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Journal articles on the topic 'RNA fingerprinting'

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Published: 9 March 2023
Last updated: 10 March 2023

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1

Gegenheimer, Peter. "Electronic fingerprinting of RNA." Nucleic Acids Research 16, no. 5 (1988): 1799–800. http://dx.doi.org/10.1093/nar/16.5.1799.

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2

Gegenheimer, Peter. "Electronic fingerprinting of RNA." Nucleic Acids Research 16, no. 5 (1988): 1801–12. http://dx.doi.org/10.1093/nar/16.5.1801.

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3

Kato, K. "RNA fingerprinting by molecular indexing." Nucleic Acids Research 24, no. 2 (January 15, 1996): 394–95. http://dx.doi.org/10.1093/nar/24.2.394.

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4

Singh, Ankita, Akhilesh Mishra, Ali Khosravi, Garima Khandelwal, and B. Jayaram. "Physico-chemical fingerprinting of RNA genes." Nucleic Acids Research 45, no. 7 (December 8, 2016): e47-e47. http://dx.doi.org/10.1093/nar/gkw1236.

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5

Welsh, John, Kiran Chada, Seema S. Dalal, Rita Cheng, David Relph, and Michael McClelland. "Arbitrarily primed PCR fingerprinting of RNA." Nucleic Acids Research 20, no. 19 (1992): 4965–70. http://dx.doi.org/10.1093/nar/20.19.4965.

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6

McClelland, M., and J. Welsh. "RNA fingerprinting by arbitrarily primed PCR." Genome Research 4, no. 1 (August 1, 1994): S66—S81. http://dx.doi.org/10.1101/gr.4.1.s66.

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7

Carter, R. E., J. H. Wetton, and D. T. Parkin. "Improved gentic fingerprinting using RNA probes." Nucleic Acids Research 17, no. 14 (1989): 5867. http://dx.doi.org/10.1093/nar/17.14.5867.

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8

Rymerson, R. T., R. P. Bodnaryk, S. Haber, and J. D. Procunier. "Arbitrary primed RNA fingerprinting in plants." Biotechnology Techniques 9, no. 8 (August 1995): 563–66. http://dx.doi.org/10.1007/bf00152444.

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9

Augéde Mello, P., R. C. Olascoaga, M. P. Costa Giomi, A. Alonso Fernández, E. A. Scodeller, J. L. La Torre, and I. E. Bergmann. "RNA fingerprinting of South American prototype aphthovirus strains." Vaccine 4, no. 2 (June 1986): 105–10. http://dx.doi.org/10.1016/0264-410x(86)90047-2.

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10

Lozano, Gloria, Reyes Jimenez-Aparicio, Santiago Herrero, and Encarnacion Martinez-Salas. "Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound." RNA 22, no. 3 (January 12, 2016): 330–38. http://dx.doi.org/10.1261/rna.054353.115.

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11

Dvorská, L., M. Bartoš, G. Martin, W. Erler, and I. Pavlík. "Strategies for differentiation, identification and typing of medically important species of mycobacteria by molecular methods." Veterinární Medicína 46, No. 11–12 (January 1, 2001): 309–28. http://dx.doi.org/10.17221/7890-vetmed.

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Molecular biology methods offer new opportunities to differentiate, identify and type bacterial species and strains. These methods use the variability of nucleic sequences of genes such as 16S rDNA, beta subunit RNA-ase (rpoB), gyrase (gyrB), rDNA internal transcribed spacer and other genes. The aim of this paper is to provide comprehensive information about the methods available to differentiate and identify species of mycobacteria at the DNA sequence level. The methods discussed in the review include PCR, PCR-REA, sequencing analysis, spoligotyping and DNA fingerprinting. These methods have been applied to both the “universal” part of the genome and to specific mycobacterial genes.
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12

Collin, Mattias, and Arne Olsén. "Identification of conditionally expressed genes inStreptococcus pyogenesusing RNA fingerprinting." FEMS Microbiology Letters 196, no. 2 (March 2001): 123–27. http://dx.doi.org/10.1111/j.1574-6968.2001.tb10552.x.

