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Journal articles on the topic 'Degenerate Oligonucleotide Primed PCR'

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Published: 4 June 2021
Last updated: 12 February 2022

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1

Arneson, N., S. Hughes, R. Houlston, and S. Done. "Whole-Genome Amplification by Degenerate Oligonucleotide Primed PCR (DOP-PCR)." Cold Spring Harbor Protocols 2008, no. 2 (2008): pdb.prot4919. http://dx.doi.org/10.1101/pdb.prot4919.

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2

Telenius, Ha˚kan, Nigel P. Carter, Charlotte E. Bebb, Magnus Nordenskjo¨ld, Bruce A. J. Ponder, and Alan Tunnacliffe. "Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single degenerate primer." Genomics 13, no. 3 (1992): 718–25. http://dx.doi.org/10.1016/0888-7543(92)90147-k.

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3

Kiss, Csaba, Maria Kost-Alimova, George Klein, and Laszlo Szekely. "Optimisation of the degenerate oligonucleotide primed PCR (DOP-PCR) for capillary thermocycler." Biomolecular Engineering 19, no. 1 (2002): 31–34. http://dx.doi.org/10.1016/s1389-0344(02)00008-4.

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4

Janiak, Agnieszka, Moon Young Kim, Kyujung Van, and Suk-Ha Lee. "Application of degenerate oligonucleotide primed PCR (DOP-PCR) for SNP discovery in soybean." Euphytica 162, no. 2 (2007): 249–56. http://dx.doi.org/10.1007/s10681-007-9599-8.

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5

Rose, T. "CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design." Nucleic Acids Research 31, no. 13 (2003): 3763–66. http://dx.doi.org/10.1093/nar/gkg524.

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6

He, Yu, Hongmei Li, Derek Brown, Franco Lamberti, and Maurice Moens. "Isolation and characterisation of microsatellites for Xiphinema index using degenerate oligonucleotide primed PCR." Nematology 5, no. 6 (2003): 809–19. http://dx.doi.org/10.1163/156854103773040718.

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Abstract A short insert genomic library for Xiphinema index, the natural vector of Grapevine Fanleaf Virus, was constructed from degenerate oligonucleotide primed PCR (DOP-PCR) products. The genomic library was screened for (CA)n microsatellites. Screening of 6200 colonies and comparison of the sequencing results revealed seven (CA)n containing microsatellites, coded here as XIMSL1, XIMSL2, XIMSL3, XIMSL4, XIMSL5, XIMSL6 and XIMSS1. XIMSL prefixed microsatellites were followed by the motif of the same long interspersed element. Microsatellite XIMSS1 has some similarity to the short intersperse
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7

Barbaux, Sandrine, Odette Poirier, and François Cambien. "Use of degenerate oligonucleotide primed PCR (DOP-PCR) for the genotyping of low-concentration DNA samples." Journal of Molecular Medicine 79, no. 5-6 (2001): 329–32. http://dx.doi.org/10.1007/s001090100214.

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8

Isagi, Y., M. Honjo, and I. Washitani. "Development of microsatellite markers for Primula sieboldii using degenerate oligonucleotide-primed PCR-amplified DNA." Molecular Ecology Notes 1, no. 1-2 (2001): 22–24. http://dx.doi.org/10.1046/j.1471-8278.2000.00009.x.

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9

Jamshidian-Mojaver, M., S.-E. Tabatabaeizadeh, M. Naeemipour, H. R. Farzin, and M. R. Bassami. "Use of degenerate oligonucleotide primed polymerase chain reaction for detection of chicken anaemia virus contamination in avian viral vaccines." BULGARIAN JOURNAL OF VETERINARY MEDICINE 23, no. 3 (2020): 304–9. http://dx.doi.org/10.15547/bjvm.2230.

