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Nucleic Acids Research Jun 1974SV40 DNA is cleaved by the Eco RII and Hae restriction endonucleases to give rise to two different sets of 16 fragments each. These fragments have been ordered by...
SV40 DNA is cleaved by the Eco RII and Hae restriction endonucleases to give rise to two different sets of 16 fragments each. These fragments have been ordered by analysis of the products of redigestion of one set of fragments with another restriction enzyme. The cleavage sites have been precisely mapped based on length measurements of the products of each cleavage. This provides a convenient group of small DNA fragments suitable for sequence analysis investigation of the transcripts present in infected cells, or construction of deletion substitution variants of the virus.
Topics: DNA Restriction Enzymes; DNA, Viral; Electrophoresis, Polyacrylamide Gel; Restriction Mapping; Simian virus 40
PubMed: 10793753
DOI: 10.1093/nar/1.6.727 -
Journal of Bacteriology Apr 1992We present the complete maps of five Mycoplasma hominis genomes, including a detailed restriction map and the locations of a number of genetic loci. The restriction...
We present the complete maps of five Mycoplasma hominis genomes, including a detailed restriction map and the locations of a number of genetic loci. The restriction fragments were resolved by field inversion gel electrophoresis or by the contour-clamped homogeneous-electric-field system of pulsed-field gel electrophoresis. All the ApaI, SmaI, BamHI, XhoI, and SalI restriction sites (total of 21 to 33 sites in each strain) were placed on the physical map, yielding an average resolution of 26 kb. The maps were constructed using three different approaches: (i) size determination of DNA fragments partially or completely cleaved with one or two restriction enzymes, (ii) hybridization analysis with purified restriction fragments and specific probes, and (iii) use of linking clones. A genetic map was constructed by hybridization with gene-specific probes for rpoA, rpoC, rrn, tuf, gyrB, hup, ftsY, the unc operon, the genes for two M. hominis-specific antigenic membrane proteins, and one gene encoding a protein with some homology to Escherichia coli alanyl-tRNA synthetase. The positions of mapped loci were partially conserved in the five strains except in one strain in which a 300-kb fragment was inverted. The numbers and order of mapped restriction sites were only partly conserved, and this conservation was restricted to certain regions. The gene order was compared with the gene order established for other bacteria and was found to be identical to that of the phylogenetically related Clostridium perfringens. The genome size of the M. hominis strains varied from 704 to 825 kb.
Topics: Blotting, Southern; Chromosome Mapping; Cloning, Molecular; DNA, Bacterial; Electrophoresis, Gel, Pulsed-Field; Genes, Bacterial; Mycoplasma; Restriction Mapping
PubMed: 1551841
DOI: 10.1128/jb.174.7.2199-2207.1992 -
Journal of Bacteriology May 1997PacI and SpeI restriction maps were obtained for the two chromosomes of each of the six species of the genus Brucella: B. melitensis, B. abortus, B. suis, B. canis, B.... (Comparative Study)
Comparative Study
PacI and SpeI restriction maps were obtained for the two chromosomes of each of the six species of the genus Brucella: B. melitensis, B. abortus, B. suis, B. canis, B. ovis, and B. neotomae. Three complementary techniques were used: hybridization with the two replicons as probes, cross-hybridization of restriction fragments, and a new mapping method. For each type strain, a unique I-SceI site was introduced in each of the two replicons, and the location of SpeI sites was determined by linearization at the unique site, partial digestion, and end labeling of the fragments. The restriction and genetic maps of the six species were highly conserved. However, numerous small insertions or deletions, ranging from 1 to 34 kb, were observed by comparison with the map of the reference strain of the genus, B. melitensis 16M. A 21-kb Spel fragment specific to B. ovis was found in the small chromosome of this species. A 640-kb inversion was demonstrated in the B. abortus small chromosome. All of these data allowed the construction of a phylogenetic tree, which reflects the traditional phenetic classification of the genus.
Topics: Brucella; Deoxyribonucleases, Type II Site-Specific; Electrophoresis, Gel, Pulsed-Field; Genome, Bacterial; Phylogeny; Polymorphism, Restriction Fragment Length; Replicon; Restriction Mapping; Saccharomyces cerevisiae Proteins
PubMed: 9150220
DOI: 10.1128/jb.179.10.3244-3249.1997 -
Bioinformatics (Oxford, England) Nov 2012The R/Bioconductor package HiTC facilitates the exploration of high-throughput 3C-based data. It allows users to import and export 'C' data, to transform, normalize,...
