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Molecular cloning and characterization of ARO7-OSM2, a single yeast gene necessary for chorismate mutase activity and growth in hypertonic medium.

The chorismate mutase structural gene, ARO7, which is necessary for both phenylalanine and tyrosine biosynthesis was cloned by complementation in yeast. Genetic analysis showed that ARO7 was identical to a gene necessary for growth in hypertonic medium, OSM2, which mapped nearby. After restriction mapping and subcloning of the plasmid, the cloned gene was used to detect mRNA levels in several growth conditions. Enzyme activities were measured in various genotypes. At our level of detection ARO7-OSM2 is a low level constitutively expressed gene.

Chorismate Mutase↗

Application of natural partial digests to pulsed-field gel analysis of the amplified MDR locus.

The analysis by pulsed-field gel electrophoresis of partial digestion products visualized by probes for the human multidrug resistance (MDR) locus has been used to further establish the restriction map of this region. Results place the MDR1 and MDR2 genes on a single SfiI fragment, with partial digestion products establishing the distance between these genes to be 230-250 kb. The feasibility and potential advantages of using "natural" partials to generate detailed restriction maps within an amplified DNA domain are discussed.

Blotting, Southern↗

A rapid method for identifying the thymidine kinase genes of avipoxviruses.

The thymidine kinase (TK) genes of poxviruses can be rapidly located without using TK- mutants or having to restriction map and clone the viral genomes. Identification of the TK gene is based on in situ gel hybridization with an end-labelled degenerate oligonucleotide probe, representing a consensus sequence near the 3' end of the gene. Restriction fragments of the viral DNAs are electrophoresed in agarose gels and annealed with the probe. Using this method, the TK genes of fowl pox (FPV) and quail pox (QPV) viruses were initially localized to HindIII fragments of approximately 3.8 and 6.7 kb, respectively. After inserting these fragments into pUC 19, recombinant plasmids containing the TK genes were screened by a modified in situ gel annealing procedure. Restriction mapping of the two cloned fragments and subsequent hybridization analysis more precisely placed at least the 3' portion of the FPV and QPV TK genes within a 1.4 kb ClaI-XbaI and 1.7 kb ClaI-PstI fragment, respectively. The site of the FPV TK gene was verified by comparison to the mapped position of the similar gene in an Australian FPV. The location of the QPV TK gene was confirmed by hybridization with the FPV TK gene, despite the apparent divergency of these two genes.

Cloning, Molecular↗

Restriction enzyme maps of the macropodid herpesvirus 2 genome.

The DNA of macropodid herpesvirus 2 (dorcopsis wallaby herpesvirus) was analysed using restriction enzymes and molecular cloning techniques. Sets of EcoRI and SalI clones were prepared which represented approximately 85 per cent of the genome, and these clones were used to map the DNA by double-digestion and hybridization experiments. Data on uncloned regions were obtained by analysing fragments excised from agarose gels, and terminal fragments were identified by exonuclease III digestion. The genome was shown to be approximately 135 kilobases (kb) long. It has a long unique sequence (95 kb) bounded by repeat sequences (5.5 kb) and joined at one end to a short unique sequence (15 kb) also bounded by repeat sequences (7.0 kb) in a manner similar to that of herpes simplex viruses 1 and 2.

Animals↗

Cellular gels. Purifying and mapping long DNA molecules.

Long DNA molecules of greater than 10(5) bp (0.1 Mbp) are easily broken by pipetting. Therefore, chromosomal DNA is generally isolated after embedding cells in a protective coat of agarose. The embedded DNA can then be cut into long pieces and fractionated on gels using pulsed fields, but these pieces are again easily broken if the resolved DNA molecules are recovered from the gels. We now describe a novel gel matrix, a 'cellular' gel, that permits the recovery of resolved fragments from gels in a form that enables facile manipulation without shear. This facilitates purification and restriction mapping of fragments of 0.1-1.0 Mbp. We illustrate the utility of the method by mapping chromosome III of baker's yeast, which has a length of approximately 0.36 Mbp. This method should facilitate purification and restriction mapping of yeast artificial chromosomes.

Chromosomes, Fungal↗

Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.).