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For quality control of biologicals of veterinary use, the absence of extraneous agents needs to be certified. One of the requirements for quality control of avian viral vaccines is to demonstrate freedom from extraneous and adventitious pathogenic agents, like chicken anaemia virus (CAV). In this study, a degenerate oligonucleotide primed PCR (DOP-PCR) for the detection of CAV was developed. Degenerate oligonucleotide primers were selected based on sequences corresponding to conserved regions of VP1 gene. After spiking of CAV genomic DNA to an infectious laryngotracheitis virus (ILTV) vaccine,
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10

Larsen, Jacob, Anne Marie Ottesen, Maria Kirchhoff, Claes Lundsteen, and Jørgen K. Larsen. "High Resolution Comparative Genomic Hybridization Detects 7–8 Megabasepair Deletion in PCR Amplified DNA1." Analytical Cellular Pathology 23, no. 2 (2001): 61–64. http://dx.doi.org/10.1155/2001/301570.

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We investigated if any change in spatial resolution of comparative genomic hybridization analysis could be detected when using DNA amplified by degenerate oligonucleotide primed PCR (DOP‐PCR) as opposed to the use of unamplified DNA. Five DNA samples from B‐cell leukemias with small 11q deletions were amplified by DOP‐PCR and analysed by means of high resolution comparative genomic hybridization (HR‐CGH) for the evaluation of aberration size detection limit. By means of HR‐CGH, we found the detection limit of DOP‐PCR CGH for deletions to be between 3 Mbp and 7–8 Mbp.
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11

Lee, Ji-Young, Young-Nyun Park, Kyung-Ok Uhm, Soo-Yeun Park, and Sun-Hwa Park. "Genetic Alterations in Intrahepatic Cholangiocarcinoma as revealed by Degenerate Oligonucleotide Primed PCR-Comparative Genomic Hybridization." Journal of Korean Medical Science 19, no. 5 (2004): 682. http://dx.doi.org/10.3346/jkms.2004.19.5.682.

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12

Sanchez-Cespedes, Montserrat, Paul Cairns, Jin Jen, and David Sidransky. "Degenerate Oligonucleotide-Primed PCR (DOPPCR): Evaluation of its Reliability for Screening of Genetic Alterations in Neoplasia." BioTechniques 25, no. 6 (1998): 1036–38. http://dx.doi.org/10.2144/98256cr01.

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13

Hoebee, B., J. M. de Stoppelaar, R. F. Suijkerbuijk, and S. Monard. "Isolation of rat chromosome-specific paint probes by bivariate flow sorting followed by degenerate oligonucleotide primed-PCR." Cytogenetic and Genome Research 66, no. 4 (1994): 277–82. http://dx.doi.org/10.1159/000133712.

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14

Huang, Qiang, Stimson P. Schantz, Pulivarthi H. Rao, Juan Mo, Steven A. McCormick, and R. S. K. Chaganti. "Improving degenerate oligonucleotide primed PCR-comparative genomic hybridization for analysis of DNA copy number changes in tumors." Genes, Chromosomes and Cancer 28, no. 4 (2000): 395–403. http://dx.doi.org/10.1002/1098-2264(200008)28:4<395::aid-gcc5>3.0.co;2-j.

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15

Pich, Uta, Andreas Houben, Jörg Fuchs, Armin Meister, and Ingo Schubert. "Utility of DNA amplified by degenerate oligonucleotide-primed PCR (DOP-PCR) from the total genome and defined chromosomal regions of field bean." Molecular and General Genetics MGG 243, no. 2 (1994): 173–77. http://dx.doi.org/10.1007/bf00280314.

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16

Jin, F., CD Matthews, and N. Hussey. "P-11. Study on amplification uniformity of whole genome DNA in a single cell by degenerate oligonucleotide-primed PCR." Reproductive BioMedicine Online 4 (January 2002): 44. http://dx.doi.org/10.1016/s1472-6483(12)60094-7.

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17

Van, Kyujung, Yang Jae Kang, Sang Rea Shim, and Suk-Ha Lee. "Genome-wide scan of the soybean genome using degenerate oligonucleotide primed PCR: an example for studying large complex genome structure." Genes & Genomics 34, no. 5 (2012): 467–74. http://dx.doi.org/10.1007/s13258-011-0238-3.

