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PubMed1995

Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces.

We have developed a surface mounting technology for the rapid construction of ordered restriction maps from individual DNA molecules. Optical restriction maps constructed from yeast artificial chromosome DNA molecules mounted on specially derivatized glass surfaces are accurate and reproducible, and the technology is amenable to automation. The mounting procedures described here should also be useful for fluorescence in situ hybridization studies. We believe these improvements to optical mapping will further stimulate the development of nonelectrophoretic approaches to genome analysis.

Automation↗
PubMed1992

Enteric adenovirus type 41 isolates: cloning, physical maps and diversity in restriction enzyme cleavage pattern.

Adenovirus (Ad) type 40 and 41 DNAs were directly extracted from stool specimens of children with gastroenteritis. Two new strains of Ad41, Sanekata and Ehime strain, were cloned and their restriction maps were constructed. The left terminal end of the cloned Ad41 genome, EcoRI-E fragment of the Sanekata strain and EcoRI-F fragment of the Ehime strain, had transforming ability in rat 3Y1 cells. Only one of the 35 isolates of Ad40 tested showed a different restriction profile, while three different restriction profiles were found in DNAs from Ad41 isolates.

Adenovirus Infections, Human↗
PubMed1996

A contribution to the systematization of bovine herpesvirus 1 based on genomic mapping by restriction fragment pattern analysis.

Fourteen isolates of bovine herpesvirus 1 (BHV-1) found representative of more than 100 isolates studied, were compared by restriction fragment pattern analyses and molecularly characterized. A number of evolutionary links between the variants originally associated with infectious bovine rhinotracheitis and the variants originally associated with infectious pustular vulvovaginitis were identified. These findings, as well as the lack of any correlation between genome type and clinical manifestation, confirm that there is no phylogenetic basis for a distinction between groups of strains associated with genital and respiratory disease. Two attenuated vaccine strains can be identified as deviating from field isolates.

Animals↗
PubMed1995

A novel amber mutation in a beta zero-thalassaemia gene (beta 37TGG-->TAG), with direct detection by mapping the restriction fragments in amplified genomic DNA.

A novel amber mutation, a G to A substitution at the second position of codon 37 in the beta-globin gene that changes the tryptophan coding triplet (TGG) to a termination codon (TAG), was found in a Chinese beta-thalassaemia carrier. The mutant gene creates an additional Dde I recognition site and eliminates the Ava II site, so this point mutation can be directly identified by restriction enzyme analysis.

Adult↗
PubMed1987

Measuring the human T cell receptor gamma-chain locus.

The human T cell receptor gamma locus, including eleven variable-region, five joining-region, and two constant-region segments, is contained in 160 kilobases. During T cell somatic development these genes undergo rearrangement by deletion of the sequences separating the variable and joining regions. The molecular map of this locus was completely defined by deletion mapping and restriction mapping. Restriction fragments were resolved by standard agarose electrophoresis and field inversion electrophoresis. These studies demonstrate that the deletions in this locus, which occur during the formation of a functional T cell receptor gamma-chain gene, range from 50 to 145 kilobases in length. These studies also provide a structural basis for understanding the development of the gamma-chain peptide repertoire, and extends the potential of the emerging pulsed-field electrophoretic technology.

Cell Line↗
PubMed1991

Evolution of the dec-1 eggshell locus in Drosophila. I. Restriction site mapping and limited sequence comparison in the melanogaster species subgroup.

We have analyzed approximately 18 kb of DNA in and upstream of the defective chorion-1 (dec-1) locus of the eight known species of the melanogaster species subgroup of Drosophila. The restriction maps of D. simulans, D. mauritiana, D. sechellia, D. erecta, and D. orena are shown to have basically the restriction map of D. melanogaster, whereas the maps of D. teissieri and D. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65-200 bp) is found in a repeated sequence of the central transcribed region of D. melanogaster, D. simulans, and D. erecta. Restriction site mapping indicated that the dec-1 gene is highly conserved in the melanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5' translated region. The 5' flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within the melanogaster species subgroup except that the erecta-orena pair is placed closer to the melanogaster complex than to D. teissieri and D. yakuba.

