Positions Of Restriction Sites Research Articles

RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

Background: Reduced-representation sequencing technology is widely used in genotyping for its economical and efficient features. A popular way to construct the reduced-representation sequencing libraries is to digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the restriction enzyme(s). But there are few computer programs which can evaluate the usability of restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as fragments number. But for linkage mapping analysis, enzyme loci distribution is also an important factor to evaluate the enzyme. For phylogenetic studies, comparison of the enzyme performance across multiple genomes is important. It is strongly needed to develop a simulation tool to implement these functions. Results: Here, we introduce a Perl module named RestrictionDigest with more functions and improved performance. It can analyze multiple genomes at one run and generate concise comparison of enzyme performance across the genomes. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process and generate comprehensive information of the simulation including enzyme loci number, fragments number, sequences of the fragments, positions of restriction sites on the genome, the coverage of digested fragments on different genome regions and detailed fragments lengths distribution. Conclusions: RestrictionDigest is an easy-to-use Perl module with flexible parameter settings. With the help of the information produced by the module, researchers can easily determine the most appropriate enzymes to construct the reduced-representation libraries to meet their experimental requirements.

Spodoptera frugiperda multiple nucleopolyhedrovirus as a potential biological insecticide: Genetic and phenotypic comparison of field isolates from Colombia

Thirty-eight isolates of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV), collected from infected larvae on pastures, maize, and sorghum plants in three different geographical regions of Colombia, were subjected to molecular characterization and were compared with a previously characterized Nicaraguan isolate (SfNIC). Restriction endonuclease analysis (REN) using six different enzymes showed two different patterns among Colombian isolates, one profile was particularly frequent (92%) and was named SfCOL. The physical map of SfCOL was constructed and the genome was estimated to be 133.9kb, with few differences in terms of number and position of restriction sites between the genomes of SfNIC and SfCOL. The PstI-K and PstI-M fragments were characteristic of SfCOL. These fragments were sequenced to reveal the presence of seven complete and two partial ORFs. This region was collinear with SfMNPV sf20–sf27. However, two ORFs (4 and 5) had no homologies with SfMNPV ORFs, but were homologous with Spodoptera exigua MNPV (se21 and se22/se23) and Spodoptera litura NPV (splt20 and splt21). Biological characterization was performed against two different colonies of S. frugiperda, one originating from Colombia and one from Mexico. Occlusion bodies (OBs) of the SfCOL isolate were as potent (in terms of concentration–mortality metrics) as SfNIC OBs towards the Mexican insect colony. However, SfCOL OBs were 12 times more potent for the Colombian colony than SfNIC OBs and three times more potent for the Colombian colony than for the Mexican colony. SfCOL and SfNIC showed a slower speed of kill (by ∼50h) in insects from the Colombian colony compared to the Mexican colony, which was correlated with a higher production of OBs/larvae. SfCOL is a new strain of SfMNPV that presents pathogenic characteristics that favor its development as the basis for a biopesticide product in Colombia.

Partial characterization and cloning of the genome of PvSNPV (= BP-type virus) pathogenic for Penaeus vannamei

DAO Diseases of Aquatic Organisms Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials DAO 23:59-66 (1995) - doi:10.3354/dao023059 Partial characterization and cloning of the genome of PvSNPV (= BP-type virus) pathogenic for Penaeus vannamei Bonami JR, Bruce LD, Poulos BT, Mari J, Lightner DV PvSNPV isolated from the shrimp Penaeus vannamei was characterized after purification. In negative staining, the rod-shaped, enveloped particles were 312 to 320 nm in length and 75 to 87 nm in diameter. The nucleocapsids, 306 to 312 nm in length and 62 to 68 nm in diameter, showed a cross-hatched surface arranged in a helical pattern and a trilaminar structure capping both extremities. Purified occlusion body subunits (polyhedrin subunits) were 17 to 19 nm in diameter and, in SDS-PAGE, demonstrated 1 major polypeptide of 52 kDa. BamHI digested viral genome revealed at least 7 different fragments. Cloning of these DNA fragments, and the resulting study of them, revealed the presence of 2 more fragments which had co-migrated in gel electrophoresis. The cloned fragments, which represent about 40% of the estimated size of the genome, were characterized by their size and by the position of restriction sites. When the cloned fragments were labeled and used as probes, no homology was found among the different inserts. These gene probes reacted with different BP-type strains, but not with uninfected shrimp tissue. The gene probes also did not react with shrimp tissues infected with other shrimp viruses, indicating their specificity for the BP-type viruses. BP . PvSNPV . Penaeid shrimp . Genome cloning . Gene probes Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in DAO Vol. 23, No. 1. Publication date: September 14, 1995 Print ISSN:0177-5103; Online ISSN:1616-1580 Copyright © 1995 Inter-Research.