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13

Emerick, V. L., and S. A. Woodson. "Fingerprinting the folding of a group I precursor RNA." Proceedings of the National Academy of Sciences 91, no. 21 (October 11, 1994): 9675–79. http://dx.doi.org/10.1073/pnas.91.21.9675.

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14

Lynch, M., F. O'Halloran, D. Whyte, B. Cryan, and S. Fanning. "Epidemiology and RNA fingerprinting of rota virus in Ireland." Journal of Infection 39, no. 1 (July 1999): A28. http://dx.doi.org/10.1016/s0163-4453(99)90217-7.

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15

McClelland, M. "RNA fingerprinting and differential display using arbitrarily primed PCR." Trends in Genetics 11, no. 6 (June 1995): 242–46. http://dx.doi.org/10.1016/s0168-9525(00)89058-7.

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16

McClelland, Michael, David Ralph, Rita cheng, and John Welsh. "Interactions among regualators of RNA abundance characterized using RNA fingerprinting by arbitrarily primed PCR." Nucleic Acids Research 22, no. 21 (1994): 4419–31. http://dx.doi.org/10.1093/nar/22.21.4419.

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17

Steen, Kady-Ann, Greggory M. Rice, and Kevin M. Weeks. "Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity." Journal of the American Chemical Society 134, no. 32 (August 2012): 13160–63. http://dx.doi.org/10.1021/ja304027m.

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18

Yamada, M., Mi Yamada, T. Hisamitsu, N. Uchida, and E. Richelson. "The use of RNA fingerprinting technique in the neuropsychiatry research." Biological Psychiatry 39, no. 7 (April 1996): 658. http://dx.doi.org/10.1016/0006-3223(96)84475-1.

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19

Marques, Ana Paula, Maria Vitória San Romão, and Rogério Tenreiro. "RNA fingerprinting analysis of Oenococcus oeni strains under wine conditions." Food Microbiology 31, no. 2 (September 2012): 238–45. http://dx.doi.org/10.1016/j.fm.2012.02.006.

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20

Furdon, Paul J., and Ryszard Kole. "RNA fingerprinting using a small horizontal agarose gel electrophoresis apparatus." Analytical Biochemistry 162, no. 1 (April 1987): 74–79. http://dx.doi.org/10.1016/0003-2697(87)90011-x.

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21

Fuchs, Bruno, Kunbo Zhang, Mark E. Bolander, and Gobinda Sarkar. "Identification of Differentially Expressed Genes by Mutually Subtracted RNA Fingerprinting." Analytical Biochemistry 286, no. 1 (November 2000): 91–98. http://dx.doi.org/10.1006/abio.2000.4792.

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22

VALLE, Paulo Renato, Maria Betânia G. SOUZA, Edna M. PIRES, Edward F. SILVA, and Maria A. GOMES. "Arbitrarily primed PCR fingerprinting of RNA and DNA in Entamoeba histolytica." Revista do Instituto de Medicina Tropical de São Paulo 42, no. 5 (October 2000): 249–53. http://dx.doi.org/10.1590/s0036-46652000000500003.

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Differences were detected in the gene expression of strains of E. histolytica using RNA (RAP-PCR) and DNA fingerprinting (RAPD). Analysis of the electrophoretic profiles of the gels revealed some polymorphic markers that could be used in the individual characterization of the strains. The 260 bands generated by using five different primers for RAP-PCR, as well as RAPD, were employed in the construction of dendograms. The dendogram obtained based on the RAPD products permitted the distinction of symptomatic and asymptomatic isolates, as well the correlation between the polymorphism exhibited and the virulence of the strains. The dendogram obtained for the RAP-PCR products did not show a correlation with the virulence of the strains but revealed a high degree of intraspecific transcriptional variability that could be related to other biological features, whether or not these are involved in the pathogenesis of amebiasis.
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23

Martincic, D., M. J. Koury, K. Gale, and J. A. Whitlock. "Detection of mutations by automated fluorescence/RNA-based dideoxy fingerprinting (ARddF)." Oncogene 18, no. 3 (January 21, 1999): 617–21. http://dx.doi.org/10.1038/sj.onc.1202295.

