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Journal articles on the topic 'Fragment restriction'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

WU, Z., I. NAGANO, E. POZIO, and Y. TAKAHASHI. "Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) for the identification of Trichinella isolates." Parasitology 118, no. 2 (February 1999): 211–18. http://dx.doi.org/10.1017/s0031182098003679.

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In the present study, polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis was developed to identify 5 species (Trichinella spiralis, Trichinella britovi, Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis) and 3 phenotypes of uncertain taxonomic status (Trichinella T5, T6, and T8). Eleven restriction endonucleases were used to restrict 3 DNA fragments (1) a 2800 bp fragment of the 43 kDa excretory–secretory (E–S) protein gene, (2) a 1250 bp fragment amplified with the primer pair SB147A and (3) a 372 bp fragment amplified with the primer pair SB372A. This RFLP method allows the identification of the 8 Trichinella phenotypes as follows: T. spiralis by the HinfI or DdeI endonuclease restriction of the 2800 bp fragment; T. nativa by the RsaI restriction of the 2800 bp fragment, or by the AluI restriction of the 1250 bp fragment; T. britovi and Trichinella T8 by the AluI restriction of the 1250 bp fragments, and can be discriminated between them by the SspI restriction of the 2800 bp fragment; T. pseudospiralis by the MspI restriction of the 372 bp fragment; T. nelsoni by the HhaI or AluI restriction of the 2800 bp fragment; Trichinella T5 by the HhaI restriction of the 2800 bp fragment; Trichinella T6 by the AluI restriction of the 1250 bp fragment; and Trichinella T8 by the SspI or RsaI restriction of the 2800 bp fragment. This study reveals also an intraspecifies polymorphism in the 2800 bp and 1250 bp fragments for T. britovi, Trichinella T5 and T6.

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2

Hall, Lucinda M. C., and Brigid Duke. "Conservation of Restriction Sites in Isolates ofStreptococcus pneumoniae with Diverse Restriction Fragment Patterns." Journal of Clinical Microbiology 36, no. 6 (1998): 1805–7. http://dx.doi.org/10.1128/jcm.36.6.1805-1807.1998.

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Separation of large restriction fragments by pulsed-field gel electrophoresis is a commonly used method for epidemiological typing ofStreptococcus pneumoniae and many other bacterial species. Information on the genetic changes underlying the restriction fragment polymorphisms that allow discrimination between isolates is scarce. In this study fragments adjacent to ApaI sites in a clinical isolate of S. pneumoniae were cloned and used to probeHindIII and HindIII-plus-ApaI genomic DNA digests from other isolates with very differentApaI fragment patterns. If for a given isolate theHindIII fragment detected by the probe was reduced in size on digestion with ApaI, it was deduced that theApaI site was conserved in that isolate. The results demonstrate that of six ApaI sites in PN93/908 examined, five were retained in 11 genetically different isolates and one was retained in 2 isolates but lost in 9 others. It was concluded that point mutations at restriction sites are unlikely to account for the restriction fragment length polymorphism observed and that much of the polymorphism may be due to DNA rearrangements, possibly resulting from the insertion or deletion of mobile DNA elements.

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3

Bobola, Michael S., Robert T. Eckert, and Anita S. Klein. "Restriction fragment variation in the nuclear ribosomal DNA repeat unit within and between Picearubens and Piceamariana." Canadian Journal of Forest Research 22, no. 2 (February 1, 1992): 255–63. http://dx.doi.org/10.1139/x92-033.

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The frequencies of polymorphic restriction fragments for the nuclear ribosomal DNA repeat were compared for 12 provenances of red spruce (Picearubens Sarg.) and 34 provenances of black spruce (Piceamariana (Mill.) B.S.P.). Within an individual as many as five distinct ribosomal DNA repeat unit types could be distinguished. Canonical correlation analysis revealed significant variation of restriction fragment frequencies with a geographic variate comprising latitude and longitude of provenances. Geographic origins accounted for 24.7% of the variation in polymorphic restriction fragments in black spruce and 31.8% of the variation in polymorphic restriction fragments in red spruce. Discriminant analysis, using the restriction fragment frequencies for the ribosomal DNA, was used to develop a classification model for the two species. Tenfold verification of the model produced an average correct classification of 99% for black spruce and 96% for red spruce. Plots of canonical scores for the first and second canonical variâtes clearly separated red spruce from black spruce. This study presents a novel combination of restriction fragment frequency data and multivariate analysis to distinguish species that may not always be differentiated using morphological traits.

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4

Moore, Patrick P. "CHLOROPLAST RESTRICTION FRAGMENT VARIABILITY IN RASPBERRY." HortScience 25, no. 9 (September 1990): 1159f—1159. http://dx.doi.org/10.21273/hortsci.25.9.1159f.

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Cultivated raspberries may include North American red raspberry (Rubus idaeus strigosus Michx), European red raspberry (R. idaeus vulgatus Arrhen.) or black raspberry (R. occidentalis in their pedigrees. Twenty-one raspberry clones were investigated using chloroplast restriction fragment length polymorphisms to determine the cytoplasm type and the amount of cytoplasmic diversity among these selected clones. The raspberry clones were selected representing North American red raspberry, European red raspberry, black raspberry and cultivars with divergent maternal lineages. Total cellular DNA was probed with two 32P-labelled fragments of tomato chloroplast DNA. Probe-restriction enzyme combinations were selected which discriminated between representatives of the two red raspberry subspecies. Raspberry clones were grouped according to the chloroplast restriction fragment patterns. The composition of the groups was compared with their pedigrees.

