been mapped on group 7 chromosomes or located specifically on chromosome 7A. The osmoregulation gene had previously been located on chromosome 7A, but its specific position was unknown. Analysis of linkage with the RFLP loci suggested a probable position on the short arm approximately 13 cM towards the centromere from RFLP locus Xpsr119. The findings, which were based on a relatively small sample, are of a preliminary nature and require confirmation with a larger set of genetic stocks.
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25

Grafe, Simon F., Céline Boutin, Frances R. Pick, and Roger D. Bull. "A PCR-RFLP method to detect hybridization between the invasive Eurasian watermilfoil (Myriophyllum spicatum) and the native northern watermilfoil (Myriophyllum sibiricum), and its application in Ontario lakes." Botany 93, no. 2 (February 2015): 117–21. http://dx.doi.org/10.1139/cjb-2014-0135.

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The discovery of hybridization between the invasive Eurasian watermilfoil (Myriophyllum spicatum L.) and native northern watermilfoil (Myriophyllum sibiricum Kom.) has generated interest in establishing the hybrid’s distribution and invasiveness. Identification of hybrid M. spicatum × M. sibiricum requires molecular genetic analysis, however, as the hybrid’s morphology overlaps with both parent species. Using plants collected from 10 lakes in Ontario, Canada, we compared a previous method of identification (sequencing the nuclear ITS region) with a simpler screening method (PCR-RFLP of the ITS region). Both methods agreed on the identification of hybrid M. spicatum × M. sibiricum and both parent species, supporting the suitability of PCR-RFLP to screen for the hybrid. Four of 29 samples were identified as hybrid M. spicatum × M. sibiricum, which were all found in three adjacent lakes associated with the Rideau Canal Waterway. The PCR-RFLP method should enable greater sampling effort to screen for hybrid M. spicatum × M. sibiricum and establish its geographic distribution across connected waterways.
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26

ŻACZEK, ANNA, MAŁGORZATA ZIÓŁKIEWICZ, ARKADIUSZ WOJTASIK, JAROSŁAW DZIADEK, and ANNA SAJDUDA. "IS6110-based Differentiation of Mycobacterium tuberculosis Strains." Polish Journal of Microbiology 62, no. 2 (2013): 201–4. http://dx.doi.org/10.33073/pjm-2013-026.

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In this study, 62 Mycobacterium tuberculosis strains were characterized by fast ligation-mediated PCR (FLiP) and, previously performed, IS6110 restriction fragment length polymorphism (RFLP). FLiP proved a reproducible and specific method for differentiation between M. tuberculosis strains. The discriminatory power of FLiP was close to that of the reference IS6110 RFLP suggesting its usefulness in studying the genetic diversity of M. tuberculosis strains.
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Carvalho, C. M., A. Rocha, M. L. F. Estevinho, and A. Choupina. "IDENTIFICATION OF HONEY YEAST SPECIES BASED ON RFLP ANALYSIS OF THE ITS REGION IDENTIFICACIÓN DE ESPECIES DE LEVADURAS DE MIEL BASADA EN ANÁLISIS RFLP DE LA REGION ITS IDENTIFICACIÓN DE ESPECIES DE LEVADURAS DE MEL BASADA EN ANÁLISES RFLP DA REXIÓN ITS." Ciencia y Tecnologia Alimentaria 5, no. 1 (December 2005): 11–17. http://dx.doi.org/10.1080/11358120509487665.

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Anderson, Ian C., Susan M. Chambers, and John W. G. Cairney. "ITS–RFLP and ITS sequence diversity in Pisolithus from central and eastern Australian sclerophyll forests." Mycological Research 105, no. 11 (November 2001): 1304–12. http://dx.doi.org/10.1017/s0953756201005044.

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Pandey, Ajay K., M. Sudhakara Reddy, and Trichur S. Suryanarayanan. "ITS-RFLP and ITS sequence analysis of a foliar endophytic Phyllosticta from different tropical trees." Mycological Research 107, no. 4 (April 2003): 439–44. http://dx.doi.org/10.1017/s0953756203007494.

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30

Sacco, F., E. Y. Suárez, and T. Naranjo. "Mapping of the leaf rust resistance gene Lr3 on chromosome 6B of Sinvalocho MA wheat." Genome 41, no. 5 (October 1, 1998): 686–90. http://dx.doi.org/10.1139/g98-067.

