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PubMed1994

A long range restriction map spanning the myxoid liposarcoma breakpoint in the q13-14 region of human chromosome 12.

We have used pulsed-field gel electrophoresis to construct a long range restriction map of the myxoid liposarcoma (MLS) breakpoint region in 12q13-14. The CHOP/GADD153 gene, consistently translocated in myxoid liposarcomas, is located less than 55 kb from the putative oncogene GLI. We have used fluorescent in situ hybridization to orient the map with respect to the chromosome, and to show that GLI (and thus A2MR) is located proximal to the MLS breakpoint.

CCAAT-Enhancer-Binding Proteins↗
PubMedDate not supplied

Long-range restriction mapping of megabase-sized chromosomes that may be homologs in Trypanosoma brucei.

Trypanosoma brucei is a blood-borne pathogen that changes its variant surface glycoprotein coat, thus evading immune destruction. Restriction digestion, combined with probe hybridization studies, was used to construct long-range restriction maps of the 1.4 (M4) and 1.5 megabase (M3) chromosomes from the IsTaR1 serodeme of T. b. brucei. Comparison of the two chromosomes suggests that they are a homologous pair. Hybridization with a repetitive sequence probe also identifies several copies on the M4 chromosome and a relative paucity of cross-hybridizing repetitive sequence on the larger M3 chromosome.

Animals↗
PubMedDate not supplied

A partial restriction map of the proA-purE region of the Escherichia coli K12 chromosome.

EcoRI restriction mapping data for fragments larger than 0.7 kb and contained in a 350-kb region of the Escherichia coli K-12 chromosome are presented. 75% of these fragments have been located relative to proA, B, argF, lac, proC, purE, and various insertion sequence elements normally present in this region. BglII and BamHI maps for the regions near argF and purE are also provided.

Bacterial Proteins↗
PubMed1994

A subgraph problem from restriction maps of DNA.

Computing the minimum number of edge removals needed to convert a bipartite graph into an interval graph was proposed by Waterman and Griggs in the study of restriction maps of DNA. We show that this problem is N P-complete and we give a polynomial algorithm that finds an edge-maximum interval subgraph for trees. Then various heuristics can be devised using this algorithm.

Algorithms↗
PubMed1996

The location of four fimbrin-encoding genes, agfA, fimA, sefA and sefD, on the Salmonella enteritidis and/or S. typhimurium XbaI-BlnI genomic restriction maps.

Four fimbrin-encoding genes, fimA (type-1 or SEF21 fimbriae), agfA (thin aggregative or SEF17 fimbriae), sefA (SEF14 fimbriae and sefD (SEF18 fimbriae) from Salmonella enteritidis (Se) 27655-3b were located onto the XbaI-BlnI genomic restriction maps of Salmonella typhimurium (St) LT2 and Se strains SSU7998 and 27655-3b. The XbaI or BlnI genomic fragments carrying these genes were identified by hybridization with labeled oligodeoxyribonucleotides or fimbrin-encoding genes. The fimbrin-encoding genes were not encoded by the virulence plasmids, but were located on chromosomal DNA fragments. The position of each gene on a given XbaI fragment was determined by hybridization of a series of XbaI-digested genomic DNA samples from previously characterized Tn10 mutants of Se and St with its respective probe. The fimA gene mapped near 13 centisomes (Cs) between purE884::Tn10 at 12.6 Cs (11.8 min) and apeE2::Tn10 at 12.8 Cs (12.3 min) beside the first XbaI site at 13.0 Cs in St or between purE884::Tn10 at 12.6 Cs and the XbaI site at 13.6 Cs in Se. The agfA gene mapped near 26 Cs between putA::Tn10 and pyrC691::Tn10 in St, but near 40 Cs between pncX::Tn10 and the XbaI site at 43.3 Cs in Se. This difference in map position was due to the location of agfA near one end of the 815-kb chromosomal fragment inverted between Se and St. The sefA and sefD genes mapped precisely at 97.6 Cs in Se, but were absent from the genome of St LT2. To verify the mapping procedures used herein, tctC was also mapped in both Salmonella serovars. As expected, tctC mapped near 60 Cs in both St and Se, thereby confirming previous studies.