Amino Acid Sequence↗
PubMed1992

Analysis of chromosome-sized DNA from the bacterial genome of thermophilic Campylobacter laridis by pulsed-field gel electrophoresis and physical mapping.

Three restriction enzymes ApaI, SalI and SmaI, among nine enzymes tested, were found to produce distributions of DNA fragments which were useful for analysis of chromosome-sized DNA from thermophilic Campylobacter laridis by pulsed-field gel electrophoresis. From experiments with C. laridis JCM2530T and four isolates of C. laridis, the size of the genome of C. laridis was calculated to range from 1,590 to 1,700 kb, with a mean of 1,640 kb. An SmaI restriction map was derived by the partial digestion of the DNA from C. laridis JCM2530T.

Base Sequence↗
PubMed1981

Physical map of the Salmonella typhimurium histidine transport operon: correlation with the genetic map.

A detailed restriction map of a 12.4-kilobase EcoRI fragment of Salmonella typhimurium deoxyribonucleic acid (DNA) containing the entire histidine transport operon and the argT gene is presented. Subclones of specific regions of the transport operon of S. typhimurium were constructed in plasmid vectors. An accurate correlation between the restriction map and the location of genetically defined deletions was obtained by hybridizing restriction digests of chromosomal DNA from strains carrying each deletion with cloned transport operon DNA as a probe. These data were used to position the histidine transport genes on the cloned 12.4-kilobase fragment of DNA.

Biological Transport↗
PubMed2006

Using universal degenerate primers for restriction digestion mapping by PCR.

In this study, a polymerase chain reaction (PCR) is developed to determine the restriction map without using restriction endonucleases. A 937 bp fragment of pUC 19 which contained one cut site for EcoRI and two recognition sites for PvuII was used as a model. The PCR was carried out using designed degenerate primers and the products were analyzed on 1.5% agarose gel. The number of cut sites, length of fragments and the arrangement of the fragments from 3' or 5' end of desired sequence were determined.

DNA Primers↗
PubMed1992

Cloning and restriction endonuclease mapping of the genome of an equine herpesvirus 4 (equine rhinopneumonitis virus), strain 405/76.

Purified virion DNA of an Australian isolate of equine herpesvirus 4(EHV 4.405/76) was digested with restriction enzymes and the DNA fragments were cloned into pUC19. The resulting recombinant plasmid library, representing 92% of the virus genome, was used in hybridization analyses to construct restriction maps for BamHI, EcoRI, and SalI for the EHV4 genome. The results show that the genome of EHV 4.405/76 was approximately 145 kb and comprised a unique long (UL) region of 112 kb and a unique short (US) region of 12.4 kb. US is flanked by an internal and terminal repetitive sequence (IRS and TRS) of about 10.3 kb. The BamHI and EcoRI restriction maps are similar to those previously published for an English isolate EHV 4.1942 strain although some differences such as location of an additional fragment and changes in positions of two other small fragments were found.

Animals↗
PubMed1984

Restriction endonuclease mapping and cloning of Mycobacterium intracellulare plasmid pLR7.

A restriction map of Mycobacterium intracellulare plasmid pLR7 was developed. This 15.3-kb plasmid had unique sites for BamHI, HindIII, and XbaI. Various large fragments of pLR7 were cloned into pBR322 or pHP34 and propagated in Escherichia coli. A hybrid pLR7 ::pBR322 plasmid carrying the complete pLR7 sequence was constructed by joining the plasmids at their HindIII sites. The construction of these hybrids will facilitate the analysis and manipulation of pLR7 and may allow the development of this plasmid as a model system for genetic analysis in mycobacteria.

Chromosome Mapping↗
PubMed1983

Isolation and characterization of the dut gene of Escherichia coli. II. Restriction enzyme mapping and analysis of polypeptide products.