A short, highly repeated, interspersed DNA sequence from rice was characterized using a combination of techniques and genetically mapped to rice chromosomes by restriction fragment length polymorphism (RFLP) analysis. A consensus sequence (GGC)n, where n varies from 13-16, for the repeated sequence family was deduced from sequence analysis. Southern blot analysis, restriction mapping of repeat element-containing genomic clones, and DNA sequence analysis indicated that the repeated sequence is interspersed in the rice genome, and is heterogeneous and divergent. About 200,000 copies are present in the rice genome. Single copy sequences flanking the repeat element were used as RFLP markers to map individual repeat elements. Eleven such repeat elements were mapped to seven different chromosomes. The strategy for characterization of highly dispersed repeated DNA and its uses in genetic mapping, DNA fingerprinting, and evolutionary studies are discussed.

Amino Acid Sequence↗

[Phylogenetic relationships among six species of Macaca inferred from ribosomal DNA variations].

Restriction maps of ribosomal DNA repeating units of six species of Macaca (M. mulatta, M. facsicularis, M. arctoides, M. assamensis, M. thibetana, M. nemestrina) and two outgroup species, Rhinopithecus bieti and Hylobates leucogenys, were constructed with 15 restriction endonucleases and 28S, 18S rDNA probes cloned from human, M. arctoides shares a common restriction map with M. assamensis. Phylogenetic tree derived from the neighbor-joining was somewhat different that derived from the maximum likelihood methods using the NEIGHBOR and RESTML program in PHYLIP version 3.5c. However, the consensus of our phylogenetic trees supports the viewpoint that M. facsicularis and M. mulatta were maybe diverged first in the genus Macaca. Further studies using DNA sequencing method are required to resolve the phylogeny of the genus Macaca.

Animals↗

Isolation, characterization and restriction endonuclease mapping of the Petunia hybrida chloroplast DNA.

A procedure is developed for the isolation of intact chloroplast DNA (ctDNA) from Petunia hybrida. The molecular weight, calculated from contour length measurements, is 96.0 +/- 4.5 x 10(6) daltons. This value is in good agreement with the value of 101.2 x 10(6) daltons that was estimated from the electrophoretic mobilities of restriction endonuclease fragments of ctDNA. Analysis of petunia ctDNA in neutral CsCl gradients revealed the presence of only one type of DNA at a buoyant density of 1.6987 +/- 0.0005 gcm-3. This corresponds with a GC-content of 39.3 +/- 0.5%. A physical map of petunia ctDNA was constructed by using the restriction endonucleases Sal I, Bgl I, Hpa I and Kpn I. The map indicates that petunia ctDNA contains two copies of a sequence in an inverted orientation. The inverted repeat regions have a minimum length of 10 x 10(6) daltons. Hybridization data indicate that part of the inverted repeat regions contain the genes for chloroplast ribosomal RNAs.

Chloroplasts↗

Interactions of Tn7 and temperate phage F116L of Pseudomonas aeruginosa.

Tn7 insertions into the genome of F116L, a Pseudomonas aeruginosa generalized transducing phage, were isolated by repeated cycles of transduction and induction isolated by repeated cycles of transduction and induction of strains lysogenic for F116cts mutants with selection for trimethoprim resistance (Tpr). Two non-defective F116Lcts:: Tn7 phage were characterized. They have reduced plaquing ability, produced non-lysogenic Tpr transductants, and have yielded a deletion mutant of the phage genome upon selection for plaque formation in single infection. F116L DNA is circularly permuted and terminally redundant. A circular restriction map of 61.7 kb has been defined, and a cleavage site common to many enzymes has been identified at coordinate 23.3 kb on the map. It is presumed that this site represents the sequence for the initiation of DNA encapsidation by a headful packaging mode. The Tn7 insertion targets and a 13.4 kb deletion define regions of the F116L genome non-essential for either vegetative growth or lysogenization. The restriction map of Tn7 has been determined for five enzymes. Non-lysogenic Tpr transductants reveal a Tn7 insertion hot-spot in the P. aeruginosa genome.

Bacteriophages↗

Identification of a highly promiscuous and an HLA allele-specific T-cell epitope in the birch major allergen Bet v 1: HLA restriction, epitope mapping and TCR sequence comparisons.

