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At least 811 records · Page 45Linked to original sources
PubMed1981

A simulation study on Nei and Li's model for estimating DNA divergence from restriction enzyme maps.

A simulation study has been conducted to check the accuracy of Nei and Li's (1979) formulas for the mean and variance of the proportion (S) of identical restriction sites between two DNA sequences and for estimating the mean and variance of the number (delta) of base substitutions per nucleotide site between two DNA sequences. The results show that these formulas are quite accurate as long as the probability of S becoming zero is negligibly. In addition to the simulation, approximate formulas have also been obtained for the probability for S to become zero at time t and for the contribution to S due to parallel mutation.

Base Sequence↗
PubMed1983

Molecular cloning of the unintegrated squirrel monkey retrovirus genome: organization and distribution of related sequences in primate DNAs.

The closed circular form of the endogenous squirrel monkey type D retrovirus (SMRV) was molecularly cloned in a bacteriophage vector. The restriction map of the biologically active clone was determined and found to be identical to that of the parental SMRV linear DNA except for the deletion of one long terminal repeat. Restriction enzyme analysis and Southern blotting indicated that the SMRV long terminal repeat was approximately 300 base pairs long. The SMRV restriction map was oriented to the viral RNA by using a gene-specific probe from baboon endogenous virus. Restriction enzyme digests of a variety of vertebrate DNAs were analyzed for DNA sequence homology with SMRV by using the cloned SMRV genome as a probe. Consistent with earlier studies, multiple copies of SMRV were detected in squirrel monkey DNA. Related fragments were also detected in the DNAs from other primate species, including humans.

Animals↗
PubMed1983

Genetic recombination of bacterial plasmid DNA. Physical and genetic analysis of the products of plasmid recombination in Escherichia coli.

Derivatives of plasmid pBR322 DNA containing tet mutations were constructed by inserting XhoI linkers at various sites in the tetracycline resistance gene. Monomer plasmids containing either the tet-10 allele located at nucleotide position 23 or the tet-14 allele located at nucleotide position 1267 were used to construct a circular dimer containing one copy of each allele and a circular trimer containing one copy of the tet-10 allele and two copies of the tet-14 allele. Genetic recombination of these plasmid DNAs to produce a functional tetracycline resistance gene could be detected as the production of tetracycline-resistant progeny during the growth of transformants or using a restriction mapping assay which detected the rearrangement of the mutant alleles. The structure of individual tetracycline-resistant recombination products was determined by restriction mapping. This analysis suggested that as many as 70% of the plasmid recombination events in Escherichia coli AB1157 could have involved gene conversion events. The formation of these recombination products was most easily predicted by a model involving figure 8 recombination intermediates and the formation of symmetric regions of heteroduplex. Recombination in JC10287 delta(srlR-recA)304 occurred at 5% of the wild-type frequency and appeared to occur by a similar mechanism. Recombination in JC9604 recA56 recB21 recC22 sbcA23 occurred at 20 times the wild-type frequency and appeared to involve multiple independent recombination events.

DNA Restriction Enzymes↗
PubMed1988

Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms.

The conflict between the Mendelian theory of particulate inheritance and the observation of continuous variation for most traits in nature was resolved in the early 1900s by the concept that quantitative traits can result from segregation of multiple genes, modified by environmental effects. Although pioneering experiments showed that linkage could occasionally be detected to such quantitative trait loci (QTLs), accurate and systematic mapping of QTLs has not been possible because the inheritance of an entire genome could not be studied with genetic markers. The use of restriction fragment length polymorphisms (RFLPs) has made such investigations possible, at least in principle. Here, we report the first use of a complete RFLP linkage map to resolve quantitative traits into discrete Mendelian factors, in an interspecific back-cross of tomato. Applying new analytical methods, we mapped at least six QTLs controlling fruit mass, four QTLs for the concentration of soluble solids and five QTLs for fruit pH. This approach is broadly applicable to the genetic dissection of quantitative inheritance of physiological, morphological and behavioural traits in any higher plant or animal.

Chromosome Mapping↗
PubMed1993

Physical mapping of multiple homologous genes in the Bacillus subtilis 168 chromosome: identification of ten ribosomal RNA operon loci.

Ten ribosomal RNA operons (rrn) of the Bacillus subtilis 168 strain were precisely located in the complete physical map, i.e., the NotI and SfiI restriction map [M. Itaya and Tanaka, J. Mol. Biol., 220, 631-648 (1991)]. Mapping was done by identification of the NotI and the SfiI fragments to which the rrnO operon hybridized. This protocol proved that homologous multiple genes dispersed on the chromosome can be physically mapped by using a single membrane filter. A previously unidentified deletion formation was shown to be that caused by homologous recombination between rrnJ-W.

Bacillus subtilis↗
PubMedDate not supplied

[Molecular cloning of MuLV proviruses integrated into the genome of mouse erythroleukemia cells. I. Characteristics of endogenous proviruses].

