Journal articles: 'Restriction digestion'

1

Sugimoto, Keiki, Tohru Makihara, Aya Saito, Nobuya Ohishi, Takahide Nagase, and Daiya Takai. "Betaine improved restriction digestion." Biochemical and Biophysical Research Communications 337, no. 4 (December 2005): 1027–29. http://dx.doi.org/10.1016/j.bbrc.2005.09.145.

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2

Milavetz, Barry. "Oligonucleotide-directed restriction endonuclease digestion." Nucleic Acids Research 17, no. 8 (1989): 3322. http://dx.doi.org/10.1093/nar/17.8.3322.

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Coucheron, Dag H. "Acetobacterstrains contain DNA modified at GAATTC and GANTC." Canadian Journal of Microbiology 43, no. 5 (May 1, 1997): 456–60. http://dx.doi.org/10.1139/m97-064.

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Total DNAs from nine strains of Acetobacter xylinum, two strains of Acetobacter aceti, and one Acetobacter pasteurianus strain were examined for the extent of digestion by various restriction endonucleases. The majority of the endonucleases cleaved the total DNAs with a frequency expected from the number of sites present in DNA sequences deposited in the GenBank data base. However, the restriction enzyme digestions identified two different genomic DNA modifications in Acetobacter. One sequence-specific modification protected total DNAs from seven of the A. xylinum strains against cleavage by EcoRI (GAATTC). Digestion of total DNAs from A. xylinum ATCC 10245 (DNA not cut by EcoRI) and the closely related A. xylinum NRCC 17005 (DNA cut by EcoRI) with Tsp509I (AATT) revealed differences in restriction frequencies that indicated methylation of the first or second adenine within GAATTC. Another sequence-specific modification rendered total DNAs from all the 12 strains recalcitrant to digestion by HinfI. The latter modification indicated that species of the genus Acetobacter contain a solitary DNA methyltransferase that probably methylates adenine in GANTC.Key words: Acetobacter, genomic DNA, modifications, EcoRI, HinfI.

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Simonet, P., P. Normand, A. Moiroud, and M. Lalonde. "Restriction enzyme digestion patterns ofFrankia plasmids." Plant and Soil 87, no. 1 (February 1985): 49–60. http://dx.doi.org/10.1007/bf02277647.

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5

Mezzanotte, R., U. Bianchi, and A. Marchi. "In situ digestion of Drosophila virilis polytene chromosomes by AluI and HaeIII restriction endonucleases." Genome 29, no. 4 (August 1, 1987): 630–34. http://dx.doi.org/10.1139/g87-105.

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Polytene chromosomes of Drosophila virilis were treated with AluI and HaeIII restriction endonucleases. Both enzymes were capable of extensively digesting chromosomal DNA, with the exception of some regions that contain repetitive DNAs. Moreover, a comparison was made between our data and the data already obtained with the same enzymes in D. melanogaster. On this basis, AluI digestion showed that the 5S RNA genes of D. virilis and D. melanogaster have different base composition, while digestion with HaeIII revealed resistance of the histone genes in D. virilis, contrary to what was previously found in D. melanogaster. Key words: restriction endonucleases, 5S RNA genes, histone genes, polytene chromosomes, Drosophila species.

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6

Lauer, Ulrich, and Erich Seemüller. "Physical Map of the Chromosome of the Apple Proliferation Phytoplasma." Journal of Bacteriology 182, no. 5 (March 1, 2000): 1415–18. http://dx.doi.org/10.1128/jb.182.5.1415-1418.2000.

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ABSTRACT A physical map of the apple proliferation phytoplasma strain AT chromosome was constructed from genomic DNA extracted from diseased tobacco plants. The map was generated with single and double digestions of the chromosome with BssHII, SmaI,MluI, and ApaI restriction endonucleases and resolving the fragments by pulsed-field gel electrophoresis. Partial digestion and Southern blot analysis were used to assist in the arrangement of the 14 contiguous restriction fragments obtained. From the restriction fragments generated by double digestions, the size of the circular chromosome was calculated to be approximately 645 kb. Locations of the two rRNA operons, the operon including thefus and tuf genes, and three other genes were placed on the map. Genome sizes and BssHII restriction profiles of apple proliferation strain AP15 and the pear decline and European stone fruit yellows phytoplasmas were different from that of strain AT.

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Rodriguez, Jose L., Richard W. Ermel, Thomas P. Kenny, Dale L. Brooks, and Al J. DaMassa. "Polymerase Chain Reaction and Restriction Endonuclease Digestion for Selected Members of the “Mycoplasma Mycoides Cluster” and Mycoplasma Putrefaciens." Journal of Veterinary Diagnostic Investigation 9, no. 2 (April 1997): 186–90. http://dx.doi.org/10.1177/104063879700900213.

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A specific diagnostic method using the polymerase chain reaction, together with restriction endonuclease digestion patterns, was developed for members of the “ Mycoplasma mycoides cluster” that normally occur in the United States (i.e., Mycoplasma mycoides subsp. mycoides Large Colony and Mycoplasma capricolum subsp. capricolum in addition to “cluster” mycoplasma, bovine serogroup 7, and Mycoplasma putrefaciens. The digestion of “cluster” polymerase chain reaction DNA (1,225 bp) amplification products with restriction enzymes Asel and SspI gave mycoplasma species-specific patterns for all strains of M. mycoides subsp. mycoides Large Colony, M. capricolum subsp. capricolum, and bovine group 7 tested. Moreover, we found a nonspecific amplification product for M. putrefaciens that occurred with the oligonucleotide primers used for the “ M. mycoides cluster” reaction. However, the restriction endonuclease digestion patterns observed with the restriction enzymes AluI, AseI, and SspI for M. putrefaciens were different than the digestion patterns obtained for the other “cluster” mycoplasmas. This report confirms the usefulness of polymerase chain reaction DNA amplification allied with restriction enzyme digestion profile analysis for the rapid and specific identification of mycoplasmas belonging to the “ M. mycoides cluster” and M. putrefaciens.