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18

JIN, Fan. "SINGLE CELL DEGENERATE OLIGONUCLEOTIDE PRIMER-PCR AND COMPARATIVE GENOMIC HYBRIDIZATION WITH MODIFIED CONTROL REFERENCE." Journal of Zhejiang University SCIENCE 2, no. 3 (2001): 318. http://dx.doi.org/10.1631/jzus.2001.0318.

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19

Li, Ya-zhong, Xiao-dan Li, Yu-mei Jiang, Ren Wang та Bing Xia. "Cloning and Heterologous Expression of a New 3ʹ-Hydroxylase Gene from Lycoris radiata". Zeitschrift für Naturforschung C 64, № 1-2 (2009): 138–42. http://dx.doi.org/10.1515/znc-2009-1-222.

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A full-length cDNA (LC3ʹH) was obtained from a cDNA library of Lycoris radiata by DOP-PCR (degenerate oligonucleotide primer PCR), 3ʹrace and 5ʹrace methods. Compared with the other reported enzymes from different plants, the deduced amino acid sequence of LC3ʹH exhibits significant homologies to 3ʹ-hydroxylases that are involved in the caffeic acid biosynthesis. These findings suggest that the new gene is closely related to the biosynthesis of caffeic acid, which is also an important step of the galanthamine biosynthesis in Amaryllidaceae plants.
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20

Green, E. K., S. C. Bain, P. J. Day, et al. "Detection of human apolipoprotein E3, E2, and E4 genotypes by an allele-specific oligonucleotide-primed polymerase chain reaction assay: development and validation." Clinical Chemistry 37, no. 7 (1991): 1263–68. http://dx.doi.org/10.1093/clinchem/37.7.1263.

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Abstract A polymerase chain reaction (PCR) assay has been developed and validated by using allele-specific oligonucleotide (ASO) primers to specifically amplify E3, E2, and E4 polymorphic sequences of the human apolipoprotein E (apo E) genes. Degenerate ASOs containing one or two additional 3' mismatches provided greater specificity than did ASOs containing a single mid-sequence or 3' allele-specific mismatch with plasmid pEB4 or genomic DNA as template. Optimal specificity and efficiency of amplification did not correlate with primer annealing conditions, whether determined theoretically or v
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21

Scutt, Charles P., Yasuko Kamisugi, Philip M. Gilmartin, and Fukumi Sakai. "Laser isolation of plant sex chromosomes: studies on the DNA composition of the X and Y sex chromosomes of Silene latifolia." Genome 40, no. 5 (1997): 705–15. http://dx.doi.org/10.1139/g97-793.

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X and Y sex chromosomes from the dioecious plant Silene latifolia (white campion) were isolated from mitotic metaphase chromosome preparations on polyester membranes. Autosomes were ablated using an argon ion laser microbeam and isolated sex chromosomes were then recovered on excised fragments of polyester membrane. Sex chromosome associated DNA sequences were amplified using the degenerate oligonucleotide primed polymerase chain reaction (DOP–PCR) and pools of DOP–PCR products were used to investigate the genomic organization of the S. latifolia sex chromosomes. The chromosomal locations of c
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22

Arneson, Nona, Juan Moreno, Vladimir Iakovlev, et al. "Comparison of Whole Genome Amplification Methods for Analysis of DNA Extracted from Microdissected Early Breast Lesions in Formalin-Fixed Paraffin-Embedded Tissue." ISRN Oncology 2012 (March 14, 2012): 1–10. http://dx.doi.org/10.5402/2012/710692.