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The Lr3 gene for resistance to race 66 of Puccinia recondita present in hexaploid wheat cv. Sinvalocho MA was mapped on chromosome 6B, using intervarietal polymorphic RFLP loci and the Amp-B1 isozyme gene as a centromere marker. The RFLP markers were located mainly in two subregions of chromosome 6BL. Six RFLP loci clustered in the centromeric region and one other, Xmwg798, cosegregated with the Lr3 gene. C-banding analysis of the leaf rust resistant standard 'Sinvalocho MA' line and three naturally occurring susceptible lines of 'Sinvalocho MA' revealed a terminal deletion on 6BL that covered 20% of its length in one susceptible line. Because Xmwg798 was missing in this line, both Xmwg798 and Lr3 were allocated to the deleted segment. Distorted segregations were observed for the proximal markers, suggesting a selection against gametes carrying the centromeric region of 'Sinvalocho MA'.Key words: wheat, RFLP, Lr3 gene, chromosome 6B, C-banding.
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Reinoso, Elina, Silvana Dieser, Luis Calvinho, Cristina Bogni, and Liliana Odierno. "Phenotyping and genotyping of streptococci in bovine milk in Argentinean dairy herds." Acta Veterinaria Hungarica 58, no. 3 (September 1, 2010): 287–95. http://dx.doi.org/10.1556/avet.58.2010.3.2.

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Most veterinary and milk hygiene laboratories identify streptococci and enterococci based on serological and biochemical tests. The analysis of 16S rDNA was suggested to be used for more exact identification; however, its use has not been considered so far in monitoring studies. The objective of the present study was to compare a conventional phenotypic method with restriction fragment length polymorphism analysis of 16S rDNA (16S rDNA RFLP) for identification of streptococci isolated from composite milk samples collected in connection with intramammary infection (IMI) in six Argentinean dairy farms. Composite milk samples (n = 1223) from cows belonging to six herds were collected for bacteriological analysis. Twelve reference strains and fifty streptococci or streptococcuslike isolates were identified to species level by the API 20 Strep system, conventional biochemical tests and 16S rDNA RFLP in a blind assay. The remaining streptococci or streptococcus-like isolates (n = 40) were identified to the species level both by 16S rDNA RFLP and conventional biochemical tests. As indicated by Kappa values, agreement between the 16S rDNA RFLP and the conventional scheme for identification ofStreptococcus agalactiae, S. dysgalactiae, S. uberis, S. equinusandEnterococcus faecaliswas 0.91, 0.73, 0.92, 0.81 and 0.85, respectively. Together with the less frequently isolated streptococcal species, the conventional scheme correctly identified 77 out of 90 isolates (85.5%). Thus, the use of 16S rDNA RFLP is considered valuable for monitoring studies due to its affordable cost for standard laboratories.
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Vijayakumar, Ramraj, Sidhartha Giri, and Anupma Jyoti Kindo. "Molecular Species Identification of Candida from Blood Samples of Intensive Care Unit Patients by Polymerase Chain Reaction – Restricted Fragment Length Polymorphism." Journal of Laboratory Physicians 4, no. 01 (January 2012): 001–4. http://dx.doi.org/10.4103/0974-2727.98661.

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ABSTRACT Introduction: Candida spp is an emerging cause of blood stream infections worldwide. Delay in speciation of Candida isolates by conventional methods and resistance to antifungal drugs (especially fluconazole, amphotericin B, etc.) in various Candida species are some of the factors responsible for the increase in morbidity and mortality due to candidemia. So, the rapid detection and identification of Candida isolates from blood is very important for the proper management of patients having candidemia. Materials and Methods: In this study, we have used polymerase chain reaction (PCR) - restriction fragment length polymorphism (RFLP) as a method for the speciation of Candida isolates from blood samples of intensive care unit (ICU) patients. PCR was used to amplify the ITS-1 and ITS-2 regions of Candida spp using universal primers ITS-1 and ITS-4. The amplified product was digested using Msp I restriction enzyme by RFLP. Results and Discussion: The method PCR-RFLP helped in identifying five medically important Candida spp (C. tropicalis, C. albicans, C. parapsilosis, C. krusei and C. glabrata) from blood. This method is rapid, reliable, easy and cost-effective and can be used in routine laboratory diagnostics for the rapid identification of Candida isolates from blood. Conclusion: PCR-RFLP is an easy, rapid and highly valuable tool which can be used in routine diagnostic laboratories to speciate Candida isolates obtained from blood. This rapid method of speciation will help clinicians to decide on empirical therapy in candidemia cases before antifungal susceptibility results are available.
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Pulvirenti, Andrea, Lisa Solieri, Luciana De Vero, and Paolo Giudici. "Limitations on the use of polymerase chain reaction – restriction fragment length polymorphism analysis of the rDNA NTS2 region for the taxonomic classification of the speciesSaccharomyces cerevisiae." Canadian Journal of Microbiology 51, no. 9 (September 1, 2005): 759–64. http://dx.doi.org/10.1139/w05-062.