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8

Tiwari, P. K., and S. C. Lakhotia. "Restriction enzyme digestion of heterochromatin inDrosophila nasuta." Journal of Biosciences 16, no. 4 (December 1991): 187–97. http://dx.doi.org/10.1007/bf02703284.

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9

GIDENNE, T., L. FORTUN-LAMOTHE, and S. COMBES. "Restreindre l’ingestion du jeune lapin : de nouvelles stratégies pour renforcer sa santé digestive et améliorer son efficacité alimentaire." INRAE Productions Animales 25, no. 4 (October 1, 2012): 323–36. http://dx.doi.org/10.20870/productions-animales.2012.25.4.3221.

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La restriction temporaire de l'ingestion du lapin après son sevrage est maintenant une stratégie d'alimentation couramment employée en cuniculture. L'objet de cette synthèse est de présenter les différents effets d'une limitation de l'ingestion sur la santé, la physiologie digestive et l'efficacité alimentaire du lapin en croissance. Même si une restriction alimentaire conduit à une croissance plus lente, ces stratégies sont désormais utilisées par plus de 85% des éleveurs français. En effet, elles permettent de réduire les risques de mortalité et de morbidité post-sevrage par troubles digestifs, par exemple par l'entéropathie épizootique du lapin. De plus, la conversion alimentaire est améliorée, plus particulièrement lorsque les lapins sont de nouveau alimentés librement, en raison d'une importante croissance compensatrice. Cette meilleure efficacité alimentaire est associée à un transit plus lent et à une meilleure digestion, bien qu'on observe des interactions avec la composition chimique de l'aliment. La physiologie digestive est par ailleurs peu modifiée, en particulier la morphométrie de la muqueuse intestinale, l’activité fermentaire et le microbiote caecal. La qualité de la viande est peu affectée par la restriction alimentaire, alors qu'on observe une baisse de l'état d'engraissement des carcasses et une légère dégradation du rendement à l'abattage. Les effets d'une limitation de l'ingestion sur le comportement et le bien-être animal sont discutés, sachant que le jeune lapin présente une adaptation très rapide aux stratégies de restriction. Ainsi, les stratégies de restriction peuvent améliorer la rentabilité de l'atelier cunicole, mais elles doivent être adaptées à chaque situation d'élevage.

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10

Diniz, Leandro Eugênio Cardamoni, Claudete de Fátima Ruas, Valdemar de Paula Carvalho, Fabrício Medeiros Torres, Eduardo Augusto Ruas, Melissa de Oliveira Santos, Tumoru Sera, and Paulo Maurício Ruas. "Genetic diversity among forty coffee varieties assessed by RAPD markers associated with restriction digestion." Brazilian Archives of Biology and Technology 48, no. 4 (July 2005): 511–21. http://dx.doi.org/10.1590/s1516-89132005000500002.

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The genetic variability of 40 accessions of_C. arabica was evaluated using a combination of the random amplified polymorphic DNA (RAPD) technique and restriction digestion of genomic DNA. The genetic variability and the relatedness among all accessions were initially evaluated using 195 RAPD primers which revealed a very low level of genetic variation. To improve the efficiency in the detection of polymorphism, the genomic DNA of all accessions were submitted to digestion with restriction endonucleases prior to PCR amplification. A total of 24 primers combined with restriction digestion of DNA rendered 318 bands, of which 266 (83.65%) were polymorphic. The associations among genotypes were estimated using UPGMA-clustering analysis. The accessions were properly clustered according to pedigree and agronomic features. The ability to distinguish among coffee accessions was greater for RAPD plus restriction digestion than for RAPD alone, providing evidences that the combination of the techniques was very efficient for the estimation of genetic relationship among_C. arabica genotypes.

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11

Kamisugi, Y., Y. Ikeda, M. Ohno, M. Minezawa, and K. Fukui. "In situ digestion of barley chromosomes with restriction endonucleases." Genome 35, no. 5 (October 1, 1992): 793–98. http://dx.doi.org/10.1139/g92-121.

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In situ digestion of barley chromosomes with restriction endonucleases was examined. All the treatments with five restriction endonucleases, MboII, RsaI, HaeIII, HinfI, and DraII, showed various band patterns on the barley chromosomes. Differences were observed in the band patterns produced with different restriction endonucleases. Uneven staining patterns, similar to the band patterns by the endonuclease treatments, also appeared when the chromosomes were treated with the buffer solution without the enzyme. The band patterns observed both with and without the endonucleases were classified into the four types and the frequency of each type among the different treatments was investigated. The change of the band types along with treatment time was accelerated by the addition of the restriction endonuclease. As a result, it was concluded that there existed chromosome band patterns that were specific to the endonuclease treatments and that the buffer solution also affected to the production of the bands on the chromosomes.Key words: Hordeum vulgare L., chromosome band pattern, in situ digestion, restriction endonuclease, restriction banding.

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12

Turceková, Ľ., and I. Kráľová. "Characterization of DNA restriction profiles and rRNA gene restriction fragment length polymorphisms of Proteocephalus exiguus and P. neglectus from geographically distinct regions." Journal of Helminthology 69, no. 2 (June 1995): 159–63. http://dx.doi.org/10.1017/s0022149x0001405x.