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To understand cancer progression, it is desirable to study the earliest stages of its development, which are often microscopic lesions. Array comparative genomic hybridization (aCGH) is a valuable high-throughput molecular approach for discovering DNA copy number changes; however, it requires a relatively large amount of DNA, which is difficult to obtain from microdissected lesions. Whole genome amplification (WGA) methods were developed to increase DNA quantity; however their reproducibility, fidelity, and suitability for formalin-fixed paraffin-embedded (FFPE) samples are questioned. Using a
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23

Hirose, Yuichi, Kenneth Aldape, Michelle Takahashi, Mitchel S. Berger, and Burt G. Feuerstein. "Tissue Microdissection and Degenerate Oligonucleotide Primed-Polymerase Chain Reaction (DOP-PCR) Is an Effective Method to Analyze Genetic Aberrations in Invasive Tumors." Journal of Molecular Diagnostics 3, no. 2 (2001): 62–67. http://dx.doi.org/10.1016/s1525-1578(10)60653-8.

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24

Deng, Chuanliang, Lili Bai, Shufen Li, et al. "DOP–PCR based painting of rye chromosomes in a wheat background." Genome 57, no. 9 (2014): 473–79. http://dx.doi.org/10.1139/gen-2014-0110.

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To determine the appropriateness of chromosome painting for identifying genomic elements in rye, we microdissected the 1R and 1RS chromosomes from rye (Secale cereale L. var. King II) and wheat–rye addition line 1RS, respectively. Degenerate oligonucleotide primed – polymerase chain reaction (DOP–PCR) amplification of 1R and 1RS products from dissected chromosomes were used as probes to hybridize to metaphase chromosomes of rye, wheat–rye addition lines 1R and 1RS, translocation line 1RS.1BL, and allohexaploid triticale. The results showed that (i) the hybridization signal distribution pattern
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25

Provencher, Cathy, Gis�le LaPointe, St�phane Sirois, Marie-Rose Van Calsteren, and Denis Roy. "Consensus-Degenerate Hybrid Oligonucleotide Primers for Amplification of Priming Glycosyltransferase Genes of the Exopolysaccharide Locus in Strains of the Lactobacillus casei Group." Applied and Environmental Microbiology 69, no. 6 (2003): 3299–307. http://dx.doi.org/10.1128/aem.69.6.3299-3307.2003.

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ABSTRACT A primer design strategy named CODEHOP (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (GT) gene in strains of the Lactobacillus casei group. Each hybrid primer consisted of a short 3′ degenerate core based on four highly conserved amino acids and a longer 5′ consensus clamp region based on six sequences of the priming GT gene products from exopolysaccharide (EPS)-producing bacteria. The hybrid primers were used to detect the priming GT gene of 44 commercial isolates and reference
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26

CULLINGFORD, E. Tim, T. Colin DOLPHIN, K. Kishore BHAKOO, Stefan PEUCHEN, Laura CANEVARI, and B. John CLARK. "Molecular cloning of rat mitochondrial 3-hydroxy-3-methylglutaryl-CoA lyase and detection of the corresponding mRNA and of those encoding the remaining enzymes comprising the ketogenic 3-hydroxy-3-methylglutaryl-CoA cycle in central nervous system of suckling rat." Biochemical Journal 329, no. 2 (1998): 373–81. http://dx.doi.org/10.1042/bj3290373.

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We have investigated, by RNase protection assays in rat brain regions and primary cortical astrocyte cultures, the presence of the mRNA species encoding the three mitochondrially located enzymes acetoacetyl-CoA thiolase, mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase (mt. HMG-CoA synthase) and HMG-CoA lyase (HMG-CoA lyase) that together constitute the ketogenic HMG-CoA cycle. As a prerequisite we obtained a full-length cDNA encoding rat HMG-CoA lyase by degenerate oligonucleotide-primed PCR coupled to a modification of PCR-rapid amplification of cDNA ends (PCR-RACE). We report here: (1)
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27

Zhou, Jian, Shaojing Wang, Li'ang Yu, et al. "Cloning and physical localization of male-biased repetitive DNA sequences in Spinacia oleracea (Amaranthaceae)." Comparative Cytogenetics 15, no. 2 (2021): 101–18. http://dx.doi.org/10.3897/compcytogen.v15i2.63061.