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5

Fani, Renato, Marco Bazzicalupo, Enzo Gallori, Luciana Giovannetti, Stefano Ventura, and Mario Polsinelli. "Restriction fragment length polymorphism ofAzospirillumstrains." FEMS Microbiology Letters 83, no. 2 (October 1991): 225–29. http://dx.doi.org/10.1111/j.1574-6968.1991.tb04444.x-i1.

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6

Williams, Robert C. "Restriction fragment length polymorphism (RFLP)." American Journal of Physical Anthropology 32, S10 (1989): 159–84. http://dx.doi.org/10.1002/ajpa.1330320508.

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7

Jarcho, John. "Restriction Fragment Length Polymorphism Analysis." Current Protocols in Human Genetics 1, no. 1 (May 1994): 2.7.1–2.7.15. http://dx.doi.org/10.1002/0471142905.hg0207s01.

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8

Chowdhury, SMZH, AR Omar, A. Ideris, H. Bejo, and AA Jamaluddin. "Restriction endonuclease analysis of the genomes of different isolates of chicken anemia virus amplified by polymerase chain reaction." SAARC Journal of Agriculture 15, no. 2 (January 25, 2018): 1–18. http://dx.doi.org/10.3329/sja.v15i2.35155.

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Four DNA fragments (fragments A, B, C and D) covering the whole genome of chicken anemia virus (CAV) were amplified enzymatically by polymerase chain reaction (PCR) using four pairs of oligonucleotide primers. The DNA fragments were amplified from each of nine CAV isolates including eight Malaysian isolates and one European isolate (Cux-1). For all nine CAV isolates, fragment A (1518 bp) was digested with one restriction enzyme, Eco130I (StyI); fragment B (926 bp) with three enzymes, Eco130I (StyI), HpaII and MboI separately; fragment C (675 bp) with also three enzymes, BsuRI (HaeIII), HinfI, and HpaII separately; and the fragment D (552 bp) with one enzyme, EcoRI. Enzyme digested products of different fragments were separated by agarose gel or polyacrylamide gel electrophoresis. Each of the eightenzymatic reactions differentiated at least two isolates except the HpaII digestion of fragment C where no isolate was distinguished. The overall restriction endonuclease (RE) analysis separated four isolates (BL-1, BL- 2, BL-4 and BL-5) in one group and the rest five isolates (SMSC-1, SMSC-2, 3-1, BL-3 and Cux-1) were differentiated from each other and also from the group of four isolates, based on the number of restriction site differences and the fragments generated by different enzymatic digestions. The study revealed that RE analysis could be used to identify and differentiate CAV isolates based on the number of restriction site differences. The study showed that more isolates, even the isolates from the same poultry farm, could be differentiated with proper genomic diversity after RE analysis of more genome fragments compared to that of single genome fragment.SAARC J. Agri., 15(2): 1-18 (2017)

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9

Curran, J., D. L. Baillie, and J. M. Webster. "Use of genomic DNA restriction fragment length differences to identify nematode species." Parasitology 90, no. 1 (February 1985): 137–44. http://dx.doi.org/10.1017/s0031182000049088.

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Restriction endonuclease digestion of genomic DNA generates DNA fragments of unique size, dependent upon the particular base sequence. Following fractionation by agarose gel electrophoresis, repetitive DNA can be visualized as distinct bands in stained gels and the restriction fragment length of such bands used as diagnostic characters. Restriction fragment length differences were detected between species within the genera Trichinella, Caenorhabditis, Romanomermis, Steinernema (syn. Neoaplectana) and Meloidogyne. This technique provides a new tool for the taxonomist, which is independent of phenotypic variation and it enables the rapid and reliable separation of closely related species.

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10

Traut, W. "Hypervariable Bkm DNA Loci in a Moth, Ephestia kuehniella : Does Transposition Cause Restriction Fragment Length Polymorphism?" Genetics 115, no. 3 (March 1, 1987): 493–98. http://dx.doi.org/10.1093/genetics/115.3.493.

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ABSTRACT Bkm sequences, originally isolated from snake satellite DNA, are a component of eukaryote genomes with a preferential location on sex chromosomes. In the Ephestia genome, owing to the presence of only a few Bkm-positive BamHI restriction fragments and to extensive restriction fragment length polymorphisms between and within inbred strains, a genetic crossbreeding analysis was feasible. No sex linkage of Bkm was detected. Instead-depending on the strain-two or three autosomal Bkm DNA loci were identified. All three loci were located on different chromosomes. Fragment length and transmission of fragments was stable in some crosses. In others, changes in fragment length or loss of the Bkm component were observed, probably depending on the source strain of the fragment. The anomalous genetic behaviour is best accounted for by the assumption that Bkm sequences are included in mobile genetic elements.

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11

Matsuura, T., G. Bylund, and K. Sugane. "Comparison of restriction fragment length polymorphisms of ribosomal DNA between Diphyllobothrium nihonkaiense and D. latum." Journal of Helminthology 66, no. 4 (December 1992): 261–66. http://dx.doi.org/10.1017/s0022149x00014693.

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ABSTRACTRestriction fragment length polymorphisms (RFLPs) of ribosomal DNA (rDNA) were compared between Diphyllobothrium latum and D. nihonkaiense using seven kinds of restriction endonucleases. No intra-specific variation in restriction fragment profiles was shown within both species of Diphyllobothrium. Digestion of the genomic DNA with three endonucleases, Smal, Hinfl and Hhal, provided one or two different bands between two species, although the hybridization patterns generated with the others, Hindlll, Xbal, Styl and Haelll, were the same in both. RFLPs in the digested profiles with Smal, Hinfl and Hhal could be used as species-specific markers even if only fragments of strobilae with morphological similarity were available. Other cestodes, Spirometra erinacei and Taenia saginata, used as controls showed quite different restriction fragment patterns with all the enzymes used.