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AbstractThe total DNA of two morphologically similar cestode species of the genus Proteocephalus parasitizing coregonid and salmonid fish, P. exiguus La Rue, 1911 and P. neglectus La Rue, 1911, was compared. The methods of DNA analysis involved digestion of the total DNA with restriction endonucleases and Southern blotting hybridization with the ribosomal DNA probes pSM 889, pSM 389 and pSM 890. No inter-specific variation was found between the two proteocephalid species. Distinct differences in RFLP patterns were recorded between two geographically distinct population of P. neglectus after BspRI digestion; after EcoRI digestion and following hybridization with the 32P-labelled probe pSM 890 and after BamHI digestion and hybridization with the 32P-labelled probe pSM 889. The high degree of genetic similarity revealed in the two Proteocephalus spp. could be a further argument for the conspecifity of both taxa.

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13

Ko, Yong Jun, Dae Jin Kim, Woong Cho, Yoo Min Ahn, and Seung Yong Hwang. "Glass-Polydimethysiloxane Hybrid Microthermostat for Restriction Enzyme Digestion." Materials Science Forum 544-545 (May 2007): 335–38. http://dx.doi.org/10.4028/www.scientific.net/msf.544-545.335.

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This paper reports a low-cost microthermostat that is able to maintain a constant temperature necessary for restriction enzyme digestion. Polydimethylsiloxane (PDMS) and Pyrex glass were used to make the microthermostat, because PDMS is a cheap and mass-producible material and both PDMS and glass have very good biocompatibility compared to the more commonly used silicon. A heater made of Au wiring patterned on Pyrex glass was used to control the temperature. A PDMS replica molding technique was used to fabricate a reaction chamber with 3.6 μl capacity. Restriction enzyme digestion was performed by using the fabricated microthermostat and by a conventional method. Then, using gel electrophoresis, we compared results between the microthermostat and conventional methods. It was found that restriction enzyme digestion using the microthermostat required 5 min of heating.

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14

Hedemann, Ute, M. Schürmann, and E. Schwinger. "The effect of restriction enzyme digestion of human metaphase chromosomes on C-band variants of chromosomes 1 and 9." Genome 30, no. 5 (October 1, 1988): 652–55. http://dx.doi.org/10.1139/g88-110.

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Human metaphase chromosomes, fixed on slides, have been treated with 8 different restriction endonucleases and 29 combinations of 2 restriction enzymes prior to staining with Giemsa. The endonucleases AluI and DdeI and the combinations AluI + DdeI, AluI + HaeIII, AluI + HinfI, and AluI + MboI have then been used to digest metaphase chromosomes of nine individuals with C-band variants of chromosomes 1 or 9, obtained by the CBG technique. The restriction enzyme resistant chromatin of the paracentromeric regions of chromosomes 1 and 9 has been measured and compared with the corresponding CBG-bands. The size of the enzyme resistant chromatin regions depend upon the type of enzyme(s) used. Treatment with AluI + MboI was the only digestion that acted differently on different chromosome pairs. However, within one pair of homologous chromosomes, all digestions revealed the same variations as conventional C-banding.Key words: C-band variants, heterochromatin, human chromosomes, restriction endonucleases.

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15

Spear, Matthew A. "Efficient DNA Subcloning through Selective Restriction Endonuclease Digestion." BioTechniques 28, no. 4 (April 2000): 660–68. http://dx.doi.org/10.2144/00284st01.

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16

Her, Chengtao, and Richard Weinshilboum. "Long PCR: Selective Suppression by Restriction Endonuclease Digestion." BioTechniques 21, no. 5 (November 1996): 764–66. http://dx.doi.org/10.2144/96215bm01.

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17

Gosálvez, J., and V. Goyanes. "Selective digestion of mouse chromosomes with restriction endonucleases." Cytogenetic and Genome Research 48, no. 4 (1988): 198–200. http://dx.doi.org/10.1159/000132627.

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18

Gosálvez, J., R. Mezzanotte, C. López-Fernández, P. Del Castillo, J. C. Stockert, V. Goyanes, and A. T. Sumner. "Selective digestion of mouse chromosomes with restriction endonucleases." Cytogenetic and Genome Research 56, no. 2 (1991): 82–86. http://dx.doi.org/10.1159/000133055.

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19

Corneo, Gianmarco, Enrico Pogliani, Daniela Biassoni, and Pasquale Tripputi. "Inhibition of DNA restriction enzyme digestion by anthracyclines." La Ricerca in Clinica e in Laboratorio 18, no. 1 (January 1988): 19–22. http://dx.doi.org/10.1007/bf02918815.

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20

Jones, David S., Fumiko Nemoto, Yoshiyuki Kuchino, Eiko Ohtsuka, and Susumu Nishimura. "8-Hydroxydeoxyguanosine in dna Inhibits Restriction Endonuclease Digestion." Nucleosides and Nucleotides 9, no. 2 (February 1990): 223–33. http://dx.doi.org/10.1080/07328319008045134.

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21

Sambrook, Joseph, and David W. Russell. "Restriction Endonuclease Digestion of DNA in Agarose Plugs." Cold Spring Harbor Protocols 2006, no. 1 (June 2006): pdb.prot4031. http://dx.doi.org/10.1101/pdb.prot4031.

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22

Parent, Michelle. "Restriction Enzyme Digestion Exercise – An In-class Activity." Journal of Microbiology & Biology Education 11, no. 1 (May 20, 2010): 56–57. http://dx.doi.org/10.1128/jmbe.v1.i2.129.

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23

Griffith, Gareth W., and David S. Shaw. "Polymorphisms in Phytophthora infestans: Four Mitochondrial Haplotypes Are Detected after PCR Amplification of DNA from Pure Cultures or from Host Lesions." Applied and Environmental Microbiology 64, no. 10 (October 1, 1998): 4007–14. http://dx.doi.org/10.1128/aem.64.10.4007-4014.1998.