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Spinach (Spinacia oleracea Linnaeus, 1753) is an ideal material for studying molecular mechanisms of early-stage sex chromosome evolution in dioecious plants. Degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) technique facilitates the retrotransposon-relevant studies by enriching specific repetitive DNA sequences from a micro-dissected single chromosome. We conducted genomic subtractive hybridization to screen sex-biased DNA sequences by using the DOP-PCR amplification products of micro-dissected spinach Y chromosome. The screening yielded 55 male-biased DNA sequences with
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28

Zhou, Jian, Shaojing Wang, Li'ang Yu, et al. "Cloning and physical localization of male-biased repetitive DNA sequences in Spinacia oleracea (Amaranthaceae)." Comparative Cytogenetics 15, no. 2 (2021): 101–18. http://dx.doi.org/10.3897/compcytogen.v15.i2.63061.

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Spinach (Spinacia oleracea Linnaeus, 1753) is an ideal material for studying molecular mechanisms of early-stage sex chromosome evolution in dioecious plants. Degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) technique facilitates the retrotransposon-relevant studies by enriching specific repetitive DNA sequences from a micro-dissected single chromosome. We conducted genomic subtractive hybridization to screen sex-biased DNA sequences by using the DOP-PCR amplification products of micro-dissected spinach Y chromosome. The screening yielded 55 male-biased DNA sequences with
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29

Sharbel, Timothy F., David M. Green, and Andreas Houben. "B-chromosome origin in the endemic New Zealand frog Leiopelma hochstetteri through sex chromosome devolution." Genome 41, no. 1 (1998): 14–22. http://dx.doi.org/10.1139/g97-091.

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The endemic New Zealand frog Leiopelma hochstetteri has variable numbers of mitotically stable B chromosomes. To assess whether the B chromosomes were derived from the autosome complement, they were isolated by micromanipulation and their DNA amplified by degenerate oligonucleotide primed PCR. Southern hybridizations of B chromosome DNA probes to genomic DNA from males and females characterized by differing numbers of B chromosomes demonstrated that the B chromosomes were derived from the univalent W sex chromosome characteristic of North Island populations. The presence of homologous B chromo
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30

Patreze, C. M., D. B. Felix, F. R. Scarano, and M. Alves-Ferreira. "Isolating of a putative glyceraldehyde-3 phosphate dehydrogenase (GAPDH) from Calophyllum brasiliense, an important tropical forest tree." Silvae Genetica 61, no. 1-6 (2012): 44–51. http://dx.doi.org/10.1515/sg-2012-0006.

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Abstract Calophyllum brasiliense Cambess. has characteristics that made it an excellent candidate model for ecogenomics in rain forest trees such as widespread natural occurrence and geographical patterns of adaptive genetic variation. Besides, it is also becoming a popular species for reforestation efforts in Brazil. Although, very little is known about its genetic diversity and the molecular mechanisms involved genetic adaptation traits. The first difficulty in launching genetic studies in a wild wood species is the lack of an optimized protocol for RNA and DNA isolation. In this work we bui
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31

Franke, Sabine, Iwona Wlodarska, Brigitte Maes, et al. "Lymphocyte predominance Hodgkin disease is characterized by recurrent genomic imbalances." Blood 97, no. 6 (2001): 1845–53. http://dx.doi.org/10.1182/blood.v97.6.1845.

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Single-cell polymerase chain reaction (PCR) has been used as a tool to demonstrate clonality and B-cell origin of Reed-Sternberg (RS) cells in Hodgkin disease (HD). An analogous approach was used to investigate genomic imbalances in a (cyto)genetically poorly characterized subentity: lymphocyte predominance Hodgkin disease (LPHD). Nineteen cases of LPHD were selected for a comparative genomic hybridization (CGH) study. CGH was performed with degenerate oligonucleotide primed–PCR (DOP-PCR)–amplified DNA from 4-5 microdissected CD20+ malignant cells. All analyzed cases revealed a high number of
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32

Cheng, Ya-Ming, and Bor-Yaw Lin. "Cloning and Characterization of Maize B Chromosome Sequences Derived From Microdissection." Genetics 164, no. 1 (2003): 299–310. http://dx.doi.org/10.1093/genetics/164.1.299.