SUMMARY
The R/Bioconductor package HiTC facilitates the exploration of high-throughput 3C-based data. It allows users to import and export 'C' data, to transform, normalize, annotate and visualize interaction maps. The package operates within the Bioconductor framework and thus offers new opportunities for future development in this field.
AVAILABILITY AND IMPLEMENTATION
The R package HiTC is available from the Bioconductor website. A detailed vignette provides additional documentation and help for using the package.
Topics: Animals; Chromosome Mapping; Chromosomes, Human, Pair 14; Data Display; Humans; Mice; Molecular Conformation; Restriction Mapping; Software
PubMed: 22923296
DOI: 10.1093/bioinformatics/bts521 -
Genes Apr 2019The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, , is an economically important...
The sex of an animal influences its economic traits, especially in species displaying sexual dimorphism. The Chinese soft-shelled turtle, , is an economically important aquatic species that shows significant male sexual dimorphism, with a large body size, faster growth, a thick and wide calipash, and lower body fat. In this study, ten male and ten female turtles were subjected to restriction site-associated DNA sequencing (RAD-seq) using the Hi-Seq 4000 sequencing platform to isolate female-specific DNA fragments. We identified 5967 bp and 6532 bp fragments using genome walking. Three female-specific markers designed from these two fragments were confirmed to separate the sexes of perfectly. One of the female-specific markers showed dosage association in female and male individuals. Individuals from different populations (n = 296) were used to validate that the female-specific markers could identify the genetic sex of with 100% accuracy. The results of the present study demonstrated that RAD-seq was useful to develop sex-related markers in animals, and verified that the sex determination system of belonged to the ZZ/ZW heterogametic system. Importantly, the developed markers could lead to a method for sex-controlled breeding in the Chinese soft-shelled turtle.
Topics: Animals; Body Size; Female; Gene Dosage; Genetic Markers; Genome-Wide Association Study; Male; Restriction Mapping; Sequence Analysis, DNA; Sex Characteristics; Turtles
PubMed: 30991756
DOI: 10.3390/genes10040302 -
Anaerobe Dec 2018Restriction endonuclease analysis (REA) and PCR ribotyping are two typing systems that have been frequently utilized for molecular epidemiologic characterization of... (Comparative Study)
Comparative Study
Restriction endonuclease analysis (REA) and PCR ribotyping are two typing systems that have been frequently utilized for molecular epidemiologic characterization of Clostridioides (Clostridium) difficile. To correlate typing data obtained from each method, we performed both REA and PCR ribotyping on a large and diverse set of historical and contemporary C. difficile infection clinical isolates. Eighty isolates were selected from each reference laboratory in the United States (Microbiology Reference Laboratory, Hines VA Medical Center) and United Kingdom (Clostridium difficile Network for England and Northern Ireland laboratory, University of Leeds). The 160 isolates were assigned to 82 unique ribotypes and 51 unique REA groups (116 unique REA types). In general, concordance between typing methods was good. Dendrogram analysis of PCR ribotype band patterns demonstrated close genetic relationships among strain types with discordant REA and ribotype assignments. While REA typing was more discriminatory, several REA types in this study were further discriminated by PCR ribotyping, indicating that discriminatory value of these typing methods may be strain dependent. These data will assist with molecular epidemiologic surveillance of strains identified by these two commonly used C. difficile typing systems.
Topics: Clostridioides difficile; Clostridium Infections; DNA Restriction Enzymes; Humans; Phylogeny; Polymerase Chain Reaction; Prohibitins; Restriction Mapping; Ribotyping
PubMed: 30009944
DOI: 10.1016/j.anaerobe.2018.07.004 -
Revue Scientifique Et Technique... Dec 2000The lack of a typing system for Mycobacterium bovis has, until recently, been an impediment to undertaking sophisticated epidemiological studies to assist in the control... (Review)
Review
The lack of a typing system for Mycobacterium bovis has, until recently, been an impediment to undertaking sophisticated epidemiological studies to assist in the control and eradication of tuberculosis in domestic animals. Molecular biology techniques for mycobacteria have been in development since the mid-1980s, leading to the availability of a number of genetic typing systems for M. bovis. The authors summarise the available techniques, identify those which are most useful at present and those which might prove useful in the future. The present recommendation is to use spoligotyping analysis for rapid, large scale screening of M. bovis isolates, and to use restriction fragment length polymorphism analysis using the polymorphic guanine and cytosine-rich repeat sequences probe where greater differentiation of isolates is required. In the future, systematic analysis of the genome sequence of M. bovis will allow the development of improved techniques that combine good discrimination with ease of use.