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24

Cavallaro, S., N. Meiri, C. L. Yi, S. Musco, W. Ma, J. Goldberg, and D. L. Alkon. "Late memory-related genes in the hippocampus revealed by RNA fingerprinting." Proceedings of the National Academy of Sciences 94, no. 18 (September 2, 1997): 9669–73. http://dx.doi.org/10.1073/pnas.94.18.9669.

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25

Dorn, G. W., M. G. Davis, and D. D. D'Angelo. "Gene expression during phorbol ester-induced differentiation of cultured human megakaryoblastic cells." American Journal of Physiology-Cell Physiology 266, no. 5 (May 1, 1994): C1231—C1239. http://dx.doi.org/10.1152/ajpcell.1994.266.5.c1231.

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Platelet protein makeup is determined during transformation of megakaryoblasts to mature megakaryocytes, the immediate precursor of circulating platelets. To better understand the molecular mechanisms of megakaryocyte formation, gene expression was characterized by Northern analysis and RNA fingerprinting of cultured human CHRF-288 megakaryoblastic cells undergoing phorbol ester-stimulated megakaryocytic differentiation or serum-stimulated megakaryoblast proliferation. Protooncogenes c-fos and c-jun were coordinately upregulated in both proliferating and differentiating cells, whereas c-myc transcripts were upregulated during proliferation only. In contrast, mRNAs for transforming growth factor-beta 1 (TGF-beta 1) and thromboxane receptors were coordinately upregulated during differentiation but differentially regulated during proliferation. RNA fingerprinting revealed multiple transcripts specific to either proliferating or differentiated cells. Three of these were identified by homology to known DNA sequence: CDw44 adhesion molecule (upregulated during differentiation), glutathione sulfhydryl peroxidase (downregulated during differentiation), and plectin cytoskeletal protein (upregulated during differentiation). Thus, although megakaryoblast proliferation and megakaryocyte differentiation both involve DNA and protein synthesis, each growth response is characterized by a distinct pattern of gene expression.
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26

Sharma, S., M. K. Aneja, J. Mayer, M. Schloter, and J. C. Munch. "RNA fingerprinting of microbial community in the rhizosphere soil of grain legumes." FEMS Microbiology Letters 240, no. 2 (November 2004): 181–86. http://dx.doi.org/10.1016/j.femsle.2004.09.026.

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27

Gardner, Ian A., Rick Kasten, Graeme J. Eamens, Kurt P. Snipes, and Randall J. Anderson. "Molecular Fingerprinting of Pasteurella Multocida Associated with Progressive Atrophic Rhinitis in Swine Herds." Journal of Veterinary Diagnostic Investigation 6, no. 4 (October 1994): 442–47. http://dx.doi.org/10.1177/104063879400600407.