The library of genes was obtained from erythroleukemic AKR cells (C-1), that were maintained as suspension culture. Thirty four clones that had homology with 60-70S RNA of Rauscher Leukemia virus (RLV) were separated from this library. The restriction mapping was carried out with 14 clones, that contained most extensive proviral sequences. One clone (107) contains proviral sequences that are derived from one of the components of the RLV complex. The other 13 clones contain sequences of endogenous xenotropic viruses. The endogenous retroviral sequences obtained differ in restrictive maps from proviruses of ecotropic and xenotropic infectious endogenous MuLV and, apparently, might be attributed as non-inducible infectious xenotropic MuLV of class III. Some of the cloned retroviral sequences had symmetrical structure, that is typical for integrated proviruses, i. e. these sequences were separated from flanking cellular ones by long terminal repeats. All investigated retroviral sequences are deletion mutants of MuLV proviruses. It was shown that the inner regions of proviruses diverged more than the long terminal repeats. The expression of the main inner MuLV polypeptide (p30) was detected in NIH 3T3 cells, transfected with DNA of some clones.

Animals↗
PubMed2005

[Cloning and sequence analysis of human uric acid transporter gene].

OBJECTIVE: To obtain full-length human urate transporter (hUAT) gene. METHODS: Primers was designed according to the sequence of hUAT reported in Genbank. The target fragments were obtained by reverse transcriptional (RT) PCR from the mRNA extracted from human renal tubular epithelial cell lines (HK-2), followed by cloning into pEGFP-C1 plasmid. The cloned fragment was subjected to restriction mapping and sequence analysis for confirmation. RESULTS AND CONCLUSION: hUAT gene with correct sequence is successfully cloned from HK-2 cells. The restriction maps and sequence analysis of the selected clones were consistent with the sequence reported in Genbank.

Base Sequence↗
PubMed1987

Restriction site polymorphism in genes encoding type 2 but not type 1 gonococcal IgA1 proteases.

Neisseria gonorrhoeae produces two phenotypically distinct types of IgA1 proteases, each of which cleaves a specific peptide bond in the hinge region of the human IgA1 heavy chain. The genes encoding IgA1 protease from twenty-eight different strains of N. gonorrhoeae, including twelve which produce type 1 enzyme, thirteen which produce type 2 enzyme, and three which are protease negative, were analyzed. Nine restriction site patterns were found in the iga genes. All twelve type 1 strains showed identical restriction maps of the iga gene, which differed from all the iga-2 variants. The three protease negative strains each contained DNA homologous to the probe. While strain to strain variation in restriction maps of specific genes is not unique and has been reported in N. gonorrhoeae previously, the existence of such restriction site polymorphism among iga-2 genes contrasts strongly with the lack of such variation among iga-1 genes. The basis for this lack of diversity among the iga-1 genes is under further investigation.

DNA Restriction Enzymes↗
PubMed1997

Human histone gene organization: nonregular arrangement within a large cluster.

We have previously located the genes of the five human main type H1 genes and the gene encoding the testicular subtype H1t to the region 21.1 to 22.2 on the short arm of chromosome 6. To investigate the organization of the histone genes in this region, we isolated two YACs from a human YAC library by PCR screening with primers specific for histone H1.1. This screen revealed two YAC clones, YAC Y23 (corresponding to ICRFy901D1223) contains an insert of about 480 kb, whereas the smaller YAC 4A (corresponding to ICRFy900C104) spans about 340 kb and is completely covered by YAC Y23. We have subcloned the YAC inserts in cosmids, determined the linear orientation of the cosmids by cosmid walking, and constructed a restriction map of the entire region by mapping the individual cosmids using partial digests and hybridization with labeled oligonucleotides complementary to the cos site of the vector. Hybridization analysis, subcloning, restriction mapping, and sequencing revealed that most of the previously isolated phage and cosmid clones containing histone genes are part of this YAC including the clones containing the four human main type H1 histone genes H1.1 to H1.4, the H1t gene, and core histone genes. Thirty-five histone genes map within 260 kb of the YAC Y23 insert. All newly identified histone genes were sequenced, and the sequences were deposited with the EMBL nucleotide sequence database. The histone H1.5 gene is not part of this region, and we therefore conclude that the H1.5 gene and the associated core histone genes form a separate subcluster within this chromosomal region.

Chromosome Mapping↗
PubMed1989

Intraspecific evolution of a gene family coding for urinary proteins.