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Different molecular techniques were tested to determine which was the most effective in the identification of Saccharomyces cerevisiae strains. In particular, polymerase chain reaction – restriction fragment length polymorphism (PCR–RFLP) analysis of the internal transcribed spacer (ITS) regions and the nontranscribed spacer 2 (NTS2) region, sequencing of the D1/D2 domain, and electrophoretic karyotyping were applied to 123 yeast strains isolated from different sourdoughs and tentatively attributed to the species S. cerevisiae. All of the strains tested showed an identical PCR–RFLP pattern for the ITS regions, an identical nucleotide sequence of the D1/D2 domain, and the typical electrophoretic karyo type of S. cerevisiae. In contrast, 14 out of the 123 strains tested showed some polymorphism with BanI restriction analysis of the NTS2 region. Our results indicate that while the sequencing of the D1/D2 domain, the PCR–RFLP analysis of the ITS regions, and the electrophoretic karyotype can be employed successfully to identify S. cere visiae strains, PCR–RFLP analysis of the NTS2 region does not allow a consistent and accurate grouping for S. cere visiae strains. The fact that the NTS2 region of a small number of strains (8.78% of the total strains tested) is different from that of the other S. cerevisiae strains confirms that molecular methods should always be tested on a great number of strains.Key words: ribosomal DNA, Saccharomyces cerevisiae, yeast identification.
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Tarach, Piotr. "Application of polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) in the analysis of single nucleotide polymorphisms (SNPs)." Acta Universitatis Lodziensis. Folia Biologica et Oecologica 17 (September 29, 2021): 48–53. http://dx.doi.org/10.18778/1730-2366.16.14.

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Polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) is a technique used to identify single nucleotide polymorphisms (SNPs) based on the recognition of restriction sites by restriction enzymes. RFLP-PCR is an easy-to-perform and inexpensive tool for initial analysis of SNPs potentially associated with some monogenic diseases, as well as in genotyping, genetic mapping, lineage screening, forensics and ancient DNA analysis. The RFLP-PCR method employs four steps: (1) isolation of genetic material and PCR; (2) restriction digestion of amplicons; (3) electrophoresis of digested fragments; and (4) visualisation. Despite its obsolescence and the presence of high-throughput DNA analysis techniques, it is still applied in the analysis of SNPs associated with disease entities and in the analysis of genetic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RFLP-PCR is a low-cost and low-throughput research method allowing for the analysis of SNPs in the absence of specialised equipment, and it is useful when there is a limited budget.
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Hanoğlu, Şakire, S. Elif Korcan, S. Feyza Erdoğmuş, and Muhsin Konuk. "Comparison of 16S-ITS rDNA RFLP Profiles of Bacillus sp. Isolated from Milk and Different Water Sources." Afyon Kocatepe University Journal of Sciences and Engineering 14, no. 2 (June 10, 2014): 29–38. http://dx.doi.org/10.5578/fmbd.8061.

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36

Donnik, Irina, Irina Donnik, Ramil Vafin, Ramil Vafin, Aram Galstyan, Aram Galstyan, Anna Krivonogova, et al. "Genetic identification of bovine leukaemia virus." Foods and Raw Materials 6, no. 2 (December 20, 2018): 314–24. http://dx.doi.org/10.21603/2308-4057-2018-2-314-324.