Topics: Animals; Bacterial Typing Techniques; Cattle; DNA, Bacterial; Electrophoresis, Gel, Pulsed-Field; Genome, Bacterial; Genotype; Mycobacterium bovis; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Restriction Mapping; Tuberculosis, Bovine
PubMed: 11107611
DOI: 10.20506/rst.19.3.1241 -
Brain Pathology (Zurich, Switzerland) Mar 2010Hotspot mutations in codon 132 of the gene encoding isocitrate dehydrogenase 1 (IDH1) have emerged as the most frequent DNA alteration in astrocytomas,...
Hotspot mutations in codon 132 of the gene encoding isocitrate dehydrogenase 1 (IDH1) have emerged as the most frequent DNA alteration in astrocytomas, oligodendrogliomas and oligoastrocytomas. These mutations have been shown to be of significant diagnostic and prognostic value. So far, assessment of IDH1 mutation relied on DNA sequencing techniques. We generated a set of primers suitable for endonuclease-based detection of hotspot mutations in codon 132 of IDH1. This primer set will allow determining these mutations without the need of DNA sequencing. One set of primer sets is designed to detect the presence or absence of IDH1 mutations in codon 132, while the other primer sets individually recognize the R132H, R132C, R132S, R132G and R132L mutations.
Topics: Amino Acid Sequence; Codon; DNA Primers; Humans; Isocitrate Dehydrogenase; Molecular Sequence Data; Mutation; Mutation, Missense; Polymerase Chain Reaction; Restriction Mapping
PubMed: 19744125
DOI: 10.1111/j.1750-3639.2009.00327.x -
Briefings in Functional Genomics Dec 2010Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis of genetic diversity in populations. However,... (Comparative Study)
Comparative Study
Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis of genetic diversity in populations. However, genome-scale population genetic studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promises to deliver high resolution population genomic data-thousands of sequenced markers across many individuals-for any organism at reasonable costs. It has found application in wild populations and non-traditional study species, and promises to become an important technology for ecological population genomics.
Topics: Animals; Base Sequence; Genetic Variation; Genetics, Population; Genome; Humans; Phylogeny; Polymorphism, Single Nucleotide; Restriction Mapping; Sequence Analysis, DNA
PubMed: 21266344
DOI: 10.1093/bfgp/elq031 -
DNA Research : An International Journal... Feb 1997The chromosomal DNAs of nine strains of seven Bacteroides species including B. fragilis, the type species of the genus Bacteroides, were digested with rare-cutting... (Comparative Study)
Comparative Study
The chromosomal DNAs of nine strains of seven Bacteroides species including B. fragilis, the type species of the genus Bacteroides, were digested with rare-cutting restriction enzymes I-Ceu I, Not I, and Asc I and analysed by pulsed-field gel electrophoresis. The genome sizes of B. fragilis, B. distasonis, B. eggerthii, B. ovatus, B. thetaiotaomicron, B. uniformis, and B. vulgatus were determined to be 5.3, 4.8, 4.4, 6.9, 4.8, 4.6, and 5.1 Mbp, respectively. B. distasonis and B. vulgatus, and also B. uniformis and B. eggerthii, showed similar I-Ceu I restriction profiles. I-Ceu I cut B. uniformis and B. eggerthii genomes into four, B. ovatus into five, B. fragilis and B. thetaiotaomicron into six, and B. distasonis and B. vulgatus into seven fragments. On the basis of genome size, restriction profile, and I-Ceu I fragment number, a phylogenetic tree of the Bacteroides species was proposed. This was in overall agreement with the previous phylogenetic tree obtained by 16S rRNA data, with the exceptions of B. distasonis and B. ovatus.
Topics: Bacteroides; Chromosomes, Bacterial; DNA, Bacterial; Deoxyribonucleases, Type II Site-Specific; Electrophoresis, Gel, Pulsed-Field; Endodeoxyribonucleases; Genome, Bacterial; Phylogeny; Restriction Mapping
PubMed: 9179492
DOI: 10.1093/dnares/4.1.19