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PubMed1993

PFGE MAPPER: a tool to aid in the analysis of pulse field gel electrophoresis maps.

Pulse field gel electrophoresis mapping is an important technique for characterizing large segments of DNA and constructing long-range restriction maps. We have developed a tool, PFGE MAPPER, to aid in the construction of pulse field electrophoresis gel maps. This tool helps construct pulse field gel maps from single and double digest experiments visualized by hybridization with single copy probes. The program is written in Think C and runs on Macintosh computers. An intuitive interface allows the user to interactively modify fragment sizes or errors, select fragments for analysis and recalculate the maps. Maps can be printed or saved for later viewing. After constructing and saving several maps in a region, PFGE MAPPER can be used to refine and extend the overall map by merging individual maps. This tool should be useful for constructing long-range restriction maps of genomic DNA and yeast artificial chromosomes.

Algorithms↗
PubMed1986

Characterisation of chloramphenicol resistance plasmids of Staphylococcus aureus and S. epidermidis by restriction enzyme mapping techniques.

Chloramphenicol resistance (Cmr) plasmids pSK2 and pSK5 from Staphylococcus aureus and pSK102 and pSK103 from S. epidermidis have been characterised and detailed restriction endonuclease cleavage maps constructed. TaqI digestion profiles illustrated the identity of pSK5 and pSK102 and also revealed a high degree of similarity between these four Cmr plasmids from Australian staphylococci and three Cmr plasmids from S. aureus strains of geographically unrelated origin. DNA-DNA hybridisation indicated that the chloramphenicol acetyltransferase determinant carried by pSK5/pSK102 could be found on other structurally-distinct Cmr plasmids. The role of S. epidermidis as a reservoir for Cmr plasmids found in S. aureus is discussed.

Base Sequence↗
PubMed1977

HindIII and Sst I restriction sites mapped on rabbit poxvirus and vaccinia virus DNA.

The DNAs of two closely related orthopoxviruses, rabbit poxvirus (RPV) and vaccinia virus (VV), were mapped by overlapping-fragment analysis using restriction endonucleases HindIII and Sst I. The exact arrangement of these fragments was accomplished by total digestion of isolated partial restriction products and by end-fragment determination. RPV and VV DNAs showed identical restriction patterns in an internal region comprising approximately 60% of the genome. The size, by electrophoretical analysis of the RPV DNA, was 118 X 10(6) daltons, some 6 X 10(6) daltons less than VV DNA. The two opposite terminal restriction fragments of RPV DNA cross-hybridized to each other.

Base Sequence↗
PubMed1990

Restriction site mapping of bovine adenovirus type 1.

Physical maps of the DNA of bovine adenovirus (BAV) type 1 were established using ApaI, BamHI, BstEII, EcoRI and KpnI enzymes. The size of the viral genome was found to be around 35,000 base pairs. The orientation of the maps was determined by hybridizing Southern blots of BAV-1 DNA with the cloned hexon gene region of BAV-3.

Adenoviridae↗
PubMed1990

Restriction endonuclease mapping of the fowlpox virus genome.

The genome of fowlpox virus (Webster's mild vaccine strain) is composed of a single, double-stranded DNA molecule with covalently linked terminal hairpins and approximately 300 kb in length. Sites for cleavage by restriction endonucleases Pstl, Sal/l, Smal, and Notl have been identified with partial maps for EcoRI and BamHI. Differences in Pstl restriction fragment profiles for two separately prepared viruses (FPV-M and FPV-M3), both derived from the vaccine strain, indicate the presence of a nonessential region and potential insertion site for foreign DNA, toward one end of the viral genome. The size of the fowlpox virus genome, which is more than 100 kb larger than the orthopoxvirus vaccinia, indicates that the avipox viruses have the potential to code for more proteins than other groups of poxviruses.

Animals↗
PubMed1979

Mapping of restriction sites in the argF gene of Escherichia coli by partial endonuclease digestion of end-labeled DNA.

A detailed physical map depicting the cleavage sites generated by ten different restriction endonucleases was prepared for the argF region of the Escherichia coli K-12 genome carried on a 1650 base pair fragment capable of directing the in vitro synthesis of ornithine transcarbamylase (OTCase; ec 2.1.3.3) under the control of arginine holorepressor. The method employed was originally developed by Smith and Birnstiel (1976), and involved the electrophoretic sizing of partial endonuclease digestion products of DNA radiolabeled at one end. This novel technique proved to be rapid, simple, amenable to the simultaneous mapping of numerous cleavage sites, and provided the essential information for determining the map order of restriction fragments. A facile method which involved magnesium phosphate as the DNA-binding agent was presented for the isolation of DNA fragments. The discovery of a 117 base pair leader sequence in the argF gene is also discussed.

Arginine↗
PubMed1985

Restriction endonuclease mapping of adenovirus 35, a type isolated from immunocompromised hosts.