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Ninety-six nasal isolates of Pasteurella multocida from swine herds with progressive atrophic rhinitis were characterized by restriction endonuclease analysis (REA) of whole-cell DNA, ribotyping, and plasmid analysis. For REA, bacterial DNA was digested with SmaI and electrophoresed in 0.7% agarose, and fragments were visualized with UV light. For ribotyping, EcoRI-digested and electrophoresed restriction fragments of whole-cell DNA were transferred to nitrocellulose membranes, hybridized with γ-32P-labeled Escherichia coli ribosomal RNA, and visualized by autoradiography. Phenotypes of isolates were toxigenic capsular type D ( n = 51), nontoxigenic type D ( n = 28), nontoxigenic type A ( n = 16), and toxigenic type A ( n = 1). Plasmids of various sizes were evident in 92.2% and 17.9% of toxigenic and nontoxigenic D strains, respectively, but were absent from all type A strains. Among the 4 phenotypes, there were 17 REA profiles and 6 ribotypes. For 3 of 17 REA patterns, multiple ribotypes were evident, and several REA types were evident in 5 of 6 ribotypes. Thirty-seven isolates of toxigenic capsular type D from Australian herds were either SmaI type B or C and ribotype 2, whereas 14 toxigenic D isolates from the USA and other countries were more heterogeneous (7 REA types and 6 ribotypes). The fingerprinting results provided evidence in support of the hypothesis of a single source infection in Australia associated with the introduction of breeding pigs from overseas.
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28

Miller, David, Pei-Zhong Tang, Clare Skinner, and Richard Lilford. "Differential RNA fingerprinting as a tool in the analysis of spermatozoal gene expression." Human Reproduction 9, no. 5 (May 1994): 864–69. http://dx.doi.org/10.1093/oxfordjournals.humrep.a138607.

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29

Palmieri, Steven, and Bailey W. Mitchell. "Comparison of Three Velogenic Strains of Newcastle Disease Virus by RNA Oligonucleotide Fingerprinting." Avian Diseases 35, no. 2 (April 1991): 384. http://dx.doi.org/10.2307/1591194.

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30

Storch, G. A., C. S. Park, and D. E. Dohner. "RNA fingerprinting of respiratory syncytial virus using ribonuclease protection. Application to molecular epidemiology." Journal of Clinical Investigation 83, no. 6 (June 1, 1989): 1894–902. http://dx.doi.org/10.1172/jci114096.

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31

Krause, Katrin, and Erika Kothe. "Use of RNA fingerprinting to identify fungal genes specifically expressed during ectomycorrhizal interaction." Journal of Basic Microbiology 46, no. 5 (October 2006): 387–99. http://dx.doi.org/10.1002/jobm.200610153.

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32

Guarino, Linda A., Bin Xu, Jianping Jin, and Wen Dong. "A Virus-Encoded RNA Polymerase Purified from Baculovirus-Infected Cells." Journal of Virology 72, no. 10 (October 1, 1998): 7985–91. http://dx.doi.org/10.1128/jvi.72.10.7985-7991.1998.

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ABSTRACT A DNA-dependent RNA polymerase was purified to homogeneity, starting from insect cells infected with the baculovirusAutographa californica nuclear polyhedrosis virus (AcNPV). The purified polymerase supported accurate and specific transcription from late and very late promoters but was not active on viral early promoters. Thus, promoter recognition is an integral function of the purified enzyme. The purified RNA polymerase was composed of only four equimolar subunits, which makes it the simplest DNA-directed RNA polymerase from a eukaryotic source described so far. Amino-terminal protein sequencing, peptide fingerprinting, and immunochemical analyses were used to identify the four subunits, all of which are virus encoded. Overexpression of the four viral proteins (LEF-8, LEF-4, LEF-9, and p47) in baculovirus-infected cells resulted in a significant increase in the levels of RNA polymerase produced in the infected cells. Thus, the overexpression data are consistent with our identification of the RNA polymerase subunits.
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33

Yin, Bei, Lea Valinsky, Xuebiao Gao, J. Ole Becker, and James Borneman. "Identification of Fungal rDNA Associated with Soil Suppressiveness Against Heterodera schachtii Using Oligonucleotide Fingerprinting." Phytopathology® 93, no. 8 (August 2003): 1006–13. http://dx.doi.org/10.1094/phyto.2003.93.8.1006.