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12

Wilson, J. G., E. E. Murphy, W. W. Wong, L. B. Klickstein, J. H. Weis, and D. T. Fearon. "Identification of a restriction fragment length polymorphism by a CR1 cDNA that correlates with the number of CR1 on erythrocytes." Journal of Experimental Medicine 164, no. 1 (July 1, 1986): 50–59. http://dx.doi.org/10.1084/jem.164.1.50.

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A genetic basis for the regulation of the number of CR1 on E of different normal individuals was investigated by probing Southern blots of their genomic DNA with a 0.75-kb fragment of CR1 cDNA. Using Hind III, we observed a RFLP involving fragments of 7.4 kb and 6.9 kb that correlated with the number of CR1 on E. 32 individuals having only the 7.4-kb restriction fragment had a mean of 661 +/- 33 (SEM) CR1/E, 11 donors having both restriction fragments had a mean of 455 +/- 52 CR1/E, and 7 individuals having only the 6.9-kb fragment had a mean of 156 +/- 13 CR1/E, all means being significantly different (p less than 0.005). Cosegregation in a normal family of the Hind III restriction fragments with the S, F, and F' structural allotypes of CR1 confirmed that the regulatory element identified by these fragments is linked to the CR1 gene. Moreover, an analysis of the relative expression on E of these structural allotypes in association with either the 7.4-kb Hind III fragment or the 6.9-kb fragment showed that this regulatory element is cis-acting. In contrast, quantitation of CR1 of B lymphocytes and neutrophils revealed no differences in total CR1 expression between individuals homozygous for the 7.4-kb and 6.9-kb Hind III fragments. Thus, we have identified a genomic polymorphism that is linked to the CR1 gene and is associated with a cis-acting regulatory element for the expression of CR1 on E.

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13

Sugane, Kazuo, Liu Qing, and Tadashi Matsuura. "Restriction fragment length polymorphisms of Anisakinae larvae." Journal of Helminthology 63, no. 4 (December 1989): 269–74. http://dx.doi.org/10.1017/s0022149x00009123.

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ABSTRACTThe analysis of restriction fragment length polymorphisms (RFLPs) was applied to distinguish several kinds of Anisakinae larvae, Anisakis larvae (type I) collected from two different paratenic hosts, Anisakis larvae (type II) and Contracaecum larvae. The patterns of the two different paratenic host-derived DNA of Anisakis larva (I) were exactly the same in hybridized fragments generated by six endonucleases. The quite different patterns in RFLPs of genomic DNA were observed among the Anisakis larva (I), Anisakis larva (II) and Contracaecum larvae. The results suggest that the RFLPs analysis may be useful for distinguishing Anisakinae larvae and clarifying the relationships between Anisakis larvae and their adult worms.

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14

Skow, Loren C., Joseph N. Nadeau, Jong Cheol Ahn, Hee-Sup Shin, Karen Artzt, and Dorothea Bennett. "Polymorphism and Linkage of the αA-Crystallin Gene in t-Haplotypes of the Mouse." Genetics 116, no. 1 (May 1, 1987): 107–11. http://dx.doi.org/10.1093/genetics/116.1.107.

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ABSTRACT Restriction fragment polymorphisms were used to order the αA-crystallin locus (Crya-1) relative to other genes in mouse t-chromatin and to investigate the relatedness of α-A-crystallin sequences among different t-haplotypes. Analysis of DNA from t-recombinant mice mapped Crya-1 to the K end of the H-2 complex and within the distal inverted region characteristic of t-haplotypes. Hybridization with Crya-1 cDNA revealed three distinct phenotypic groups among the 17 different t-haplotypes studied. A majority (9 of 17) of the t-haplotypes were classified into a novel group (Crya-1t) characterized by restriction fragments apparently unique to t-chromosomes and therefore thought to contain αA-crystallin sequences descended from the original t-chromosome. A second group of t-haplotypes had restriction fragment patterns indistinguishable from those observed among many common inbred strains of mice of the Crya-1a type, and a third restriction fragment pattern, observed only in the tw121 haplotype, was indistinguishable from the fragment pattern for C3H/DiSn (Crya-1b) and several other inbred strains of mice. Thus, with respect to sequences around the Crya-1 locus, different t-haplotypes show restriction fragment polymorphisms, some of which are comparable to those found in wild-type chromosomes and provide further evidence for genetic heterogeneity in DNA from the distal region of t-haplotypes.

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15

Straus, Steven H., and Allan H. Doerksen. "Restriction Fragment Analysis of Pine Phylogeny." Evolution 44, no. 4 (July 1990): 1081. http://dx.doi.org/10.2307/2409568.

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16

Strauss, Steven H., and Allan H. Doerksen. "RESTRICTION FRAGMENT ANALYSIS OF PINE PHYLOGENY." Evolution 44, no. 4 (July 1990): 1081–96. http://dx.doi.org/10.1111/j.1558-5646.1990.tb03827.x.

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17

SIEGEL, ANDREW F., JARED C. ROACH, CHARLES MAGNESS, ED THAYER, and GER VAN DEN ENGH. "Optimization of Restriction Fragment DNA Mapping." Journal of Computational Biology 5, no. 1 (January 1998): 113–26. http://dx.doi.org/10.1089/cmb.1998.5.113.

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18

MacMurray, Armand. "DIGICALC: a restriction fragment analysis program." Nucleic Acids Research 14, no. 1 (1986): 529–36. http://dx.doi.org/10.1093/nar/14.1.529.

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19

Singh, Brajesh K., and Nadine Thomas. "Multiplex-terminal restriction fragment length polymorphism." Nature Protocols 1, no. 5 (December 2006): 2428–33. http://dx.doi.org/10.1038/nprot.2006.392.