The DNA of adenovirus 35 (Ad35), a type recently associated with infections in immunocompromised hosts, was mapped by the use of BamHI, SmaI, PstI, EcoRI, and HpaI restriction endonucleases. In addition to standard mapping procedures, we used the in vitro adenovirus DNA replication system with origins at both physical ends of the linear molecule to determine the terminal fragments. Deletions of single restriction endonuclease sites in a group of closely related adenovirus isolates from patients with acquired immunodeficiency syndrome helped determine the location of some DNA fragments on the genome.

Acquired Immunodeficiency Syndrome↗
PubMed1989

Structure of the human CR1 gene. Molecular basis of the structural and quantitative polymorphisms and identification of a new CR1-like allele.

Structural and quantitative polymorphisms have been described in human CR1. In the former, the S allotype is larger than the F allotype by 40-50 kD, the size of a long homologous repeat (LHR). In the latter, homozygotes for a 7.4-kb Hind III fragment express fourfold more CR1 per erythrocyte than do homozygotes for the allelic 6.9-kb restriction fragment. The basis for these genomic polymorphisms has been determined by restriction mapping the entire S allele and part of the F allele. The S allele is 158 kb and contains 5 LHRs of 20-30 kb, designated -A, -B/A, -B, -C, and -D, respectively, 5' to 3'. Extensive homology was found among the LHRs in their restriction maps, exon organization, and the coding and noncoding sequences. The presence of LHR-B/A in the S allele but not in the F allele accounts for the longer transcripts and polypeptide associated with the former allotype. At least 42 exons are present in the S allele, with distinct exons for the leader sequence, the transmembrane and cytoplasmic regions and most of the SCRs comprising the extracellular portion of CR1. Consistent with the mapping of the ligand binding site to the first two SCRs in each LHR, the second SCRs in LHR-A, -B/A, -B, and -C are encoded by two exons, reflecting a specialized function for this unit. The allelic 7.4/6.9-kb Hind III fragments extend from the 3' region of LHR-C to LHR-D. The 6.9-kb restriction fragment is the result of a new Hind III site generated by a single base change in the intron between the exons encoding the second SCR of LHR-D. A second cluster of genomic clones has been identified by hybridization to CR1 probes. Although they contain regions of hybridization to the cDNA and genomic probes derived from CR1, these cannot be overlapped with the structural gene owing to their distinct restriction maps. Three genomic polymorphisms previously identified by CR1 cDNA probes map to this region. These additional clones may represent part of a duplicated allele located nearby within the CR1 locus.

Alleles↗
PubMed1993

CpG island mapping of a mouse double-minute chromosome.

The development of double-minute chromosomes (DMs) and subsequent gene amplification are important genomic alterations resulting in increased oncogene expression in a variety of tumors. The molecular mechanisms mediating the development of these acentric extrachromosomal elements have not been completely defined. To elucidate the mechanisms involved in DM formation, we have developed strategies to map amplified circular DM DNA. In this study, we present a long-range restriction map of a 980-kb DM. A cell line cloned from mouse EMT-6 cells was developed by stepwise selection for resistance to methotrexate. This cloned cell line contains multiple copies of the 980-kb DM carrying the dihydrofolate reductase (DHFR) gene. A long-range restriction map was developed in which a hypomethylated CpG-rich region near the DHFR gene served as a landmark. This strategy was combined with plasmid-like analysis of ethidium bromide-stained pulsed-field gels and indicated that a single copy of the DHFR gene was located near a hypomethylated region containing SsII and NotI sites. At least 490 kb of this DM appears to be composed of unrearranged chromosomal DNA.

Animals↗
PubMed1992

Restriction enzyme mapping of carcinogen binding regions on pBR322.

Previous equilibrium binding experiments (S.A. Winkle and T.R. Krugh, Nucleic Acids Res. 9, 3175-3186 (1981)) suggested that the carcinogen N-hydroxy-N-acetyl-2-aminofluorene might exhibit preferential binding to a small number of sites on phiX174 DNA. To examine whether the covalently binding analogue N-acetoxy-N-acetyl-2-aminofluorene (acetoxyAAF) also possesses high affinity sites, the plasmid pBR322 was reacted with 3H labeled acetoxyAAF to give one to sixteen adducts per DNA molecule. Thus only higher affinity sites would be affected. The DNA was subsequently cleaved with either Alu I, Hae III, Hha I, Hinf I or Hpa II restriction endonuclease and the restriction fragments isolated by gel electrophoresis. Examination of the distribution of 3H acetoxyAAF among the fragments was not random but, rather, with each enzyme, the acetoxyAAF was found predominantly in a few fragments. The locations of the bands containing the acetoxyAAF for each enzyme overlap--suggesting that there are regions on pBR 322 which contain high affinity sites for acetoxyAAF binding.