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To understand the nature of a soil with suppressiveness against Heterodera schachtii, an rDNA analysis was used to identify fungi associated with H. schachtii cysts obtained from soils possessing various levels of suppressiveness. Because H. schachtii cysts isolated from these suppressive soils can transfer this beneficial property to nonsuppressive soils, analysis of the microorganisms associated with the cysts should lead to the identification of the causal organisms. Five soil treatments, generated by mixing different amounts of suppressive and fumigation-induced nonsuppressive soils, were infested with second-stage juveniles of H. schachtii and cropped with mustard-greens. Fungi were identified through an rDNA analysis termed oligonucleotide fingerprinting of ribosomal RNA genes (OFRG). Cysts obtained from soil mixtures consisting of 10 and 100% suppressive soil predominantly contained fungal rDNA with high sequence identity to Dactylella oviparasitica. The dominant fungal rDNA in the cysts isolated from the soil mixtures composed of 0.1 and 1% suppressive soil had high sequence identity to Fusarium oxysporum. Polymerase chain reaction (PCR) amplifications performed with sequence-selective primers corroborated the treatment-specific distribution of rDNA clones obtained by the OFRG analysis. When these sequence-selective PCR primers were used to examine H. schachtii cysts from biocidal soil treatments that produced various levels of suppressiveness, only the D. oviparasitica-like rDNA was consistently identified in the highly suppressive soils.
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34

Menke, Ulrich, and Bernd Mueller-Roeber. "RNA fingerprinting of specific plant cell types: Adaptation to plants and optimization of RNA arbitrarily primed PCR (RAP-PCR)." Plant Molecular Biology Reporter 19, no. 1 (March 2001): 33–48. http://dx.doi.org/10.1007/bf02824076.

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35

Gill, Kulvinder S., and Devinder Sandhu. "Candidate-gene cloning and targeted marker enrichment of wheat chromosomal regions using RNA fingerprinting - differential display." Genome 44, no. 4 (August 1, 2001): 633–39. http://dx.doi.org/10.1139/g01-047.

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The usefulness of the RNA fingerprinting – differential display technique in gene cloning and targeted marker enrichment in wheat is demonstrated. A small region of chromosome 5BL was targeted that contains Ph1, a chromosome-pairing regulator gene. The cultivar Chinese Spring (CS) and mutant ph1b are almost identical except for chromosome 5BL, which, in the mutant line, carries an interstitial deletion encompassing the Ph1 gene. Poly(A)+ RNA of the two lines from anthers at developmental stages ranging from pre-meiotic mitosis to anaphase II was PCR-amplified using 38 pairwise combinations of 19 primers. The 35S-labeled amplified products were size-separated on denaturing polyacrylamide-urea gels. A total of 3154 fragment bands were observed, of which 43 were present in CS but absent in the ph1b mutant. These 43 fragment bands were eluted, re-amplified, and used as probes in gel-blot DNA analyses of wheat group 5 nullisomic-tetrasomic lines and the ph1b mutant. Twenty-four of these 43 probes were single- or few-copy sequences. Eight of the 24 probes mapped to wheat group 5 and five mapped to the deletion of the ph1b mutant. Three of these five probes were further localized to the submicroscopic region containing the Ph1 gene, by using two deletion lines flanking the region. Northern-blot analysis revealed that the gene corresponding to one of these three probes expresses mainly during meiosis and is from the B genome.Key words: RNA fingerprinting – differential display, wheat, gene cloning, marker enrichment, Ph1 gene.
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36

Frolková, Petra, Pavel Švec, Ivo Sedláček, Ivana Mašlaňová, Jitka Černohlávková, Anuradha Ghosh, Ludek Zurek, Tomáš Radiměřský, and Ivan Literák. "Enterococcus alcedinis sp. nov., isolated from common kingfisher (Alcedo atthis)." International Journal of Systematic and Evolutionary Microbiology 63, Pt_8 (August 1, 2013): 3069–74. http://dx.doi.org/10.1099/ijs.0.049833-0.