Physical mapping of differences in chloroplast DNA of the five wild-type plastomes in Oenothera subsection Euoenothera

1) DNA has been isolated from the five genetically distinguishable plastid types of Oenothera, subsection Euoenothera. DNA of plastomes I to IV was obtained from plants with identical nuclear backgrounds containing the genotype AA of Oenothera hookeri whereas the DNA of plastome V came from Oenothera argillicola (genotype CC). 2) The DNAs of the five basic Euoenothera wild-type plastomes can be distinguished by restriction endonuclease analysis with Sal I, Pst I, Kpn I, Eco RI and Bam HI. The fragment patterns exhibit distinct common features as well as some degree of variability. 3) Physical maps for the circular DNAs of plastome I, II, III and V could be constructed using the previously detailed map of plastome IV DNA (Gordon et al. 1981). This has been achieved by comparing the cleavage products generated by restriction endonucleases Sal I, Pst I and Kpn I which collectively result in 36 sites in each of the five plastome DNAs, and by hybridization of radioactively labelled chloroplast rRNA or chloroplast cRNA probes of spinach to Southern blots of appropriate restriction digests. The data show that the overall fragment order is the same for all five plastome DNAs. Each DNA molecule is segmentally organized into four regions represented by a large duplicated sequence in inverted orientation whose copies are separated by two single-copy segments. 4) The alterations in position of restriction sites among the Euoenothera plastome DNAs result primarily from insertions/deletions. Eleven size differences of individual fragments in the Sal I, Pst I and Kpn I patterns measuring 0.1-0.8 Md (150-1,200 bp) relative to plastome IV DNA have been located. Most changes were found in the larger of the two single-copy regions of the five plastomes. Changes in the duplication are always found in both copies. This suggests the existence of an editing mechanism that, in natural populations, equalizes or transposes any change in one copy of the repeat to the equivalent site of the other copy. 5) Detailed mapping of the two rDNA regions of the five plastomes, using the restriction endonucleases Eco RI and Bam HI which each recognize more than 60 cleavage sites per DNA molecule, disclosed a 0.3 Md deletion in plastome III DNA and a 0.1 Md insertion in plastome V DNA relative to DNA of plastome IV, I and II. These changes are most probably located in the spacer between the genes for 16S and 23S rRNA and are found in both rDNA units.

Molecular cloning vectors derived from the CoLEl type plasmid pMBl

In vitro recombination via restriction endonucleases and in vivo genetic translocation of an impicillin resistance gene, have been utilized for the construction of a series of cloning vehicles. These vectors have been derived by combining the essential replication properties of plasmid pMBl, a CoLEl type plasmid, with one, two or three resistance markers (tetracycline, ampicillin, chloramphenicol and colicin El production). During the construction of these vectors, the position of restriction sites used for cloning DNA fragments, relative to the antibiotic resistance genes and the origin of DNA replication, have been determined. The use of the cloning vectors pMB9, pBR313, pBR322, pBR324, pBR325 permits the molecular cloning and easy selection of Eco RI, Bam HI, Bgl II, Dpn II, Hind III, Sal I, Xho I, Xam I, Taq I, Pst I, Hinc II, Pvu I, Sma I, Xma I, Ba l I, Hpa I, Ava I, Pvu II, Hae III, Alu I, Hpa II, Eco RII and virtually any blunt-ended generated DNA fragment.