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ABSTRACT Four pairs of primers were designed for PCR amplification of known polymorphic regions of the mitochondrial genome of Phytophthora infestans. Digestion of the amplified products with restriction enzymes allows identification of previously identified haplotypes. Product P2 cut with MspI uniquely identifies haplotypes Ib and IIa, while types Ia and IIb are differentiated by digestion of product P4 with EcoRI. Digestion of products P1 and P3 gave results similar to that with digestion of P4, but amplification of these products was less robust. Thus, all four common haplotypes are identified by amplifying and digesting products P2 and P4. Identification of haplotypes was also possible from DNA extracted directly from small, late-blight lesions on both tomato and potato leaves, making isolation of the fungus unnecessary. A rapid and efficient method of monitoring changes in the pathogen population is facilitated. These PCR primers were also useful for differentiating other Phytophthora species.

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Tagarro, I., J. J. González-Aguilera, and A. Ma Fernández-Peralta. "TaqI digestion reveals fractions of satellite DNAs on human chromosomes." Genome 34, no. 2 (April 1, 1991): 251–54. http://dx.doi.org/10.1139/g91-039.

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Restriction endonuclease TaqI has been known as a nonbanding restriction endonuclease when it is used on fixed human chromosomes. However, a specific TaqI digestion can be obtained after varying experimental conditions such as concentration of enzyme, time of incubation, and volume of the final reaction mixture. This digestion consists of an extensive DNA loss in heterochromatin subregions of chromosomes 1, 9, 15, 16, and Y. These regions essentially coincide with those corresponding to the main chromosome locations of satellite II DNA, whose tandem repeated units contain many TaqI target sequences, and some satellite III DNA domains enriched in TaqI sites.Key words: TaqI restriction endonuclease, heterochromatin, satellite DNAs, human chromosomes.

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25

Liberator, P. A., and J. B. Lingrel. "Chromatin fine-structure mapping of the goat beta F gene in fetal erythroid tissue." Molecular and Cellular Biology 7, no. 8 (August 1987): 2772–82. http://dx.doi.org/10.1128/mcb.7.8.2772-2782.1987.

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Using a restriction enzyme accessibility assay, we have previously demonstrated that the chromatin structure immediately proximal to the goat beta F-, beta C-, and beta A-globin genes changes in a manner which parallels their developmentally regulated expression. More specifically, the PvuII recognition sequence, located 9 nucleotides upstream from the transcriptional start site in each of the three genes, is accessible to digestion only in nuclei prepared from erythroid tissue in which the respective gene product is expressed. Here we describe two restriction enzyme sites further upstream from the transcription start sites (HindIII at -700 and SacI at -480) which were not accessible to digestion in fetal erythroid nuclei. Conversely, two sites within the second coding block of the beta F gene (AccI at +276 and BamHI at +470) were accessible in fetal erythroid tissue. The corresponding sites in the beta C and beta A genes were not available for digestion in the same fetal tissue. Processive exonuclease III digestion in situ from the three accessible restriction enzyme sites in the beta F gene allowed us to define more closely the limits of these open regions. Resistance to exonuclease III digestion was encountered at or near both intron-exon junctions flanking the first intervening sequence of the beta F gene. Conversely, no resistance to exonuclease III digestion was evident in either the first or second coding blocks or the 5' untranslated region. Digestion upstream from the PvuII site of the beta F gene was negligible. High-resolution mapping by S1 nuclease analysis indicated that the endpoint of exonuclease III digestion from this site lay immediately downstream of the ATA box.

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Liberator, P. A., and J. B. Lingrel. "Chromatin fine-structure mapping of the goat beta F gene in fetal erythroid tissue." Molecular and Cellular Biology 7, no. 8 (August 1987): 2772–82. http://dx.doi.org/10.1128/mcb.7.8.2772.

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Using a restriction enzyme accessibility assay, we have previously demonstrated that the chromatin structure immediately proximal to the goat beta F-, beta C-, and beta A-globin genes changes in a manner which parallels their developmentally regulated expression. More specifically, the PvuII recognition sequence, located 9 nucleotides upstream from the transcriptional start site in each of the three genes, is accessible to digestion only in nuclei prepared from erythroid tissue in which the respective gene product is expressed. Here we describe two restriction enzyme sites further upstream from the transcription start sites (HindIII at -700 and SacI at -480) which were not accessible to digestion in fetal erythroid nuclei. Conversely, two sites within the second coding block of the beta F gene (AccI at +276 and BamHI at +470) were accessible in fetal erythroid tissue. The corresponding sites in the beta C and beta A genes were not available for digestion in the same fetal tissue. Processive exonuclease III digestion in situ from the three accessible restriction enzyme sites in the beta F gene allowed us to define more closely the limits of these open regions. Resistance to exonuclease III digestion was encountered at or near both intron-exon junctions flanking the first intervening sequence of the beta F gene. Conversely, no resistance to exonuclease III digestion was evident in either the first or second coding blocks or the 5' untranslated region. Digestion upstream from the PvuII site of the beta F gene was negligible. High-resolution mapping by S1 nuclease analysis indicated that the endpoint of exonuclease III digestion from this site lay immediately downstream of the ATA box.

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27

Ansari, Farheen, Balkrushna Brahmkshtri, Umed Ramani, Mamta Janmeda, and Thakur K. Rao. "Genetic Polymorphism of Insulin-Like Growth Factor 1 and Prolactin Receptor Genes in Surti and Mehsana Goats by PCR-RFLP." Indian Journal of Veterinary Sciences & Biotechnology 18, no. 5 (November 7, 2022): 89–92. http://dx.doi.org/10.48165/ijvsbt.18.5.18.

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The present study was planned with the objective to amplify 5’NCR Insulin-like growth factor 1 (IGF1) and 3’UTR Prolactin receptor (PRLR) genes using caprine specific primers by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) in Surti and Mehsana goats. IGF1 gene 5’NCR was found to be monomorphic on restriction digestion with HaeIII, which revealed only one genotype GG in both Surti and Mehsana goats. The allele frequency of G was found to be 1.00 in both the breeds. Restriction digestion of PRLR gene 443 bp fragment with AluI also showed monomorphic pattern. Only one genotype CC was found with an allele frequency of 1.0 in both the Surti and Mehsana goats.