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Two Gram-positive, catalase-negative bacterial strains were isolated from the cloaca of common kingfishers (Alcedo atthis). Repetitive sequence-based PCR fingerprinting using the (GTG)5 primer grouped these isolates into a single cluster separated from all known enterococcal species. The two strains revealed identical 16S rRNA gene sequences placing them within the genus Enterococcus with Enterococcus aquimarinus LMG 16607T as the closest relative (97.14 % similarity). Further taxonomic investigation using sequencing of the genes for the superoxide dismutase (sodA), phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) as well as application of whole-cell protein fingerprinting, automated ribotyping and extensive phenotyping confirmed that both strains belong to the same species. Based on data from this polyphasic study, these strains represent a novel species of the genus Enterococcus , for which the name Enterococcus alcedinis sp. nov. is proposed. The type strain is L34T ( = CCM 8433T = LMG 27164T).
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37

Švec, Pavel, Peter Vandamme, Hana Bryndová, Pavla Holochová, Marcel Kosina, Ivana Mašlaňová, and Ivo Sedláček. "Enterococcus plantarum sp. nov., isolated from plants." International Journal of Systematic and Evolutionary Microbiology 62, Pt_7 (July 1, 2012): 1499–505. http://dx.doi.org/10.1099/ijs.0.033357-0.

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Eight Gram-positive, catalase-negative bacterial strains were isolated during screening of enterococcal populations on plants. rep-PCR fingerprinting using the (GTG)5 primer showed that the isolates constituted a single cluster that was separate from all known enterococcal species. 16S rRNA gene sequence phylogenetic analysis of three representative strains showed that the isolates belonged to the genus Enterococcus and that they clustered with the Enterococcus faecalis species group. Sequencing of the genes for the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) also revealed the isolates’ separate taxonomic position. Application of whole-cell protein fingerprinting, automated ribotyping and extensive phenotyping demonstrated the genetic and phenotypic homogeneity of the isolates and confirmed their separate position within the E. faecalis species group. The isolates represent a novel species of the genus Enterococcus , for which the name Enterococcus plantarum sp. nov. is proposed; the type strain is CCM 7889T ( = LMG 26214T = C27T).
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38

Liu, S., G. Bokinsky, N. G. Walter, and X. Zhuang. "Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting"." Proceedings of the National Academy of Sciences 104, no. 31 (May 11, 2007): 12634–39. http://dx.doi.org/10.1073/pnas.0610597104.

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39

Palmieri, Steven, and Michael L. Perdue. "An Alternative Method of Oligonucleotide Fingerprinting for Resolving Newcastle Disease Virus-Specific RNA Fragments." Avian Diseases 33, no. 2 (April 1989): 345. http://dx.doi.org/10.2307/1590854.

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40

Katsivela, Eleftheria, and Manfred G. Höfle. "Low-molecular-mass RNA fingerprinting of bacteria by capillary electrophoresis using entangled polymer solutions." Journal of Chromatography A 717, no. 1-2 (November 1995): 91–103. http://dx.doi.org/10.1016/0021-9673(95)00628-5.

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41

Diachenko, Luda B., John Ledesma, Alex A. Chenchik, and Paul D. Siebert. "Combining the Technique of RNA Fingerprinting and Differential Display to Obtain Differentially Expressed mRNA." Biochemical and Biophysical Research Communications 219, no. 3 (February 1996): 824–28. http://dx.doi.org/10.1006/bbrc.1996.0317.

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42

Oxford, J. S. "Biochemical techniques for the genetic and phenotypic analysis of viruses: ‘Molecular Epidemiology’." Journal of Hygiene 94, no. 1 (February 1985): 1–7. http://dx.doi.org/10.1017/s0022172400061076.