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Abstract Isolation of sequences from the maize B chromosome is always hampered by its high homology with the normal complements. In this study, this handicap was overcome by cloning the sequences from the pachytene B chromosomes dissected out of a slide by a micromanipulator followed by degenerate oligonucleotide-primed PCR. The isolated sequences were found to hybridize with genomic DNA in a B-dosage-dependent manner and with the pachytene B chromosome by fluorescence in situ hybridization (FISH), corroborating their B origin. A total of 19 B sequences were isolated, all of which are repetiti
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33

Zitzelsberger, H., Ulrike Kulka, Lars Lehmann, et al. "Genetic heterogeneity in a prostatic carcinoma and associated prostatic intraepithelial neoplasia as demonstrated by combined use of laser-microdissection, degenerate oligonucleotide primed PCR and comparative genomic hybridization." Virchows Archiv 433, no. 4 (1998): 297–304. http://dx.doi.org/10.1007/s004280050252.

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34

de Sá, Patricia B., Wendy M. Havens, and Said A. Ghabrial. "Characterization of a Novel Broad-Spectrum Antifungal Protein from Virus-Infected Helminthosporium (Cochliobolus) victoriae." Phytopathology® 100, no. 9 (2010): 880–89. http://dx.doi.org/10.1094/phyto-100-9-0880.

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A broad-spectrum anti-fungal protein of ≈10 kDa, designated victoriocin, was purified from culture filtrates of a virus-infected isolate of the plant-pathogenic fungus Helminthosporium victoriae (teleomorph: Cochliobolus victoriae) by a multistep procedure involving ultrafiltration and reverse-phase high-performance liquid chromatography (RP-HPLC). Amino acid sequences, obtained by automated Edman degradation sequencing of RP-HPLC-purified victoriocin-derived peptides, were used to design primers for degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) amplification from H. vi
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35

Willhoeft, Ute, Jutta Mueller-Navia, and Gerald Franz. "Analysis of the sex chromosomes of the Mediterranean fruit fly by microdissected DNA probes." Genome 41, no. 1 (1998): 74–78. http://dx.doi.org/10.1139/g97-102.

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In the Mediterranean fruit fly, Ceratitis capitata, the sex-determining region maps to the long arm of the Y chromosome. DNA from this region of the Y chromosome and, for comparison, from the tip of the long arm of the X chromosome, was isolated by microdissection and amplified by degenerate oligonucleotide primer PCR (DOP-PCR). FISH of the Y-chromosomal microdissection products medY1-medY5 to mitotic chromosomes revealed hybridization signals on most of the long arm of the Y chromosome, including the male-determining region, and on the long arm of the X chromosome, as well as weaker signals o
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36

Staiber, Wolfgang. "Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus." Genome 47, no. 4 (2004): 732–41. http://dx.doi.org/10.1139/g04-026.

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The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and
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37

Pereyra, L. P., S. R. Hiibel, M. V. Prieto Riquelme, K. F. Reardon, and A. Pruden. "Detection and Quantification of Functional Genes of Cellulose- Degrading, Fermentative, and Sulfate-Reducing Bacteria and Methanogenic Archaea." Applied and Environmental Microbiology 76, no. 7 (2010): 2192–202. http://dx.doi.org/10.1128/aem.01285-09.

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ABSTRACT Cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. Compared to the study of 16S rRNA genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. However, no methods are available for the broad quantification of these genes from uncultured microbes characteristic of complex environments. In this study, consensus degenerate hybrid oligonucleotide prime
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38

Kohout, T. A., and T. B. Rogers. "Use of a PCR-based method to characterize protein kinase C isoform expression in cardiac cells." American Journal of Physiology-Cell Physiology 264, no. 5 (1993): C1350—C1359. http://dx.doi.org/10.1152/ajpcell.1993.264.5.c1350.