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Buño, Ismael, Carmen López-Fernández, Jaime Gosálvez, and José Luis Díez-Martín. "Dynamics of Sau3A in situ digestion of human chromosomes analyzed with computerized imaging." Genome 40, no. 1 (February 1, 1997): 123–26. http://dx.doi.org/10.1139/g97-017.

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The differential DNA removal obtained after in situ digestion of human metaphase chromosomes with the restriction endonuclease Sau3A was analyzed on complete and partially digested nuclei using computerized imaging. The results obtained permit the discrimination of Sau3A-resistant chromosome regions (pericentromeric constitutive heterochromatin on chromosomes 3 and 9) from those partially digested (Yq12 and pericentromeric heterochromatin on other chromosomes), according to the digestion dynamics deduced from the grey intensity profile along each chromosome. This approach permits an accurate labelling of chromosome markers for the identification of genomes from different individuals. This is of special interest for the analysis of the chimeric status found in patients after allogenic bone marrow transplantation.Key words: human cytogenetics, restriction endonucleases, in situ digestion, image processing and analysis.

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Dennis, Jonathan J., and Gerben J. Zylstra. "Rapid Generation of Nested Deletions by Differential Restriction Digestion." BioTechniques 33, no. 2 (August 2002): 310–15. http://dx.doi.org/10.2144/02332st02.

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30

Anand, Rishi D., Odeniel Sertil, and Charles V. Lowry. "Restriction digestion monitors facilitate plasmid construction and PCR cloning." BioTechniques 36, no. 6 (June 2004): 982–85. http://dx.doi.org/10.2144/04366st03.

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31

Parkes, Joan Lee, Frank C. Hubbard, and Arthur Penn. "Resistance of Tumor-Derived DNA to Restriction Enzyme Digestion." Cancer Investigation 8, no. 2 (January 1990): 169–72. http://dx.doi.org/10.3109/07357909009017562.

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32

Rogan, Peter K. "Restriction mapping by preferential ligatlon of adjacent digestion fragments." Nucleic Acids Research 14, no. 22 (1986): 9219. http://dx.doi.org/10.1093/nar/14.22.9219.

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Sweeney, P. M., and T. K. Danneberger. "Restriction Digestion of Arbitary Amplification Fragments of Annual Bluegrass." Crop Science 36, no. 5 (September 1996): 1301–3. http://dx.doi.org/10.2135/cropsci1996.0011183x003600050038x.

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34

Sappal, Navtej Pal, Robert S. Jeng, Martin Hubbes, and Fuhua Liu. "Restriction fragment length polymorphisms in polymerase chain reaction amplified ribosomal DNAs of three Trichogramma (Hymenoptera: Trichogrammatidae) species." Genome 38, no. 3 (June 1, 1995): 419–25. http://dx.doi.org/10.1139/g95-055.

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Restriction fragment length polymorphisms from PCR amplified ribosomal DNAs of three Trichogramma species, T. minutum, T. brassicae, and T. near sibiricum, were studied. Length variation in the internal transcribed spacer (ITS) region was observed. The ITS region of T. brassicae is about 1350 base pairs (bp) in length and those of T. minutum and T. near sibiricum are 1300 bp. These three species also differ in the size of their ITS1 and ITS2 regions. Restriction enzyme digestions of these regions showed unique banding patterns for each species. The amplified 18S region of ribosomal DNA is about 1800 bp in length and showed no length variation between the three species of Trichogramma. Restriction enzyme digestion of this region by BamHI differentiated T. brassicae from the other two species. Restriction site maps of the ITS and 18S regions were constructed for each species. The amplified 28S region is about 1700 bp for these three species. Restriction of this region by RsaI and SacII differentiates these three species. The reported results indicate that these species of Trichogramma can be clearly differentiated from one another by nuclear ribosomal DNA markers.Key words: rDNA, Trichogramma, PCR.

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Lorite, P., and T. Palomeque. "Effects of restriction endonucleases on nucleolar organizing regions in the ant Tapinoma nigerrimum." Genome 41, no. 6 (December 1, 1998): 872–75. http://dx.doi.org/10.1139/g98-095.

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The effects of some restriction endonucleases (REs) on the nucleolar organizing regions and on the genes for ribosomal RNA (rDNA) were analyzed using the nucleolar organizing region of the chromosome 6 of Tapinoma nigerrimum as an experimental model, since, in accordance with previous studies, the genes for ribosomal RNA seem to be present only in this chromosome. In situ non-digestion of the nucleolar organizing region was observed when EcoRI and HindIII were used. However, very evident digestion and partial digestion respectively were observed when HaeIII and Tru9I were used. Southern blot analysis realized on naked DNA digested with the same REs and using rDNA of Drosophila melanogaster as probe showed that there are target sequences for these enzymes in the rDNA. In accordance with the results obtained, the rDNA is poor in EcoRI and HindIII sequences, contains moderate amounts of Tru9I sequences, and is rich in HaeIII sequences. All the data obtained suggest that in the nucleolar organizing region of Tapinoma nigerrimum, the major, if not the only, limiting factor affecting in situ digestion by the REs used is the presence and frequency of their specific restriction targets. Consequently, extraction of DNA from this chromosome region depends on the size of the fragments originated.Key words: chromosome banding, Formicidae, NORs, rDNA, restriction endonucleases.

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ŁYP, PAWEŁ, MACIEJ SKRZYPCZAK, STANISŁAW WINIARCZYK, and ŁUKASZ ADASZEK. "Molecular typing of Polish strains of Babesia canis protozoa isolated from dogs in the years 2013-2016." Medycyna Weterynaryjna 74, no. 1 (2018): 6021–2018. http://dx.doi.org/10.21521/mw.6021.