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New technologies now enable virologists to study small genetic and antigenic differences between field isolates of animal viruses at a higher level of discrimination than has been possible using conventional serological techniques. The most important of the laboratory techniques revolve around the use of monoclonal antibodies, peptide mapping, fingerprinting of whole RNA virus genomes, RNA:RNA hybridization, ‘electropherotyping’ of virus RNA or polypeptides, restriction enzyme analysis of virus DNA genomes, cloning of genes and rapid sequencing of viral DNAs and RNAs, in the latter case using primer extension techniques (reviewed by Palese & Roizman, 1980). From a practical point of view, genetic and phenotypic heterogeneity among viruses may be of considerable importance in attempts to control certain virus diseases by chemo- or immunoprophylaxis.
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43

Iranpour, M., A. M. Schurko, G. R. Klassen, and T. D. Galloway. "DNA fingerprinting of tabanids (Diptera: Tabanidae) and their respective egg masses using PCR – restriction fragment profiling." Canadian Entomologist 136, no. 5 (October 2004): 605–19. http://dx.doi.org/10.4039/n03-076.

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AbstractPolymerase chain reaction and subsequent restriction fragment profiling analysis were used to associate collected tabanid egg masses with their respective species of adult horse flies and deer flies (Diptera: Tabanidae) in Manitoba, Canada. The ribosomal DNA (rDNA) intergenic spacer between the 28S and 18S ribosomal RNA genes was used successfully to differentiate 34 species of adult tabanids representing five genera: Atylotus (1 sp.), Chrysops (10 spp.), Haematopota (1 sp.), Hybomitra (17 spp.), and Tabanus (5 spp.). rDNA was a suitable molecular target for identifying tabanid species because of the high level of interspecific variation when comparing fragment profiles among different species, and the corresponding minimal intraspecific variation among individuals of the same species. Restriction fragment profiles from 56 field-collected tabanid egg masses were compared with those previously obtained from adults of known species. Egg masses of five species were identified: Hybomitra lasiophthalma (Macquart), Hybomitra nitidifrons nuda (McDunnough), Chrysops aestuans van der Wulp, Chrysops excitans Walker, and Chrysops mitis Osten Sacken. We also provide physical descriptions of these tabanid egg masses along with pictures.
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44

Valášková, V., and P. Baldrian. "Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities." Plant, Soil and Environment 55, No. 10 (October 21, 2009): 413–23. http://dx.doi.org/10.17221/132/2009-pse.

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In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.
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45

A. VALDECANTOS, PABLO, MART蚇 E. ARGA袮RAZ, CARLOS M. ABATE, and DORA C. MICELI. "RNA fingerprinting using RAP-PCR identifies an EBAF homologue mRNA differentially expressed in rat oviduct." BIOCELL 28, no. 3 (2004): 287–97. http://dx.doi.org/10.32604/biocell.2004.28.287.

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BUDAK, HIKMET, SENEM SU, and NESLIHAN ERGEN. "Revealing constitutively expressed resistance genes in Agrostis species using PCR-based motif-directed RNA fingerprinting." Genetical Research 88, no. 03 (December 2006): 165. http://dx.doi.org/10.1017/s0016672307008518.

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Aneja, Manish K., Shilpi Sharma, Jean C. Munch, and Michael Schloter. "RNA fingerprinting—a new method to screen for differences in plant litter degrading microbial communities." Journal of Microbiological Methods 59, no. 2 (November 2004): 223–31. http://dx.doi.org/10.1016/j.mimet.2004.07.005.

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48

ZHANG, Zhan-Feng. "RNA Fingerprinting of the Differential Expression Fragments Related to Cytoplasmic Male Sterility in Chinese Cabbage." HEREDITAS 28, no. 10 (2006): 1280. http://dx.doi.org/10.1360/yc-006-1280.

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Warbington, Blake, Daniel Weinstein, David Mallinson, Daria Olijnyk, Sarah Paterson, Susan Ridha, Vincent O'Brien, et al. "Characterization Of Bone Marrow Derived CD34+ Cells With Different Mobility Potentials By Micro RNA Fingerprinting." Blood 122, no. 21 (November 15, 2013): 4844. http://dx.doi.org/10.1182/blood.v122.21.4844.4844.