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Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.
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37

Conville, Patricia S., Steven H. Fischer, Charles P. Cartwright, and Frank G. Witebsky. "Identification of Nocardia Species by Restriction Endonuclease Analysis of an Amplified Portion of the 16S rRNA Gene." Journal of Clinical Microbiology 38, no. 1 (January 2000): 158–64. http://dx.doi.org/10.1128/jcm.38.1.158-164.2000.

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ABSTRACT Identification of clinical isolates of Nocardia to the species level is important for defining the spectrum of disease produced by each species and for predicting antimicrobial susceptibility. We evaluated the usefulness of PCR amplification of a portion of the Nocardia 16S rRNA gene and subsequent restriction endonuclease analysis (REA) for species identification. Unique restriction fragment length polymorphism (RFLP) patterns were found for Nocardia sp. type strains (except for the N. asteroides type strain) and representative isolates of the drug pattern types of Nocardia asteroides (except for N. asteroides drug pattern type IV, which gave inconsistent amplification). A variant RFLP pattern for Nocardia nova was also observed. Twenty-eight clinical isolates were evaluated both by traditional biochemical identification and by amplification and REA of portions of the 16S rRNA gene and the 65-kDa heat shock protein (HSP) gene. There was complete agreement among the three methods on identification of 24 of these isolates. One isolate gave a 16S rRNA RFLP pattern consistent with the biochemical identification but was not identifiable by its HSP gene RFLP patterns. Three isolates gave 16S rRNA RFLP patterns which were inconsistent with the identification obtained by both biochemical tests and HSP gene RFLP; sequence analysis suggested that two of these isolates may belong to undefined species. The PCR and REA technique described appears useful both for the identification of clinical isolates of Nocardia and for the detection of new or unusual species.
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38

Godoy-Lutz, G., J. R. Steadman, B. Higgins, and K. Powers. "Genetic Variation Among Isolates of the Web Blight Pathogen of Common Bean Based on PCR-RFLP of the ITS-rDNA Region." Plant Disease 87, no. 7 (July 2003): 766–71. http://dx.doi.org/10.1094/pdis.2003.87.7.766.

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Variability of 45 isolates of Rhizoctonia solani (teleomorph Thanatephorus cucumeris) causing web blight (WB) of common bean, Phaseolus vulgaris, was examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the internal transcribed spacer regions (ITS1 and ITS2) and the 5.8S subunit (5.8S) of the nuclear ribosomal DNA repeat (ITS-5.8S-rDNA). Isolates were collected from diseased bean leaves from Argentina, Costa Rica, Cuba, Dominican Republic, Honduras, Panama, and Puerto Rico. These WB isolates belong to AG-1 and AG-2 based on anastomosis reaction. Isolates of AG-1 that cause WB were separated into three distinct groups of RFLP patterns from enzymatic digestion of a 740-bp PCR fragment. Microsclerotia-producing isolates (<1 mm) were differentiated from macrosclerotia-producing isolates (5 to 20 mm) based on PCR-RFLP patterns even though they are placed in the same AG1-1B subgroup by anastomosis reaction. WB isolates of AG-2 were separated into two distinct PCR-RFLP groups as previously reported. AG-1 macrosclerotial-producing isolates were the most virulent, whereas isolates of AG-2 were the least virulent. Genetic variability of the WB pathogen may have influenced the failure or success of management practices implemented in the past in Latin America.
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39

Efriwat. "Yeast community of Indonesian Tempeh based on ITS-PCR T-RFLP analysis." Current Research in Environmental & Applied Mycology 4, no. 2 (2014): 202–10. http://dx.doi.org/10.5943/cream/4/2/7.

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40

Chung, Hoyoung, and Michael Davis . "PCR-RFLP of the Ovine Calpastatin Gene and its Association with Growth." Asian Journal of Animal and Veterinary Advances 7, no. 8 (July 15, 2012): 641–52. http://dx.doi.org/10.3923/ajava.2012.641.652.

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41

Velasquez, Viviana L. Becerra, and Paul Gepts. "RFLP diversity of common bean (Phaseolus vulgaris) in its centres of origin." Genome 37, no. 2 (April 1, 1994): 256–63. http://dx.doi.org/10.1139/g94-036.