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20

Chen, Liang Zhong, and Simon Easteal. "Renin locus restriction fragment length polymorphism." Human Genetics 82, no. 3 (June 1989): 302. http://dx.doi.org/10.1007/bf00291180.

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21

Messick, Joanne B., Geoffrey Smith, Linda Berent, and Sandra Cooper. "Genome size ofEperythrozoon suisand hybridization with 16S rRNA gene." Canadian Journal of Microbiology 46, no. 11 (November 1, 2000): 1082–86. http://dx.doi.org/10.1139/w00-088.

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The genome size of Eperythrozoon suis, an unculturable haemotropic mycoplasma, was estimated using pulsed-field gel electrophoresis (PFGE). Gamma irradiation was used to introduce one (on the average) double-strand break in the E. suis Illinois chromosome. Restriction enzymes that cut infrequently were also used to analyze genome size. The size estimate for the full-length genome was 745 kilobases (kb), whereas the size estimates based on the summation of restriction fragments ranged from 730 to 770 kb. The 16S rRNA gene was located on the 120-kb MluI fragment, 128-kb NruI fragment, 25-kb SacII fragment, and 217-kb SalI fragment by Southern blotting.Key words: Eperythrozoon suis, 16S rRNA, Mycoplasma pneumoniae group, pulsed-field gel electrophoresis, genome size.

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22

Hubbard, Mark, John Kelly, Sriyani Rajapakse, Robert Ballard, and Albert Abbott. "PRELIMINARY RESULTS OF PHYLOGENETIC STUDIES WITHIN THE GENUS ROSA (ROSACEAE)." HortScience 25, no. 9 (September 1990): 1159c—1159. http://dx.doi.org/10.21273/hortsci.25.9.1159c.

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We have initiated a phylogenetic study using restriction fragment length polymorphisms to examine nuclear DNA variation in a number of Rosa species. Random genomic clones were isolated from the cultivar `Confection'. To generate these clones, genomic DNA was digested with the restriction enzymes Hind III and Eco RI and the resulting fragments cloned into a pUC8 plasmid and transformed into the E. coli bacterial strain JM83. Individual clones from the DNA library were screened for polymorphism by Southern hybridization methods. Those clones displaying polymorphisms were used in combination with one, two, or three restriction enzymes to identify different size restriction fragments. Each fragment was treated as a unit character and was used to generate a phylogenetic tree using the computer program “Phylogenetic Analysis Using Parsimony” (PAUP version 3.0). Results of the studies on the amount of genetic diversity and phylogenetic affinities of Rosa species among the different sections of the subgenus Rosa will be presented.

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23

Winkelmann, Dianne C., Laura D. Querengesser, and Ross B. Hodgetts. "Growth hormone restriction fragment length polymorphisms that segregate with 42-day live weight of mice." Genome 33, no. 2 (April 1, 1990): 235–39. http://dx.doi.org/10.1139/g90-037.

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The known correlation between growth hormone levels and growth rate in a number of species prompted us to examine if polymorphic restriction fragment alleles at the growth hormone locus in mice might be associated with differentiable rates of growth. An F2 population of mice was generated from crosses between a line selected for high 42-day weight and an unselected control line. The original selected and control lines exhibited mean 42-day weights of 30.6 ± 3.8 and 20.5 ± 2.6 g, respectively. Since the two lines also differed with respect to the restriction fragments detected by hybridization to a rat growth hormone cDNA probe, an analysis of the F2 generation was carried out to determine whether this polymorphism could be considered a quantitative trait locus for 42-day weight. The results of the analysis indicated that a polymorphic HindIII restriction fragment was correlated (P < 0.05) with 42-day weight. However, the allele that was positively correlated with weight was the one that was fixed in the original control line, rather than the one from the selected line. While these findings support the potential use of restriction fragment length polymorphisms in quantitative trait evaluation of livestock, they also emphasize the requirement for testing such potential quantitative trait loci in the appropriate genetic background.Key words: mice, growth rate, quantitative trait loci, restriction fragment length polymorphism.

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24

Rahayu, Sri, Sutiman Bambang Sumitro, T. Susilawati, and Soemarno Soemarno. "IDENTIFIKASI POLIMORFISME GEN GH (GROWTH HORMONE) SAPI BALI DENGAN METODE PCR-RFLP." Berkala Penelitian Hayati 12, no. 1 (December 31, 2006): 7–11. http://dx.doi.org/10.23869/bphjbr.12.1.20062.

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This study was conducted to identify polymorphism of growth hormone gene of Bali cattle. A PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) procedure was developed for determining polymorphism of growth hormone gene. The DNA was isolated from blood samples by salting out method. Total DNA were amplified with forward primer, 5’-TAGGGGAGGGTGGAAAATGGA-3’ and reverse primer, 5’-GACACCTACTCAGACAATGCG-3’. The PCR product was digested by HaeIII restriction enzyme. Result of the amplification was a specific single band with fragment 450 bp. Restriction with HaeIII restriction enzyme resulted four kinds of haplotype. Haplotype I was not cut by HaeIII restriction enzyme. Haplotype II were cut into two, 225 bp and 150 bp,. Haplotype III were cut into three size, 400 bp, 225 bp and 150 bp. Haplotype IV were cut into five fragments 450 bp, 400 bp, 275 bp, 225 bp and 150 bp.

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25

Gillet, Elizabeth M. "Genetic analysis of nuclear DNA restriction fragment patterns." Genome 34, no. 5 (October 1, 1991): 693–703. http://dx.doi.org/10.1139/g91-107.