Restriction endonuclease mapping of previously constructed dut plasmids has been carried out using the enzymes PvuI, PvuII and SacI. Various dut plasmids were also tested in the "maxicell" protein-synthesizing system. They all show two protein bands in common, one of Mr 16000 in agreement with the size previously reported for the purified dUTPase subunit (Shlomai and Kornberg, 1978). With the information obtained the structural gene for dUTPase can be assigned to a 950-bp SacI-PvuII fragment of the E. coli genome. Studies, described in the preceding paper, on the overproduction of dUTPase by bacterial strains carrying different dut plasmids strongly suggest that the dut gene is transcribed in the direction from the SacI site towards the PvuII site and that the SacI site is located within the dut control region. The second protein band observed in the "maxicell" experiments has an Mr of 23500. Its identity is unknown but it may represent a precursor of dUTPase or the product of a separate gene located between dut and pyrE.

Chromosome Mapping↗
PubMed1981

Structure and restriction enzyme maps of the circularly permuted DNA of staphylococcal bacteriophage phi 11.

One restriction enzyme map of Staphylococcus aureus bacteriophage phi 11 DNA was established by reciprocal double digestions with the enzymes EcoRI, HaeII, and KpnI. The sequential order of the EcoRI fragments was thereafter established by a novel approach involving blotting of DNA partially cleaved with EcoRI and the probing the blots with nick-translated terminal fragments. A circular map of the phi 11 DNA was established, and the phage genome was circularly permuted based on the failure to end label mature viral DNA, restriction maps of replicating DNA, and finally, homoduplex analysis in the electron microscope. A restriction enzyme map of the prophage form of phi 11 DNA was obtained by analysis of chromosomal DNA from a lysogenic strain.

Chromosome Mapping↗
PubMed1990

Restriction site mapping for three or more enzymes.

Restriction site mapping requires a generator to put forward possible maps and a constraint checker to reject false maps. Ideally these combine to give an algorithm which calculates a sound and complete solution set. Three algorithms for generation are presented and compared. Two decompose a multi-enzyme problem (greater than or equal to 3) into subproblems. The constraint checker is based on separation theory. Some insights into the extent of constraint checking involved in and feasibility of more checking for three or more enzymes are discussed. The trade-off between computation time and the soundness of the solution set is examined.

Algorithms↗
PubMed1996

Mitochondrial DNA restriction site map of Cochliomyia macellaria (Diptera:Calliphoridae).

The mitochondrial DNA of the secondary screwworm, Cochliomyia macellaria (F.), was cleaved with 15 restriction endonucleases to produce 54 restriction fragments. Forty-three restriction sites recognized by 12 enzymes were assigned positions on a restriction site map. Both the restriction fragments and the restriction site map were compared with published data from the screwworm, Cochliomyia hominivorax (Coquerel). The restriction site maps were aligned using a combination of highly conserved restriction sites. Estimated nucleotide divergence between the 2 species based on the fragments was 0.052. The divergence based on the restriction site map was 0.093. The data provide a baseline for future population or phylogenetic investigations.

Animals↗
PubMed1990

Restriction site mapping of adenovirus prototypes of subgenus D.

Restriction site maps with the endonucleases HindIII, BglII, and Bam HI were elaborated for the majority of 23 adenovirus prototypes of subgenus D (AV8 to AV39). On the basis of four or five types which have been mapped by biochemical methods, the physical maps for other types were constructed by adapting restriction fragments of defined molecular weight, as the homology among types of the same subgenus is considerable. Prototypes of subgenus D shared several common restriction sites; different sites, however, were distributed at random over the genome. The gene loci for hexon and fiber did not show either higher or lower variability.

Adenoviridae↗
PubMed1999

Optical mapping of Plasmodium falciparum chromosome 2.

Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensembles of individual DNA molecules. DNA molecules were bound to derivatized glass surfaces, cleaved with NheI or BamHI, and imaged by digital fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restriction fragments were mapped. Maps were assembled from 50 molecules producing an average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by optical mapping with NheI, and 946 kb with BamHI, which compares closely to the published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optical mapping data, and good correspondence was found. Such high-resolution restriction maps may become an indispensable resource for large-scale genome sequencing projects.

Animals↗