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Molecular cloning has identified at least nine unique isozymes of protein kinase C (PKC) designated alpha, beta I, beta II, gamma, delta, epsilon, zeta, and eta/L, with the recent addition of the theta-isoform. Previous attempts to characterize PKC isoform expression in heart have been limited by low levels of protein and perhaps by the presence of novel isoforms. Thus to critically examine the diversity of PKC expression in cardiac cells, we developed a reverse transcriptase-polymerase chain reaction (RT-PCR) approach that would amplify regions of the target cDNA of all the PKC isozymes in a
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Aubele, Michaela, Margaret Cummings, Axel Walch, et al. "Heterogeneous Chromosomal Aberrations in Intraductal Breast Lesions Adjacent to Invasive Carcinoma." Analytical Cellular Pathology 20, no. 1 (2000): 17–24. http://dx.doi.org/10.1155/2000/930246.

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There is evidence that breast cancer is a heterogeneous disease phenotypically as well as molecular biologically. So far, heterogeneity on the molecular biological level has not been investigated in potential precursor lesions, such as ductal hyperplasia (DH) and ductal carcinomain situ(DCIS). In this study we applied comparative genomic hybridization (CGH) to formalin‐fixed, paraffin‐embedded breast tissue with DH and DCIS, adjacent to invasive ductal carcinoma (IDC), to screen these potential precursor lesions for whole genomic chromosomal imbalances. Laser‐microdissection was used to select
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40

Cooper, D. L., and E. W. Baptist. "Degenerate oligonucleotide sequence-directed cross-species PCR cloning of the BCP 54/ALDH 3 cDNA: priming from inverted repeats and formation of tandem primer arrays." Genome Research 1, no. 1 (1991): 57–62. http://dx.doi.org/10.1101/gr.1.1.57.

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41

Martin, R. R., and I. E. Tzanetakis. "First Report of Rosa multiflora cryptic virus in Rosa multiflora in the Eastern United States." Plant Disease 92, no. 12 (2008): 1706. http://dx.doi.org/10.1094/pdis-92-12-1706b.

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In the process of attempting to identify the rose rosette agent, double-stranded RNA was isolated from several symptomatic Rosa multiflora plants from northwestern Arkansas. The pattern of the dsRNA bands differed among the five samples used in this study, suggesting the presence of several viruses. Four of the five plants tested had two predominant bands of approximately 1.8 and 1.5 kbp, a pattern similar to that observed in plants infected with Fragaria chiloensis cryptic virus (FCCV; 3), and further steps were taken for the identification of the putative virus. One plant that only had the t
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Iserte, Javier Alonso, Betina Ines Stephan, Sandra Elizabeth Goñi, Cristina Silvia Borio, Pablo Daniel Ghiringhelli, and Mario Enrique Lozano. "Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides." Biotechnology Research International 2013 (February 21, 2013): 1–9. http://dx.doi.org/10.1155/2013/383646.

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Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus ( nucleotides), Baculovirus ( to bp), Lactobacillus sp. ( to bp), and Pseudomonas sp. ( to bp). In each case, F
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Pellegrin, F., D. Nandris, H. Chrestin, and N. Duran-Vila. "Rubber Tree (Hevea brasiliensis) Bark Necrosis Syndrome I: Still No Evidence of a Biotic Causal Agent." Plant Disease 88, no. 9 (2004): 1046. http://dx.doi.org/10.1094/pdis.2004.88.9.1046c.

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The main constraint in rubber plantations worldwide is the cessation of latex production because of two syndromes: (i) tapping panel dryness (TPD), a reversible physiological response to overexploitation; and (ii) bark necrosis (BN), an irreversible syndrome spreading from the collar toward the tapping cut. Early BN symptoms develop in the inner phloem tissues but never affect the cambium. Necrotic patches appear in the outer phloem, inducing bark cracking and peeling, but these alterations never lead to tree death. BN spreads gradually to neighboring rubber trees, and evidence of linear disea
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44

Broderick, Kevin, Christopher Pittock, Tony Arioli, Ernest H. Creaser, Jeremy J. Weinman, and Barry G. Rolfe. "Pathogenesis-Related Proteins in Trifolium subterraneum: A General Survey and Subsequent Characterisation of a Protein Inducible by Ethephon and Redlegged Earth Mite Attack." Functional Plant Biology 24, no. 6 (1997): 819. http://dx.doi.org/10.1071/pp97022.