Antigens, Bacterial↗
PubMed1990

Human chromosome 17 NotI linking clones and their use in long-range restriction mapping of the Miller-Dieker chromosome region (MDCR) in 17p13.3.

A NotI linking library constructed from flow-sorted human chromosome 17 material was screened to aid in construction of a long-range restriction map of the Miller-Dieker chromosome region (MDCR) in 17p13.3. A total of 66 clones were mapped to one of eight regions of chromosome 17 using a somatic cell hybrid panel, and 44/66 (67%) of these clones cross-hybridized to rodent DNA on Southern blots. Of these, 24 clones were tested and all mapped to mouse chromosome 11, the homolog of human chromosome 17. Four linking clones mapped to 17p13.3 and were used for pulsed-field gel electrophoresis studies along with six other anonymous probes previously mapped to this region. Clone L132 was found to be deleted in all Miller-Dieker patients tested (n = 15) and therefore lies within the critical region for this disorder. It detects two NotI fragments (180 and 320 kb), one of which (320 kb) was shared by YNZ22 and YNH37, two probes previously shown to be co-deleted in all patients with the Miller-Dieker syndrome (MDS). These results indicate that all MDS patients share a minimum deletion region of greater than 370 kb. Two other NotI clones, L53 and L125, mapped telomeric to the MDS critical region and share a 600-kb MluI fragment with each other and with YNZ22/YNH37. This provides a 930-kb MluI map that encompasses the distal boundary of the MDS critical region but does not include the proximal boundary. A total of over 2 Mbp is represented in the MluI fragments by probes in subband p13.3, a cytogenetic region estimated to be 3-4 Mbp.

Abnormalities, Multiple↗
PubMed1994

Construction of a cosmid contig and of an EcoRI restriction map of yeast chromosome X.

We report here the construction of a complete physical map of the chromosome X of yeast Saccharomyces cerevisiae. Fragments resulting from partial Sau3AI digestion of DNA from a diploid strain derived from S288C were ligated to linearized pWE15, a cosmid vector with T3 and T7 promoters. Another library, made in the cosmid vector pOU61 cos, that lacks T3 and T7 promoters, was also used as a source of target clones. Chromosome-X-specific clones were sorted out by hybridization with radiolabelled pulse-field-gel-purified chromosome X as a probe. Then, 254 cosmids were ordered by walking from one to another by hybridization with end-specific T3 or T7 RNA transcripts as probes. The construction was put to the test by hybridization with a battery of chromosome X gene markers, that showed that the physical map and the genetic map were colinear. The validity of the contig was further strengthened by the results of chromosome nested fractionation with meganuclease I-SceI. An EcoRI restriction map of the contig enabled further verification and measurement of the total length of the contig, that was found to be approximately 700 kb in size. In addition to providing a base for the ongoing yeast genome sequencing project, the physical map can be used to map any sequence belonging to chromosome X.

Chromosomes, Fungal↗
PubMed1993

DNA sequence variation and phylogenetic relationships among strains of Pseudomonas syringae pv. syringae inferred from restriction site maps and restriction fragment length polymorphism.