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The aim of the study was the molecular analysis of B. canis strains isolated from dogs from Poland based on 18S RNA and Bc28 genes. The study involved 140 protozoan strains derived from clinical disease cases. All DNA samples of parasites were analyzed in two ways (amplification and restriction digestion) which made it possible to demonstrate the polymorphism of the Bc28 gene, and to show 18S RNA gene polymorphism (amplification and restriction digestion). Amplification of the Bc28 gene fragment and digestion of the resulting PCR products allowed for the classification of 104 isolates of B. canis to the Bc28-A group, and 36 strains of protozoa to the Bc28-B group. Amplification of the Bc28 gene fragment and digestion of the resulting PCR products allowed for the classification of 33 isolates to 18S RNA-A group, while to 18S RNA-B – 107 parasite isolates. Comparison of both groups of protozoa among themselves allowed partial but not complete correlation of polymorphisms in Bc28 and 18S RNA genes..

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

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

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Sacco, Randy E., Karen B. Register, and Gwen E. Nordholm. "Restriction Endonuclease Analysis Discriminates Bordetella bronchiseptica Isolates." Journal of Clinical Microbiology 38, no. 12 (2000): 4387–93. http://dx.doi.org/10.1128/jcm.38.12.4387-4393.2000.

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One hundred ninety-five Bordetella bronchisepticaisolates from 12 different host species worldwide were characterized by restriction enzyme analysis (REA). These isolates had previously been categorized into 19 PvuII ribotypes. Twenty restriction endonucleases were evaluated for use in REA. Digestion of chromosomal DNA with HinfI, followed by submarine electrophoresis in agarose gels and staining with ethidium bromide, produced DNA fragments in the 4.0- to 10-kb range, which readily discriminated B. bronchiseptica isolates, resulting in 48 fingerprint patterns. Moreover, AluI digestion of chromosomal DNA produced 39 distinct fingerprint profiles with DNA fragments ranging from 6.0 to 20.0 kb. While REA frequently provided more discriminatory power than ribotyping, there were examples where the use of ribotyping was more discriminatory than REA. Passage of selected isolates up to passage 25 did not change the REA profile. Moreover, the Bvg phase did not alter the fingerprint profile of chromosomal DNA from B. bronchiseptica strains digested with HinfI orAluI. Based on the results presented herein, the combination of REA and ribotyping should provide valuable information in understanding the molecular epidemiology of B. bronchiseptica infections.

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Fernandez-Peralta, A. M., P. Navarro, I. Tagarro, and J. J. Gonzalez-Aguilera. "Digestion of human chromosomes by means of the isoschizomers MspI and HpaII." Genome 37, no. 5 (October 1, 1994): 770–74. http://dx.doi.org/10.1139/g94-110.

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The isoschizomers MspI and HpaII are four base cutter (C↓CGG) restriction endonucleases, HpaII being sensitive to methylation of the internal cytosine. Human chromosomes treated with MspI have produced inconsistent results between laboratories, while HpaII has always been described as a nonbanding enzyme when used on human chromosomes. These results have been explained on the basis of both rarity of the CpG doublet in vertebrate genomes and high rate of CpG methylation (5mCpG). We demonstrated consistent banding patterns subsequent to digestions with MspI and HpaII. On euchromatin, MspI (but not HpaII) digests the DNA of R regions and thus R-bands apparently contain many more CCGG sites (mostly methylated) than G-bands. In heterochromatin, extensive digestion of the 9q12 region not only by MspI but also by HpaII reveals a heterochromatic domain with a high frequency of unmethylated CCGG sites, most probably within the satellite 3 DNA fraction. In addition, enzymatic digestions of the Yq12 heterochromatin, when this region is undercondensed by 5-azacytidine, contribute to deepen the insight into the mechanism of action of this cytidine analog and at the same time reinforce the idea of the heterogeneity of this chromosome region where domains with unmethylated CCGG sites may also exist.Key words: human chromosomes, methylation, restriction endonucleases, heterochromatin, satellite DNA.

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Hilaire, Rolston St, William R. Graves, and Randall L. Small. "Variation in TaqI-digested DNA of Sugar and Black Maples Is Independent of Taxon and Plant Origin." HortScience 36, no. 7 (December 2001): 1327–28. http://dx.doi.org/10.21273/hortsci.36.7.1327.

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Morphological distinctions between sugar maples and black maples are not consistently evident, and molecular assessment of genetic diversity is lacking for these taxa. We examined restriction-site polymorphisms in the ndhA intron of the chloroplast DNA (cpDNA) in populations of sugar maples and black maples representing their zones of allopatry and sympatry in eastern North America. Restriction-site analysis of the ndhA intron after digestion with HinfI and Sau3AI yielded no polymorphisms. Restriction digestion of the ndhA intron with TaqI revealed two cpDNA haplotypes that were neither geographically localized nor taxon specific. Although testing additional accessions of sugar maples and black maples for cpDNA variation will further elucidate patterns of genetic variation, our initial results suggest that the taxa are either exchanging genes or share an ancestral cpDNA polymorphism.

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Waeyenberge, Lieven, Alexander Ryss, Maurice Moens, Jorge Pinochet, and Thierry Vrain. "Molecular characterisation of 18 Pratylenchus species using rDNA Restriction Fragment Length Polymorphism." Nematology 2, no. 2 (2000): 135–42. http://dx.doi.org/10.1163/156854100509024.