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One of the chief predators of subterranean clover (Trifolium subterraneum) pastures is redlegged earth mite (Halotydeus destructor; RLEM). Subterranean clover pathogenesis-related (PR) proteins induced by RLEM attack and ethephon treatment were surveyed, and PR proteins with peroxidase, β-1,3-glucanase and chitinase activities were detected. A protein co-migrating with a chitinase activity, induced by RLEM predation and treatment with ethephon, was isolated. It was purified and the N-terminal amino acid sequence determined. Using a degenerate oligonucleotide primer designed from this sequence,
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Limansky, Adriana S., Emma G. Sutich, María C. Guardati, Inés E. Toresani, and Alejandro M. Viale. "Genomic Diversity amongStreptococcus agalactiaeIsolates Detected by a Degenerate Oligonucleotide‐Primed Amplification Assay." Journal of Infectious Diseases 177, no. 5 (1998): 1308–13. http://dx.doi.org/10.1086/515275.

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Sayada, Chalom, Bertrand Picard, Jacques Elion, and Rajagopal Krishnamoorthy. "Genomic fingerprinting ofYersinia enterocolitica species by degenerate oligonucleotide-primed polymerase chain reaction." Electrophoresis 15, no. 1 (1994): 562–65. http://dx.doi.org/10.1002/elps.1150150176.

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Yang, Wen-Ho, Jia-Rong Wu, Tong-Hong Wang, and Lo-Chun Au. "Methylation profiling using degenerated oligonucleotide primer–PCR specific for genome-wide amplification of bisulfite-modified DNA." Analytical Biochemistry 369, no. 1 (2007): 120–27. http://dx.doi.org/10.1016/j.ab.2007.06.017.

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Sanada, Masashi, Yasuhito Nanya, Akira Hangaishi, et al. "Array-Based Comparative Genomic Hybridization for Genome-Wide Analysis of DNA Copy Number in Myelodysplastic Syndromes." Blood 104, no. 11 (2004): 3420. http://dx.doi.org/10.1182/blood.v104.11.3420.3420.

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Abstract Myelodysplastic syndrome(MDS)is a clonal disorder of hematopoietic stem cells characterized by ineffective hematopoiesis and propensity to acute myeloid leukemias. The conversion of a normal stem cell into a preleukemic and ultimately leukemic state is thought to be a multistep process requiring accumulation of a number of genetic changes. Conventional cytogenetic analysis has disclosed a number of chromosome abnormalities common to MDS and provided valuable clues to characterize these genetic lesions, rarity of balanced translocations and relative predominance of unbalanced abnormali
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Pusch, Carsten M., Graeme J. Nicholson, Lutz Bachmann, and Michael Scholz. "Degenerate Oligonucleotide-Primed Preamplification of Ancient DNA Allows the Retrieval of Authentic DNA Sequences." Analytical Biochemistry 279, no. 1 (2000): 118–22. http://dx.doi.org/10.1006/abio.1999.4463.

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Gravitt, P. E., C. L. Peyton, T. Q. Alessi, et al. "Improved Amplification of Genital Human Papillomaviruses." Journal of Clinical Microbiology 38, no. 1 (2000): 357–61. http://dx.doi.org/10.1128/jcm.38.1.357-361.2000.

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ABSTRACT Genital human papillomaviruses (HPVs) are commonly detected from clinical samples by consensus PCR methods. Two commonly used primer systems, the MY09-MY11 (MY09/11) primers and the GP5+-GP6+ (GP5+/6+) primers, amplify a broad spectrum of HPV genotypes, but with various levels of sensitivity among the HPV types. Analysis of the primer-target sequence homology for the MY09/11 primers showed an association between inefficient amplification of HPV types and the number and position of mismatches, despite accommodation of sequence variation by inclusion of degenerate base sites. The MY09/1
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