BACKGROUND: Allergen-specific CD4+ T cells play an important regulatory role in atopic allergy. OBJECTIVE: To investigate the human leucocyte antigen (HLA) restriction and T-cell receptor (TCR) usage of allergen-specific T-cell clones (TCCs) that react with defined epitopes of Bet v 1, the major birch pollen allergen. METHODS: Five Bet v 1-specific TCCs derived from two birch pollen-allergic individuals and specific for Bet v 1, were epitope-mapped with overlapping synthetic peptides. In addition, HLA-restriction and TCR CDR3 sequences were determined. RESULTS: Three TCCs reacted with a Bet v 1 peptide containing amino acid residues 21-33 (BP21), the other two TCCs reacted with a minimal peptide comprising residues 37-45 (BP37). Studies using neutralizing anti-HLA-monoclonal antibodies and HLA-typed APCs showed that the BP37-specific TCCs were restricted by a HLA-DQA1*0301/DQB1*0603 heterodimer. In contrast, BP21 was recognized in a highly promiscuous manner. TCCs recognizing this sequence were restricted by HLA-DPB1*0201, a HLA-DQA1*0201/DQB1*0201 heterodimer, or HLA-DRB3*0101. Reverse transcription-polymerase chain reaction with primers for all known TCRAV and TCRBV gene segments, followed by CDR3 region sequencing, revealed the usage of five different TCRAV and four different TCRBV gene segments by the TCCs, as well as diversity in the joining region. All BP21-specific TCCs contained a negatively charged residue in their CDR3alpha regions, the CDR3beta regions showed a high concentration of polar and OH-group bearing residues. BP37-specific TCCs shared the amino acid combination LY in the middle of their CDR3alpha regions, the CDR3beta regions showed high concentration of OH-group bearing or charged residues. CONCLUSIONS: This study shows the existence of a highly promiscuous T-cell epitope in Bet v 1. The presence of additional T-cell epitopes in Bet v 1 may, however, hamper the clinical applicability of the epitope. Likewise, the diversity in TCR usage by T cells recognizing the epitope does not support the development of TCR-directed immunotherapy for birch pollen allergy.

Alleles↗

A 9.75-Mb map across the centromere of human chromosome 10.

We present a yeast artificial chromosome (YAC) and pulsed-field gel electrophoresis (PFGE) map across the centromere of human chromosome 10 that links expressed sequences in 10p11 to expressed sequences in 10q11.2. This map is the first of its kind to link genes across a human centromere. It consists of a 2.5-Mb YAC contig extending from 10p11 to our previously published 5.35-Mb PFGE map of the centromeric satellite arrays, and a 2.65-Mb YAC contig extending from these satellite arrays to 10q11.2. This map covers approximately 6.5-7% of the total DNA of chromosome 10. Two Généthon genetic markers, D10S578 and D10S604, are included. These markers are only 1 cM apart but are separated by a physical distance of more than 9.2 Mb, including the centromere. This gives a ratio of genetic to physical distance of 0.11 cM/Mb, 9-11 times lower than average estimates for the human genome and chromosome 10. Markers linked to the centromere include the duplicated zinc finger genes ZNF11A, ZNF33A, and ZNF37A (which map to 10p11) and ZNF11B, ZNF33B, and ZNF37B (which map to 10q11.2). Restriction mapping confirms that the genes on each arm lie in opposite orientation with respect to the centromere, consistent with the hypothesis that a pericentric inversion has occurred in this region during primate evolution.

Base Sequence↗

Cloning and transcriptional analysis of the segmentation gene fushi tarazu of Drosophila.

In the course of studying the Antennapedia (Antp) locus, we found that one of the 3' Antp exons has weak cross-homology to another gene affecting segmentation, fushi tarazu (ftz; meaning "not enough segments"), which is 30 kb to the left of Antp. Homozygous ftz- embryos die before hatching and lack alternate body segments. The reduced number of segments results from the fusion of the anterior portion of one segment with the posterior portion of the next segment. The ftz gene encodes a single 1.9 kb poly(A)+ RNA expressed exclusively from the early blastoderm to gastrula stages of embryonic development. The structure of the ftz gene has been analyzed by S1 nuclease mapping and by restriction mapping of a cDNA clone. The ftz gene consists of two exons, and it is the 3' exon that cross-hybridizes with the 3' exon of Antp. The role of ftz in cell determination is discussed.

Animals↗

Deletion analysis of sucrose metabolic genes from a Salmonella plasmid cloned in Escherichia coli K12.