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AbstractThe RFLP technique was used to establish a reliable diagnostic method for 18 Pratylenchus species: Pratylenchus agilis, P. bolivianus, P. brachyurus, P. coffeae, P. crenatus, P. fallax, P. goodeyi, P. loosi, P. mediterraneus, P. neglectus, P. penetrans, P. pratensis, P. pseudocoffeae, P. scribneri, P. subranjani, P. thornei, P. vulnus and P. zeae. The polymerase chain reaction (PCR) amplified the ITS regions from all species and populations examined and revealed large differences in length, ranging in size from approximately 900 to 1250 bp. The rDNA fragments were digested with five restriction enzymes (CfoI, DdeI, HindIII, HpaII, and PstI). All Pratylenchus species can be differentiated from each other by a combination of at least two enzymes. CfoI differentiated all nematode species with the exception of P. fallax, P. penetrans and P. pseudocoffeae. P. fallax was further separated by a DdeI restriction, and P. pseudocoffeae by a PstI digestion. Intraspecific RFLP were observed. Upon CfoI, DdeI, HindIII, or HpaII digestion, it was possible to separate the three P. coffeae populations studied from each other. La technique RFLP a été utilisée pour créer une méthode fiable de diagnostic pour 18 espèces de Pratylenchus: Pratylenchus agilis, P. bolivianus, P. brachyurus, P. coffeae, P. crenatus, P. fallax, P. goodeyi, P. loosi, P. mediterraneus, P. neglectus, P. penetrans, P. pratensis, P. pseudocoffeae, P. scribneri, P. subranjani, P. thornei, P. vulnus et P. zeae. La réaction de polymérisation en chaîne (PCR) a amplifié les régions de l’ITS pour toutes les espèces et populations étudiées et a mis en évidence de grandes différences dans la taille des gammes de longueur, de 900 à 1250 bp approximativement. Les fragments de rDNA ont été digérés à l’aide de cinq enzymes de restriction (CfoI, DdeI, HindIII, HpaII, and PstI). Toutes les espèces de Pratylenchus ont pu être différenciées les unes des autres par une combinaison d’au moins deux enzymes. CfoI a différencié toutes les espèces à l’exception de P. fallax, P. penetrans et P. pseudocoffeae. P. fallax a été ultérieurement séparé par une restriction DdeI, et P. pseudocoffeae par une digestion PstI. Des RFLP intraspécifiques ont été observés. Par les digestions CfoI, DdeI, HindIII, ou HpaII, il s’est révélé possible de séparer les unes des autres les trois populations étudiées de P. coffeae.

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Tokajian, Sima, Siba Al-Medawar, and Fuad Hashwa. "Use of the 16S–23S ribosomal genes spacer region for the molecular typing of sphingomonads." Canadian Journal of Microbiology 54, no. 8 (August 2008): 668–76. http://dx.doi.org/10.1139/w08-054.

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The ability of sphingomonads in drinking water to cause community- and hospital-acquired opportunistic infections has raised the need to establish reproducible identification assays. In this study, a total of 129 isolates recovered from drinking water with yellow- to orange-pigmented colonies were distributed among 10 biotypes on the basis of colony morphology. Polymorphisms, based on the amplification and restriction digestion of the intergenic transcribed spacer (ITS) region within the 10 assigned biotypes and 18 ATCC reference strains, were used to investigate the ability of this approach to differentiate closely related sphingomonads. ITS size, which ranged between 400 and 1100 bp, did not vary enough among the different genera. However, 16 distinct banding patterns within the ATCC reference strains and 9 within the 10 biotypes were obtained through ITS restriction digestion, and the majority of the tested biotypes produced patterns similar to those generated by the ATCC strains. To our knowledge, this study is not only the first comprehensive record of the size of the ITS region in sphingomonads, it is also the first study that describes the use of ITS restriction digestion to subtype those isolates.

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Henderson, G., and J. P. Simons. "Processing of DNA prior to illegitimate recombination in mouse cells." Molecular and Cellular Biology 17, no. 7 (July 1997): 3779–85. http://dx.doi.org/10.1128/mcb.17.7.3779.

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In mammalian cells, the predominant pathway of chromosomal integration of exogenous DNA is random or illegitimate recombination; integration by homologous recombination is infrequent. Homologous recombination is initiated at double-strand DNA breaks which have been acted on by single-strand exonuclease. To further characterize the relationship between illegitimate and homologous recombination, we have investigated whether illegitimate recombination is also preceded by exonuclease digestion. Heteroduplex DNAs which included strand-specific restriction markers at each of four positions were generated. These DNAs were introduced into mouse embryonic stem cells, and stably transformed clones were isolated and analyzed to determine whether there was any strand bias in the retention of restriction markers with respect to their positions. Some of the mismatches appear to have been resolved by mismatch repair. Very significant strand bias was observed in the retention of restriction markers, and there was polarity of marker retention between adjacent positions. We conclude that DNA is frequently subjected to 5'-->3' exonuclease digestion prior to integration by illegitimate recombination and that the length of DNA removed by exonuclease digestion can be extensive. We also provide evidence which suggests that frequent but less extensive 3'-->5' exonuclease processing also occurs.

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Komatsuda, T., I. Nakamura, F. Takaiwa, and S. Oka. "Development of STS markers closely linked to the vrs1 locus in barley, Hordeum vulgare." Genome 41, no. 5 (October 1, 1998): 680–85. http://dx.doi.org/10.1139/g98-069.

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Three random amplified polymorphic DNAs (RAPDs) closely linked to the vrs1 (formerly v) locus were sequenced and converted to sequence-tagged sites (STSs). Of the three STSs, two retained the RAPD polymorphism as dominant-recessive markers between 'Kanto Nakate Gold' (KNG; a two-rowed barley) and 'Azumamugi' (AZ; a six-rowed barley), while the other was co-dominant after digestion with restriction enzymes. Six restriction fragment length polymorphisms (RFLPs) linked to vrs1 were converted to six STSs. All six STSs were co-dominant between the two cultivars after digestion with restriction enzymes. A reliable protocol for small-scale DNA isolation from leaf tissue was developed. The STS markers and the small-scale DNA isolation protocol developed in this study are useful tools for mapping the vrs1 locus of barley.Key words: vrs1 locus (two-row vs. six-row), STSs, co-dominance, Hordeum vulgare.