We evaluated the restriction fragment length polymorphism of genomic DNA among 53 strains of the phytopathogenic bacterium Pseudomonas syringae pv. syringae. Twenty-nine strains were isolated from beans, and the rest were isolated from 11 other hosts. Southern blots of DNA digested with EcoRI or HindIII were hybridized to two random probes from a cosmid library of P. syringae pv. syringae and a hrp (hypersensitive reaction and pathogenicity) cluster cloned from P. syringae pv. syringae. The size of hybridizing fragments was determined, and a similarity matrix was constructed by comparing strains on a pairwise basis for the presence or absence of fragments. The proportion of shared fragments was then used to estimate sequence divergence. Dendrograms were produced by using the unweighted pair group method with averages and the neighbor-joining method. For the hrp region, BamHI, EcoRI, EcoRV, and HindIII restriction sites were mapped for six representative bean strains and used to construct EcoRI and HindIII restriction maps for all 30 strains pathogenic on beans. Restriction mapping revealed the presence of a 3-kb insertion in nine bean strains and a probable second insertion or deletion event on the left-hand side of the hrp cluster that biased estimates of nucleotide sequence divergence from fragment comparisons. This demonstrated that the determination of phylogenetic relationships among bacteria by using restriction fragment length polymorphism data requires mapping restriction sites to remove the effect of insertion or deletion events on the analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA, Bacterial↗
PubMed1988

Errors between sites in restriction site mapping.

Restriction site mapping programs construct maps by generating permutations of fragments and checking for consistency. Unfortunately many consistent maps often are obtained within the experimental error bounds, even though there is only one actual map. A particularly efficient algorithm is presented that aims to minimize error bounds between restriction sites. The method is generalized for linear and circular maps. The time complexity is derived and execution times are given for multiple enzymes and a range of error bounds.

Algorithms↗
PubMed1998

Phylogenetic reconstruction of the yeast genus Kluyveromyces: restriction map analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers.

We have constructed restriction site maps of the 5.8S rRNA gene and two ITS regions in 60 strains of Kluyveromyces genus. We test the value of this region as a phylogenetic indicator, and its possible use as a fast and easy method to identify species of this genus. Despite some minor incongruences, our results are in good agreement with previous phylogenetic reconstructions based on the 18S rRNA gene sequencing (Cai et al., 1996; James et al., 1997). A highly significant monophyletic group was formed by K. lactis, K. marxianus, K. aestuarii, K. dobzhanskii and K. wickerhamii, which should be considered the true Kluyveromyces genus. The other species of the genus were grouped with lower bootstrap levels. Finally, the restriction map showed by three K. lactis strains, previously identified as K. marxianus var. drosophilarum, could be interpreted as indicatory of the possible existence of different species.

DNA Primers↗
PubMed1988

The rosy region of Drosophila melanogaster and Drosophila simulans. I. Contrasting levels of naturally occurring DNA restriction map variation and divergence.

A 40-kb region around the rosy and snake loci was analyzed for restriction map variation among 60 lines of Drosophila melanogaster and 30 lines of Drosophila simulans collected together at a single locality in Raleigh, North Carolina. DNA sequence variation in D. simulans was estimated to be 6.3 times greater than in D. melanogaster (heterozygosities per nucleotide of 1.9% vs. 0.3%). This result stands in marked contrast to results of studies of phenotypic variation including proteins (allozymes), morphology and chromosome arrangements which are generally less variable and less geographically differentiated in D. simulans. Intraspecific polymorphism is not distributed uniformly over the 40-kb region. The level of heterozygosity per nucleotide varies more than 12-fold across the region in D. simulans, being highest over the hsc2 gene. Similar, though less extreme, variation in heterozygosity is also observed in D. melanogaster. Average interspecific divergence (corrected for intraspecific polymorphism) averaged 3.8%. The pattern of interspecific divergence over the 40-kb region shows some disparities with the spatial distribution of intraspecific variation, but is generally consistent with selective neutrality predictions: the most polymorphic regions within species are generally the most divergent between species. Sequence-length polymorphism is observed for D. melanogaster to be at levels comparable to other gene regions in this species. In contrast, no sequence length variation was observed among D. simulans chromosomes (limit of resolution approximately 100 bp). These data indicate that transposable elements play at best a minor role in the generation of naturally occurring genetic variation in D. simulans compared to D. melanogaster. We hypothesize that differences in species effective population size are the major determinant of the contrasting levels and patterns of DNA sequence and insertion/deletion variation that we report here and the patterns of allozyme and morphological variation and differentiation reported by other workers for these two species.

Animals↗
PubMed1993

A NotI restriction map of the entire long arm of human chromosome 21.