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Restriction fragment length polymorphism (RFLP) analysis in the broad sense is the analysis of differences in restriction fragment pattern produced by defined target segments within or between cell compartments, cell types, etc., in a single individual or in different individuals. Thus both molecular hybridization and DNA amplification by two-primer extension using the polymerase chain reaction can define target segments for RFLP analysis. The two techniques are outlined with special consideration of characteristics important for genetic analysis. The mode of inheritance of restriction fragment patterns as a prerequisite for their use as genetic markers in inheritance studies is explained, leading to criticism of common usage. The importance of internal restriction sites for the determination of allelic variation is stressed. It is shown that, if target segments are under the control of a single nuclear diploid restriction fragment locus, then complete reconstruction of all parental target segments requires controlled crosses between individuals of like restriction fragment pattern.Key words: genetic analysis, inheritance, restriction fragment length polymorphism, controlled cross, polymerase chain reaction.

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26

Desrosiers, B., J. M. Sévigny, and J. P. Chanut. "Restriction fragment length polymorphism of rDNA in the redfishes Sebastes fasciatus and S. mentella (Scorpaenidae) from the Gulf of St. Lawrence." Canadian Journal of Zoology 77, no. 2 (August 1, 1999): 267–77. http://dx.doi.org/10.1139/z98-208.

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A restriction fragment length polymorphism (RFLP) analysis was carried out on nuclear ribosomal DNA (rDNA) of the redfishes Sebastes fasciatus and Sebastes mentella from the Gulf of St. Lawrence in an attempt to describe new molecular markers that would discriminate these two sibling species. The RFLP analysis revealed heterogeneity in the size of the repeat unit within and among individuals that is most likely the result of variation in the length of the intergenic spacer. Double digestion of rDNA with the restriction enzymes EcoRI and ScaI and subsequent hybridization with a 28S probe revealed the presence of three patterns of fragments. Two fragment groups seem to characterize S. mentella and S. fasciatus. Both fragment groups were present in several specimens, suggesting either a restriction-site polymorphism in S. mentella or a hybrid origin for these redfish. Discriminant analysis clearly differentiated all three rDNA patterns. Comparisons of genetic variations at the MDH* locus and of the number of soft rays in the anal fin among the three rDNA-defined groups suggest that if the individuals showing the two groups of fragments are hybrids between S. fasciatus and S. mentella, introgression has also occurred in the Gulf of St. Lawrence.

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27

Sheldon, E., D. E. Kellogg, C. Levenson, W. Bloch, L. Aldwin, D. Birch, R. Goodson, P. Sheridan, G. Horn, and R. Watson. "Nonisotopic M13 probes for detecting the beta-globin gene: application to diagnosis of sickle cell anemia." Clinical Chemistry 33, no. 8 (August 1, 1987): 1368–71. http://dx.doi.org/10.1093/clinchem/33.8.1368.

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Abstract M13 DNA probes labeled with biotinylated psoralen and a streptavidin-horseradish peroxidase conjugate provide nonradioactive detection of the sickle cell and normal alleles of the beta-globin locus. The two biotinylated probes contain single-stranded sequences complementary to two different Sau3AI restriction fragments from the 5' region of the beta-globin gene and double-stranded M13 vector sequences. These probes are labeled with biotinylated psoralen photochemically linked to DNA. After hybridization, the presence of biotinylated probe bound to target DNA is detected in 3 h by using a streptavidin-horseradish peroxidase conjugate and the substrate, 3,3',5,5'-tetramethylbenzidine. Digestion of the normal (beta A) allele of the beta-globin gene with MstII (or isoschizomers) yields a 1.14-kb restriction fragment, while digestion of the mutant beta S allele yields a 1.34-kb fragment. These fragments can be resolved by gel electrophoresis and detected by Southern blot hybridization. The nonradioisotopic probe system can detect the beta-globin restriction fragment in as little as 0.5 microgram of human DNA and can distinguish heterozygotes (beta A beta S) from homozygotes (beta A beta A or beta S beta S) in 2.0 micrograms of human DNA.

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28

Giebler, Julia, Lukas Y. Wick, Michael Schloter, Hauke Harms, and Antonis Chatzinotas. "Evaluating the Assignment ofalkBTerminal Restriction Fragments and Sequence Types to Distinct Bacterial Taxa." Applied and Environmental Microbiology 79, no. 9 (March 1, 2013): 3129–32. http://dx.doi.org/10.1128/aem.04028-12.

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ABSTRACTSequence and terminal restriction fragment length polymorphism (T-RFLP) analyses revealed multiplealkBgene copies/cell in soil bacterial isolates and an apparently high genetic mobility among various phylogenetic groups. Identifying alkane degraders byalkBterminal restriction fragments (T-RFs) and sequences is strongly biased, as the phylogenetic trees based on 16S rRNA andalkBgene sequences were highly inconsistent.

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29

Prince, James P., Fernando Loaiza-Figueroa, and Steven D. Tanksley. "Restriction fragment length polymorphism and genetic distance among Mexican accessions of Capsicum." Genome 35, no. 5 (October 1, 1992): 726–32. http://dx.doi.org/10.1139/g92-112.

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Restriction fragment length polymorphism analysis was performed on 25 accessions of pepper (Capsicum sp.) from various regions of Mexico and on the two parents currently in use for molecular mapping. The fragments detected were used to estimate genetic distances among the accessions. A dendrogram from cluster analysis and a principal component analysis diagram of the genetic distance matrix are presented. The correlation between genetic distances measured by restriction fragment length polymorphism versus genetic distances measured by isozymes is good (R2 = 0.438, p = 0.0001). All but four accessions could be differentiated with the 10 most polymorphic clones examined. Crosses were made between each of our two mapping parents and the Mexican accessions as well as among many of the Mexican accessions. F1 pollen stainability data were taken to estimate the fertility of each cross. This information along with the genetic distance data is used to select polymorphic but interfertile parents for future restriction fragment length polymorphism mapping in pepper.Key words: pepper, cluster analysis, isozyme-RFLP correlation, DNA fingerprinting.