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Oliveira, R. S., M. P. Sircili, S. Y. M. Ueki, M. A. S. Telles, B. Schnabel, M. R. S. Briones, and S. C. Leão. "PCR-Restriction Enzyme Analysis of a Bone Marrow Isolate from a Human Immunodeficiency Virus-Positive Patient Discloses Polyclonal Infection with Two Mycobacterium avium Strains." Journal of Clinical Microbiology 38, no. 12 (2000): 4643–45. http://dx.doi.org/10.1128/jcm.38.12.4643-4645.2000.

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Polyclonal infection by Mycobacterium avium was detected by hsp65 PCR-restriction enzyme analysis (PRA) in a bone marrow isolate from an AIDS patient. Two M. aviumstrains, differing in colony morphology, PRA HaeIII digestion pattern, insertion element (IS) 1245amplification, and restriction fragment length polymorphism fingerprints with IS1245 and IS1311 probes, were isolated.

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Groot, Masja Nierop, Frank Nieboer, and Tjakko Abee. "Enhanced Transformation Efficiency of Recalcitrant Bacillus cereus and Bacillus weihenstephanensis Isolates upon In Vitro Methylation of Plasmid DNA." Applied and Environmental Microbiology 74, no. 24 (October 24, 2008): 7817–20. http://dx.doi.org/10.1128/aem.01932-08.

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ABSTRACT Digestion patterns of chromosomal DNAs of Bacillus cereus and Bacillus weihenstephanensis strains suggest that Sau3AI-type restriction modification systems are widely present among the isolates tested. In vitro methylation of plasmid DNA was used to enhance poor plasmid transfer upon electroporation to recalcitrant strains that carry Sau3AI restriction barriers.

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Matar, Ghassan M., Jane E. Koehler, Georgia Malcolm, Mary Ann Lambert-Fair, Jordan Tappero, Suzan B. Hunter, and Bala Swaminathan. "Identification of Bartonella Species Directly in Clinical Specimens by PCR-Restriction Fragment Length Polymorphism Analysis of a 16S rRNA Gene Fragment." Journal of Clinical Microbiology 37, no. 12 (1999): 4045–47. http://dx.doi.org/10.1128/jcm.37.12.4045-4047.1999.

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It is now established that two species of Bartonella, namely, Bartonella henselae and B. quintana, cause bacillary angiomatosis in human immunodeficiency virus-infected patients. In addition, B. henselae causes cat scratch disease and B. quintana, B. henselae, andB. elizabethae can cause bacteremia and endocarditis in immunocompetent persons. We have developed a PCR-restriction fragment length polymorphism-based assay for direct detection and identification to species level of Bartonella in clinical specimens. This is accomplished by PCR amplification of Bartonella DNA using primers derived from conserved regions of the gene carrying the 16S ribosomal DNA, followed by restriction analysis usingDdeI and MseI restriction endonucleases. We amplified a Bartonella genus-specific 296-bp fragment from 25 clinical samples obtained from 25 different individuals. Restriction analysis of amplicons showed that identical patterns were seen from digestion of B. henselae and B. quintanaamplicons with DdeI, whereas a different unique pattern was seen by using the same enzyme with B. vinsonii and B. elizabethae. With MseI digestion, B. henselae and B. vinsonii gave nearly identical patterns while B. quintana and B. elizabethaegave a different pattern. By combining the restriction analysis data generated with MseI and DdeI, unique “signature” restriction patterns characteristic for each species were obtained. These patterns were useful in identifying theBartonella species associated with each tissue specimen.

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Thompson, D. P., and P. S. Barboza. "Responses of caribou and reindeer (Rangifer tarandus) to acute food shortages in spring." Canadian Journal of Zoology 91, no. 9 (September 2013): 610–18. http://dx.doi.org/10.1139/cjz-2013-0047.

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Migratory caribou and sedentary reindeer (Rangifer tarandus (L., 1758)) can encounter acute food shortages during spring. We examined the response to short-term food restrictions by measuring individual food intake, body mass, and activity of 2-year-old unbred female caribou and reindeer from 25 April to 29 May 2011. Caribou lost 2%–3% of body mass on days when mean dry matter (DM) intakes (60 ± 6 g DM·kg−0.75·d−1) were restricted up to 75%. Caribou regained body mass as intake increased to 98 ± 8 g DM·kg−0.75·d−1 following restriction without a change in digestibility (82%–83%). In reindeer, digestibility increased (78%–83%) as intakes decreased (67–45 g DM·kg−0.75·d−1). Food restriction did not affect activity for either subspecies. We suggest that, at high digestive efficiency, Rangifer have “spare capacity”, to increase DM intake to compensate for lost foraging opportunity or to use patches of emerging high-quality forage. Furthermore, caribou with large fat reserves lost proportionally more body mass, consumed less food, and were less active than leaner caribou. Our data indicate that Rangifer use flexible responses of food intake, digestion, and body condition to maximize survival and reproduction in both migratory and sedentary ecotypes at the end of winter.

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Yao, Binbin, Sha Zhu, Xinyu Xu, Ninghan Feng, Yaping Tian, and Nandi Zhou. "Ultrasensitive detection of the androgen receptor through the recognition of an androgen receptor response element and hybridization chain amplification." Analyst 144, no. 6 (2019): 2179–85. http://dx.doi.org/10.1039/c9an00034h.

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Swisher, K. D., and J. M. Crosslin. "Restriction Digestion Method for Haplotyping the Potato Psyllid,Bactericera Cockerelli." Southwestern Entomologist 39, no. 1 (March 2014): 49–56. http://dx.doi.org/10.3958/059.039.0106.

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Journal articles on the topic 'Restriction digestion'

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