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Eighty-five wild and cultivated accessions of common bean (Phaseolus vulgaris L.), representing a wide geographic area in the centres of domestication were tested for restriction fragment length polymorphisms (RFLPs). Genomic DNA was digested with one of three restriction enzymes (EcoRI, EcoRV, and HindIII) and hybridized to 12 probes distributed throughout the common bean genome. Accessions could be classified into two major groups with a distinct geographical distribution in Middle America and the Andes. Within each gene pool, cultivated accessions clustered together with wild forms from the same geographical area supporting the multiple domestications hypothesis for this crop. Estimates of Nei's genetic distances among the cultivated races from the two different gene pools varied from 0.12 to 0.56 and among races from the same gene pool from 0.04 to 0.12, suggesting that the divergence in Phaseolus vulgaris has reached the subspecies level. The level of genetic diversity (Ht = 0.38) was twice the value obtained with isozyme analysis. Genetic diversity within races (Hs = 0.27) was four to five times higher compared with isozymes, but genetic diversity between races (Dst = 0.11) was similar for both categories of markers. These results corroborate previous studies on the characterization of genetic diversity in common bean that clearly showed two distinct gene pools, Middle American and Andean. Moreover, RFLP markers are superior to isozymes because they provide better coverage of the genome and reveal higher level of polymorphisms.Key words: common bean, restriction fragment length polymorphism, domestication, genetic diversity.
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42

Kim, Kyung Ah, and Ki Oug Yoo. "Phylogenetic Relationships of Korean Campanulaceae Based on PCR-RFLP and ITS Sequences." Korean Journal of Plant Taxonomy 41, no. 2 (June 30, 2011): 119–29. http://dx.doi.org/10.11110/kjpt.2011.41.2.119.

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43

Yoshida, Mutsuhiro. "Intraspecific variation in RFLP patterns and morphological studies on Steinernema feltiae and S. kraussei (Rhabditida: Steinernematidae) from Hokkaido, Japan." Nematology 5, no. 5 (2003): 735–46. http://dx.doi.org/10.1163/156854103322746913.

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AbstractSteinernema feltiae and S. kraussei were isolated from Hokkaido, Japan. This is the first record of S. kraussei and the first definitive record of S. feltiae from Japan. The morphological variation of the infective juveniles and the first generation males of Japanese isolates of both species are reported. Intraspecific variation in the PCR-RFLP analysis of the ITS region of ribosomal DNA was observed in both species. The Japanese isolates of S. feltiae showed different RFLP patterns from European isolates with Dde I and Hinf I restriction digests. The Japanese isolate of S. kraussei also showed an RFLP variation from the UK and Russian isolates upon Dde I restriction digestion. Moreover, in each isolate of S. kraussei, some intra-population variations were observed with some restriction digestions. The intraspecific variation in the ITS region of the rDNA could be used as a molecular marker to distinguish the Japanese isolates from European isolates of S. feltiae if the latter was introduced as a biological insecticide.
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44

Bogiel, Tomasz, Agnieszka Mikucka, and Piotr Kanarek. "Agarose Gel Electrophoresis-Based RAPD-PCR—An Optimization of the Conditions to Rapidly Detect Similarity of the Alert Pathogens for the Purpose of Epidemiological Studies." Gels 8, no. 12 (November 22, 2022): 760. http://dx.doi.org/10.3390/gels8120760.

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Agarose gel electrophoresis is a well-known tool to detect DNA fragments amplified in polymerase chain reaction (PCR). Its usefulness has also been confirmed for epidemiological studies based on restriction fragments length polymorphism (RFLP), usually performed using pulsed-field gel electrophoresis (PFGE). Little is known on the effectiveness for alert-pathogen epidemiological studies of another less time-consuming and costly technique called randomly amplified polymorphic DNA-PCR (RAPD-PCR). Meanwhile, its usefulness is believed to be comparable to RFLP-PFGE. Therefore, the aim of the study was to establish and optimize the conditions of agarose gel electrophoresis following RAPD-PCR for 19 Enterococcus faecium strains derived from epidemic outbreaks at intensive care units. An application of different PCR primers, primer combinations, and, in particular, agarose gel concentrations and electrophoresis conditions revealed the usefulness of this relatively fast and inexpensive method based on RAPD-PCR for epidemiological studies without a compulsion to use the specialized equipment necessary for RFLP-PFGE.
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45

Trevisan, Giovani, Aditi Sharma, Phillip Gauger, Karen M. Harmon, Jianqiang Zhang, Rodger Main, Michael Zeller, Leticia C. M. Linhares, and Daniel C. L. Linhares. "PRRSV2 genetic diversity defined by RFLP patterns in the United States from 2007 to 2019." Journal of Veterinary Diagnostic Investigation 33, no. 5 (June 28, 2021): 920–31. http://dx.doi.org/10.1177/10406387211027221.