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30

Neale, David B., Nicholas C. Wheeler, and Robert W. Allard. "Paternal inheritance of chloroplast DNA in Douglas-fir." Canadian Journal of Forest Research 16, no. 5 (October 1, 1986): 1152–54. http://dx.doi.org/10.1139/x86-205.

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The inheritance of chloroplast DNA in Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) was determined using a restriction fragment length polymorphism (RFLP) as a marker. An insertion/deletion sequence homologous to a 15.3 kilobase PstI fragment from petunia chloroplast DNA was detected in SmaI and BamHI digests of total DNAs of parent trees. Full-sib progeny (36 in total) were then assayed for this polymorphism in three sets of crosses between male and female parents with different RFLP markers. The full-sib progeny had the same restriction fragment as the male parent, with three exceptions. These data provide direct evidence for the paternal inheritance of chloroplast DNA in a gymnosperm. This result is in sharp contrast to the strict maternal and occasional biparental inheritance of chloroplast DNA observed in angiosperms. The three exceptions had restriction fragments unlike either the male or female parents of the cross, suggesting that some type of mutational or recombinational event had occurred during the transmission of these genomes.

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31

Loomis, W. F., D. Welker, J. Hughes, D. Maghakian, and A. Kuspa. "Integrated maps of the chromosomes in Dictyostelium discoideum." Genetics 141, no. 1 (September 1, 1995): 147–57. http://dx.doi.org/10.1093/genetics/141.1.147.

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Abstract Detailed maps of the six chromosomes that carry the genes of Dictyostelium discoideum were constructed by correlating physically mapped regions with parasexually determined linkage groups. Chromosomally assigned regions were ordered and positioned by the pattern of altered fragment sizes seen in a set of restriction enzyme mediated integration-restriction fragment length polymorphism (REMI-RFLP) strains each harboring an inserted plasmid that carries sites recognized by NotI, SstI, SmaI, BglI and ApaI. These restriction enzymes were used to digest high molecular weight DNA prepared from more than 100 REMI-RFLP strains and the resulting fragments were separated and sized by pulsed-field gels. More than 150 gene probes were hybridized to blots of these gels and used to map the insertion sites relative to flanking restriction sites. In this way, we have been able to restriction map the 35 mb genome as well as determine the map position of more than 150 genes to with approximately 40 kb resolution. These maps provide a framework for subsequent refinement.

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32

Haertl, Rolf, and Gert Bandlow. "Genotyping ofStaphylococcus epidermidisby Small-Fragment Restriction Endonuclease Analysis and Pulsed-Field Gel Electrophoresis of Genomic Restriction Fragments." Microbiology and Immunology 38, no. 7 (July 1994): 527–34. http://dx.doi.org/10.1111/j.1348-0421.1994.tb01818.x.

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33

Ricke, Peter, Steffen Kolb, and Gesche Braker. "Application of a Newly Developed ARB Software-Integrated Tool for In Silico Terminal Restriction Fragment Length Polymorphism Analysis Reveals the Dominance of a Novel pmoA Cluster in a Forest Soil." Applied and Environmental Microbiology 71, no. 3 (March 2005): 1671–73. http://dx.doi.org/10.1128/aem.71.3.1671-1673.2005.

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ABSTRACT TRF-CUT, an ARB-implemented tool, was developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. Application of this new tool to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil revealed that novel cluster I methanotrophic bacteria were dominant.

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34

Rajapakse, Sriyani, Mark Hubbard, Albert Abbott, Robert Ballard, and John Kelly. "IDENTIFICATION OF ROSE CULTIVARS BY RESTRICTION FRAGMENT LENGTH POLYMORPHISMS." HortScience 26, no. 5 (May 1991): 484b—484. http://dx.doi.org/10.21273/hortsci.26.5.484b.

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Restriction Fragment Length Polymorphisms (RFLPs) were investigated in rose cultivars as a means of reliable cultivar identification. A random genomic DNA library was generated by shotgun cloning HindIII digested fragments of DNA extracted from rose cultivar Confection into pUC8 plasmid of Escherichia coli strain JM 83. Compared to genomic clones carrying low or highly repeated sequences, clones with moderately repeated sequences were most effective in cultivar identification. These clones were identified by hybridizing rose DNA fragments from the library with genomic DNA from `Confection'. Clones with moderately repeated copy sequences were used as probes to detect the presence of RFLPs by Southern hybridization of EcoRI digested genomic DNA of various rose cultivars. Several of these probes have revealed RFLPs useful in cultivar identification. By using a combination of two or more of these probes most of the rose cultivars compared at this time can be identified. A dichotomous key useful in identification of rose cultivars was prepared from RFLPs displayed by 3A9 probe.

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35

Bishop, R. P., B. K. Sohanpal, B. A. Allsopp, P. R. Spooner, T. T. Dolan, and S. P. Morzaria. "Detection of polymorphisms among Theileria parva stocks using repetitive, telomeric and ribosomal DNA probes and anti-schizont monoclonal antibodies." Parasitology 107, no. 1 (July 1993): 19–31. http://dx.doi.org/10.1017/s0031182000079361.