Acetoxyacetylaminofluorene↗
PubMed1988

Restriction endonuclease mapping of six novel deletions of the factor VIII gene in hemophilia A.

Hemophilia A is an X-linked disease of blood coagulation caused by deficiency of factor VIII. Using cloned cDNA, genomic and synthetic oligonucleotide factor VIII probes, we have identified six novel partial gene deletions in patients with severe hemophilia A. We have previously reported six other deletions of the factor VIII gene. The number of gross molecular defects (deletions, insertions) in the factor VIII gene in our series of 240 patients is 17 (3 insertions and 2 complicated deletions will be described elsewhere). No association was observed between the size or location of the deletions and the presence of inhibitors to factor VIII. No deletion breakpoint "hotspots" have been identified by restriction analysis. The parental origin of several of the deletions was determined.

Adolescent↗
PubMedDate not supplied

Phylogenetic relationships of three species of crows (Corvidae, Aves) based on the restriction site variation of nuclear ribosomal RNA gene.

Southern blot analysis of nuclear ribosomal DNA (rDNA) was carried out to examine phylogenetic relationships between three species of crows: Corvus cornix, C. corone and C. macrorhynchos. In this purpose DNA samples of birds were digested by 12 restriction enzymes (EcoRI, HindIII, PstI, BamHI, DraI, PvuII, KpnI, XbaI, BglII, BclI, SacI and AatI) and hybridized with the clones of mouse rDNA probes (18S, 28S and INT). Based on the data obtained and Gallus gallus restriction map as a standard the restriction site maps of the main rDNA repeating unit types (repetypes) were constructed. The length of crow rDNA genes was estimated to be 22.5 kb for Jungle and 22.0 kb for Hooded and Carrion crows. C. corone and C. cornix shared a common repetype which differed, by presence of two restriction sites (XbaI and PvuII) in the spacer region, from that of C. macrorhynchos with the estimated sequence divergence of 0.26%. Restriction-size variation was revealed between individuals of C. corone and C. cornix, although the substantial meanings of this variation remain unclear yet. These data suggest that the crow species evolve with slower rate of molecular evolution, as generally observed in other avian species, compared with the higher extent in external morphology, ecological features and behavior.

Animals↗
PubMed1997

Positional cloning of novel skin-specific genes from the human epidermal differentiation complex.

The epidermal differentiation complex, located on human chromosomal band 1q21, contains at least 20 genes expressed during epidermal differentiation. We constructed a 1.2-Mb YAC contig spanning the SPRR and S100 gene clusters. Restriction mapping and FISH confirmed the colinearity of the contig with the genomic restriction map (A. Volz et al., 1993, Genomics 18:92-99). However, the YAC clones revealed several additional restriction sites not previously detected in genomic DNA, presumably due to CpG methylation. Making use of cDNA selection, we have identified three novel cDNAs, all of which map to the SPRR/IVL region. All three transcripts are expressed at high levels in normal and psoriatic skin, but not in cultured keratinocytes or in a variety of cell lines and human tissues. The molecular cloning of this region provides a valuable tool for identifying additional epidermal differentiation genes and for elucidating the relationship between chromatin structure and gene expression during terminal differentiation.

Amino Acid Sequence↗
PubMed1981

Comparison of canine parvovirus with mink enteritis virus by restriction site mapping.

The genomes of canine parvovirus and mink enteritis virus were compared by restriction enzyme analysis of their replicative-form DNAs. Of 79 mapped sites, 68, or 86%, were found to be common for both types of DNA, indicating that canine parvovirus and mink enteritis virus are closely related viruses. Whether they evolved from a common precursor or whether canine parvovirus is derived from mink enteritis virus, however, cannot be deduced from our present data.

Animals↗
PubMed2002

A whole-genome shotgun optical map of Yersinia pestis strain KIM.

Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.

Genome, Bacterial↗
PubMed1986

Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms.

Simple single-gene disorders in humans can be genetically mapped by using traditional methods of linkage analysis and increasingly abundant restriction fragment length polymorphisms (RFLPs). Many human diseases and traits, however, can be expected to be genetically heterogeneous (i.e., caused by any one of several genes), and traditional linkage analysis is much less effective in such circumstances. We present two methods, interval mapping and simultaneous search, designed to exploit the full power of a linkage map of the DNA markers. For the simplest situations, only 1/3 as many affected families are needed to map a heterogeneous trait by using these methods. Only 1/5-1/50 as many are needed to detect that genetic heterogeneity is present.

Chromosome Mapping↗
PubMed1985

Restriction endonuclease cleavage map of the DNA of hamster papovavirus.

A detailed restriction map of hamster papovavirus (HaPV)-DNA has been constructed on the basis of the complete nucleotide sequence of the viral genome. The HaPV DNA restriction map is totally divergent from those of all other recently known papovaviruses. This map will be useful for future functional studies of the HaPV genome.

Animals↗