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The genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) increases over time. In 1998, restriction-fragment length polymorphism (RFLP) pattern analysis was introduced to differentiate PRRSV wild-type strains from VR2332, a reference strain from which a commercial vaccine (Ingelvac PRRS MLV) was derived. We have characterized here the PRRSV genetic diversity within selected RFLP families over time and U.S. geographic space, using available ISU-VDL data from 2007 to 2019. The 40,454 ORF5 sequences recovered corresponded to 228 distinct RFLPs. Four RFLPs [2-5-2 (21.2%), 1-7-4 (15.6%), 1-4-4 (11.8%), and 1-8-4 (9.9%)] represented 58.5% of all ORF5 sequences and were used for cluster analysis. Over time, there was increased detection of RFLPs 2-5-2, 1-7-4, 1-3-4, 1-3-2, and 1-12-4; decreased detection of 1-4-2, 1-18-4, 1-18-2, and 1-2-2; and different detection trends for 1-8-4, 1-4-4, 1-26-1, 1-22-2, and 1-2-4. An over-time cluster analysis revealed a single cluster for RFLP 2-5-2, supporting that sequences within RFLP 2-5-2 are still relatively conserved. For 1-7-4, 1-4-4, and 1-8-4, there were multiple clusters. State-wise cluster analysis demonstrated 4 main clusters for RFLP 1-7-4 and 1-8-4, and 6 for RFLP 1-4-4. For the other RFLPs, there was a significant genetic difference within them, particularly between states. RFLP typing is limited in its ability to discriminate among different strains of PRRSV. Understanding the magnitude of genetic divergence within RFLPs helps develop PRRSV regional control programs, placement, herd immunization strategies, and design of appropriate animal movements across borders to minimize the risk of PRRSV transmission.
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46

Garcia, G. M., H. T. Stalker, and G. Kochert. "Introgression analysis of an interspecific hybrid population in peanuts (Arachis hypogaea L.) using RFLP and RAPD markers." Genome 38, no. 1 (February 1, 1995): 166–76. http://dx.doi.org/10.1139/g95-021.

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Forty-six introgression lines (F10C9) from a cross between Arachis hypogaea L. (2n = 4x = 40) and A. cardenasii Krapov. &W.C. Gregory (2n = 2x = 20) were analyzed for the introgression of A. cardenasii chromosome segments. Seventy-three RFLP probes and 70 RAPD primers, expressing from one to four A. cardenasii-specific bands, were used to evaluate the set of introgression lines. Thirty-four RFLP probes and 45 RAPD primers identified putative A. cardenasii introgressed chromosome segments in one or more lines. Introgressed segments were detected by RFLP analysis in 10 of the 11 linkage groups; the smallest introgressed fragments were detected by single RFLP markers and the largest were detected by three or four adjacent markers and represented introgressed segments of 30–40 cM. Similar results were obtained with RAPD markers, although markers detecting introgressed fragments could not be placed on the peanut linkage map. Introgression into both A. hypogaea genomes was detected and its implication in breeding for disease resistance is discussed.Key words: peanut, Arachis hypogaea, Arachis cardenasii, RFLPs, RAPDs, introgression, reciprocal recombination, translocation, alien gene transfer, wide cross.
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47

Kobayashi, N., K. Taniguchi, K. Kojima, S. Urasawa, N. Uehara, Y. Omizu, Y. Kishi, A. Yagihashi, and I. Kurokawa. "Analysis of methicillin-resistant and methicillin-susceptibleStaphylococcus aureusby a molecular typing method based on coagulase gene polymorphisms." Epidemiology and Infection 115, no. 3 (December 1995): 419–26. http://dx.doi.org/10.1017/s095026880005857x.