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SummaryA total of 21 Theileria parva stocks from 6 countries were characterized using T. parva repetitive and ribosomal DNA probes, a Plasmodium berghei telomeric oligonucleotide and a panel of anti-schizont monoclonal antibodies (MAbs). Hybridization of the repetitive DNA probe to Southern blots of EcoRI-digested T. parva DNA revealed 20 different restriction fragment patterns among DNA samples isolated from infections initiated using 16 parasite stocks. The panel of anti-schizont MAbs defined 8 different profiles among schizont-infected lymphoblastoid cell-cultures infected with the same 16 T. parva stocks. Many stocks, which were differentiated by the repetitive DNA probe, could not be distinguished using the anti-schizont MAbs. A cloned T. parva small subunit ribosomal RNA (SSUrRNA) gene probe separated 17 T. parva stocks into 2 groups, exhibiting either 1 or 2 restriction fragments, when hybridized to EcoRI-digested T. parva DNA. When hybridized to PvuII-digested DNA from 8 T. parva stocks, the ribosomal probe identified 4 groups with similar restriction fragment patterns. A synthetic oligonucleotide derived from a P. berghei telomeric sequence hybridized to 7 or 8 size-polymorphic restriction fragments in the EcoRI-digested DNA of most T. parva stocks. The telomeric and ribosomal probes defined the same 4 groups among 8 T. parva stocks as assessed by similarities in restriction fragment patterns. Based on the comparison of repetitive DNA sequences from the T. parva Uganda and Muguga stocks, a synthetic oligonucleotide was developed which distinguished the DNA of the T. parva Uganda stock from that of 4 other T. parva stocks on a positive/negative basis.

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36

Donnison, Iain S., Jiri Siroky, Boris Vyskot, Heinz Saedler, and Sarah R. Grant. "Isolation of Y Chromosome-Specific Sequences From Silene latifolia and Mapping of Male Sex-Determining Genes Using Representational Difference Analysis." Genetics 144, no. 4 (December 1, 1996): 1893–901. http://dx.doi.org/10.1093/genetics/144.4.1893.

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The genomic subtraction method representational difference analysis (RDA) was used to identify male-specific restriction fragments in the dioecious plant Silene latifolia. Male-specific restriction fragments are linked to the male sex chromosome (the Y chromosome). Four RDA-derived male-specific restriction fragments were used to identify polymorphisms in a collection of X-ray-generated mutant plants with either hermaphroditic or asexual flowers. Some of the mutants have cytologically detectable deletions in the Y chromosome that were correlated with loss of male-specific restriction fragments. One RDA-derived probe detected a restriction fragment present in all mutants, indicating that each has retained Y chromosomal DNA. The other three probes detected genomic fragments that were linked in a region deleted in some hermaphroditic and some asexual mutants. Based on the mutant phenotypes and the correlation of cytologically visible deletions with loss of male-specific restriction fragments, these markers were assigned to positions on the Y chromosome close to the carpel suppression locus. This RDA mapping also revealed a Y-linked locus, not previously described, which is responsible for early stamen development.

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37

Simpson, June. "Amplified fragment length polymorphisms (AFLP's)." Botanical Sciences, no. 60 (May 2, 2017): 119. http://dx.doi.org/10.17129/botsci.1524.

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AFLP is a combination restriction fragment/PCR molecular marker technique which detects polymorphisms due to changes at or in the vicinity of restriction enzyme sites. The technique detects multiple polymorphic loci throughout the genome and may be used for fingerprinting and mapping purposes. The main advantages of the method are the consistency and reliability of the technique due to stringent PCR conditions and the ability to rapidly detect many polymorphic loci.

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38

Guo, J. H., D. Z. Skinner, and G. H. Liang. "Phylogenetic relationships of sorghum taxa inferred from mitochondrial DNA restriction fragment analysis." Genome 39, no. 5 (October 1, 1996): 1027–34. http://dx.doi.org/10.1139/g96-128.

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To elucidate the evolutionary history and affinity of sorghum species, 41 sorghum taxa were analyzed using variability in mitochondrial DNA. Analysis of species relationships at the molecular level can provide additional data to supplement the existing classification based on morphological characters and may also furnish unexpected but useful information. Total DNA extracted from each of the sorghum accessions was digested with each of five restriction enzymes, BamHI, HindIII, EcoRI, EcoRV, and XbaI, and probed with five mitochondrial DNAs cloned from Sorghumbicolor. A total of 180 restriction fragments was detected by the 25 probe–enzyme combinations. Forty-three fragment bands were phylogenetically informative. Multiple correspondence analysis was performed to visualize associations among the accessions and suggested that section Eusorghum species may be divided into four groups, with Sorghumlaxiflorum (section Heterosorghum) and Sorghumnitidum (section Parasorghum) appearing as outliers. A phylogenetic tree was assembled from mitochondrial restriction fragment data. The taxa analyzed formed three major groups comprising section Heterosorghum (group I), section Parasorghum (group II), and all accessions in section Eusorghum (group III). Group III is further divided into four groups: (i) two sweet sorghums and shattercane; (ii) Sorghumhalepense, Sorghummiliaceum, Sorghumhewisonii, Sorghumaethiopicum, Sorghumverticilliflorum, and S. bicolor, including Sorghumsudanense (sudangrass), the Chinese Kaoliangs, and a number of commercial sorghum inbreds from the U.S.A.; (iii) Sorghumpropinquum; and (iv) Sorghumarundinaceum, Sorghumniloticum, Sorghumalmum, Sorghumcontroversum, and the Chinese material C-401 and 5-27. Results indicate that the analysis of fragmented mitochondrial DNA was diagnostic and useful in sorghum phylogenetic and taxonomic research at the species, subspecies, and race levels, and can complement results from those analyses using nuclear ribosomal DNA and chloroplast DNA that effectively distinguish taxa at species and genus levels. Key words : Sorghum, mitochondrial DNA, phylogeny, restriction fragment.