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Abstract:
Abstract Background AMR-001, an autologous CD34+ cell product derived from mini-marrow harvest, is currently undergoing Phase II trials to treat acute myocardial infarction (AMI). AMR-001 is administered to the patient by infusion via the infarct related artery within five to ten days following coronary artery stenting post AMI. At the time of infusion, it is believed that the infarct-region SDF-1 (stromal derived factor) levels are peaked and scar formation has not yet occurred. It was found that, in addition to the quantity of CD34+ cells infused, improvement in cardiac perfusion and infarct size correlated with the mobility potential of CD34+ cells mediated by a SDF-1 gradient (Quyyumi et al, Am Heart J 2011, 161:98–105). We have developed a cell based in vitro mobility assay as a potential potency release assay for AMR-001. However, this assay is not suitable for a Phase III or commercial scale release assay due to the length of the assay, high skill level required to perform, and variability. To develop a more robust assay, we have initiated a study to identify potential microRNAs (miRNAs) that may be used as biomarkers for CD34+ cell SDF-1 driven migration. Our preliminary results suggest CD34+ cells with different mobility potentials may be characterized by miRNA fingerprinting. Methods Cryopreserved purified CD34+ cells derived from bone marrow of healthy donors were purchased from a commercial vendor. Thawed CD34+ cells were washed and the cells were assayed in an in vitro transwell system (Jo et al, J Clin Invest 2000, 105:101-111). The trans-membrane migration of CD34+ cells into the lower chamber in the presence of SDF-1, as well as the non-mobilized CD34+ cells in the upper chamber, were collected after 4 hours incubation at 37°C. Total RNA of the cells was isolated and the miRNA expression profile was analyzed using SurePrint G3 Human v16 microRNA 8x60K microarray slide (Agilent, Santa Clara, CA). A normalization algorithm was used to generate miRNA expression profiles (SistemQC™, Sistemic, Ltd) for the characterization of untreated cells, the mobilized population that migrate towards SDF-1, and non-mobilized population; from two independent donors. Results Two hundred and four (204) miRNAs were reliably detected across the cell samples. The mobilized cells had different miRNA profiles compared with non-mobilized/untreated cells. Hierarchical cluster analysis showed that mobilized cells grouped separately from the non-mobilized/untreated cells. Conclusion Analysis of the miRNA profiles of the CD34+ cells across two independent donors, identified a number of key miRNAs (kmiRs™) that represent possible markers for a mobility phenotype. Additional samples will be analyzed to confirm these preliminary findings. This approach will enable the identification of markers associated with mobility potential of CD34+ cells and the potential development of a molecular biomarker assay for potency. Disclosures: Warbington: Progenitor Cell Therapy, LLC: Employment. Weinstein:Progenitor Cell Therapy, LLC: Employment. Mallinson:Sistemic, Ltd.: Employment, Equity Ownership. Olijnyk:Sistemic, Ltd.: Employment. Paterson:Sistemic, Ltd.: Employment. Ridha:Sistemic, Ltd.: Employment. O'Brien:Sistemic, Ltd.: Employment, Equity Ownership, Membership on an entity’s Board of Directors or advisory committees. Lin:Progenitor Cell Therapy, LLC: Employment. LeBlon:Progenitor Cell Therapy, LLC: Employment. Fong:NeoStem, Inc.: Employment. Chan:Progenitor Cell Therapy, LLC: Employment.
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Velázquez, E., O. Calvo, E. Cervantes, P. F. Mateos, M. Tamame, and E. Martínez-Molina. "Staircase electrophoresis profiles of stable low-molecular-weight RNA--a new technique for yeast fingerprinting." International Journal of Systematic and Evolutionary Microbiology 50, no. 2 (March 1, 2000): 917–23. http://dx.doi.org/10.1099/00207713-50-2-917.

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