A variety of maps of the human genome have been constructed, including cloned DNA maps. We have isolated 40 of the 42 NotI sites that exist on the long arm of human chromosome 21, as NotI linking clones and constructed a complete NotI restriction map spanning the entire region. This map, which provides the most reliable ordering and distance estimation in the region from a pericentromeric locus to the terminus, demonstrates the usefulness of linking clone mapping for analysing human chromosomes.

Animals↗
PubMed1989

[Restriction map of E. coli shuttle plasmid (p# GTE5) with secretive function].

The shuttle plasmid (p# GTE5) DNA with secretive function was extracted by the alkali lysozyme method from E. coli RRI strain. Its molecular weight is 4.5 Md and DNA size is 6.9 Kb. Restriction fragments of plasmid was obtained by single and double enzymes complete digestion using five different restriction endonucleases. The restriction map of shuttle plasmid (p# GTE5) was established for the enzymes EcoRI, BglII, pstI, PvuII, and TaqI.

Escherichia coli↗
PubMed1993

Long range restriction mapping of 13q14.3 focused on the Wilson disease region.

The Wilson disease locus (WND) has been mapped by multipoint linkage analysis to a region within 13q14.3 that is flanked proximally by marker D13S31 and distally by marker D13S59 at distances of 0.4 and 1.2 cM, respectively. Long range restriction maps were constructed around these two markers to provide a framework for the detailed physical analysis that will be necessary for the cloning of the gene. The maps, together spanning over 4 Mb, include five newly isolated markers (D13S110, D13S113, D13S194, D13F71S1, and D13S196) and two established markers (D13S56 and D13S25) that were previously localized to 13q14.2-q14.3 using a hybrid panel. Markers D13F71S1 and D13S196 map to the region between D13S31 and D13S59 and will therefore be useful for the isolation of YACs for further molecular studies on Wilson disease.

Animals↗
PubMed1987

Human adenovirus from subgenus D: restriction mapping of types 9 and 19 and characterization of a new genome type.

A strain of adenovirus (AV) was isolated from the stools of a child with acute gastroenteritis. This virus (strain 208) was specifically neutralized by antiserum to AV19, a species belonging to subgenus D and previously reported to cause keratoconjunctivitis. However, restriction analysis of strain 208 showed it to be distinct from AV19 and the other 40 human AV serotypes presently known. When calculated from 18 restriction patterns, the proportion of comigrating fragments common to AV19 and strain 208 was only 57%. This percentage was no higher than that obtained by comparison of strain 208 and AV9, a randomly chosen type from subgenus D. Strain 208 therefore appeared to represent a new genome type. The restriction maps of the three viruses for BamHI, ClaI, EcoRI, HindIII, MluI, NdeI and SfiI endonucleases are presented.

Adenoviruses, Human↗
PubMed1986

[Restriction mapping of recombinant plasmids carrying the genes for arginine biosynthesis in Escherichia coli K-12].

ArgA and argECBH genes of Escherichia coli K-12 were cloned on the pBR322 vector. Restriction maps of the recombinant plasmids were constructed. Deletion mutants of these recombinant plasmids, retaining the functional argA and argE genes, were obtained using different restriction enzymes. All of the recombinant derivatives have the replication properties of the pBR322 vector.

Arginine↗
PubMed1980

Restriction map of native and cloned cauliflower mosaic virus DNA.

Cloned CaMV DNA replicates faithfully in Escherichia coli, since the restriction map of the cloned DNA can be superimposed over that of the native viral DNA. However, some short fragments were difficult to detect in the restricted native viral DNA, whereas they formed clear bands when derived from cauliflower mosaic virus (CaMV) DNA clones propagated in the E. coli host. Apparently, the small fragments that carry variable-length single-stranded gaps present only in native viral DNA, give rise to diffuse weak bands difficult to recognize in gels. Comparison of maps for several CaMV strains permits evaluation of their possible evolutionary relationship.

Chromosome Mapping↗