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39

Sampath, Vivek, and Philipp Simon. "334 RESTRICTION FRAGMENT LENGTH POLYMORPHISM IN CARROT." HortScience 29, no. 5 (May 1994): 478d—478. http://dx.doi.org/10.21273/hortsci.29.5.478d.

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Studies of genetic variation at the DNA level in the genus Daucus have been very limited. Molecular markers based on restriction fragment length polymorphism (RPLP) have been shown to be highly useful and efficient gene markers in other plant species. We have used a total of 20 carrot types (inbreds, varieties, species) for this study. Genomic DNA probes cloned in pGEM (Promega) plasmid of Escherichia coli were hybridized to DNA of these types digested with EcoRI and HindIII restriction enzymes. Based on 50 probe-enzyme combinations we have found RFLP variation to be extensive in Daucus, even among related cultivated genetic stocks. The implications of these results in the germplasm diversity in Daucus will be discussed. Also, a genetic linkage map of carrot will be constructed. The map will be used to determine the genomic regions conditioning traits like root and core diameter, root length, and nematode resistance.

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40

SOLLER, M., and J. S. BECKMANN. "Restriction Fragment Length Polymorphisms in Poultry Breeding." Poultry Science 65, no. 8 (August 1986): 1474–88. http://dx.doi.org/10.3382/ps.0651474.

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41

Yasue, Hiroshi. "Linkage analysis using restriction fragment length polymorphisms." Animal blood-group research information 1990, no. 18 (1990): 9–13. http://dx.doi.org/10.5924/abgri1983.1990.9.

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42

Quarta, R., M. T. Dettori, I. Verde, P. Laino, S. Sabatini, A. Vantaggi, and R. Sciarroni. "RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS IN PEACH." Acta Horticulturae, no. 374 (October 1996): 61–70. http://dx.doi.org/10.17660/actahortic.1996.374.7.

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43

Jacobson, Stephen C., and J. Michael Ramsey. "Integrated Microdevice for DNA Restriction Fragment Analysis." Analytical Chemistry 68, no. 5 (January 1996): 720–23. http://dx.doi.org/10.1021/ac951230c.

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44

Collins, D. M., and G. W. De Lisle. "BCG Identification by DNA Restriction Fragment Patterns." Microbiology 133, no. 6 (June 1, 1987): 1431–34. http://dx.doi.org/10.1099/00221287-133-6-1431.

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45

Grant, A., L. A. Ogilvie, C. B. Blackwood, T. Marsh, S. H. Kim, and E. A. Paul. "Terminal Restriction Fragment Length Polymorphism Data Analysis." Applied and Environmental Microbiology 69, no. 10 (October 1, 2003): 6342–43. http://dx.doi.org/10.1128/aem.69.10.6342-6343.2003.

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46

Motoyama, Miriam, Thomas S. Kilduff, Beth S. M. Lee, William C. Dement, and Hugh O. McDevitt. "Restriction fragment length polymorphism in canine narcolepsy." Immunogenetics 29, no. 2 (February 1989): 124–26. http://dx.doi.org/10.1007/bf00395862.

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47

Keim, P., R. C. Shoemaker, and R. G. Palmer. "Restriction fragment length polymorphism diversity in soybean." Theoretical And Applied Genetics 77, no. 6 (June 1989): 786–92. http://dx.doi.org/10.1007/bf00268327.

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48

Armstrong, John L., Nanci L. Fowles, and Paul T. Rygiewicz. "Restriction fragment length polymorphisms distinguish ectomycorrhizal fungi." Plant and Soil 116, no. 1 (May 1989): 1–7. http://dx.doi.org/10.1007/bf02327250.

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49

Cristina, N., B. Oury, P. Ambroise-Thomas, and F. Santoro. "Restriction-fragment-length polymorphisms amongToxoplasma gondii strains." Parasitology Research 77, no. 3 (1991): 266–68. http://dx.doi.org/10.1007/bf00930870.

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50

Rajora, Om P., and John D. Mahon. "Mitochondrial and nuclear DNA variation, genotype fingerprinting and genetic relationships in lentil (Lens culinaris Medik.)." Canadian Journal of Plant Science 77, no. 4 (October 1, 1997): 515–21. http://dx.doi.org/10.4141/p96-133.

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Mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) variations were examined in six cultivars of Lens culinaris ssp. culinaris and two (mtDNA) or one (nuDNA) accession(s) of L. culinaris ssp. orientalis. Total leaf DNA was digested with up to 15 restriction endonucleases, separated by agarose gel electrophoresis and trasferred to nylon membranes. To examine mtDNA variation, blots were probed with mtDNA coding for cytochrome c oxidase I (coxI) and ATPase 6 (atp6) of both wheat and maize as well as apocytochrome b (cob) and Orf25 (orf25) of wheat. Sixteen combinations of mtDNA probes and restriction enzymes revealed 34 fragments that discriminated between at least two lentil accessions. For nuDNA analysis, probes from cDNA and genomic DNA clones of lentil were used to probe the same blots, and identified 46 diagnostic fragments from 19 probe/enzyme combinations. Each lentil accession could be unequivocably distinguished from all others on the basis of both mitochondrial and nuclear DNA fragment patterns. The mitochondrial restriction fragment similarities ranged from 0.944 to 0.989, with a mean of 0.970 but nuclear restriction fragment similarities varied from 0.582 to 0.987, with a mean of 0.743. The apparent genetic relationships among accessions differed according to the source of DNA examined, although the commercial varieties Laird, Brewer and Redchief showed similarly high levels of mean similarity with both nuclear (0.982) and mitochondrial DNA (0.983). Key words: Lens culinaris Medik., genetic variation, mitochondrial, nuclear, DNA, lentil

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