The genome of the laboratory mouse contains about 35 major urinary protein (MUP) genes, many of which are clustered on chromosome 4. We have used distance and parsimony methods to estimate phylogenetic relationships between MUP genes from nucleotide sequence and restriction maps. By analyzing coding sequences we show that the genes fall into four main groups of related sequences (groups 1-4). Comparisons of restriction maps and the nucleotide sequences of hypervariable regions that lie 50 nucleotides 5' to the cap sites show that the group 1 genes and probably also the group 2 pseudogenes fall into subgroups. The most parsimonious trees are consistent with the evolution of the array of group 1 and 2 genes by mutation accompanied by a process tending toward homogenization such as unequal crossing-over or gene conversion. The phylogenetic grouping correlates with grouping according to aspects of function. The genomes of the inbred strains BALB/c and C57BL contain different MUP gene arrays that we take to be samples from the wild population of arrays.

Animals↗
PubMed1981

Organization of the bacteriophage T4 tail fiber gene cluster 34-38.

A correlation of the genetic, functional, and structural maps of the T4 tail fiber gene cluster has been achieved by analysis of lambda derivatives carrying genes 34-38. 31 recombinants carrying different parts of the T4 tail fiber gene cluster were identified by a marker rescue screen of 300 lambda T4 recombinant clones, generated by restriction of partial cytosine-containing T4 DNA with E coRI or with HindIII and ligation into appropriately cleaved lambda replacement vectors. Extensive genetic characterization revealed 15 recombinant classes with respect to the contiguous stretches of genome recovered and suggested the presence of 7 HindIII sites and 8 EcoRI sites in the 10 kb region. Functional analysis showed tht genes 34-38 were recovered intact. The tail fiber genes are efficiently expressed from lambda promoters and complement T4 amber mutants in a modified in vivo complementation test. Polypeptides, Mr = 145,000, 105,000, 39,000, 27,000 and 24,000 corresponding to gp34, gp37, gp35, gp38 and gp36 respectively, were detected by SDS polyacrylamide gel electrophoresis of 35S- labeled extracts of lambda T4 recombinant infected UV-treated host cells. Restriction enzyme structural analysis of the lambda T4 DNAs identified 7 HindIII and 7 EcoRI fragments and established a restriction map covering about 11 kb. The correlation of the genetic, functional and restriction maps provides a rational approach to a genetically directed DNA sequence analysis of the T4 tail fiber genes and of their mutant variants which affect particular aspects of tail fiber assembly, structure and function.

Bacteriophage lambda↗
PubMed1991

HLA DQ alpha typing of forensic specimens by amplification restriction fragment polymorphism (ARFP) analysis.

The alleles present at the HLA DQ alpha locus may be typed by either allele specific oligonucleotide (ASO) probing or by restriction mapping, referred to here as amplification restriction fragment polymorphism (ARFP) analysis. ASO typing relies upon hybridization principles, whereas ARFP typing relies upon restriction site analysis. Dot-blot ASO typings which are of doubtful interpretation may be directly checked by ARFP analysis. Aliquots of the PCR products amplified using the commercial Amplitype HLA DQ alpha system are digested with suitable restriction endonucleases. Electrophoresis, blotting and detection of biotin-labelled restriction fragments provides a sensitive and robust typing method suited to forensic analysis.

Alleles↗
PubMed1993

Automated fluorescence-based restriction fragment analysis.

We describe a procedure for the automated analysis of DNA restriction fragments in an agarose gel matrix. The procedure is based upon simultaneously digesting DNA with restriction enzymes and ligating a fluorochrome-labeled linker to the cut ends. The fluorochrome-labeled restriction fragments are loaded on a horizontal agarose gel scanning system (Applied Biosystems Model 362 GENE SCANNER Fluorescent Fragment Analyzer) for electrophoresis and data analysis. Mobility parameters for DNA fragment migration and detection sensitivity for the instrument are described. In addition, we demonstrate some unique applications, including electrophoresis and fragment size conversion of up to 72 cosmid restriction digests in 4 h, applicability of the system for subsequent DNA transfers and hybridizations, utility for establishing overlapping restriction maps of cosmids, and discrimination of restriction digest specific fragment ends following a double-digest protocol.

Base Sequence↗
PubMed1987

Physical comparison of parathion hydrolase plasmids from Pseudomonas diminuta and Flavobacterium sp.

Restriction maps of two plasmids encoding parathion hydrolase have been determined. pPDL2 is a 39-kb plasmid harbored by Flavobacterium sp. (ATCC 27551), while pCMS1 is a 70-kb plasmid found in Pseudomonas diminuta (strain MG). Both plasmids previously have been shown to share homologous parathion hydrolase genes (termed opd for organophosphate degradation) as judged by DNA-DNA hybridization and restriction mapping. In the present study, we conducted DNA hybridization experiments using each of nine PstI restriction fragments from pCMS1 as probes against Flavobacterium plasmid DNA. The opd genes of both plasmids are located within a highly conserved region of approximately 5.1 kb. This region of homology extends approximately 2.6 kb upstream and 1.7 kb downstream from the opd genes. No homology between the two plasmids is evident outside of this region.

Aryldialkylphosphatase↗