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SummaryA molecular typing method forStaphylococcus aureusbased on coagulase gene polymorphisms (coagulase gene typing) was evaluated by examining a total of 240 isolates which comprised 210 methicillin-resistantS. aureus(MRSA) and 30 methicillin-susceptibleS. aureus(MSSA) collected from a single hospital. ByAlulrestriction enzyme digestion of the PCR-amplified 3′-end region of the coagulase gene including 81-bp repeated units, the MRSA and MSSA isolates examined were divided into 6 and 12 restriction fragment length polymorphism (RFLP) patterns, respectively, whereas five patterns were commonly detected in MRSA and MSSA. MRSA isolates that showed a particular RFLP pattern were considered to be predominant in the hospital. Coagulase typing with type-specific antisera was also performed for allS. aureusisolates for comparison. Coagulase types II and VII were most frequently detected and included isolates with four and five differentAluIRFLP patterns, respectively, whereas each of the other coagulase types corresponded to a single RFLP pattern. These results indicated that RFLP typing was more discriminatory than serological typing, for typingS. aureusand demonstrated its utility in epidemiologic investigation ofS. aureusinfection in hospitals.
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48

Kauserud, Håvard, and Trond Schumacher. "Population structure of the endangered wood decay fungus Phellinus nigrolimitatus (Basidiomycota)." Canadian Journal of Botany 80, no. 6 (June 1, 2002): 597–606. http://dx.doi.org/10.1139/b02-040.

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The population structure of five Fennoscandian geographic populations of the endangered wood-decay fungus Phellinus nigrolimitatus (Romell) Bourdot et Galzin was examined by analyses of nuclear ribosomal DNA (nrDNA) spacer sequences (ITS and IGS1) and a partial sequence of the elongation factor 1α gene (efa). A high level of sequence variation was observed in ITS and IGS1, suggesting restrictions in nrDNA homogenization in this taxon. Six polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) markers, five located in nrDNA and one in efa, suggest that the geographic populations are genetically very similar, presumably owing to recent gene flow. However, linkage disequilibria were obtained in 50% of the cases in tests between the five nrDNA PCR-RFLP markers. The calculated FST values from the linked nrDNA markers and the unlinked efa marker were congruent, ranging from 0.006 to 0.042. In one geographic population, the efa locus showed significant deviation from Hardy– Weinberg expectations. Somatic incompatibility tests demonstrated that isolates derived from different basidiocarps and different logs belonged to different genets. In a microscale study including three logs, the independent assays of PCR-RFLP analysis and somatic incompatibility tests distinguished 10 genets. Life history traits and conservation status of P. nigrolimitatus are discussed in light of the results.Key words: Phellinus nigrolimitatus, population structure, somatic incompatibility, PCR-RFLP, nrDNA.
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49

Baklawa, Mohamed, Björn Niere, Holger Heuer, and Samia Massoud. "Characterisation of cereal cyst nematodes in Egypt based on morphometrics, RFLP and rDNA-ITS sequence analyses." Nematology 17, no. 1 (2015): 103–15. http://dx.doi.org/10.1163/15685411-00002855.

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Morphological and molecular diversity among populations of cereal cyst nematodes (CCN) from wheat production areas in Ismailia province, Egypt, was investigated using light microscopy, ITS-RFLP and sequencing of the rDNA-ITS. CCN were found in five out of seven regions in Ismailia, the highest incidence being found in El Shark (West Sinai). The Egyptian populations were identified as H. avenae according to morphometrics of cyst vulval cone and second-stage juveniles. No differences in ITS-RFLP patterns generated by 17 restriction enzymes were detected among the Egyptian populations although the Egyptian populations could be distinguished from German populations of H. avenae and H. filipjevi. The analyses of ITS region sequences confirmed the species identification of the Egyptian populations as they clustered with H. avenae populations from Iran, Saudi Arabia, India, Israel and China.
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Liu, Kunfeng, Maoyong Wu, Xuemei Lin, Piyanuch Lonan, Sitai Chen, Yina Wu, Xiaoping Lai, Liangwen Yu, Xiaoming Zhou, and Geng Li. "Molecular analysis of edible bird's nest and rapid authentication of Aerodramus fuciphagus from its subspecies by PCR-RFLP based on the cytb gene." Analytical Methods 12, no. 21 (2020): 2710–17. http://dx.doi.org/10.1039/c9ay02548k.

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