The sucrose operon from pUR400, a 78-kbp conjugative Salmonella plasmid, was cloned in Escherichia coli K12. The operon was located in a 5.7-kbp SalI restriction fragment and was subcloned, in each of two possible orientations, using the expression vector pUC18. The insert DNA was restriction mapped and duplicate restriction sites in the insert and in the polylinker of the vector were used to create various deletions promoter distal in the operon sequence. Additional deletions were made with the restriction exonuclease Bal31. Cells containing hybrid plasmids with specified deletions lacked the ability to transport sucrose or were constitutive for hydrolase and/or uptake activities. The scrA (enzyme IIScr) and scrR (regulatory) genes resided within 2900-bp SmaI-SalI DNA fragment and were assigned the order scrB, scrA, scrR. An amplified sucrose-inducible gene product, Mr 68,000, was detected only in the membrane fraction from recombinant cells that contained plasmid with the intact operon sequence. This protein represented 11% of the total membrane protein and was resistant to extraction with 0.5 M sodium chloride, 2% Triton X-100, and 0.5% sodium deoxycholate. The protein did not appear to be the product of either the scrA, scrB, or scrR gene and may therefore represent a previously unidentified membrane-bound sucrose protein. A new gene, scrC, is proposed. In addition, the cloned 5.7-kbp SalI and 2.5-kbp SmaI-SalI DNA fragments failed to hybridize to chromosomal DNA from Bacillus subtilis, Streptococcus lactis, Streptococcus mutans, and Lactobacillus acidophilus as well as to DNA from a sucrose plasmid from Salmonella tennessee. However, the probes showed weak homology with a 20-kbp EcoRI restriction fragment from Klebsiella pneumoniae.

Chromosome Deletion↗

Molecular cloning of the genome of human spumaretrovirus.

DNA of human spumaretrovirus (HSRV) was cloned from both cDNA and from viral DNA into phage lambda and bacterial plasmid vectors. The recombinant plasmids harboring viral DNA were characterized by Southern blot hybridization and restriction mapping. Physical maps were constructed from cDNA and found to be colinear with the restriction maps obtained from viral DNA. The recombinant clones isolated contained viral DNA inserts which range in size from 2.2 kb to 15.4 kb. The recombinant clones allowed to construct a physical map of the complete HSRV provirus of 12.2 kb.

Cloning, Molecular↗

Detection and cloning of potent transforming gene(s) from chewing tobacco-related human oral carcinomas.

High molecular weight DNA isolated from 14 primary tumour tissues of human oral carcinoma patients was analysed for transforming activity by NIH3T3 co-transfection assay using pSV2neo gene as a selectable marker, followed by nude mouse tumorigenicity assay. Ten of the patient tumour tissues demonstrated molecular lesions in myc, ras or/and EGF-R genes, whereas 4 patients did not show tumour associated aberrations in these oncogenes. The G418-resistant transfected cells from 12 of 14 individual patients demonstrated transforming potential by colony formation in soft agar and tumour induction in nude mice within 25-80 days. DNAs from the transfected cells, consequent nude mice tumours and corresponding cell lines, contained human Alu sequences. Southern blot hybridisation with ras, myc, EGF-R oncogenes demonstrated the presence of human H-ras oncogene in one of the 12 sets of nude mice tumours. In contrast, DNA from the other 11 sets of nude mice tumours indicated absence of c-myc, N-myc, L-myc, H-ras, K-ras, N-ras and EGF-R genes on Southern analysis. Further, DNAs from five first cycle tumorigenic transformants were subjected to a second cycle of transfection, and induced tumours in nude mice with a shorter latency period of 21-50 days. The secondary transformants contained discrete human Alu sequences; however, the DNA did not hybridise with myc/ras/EGF-R probes. A genomic library was constructed from a second cycle nude mice tumour, using EMBL-3 as the vector. Four human Alu sequence positive clones were isolated on screening 2 x 10(5) plaques, and one of the recombinant clones subjected to fine restriction mapping using 16 restriction enzymes. The lack of association of the nude mice tumour DNA with myc/ras/EGF-R showing aberrations in the primary human tumour, implies activation of an alternative potent transforming gene(s) in the chewing tobacco-related oral carcinomas in India.

3T3 Cells↗

Lack of association between the Glu298Asp variant of the endothelial nitric oxide synthase gene and the risk of coronary artery disease among Taiwanese.

BACKGROUND AND PURPOSE: Endothelial nitric oxide synthase (eNOS) plays a key role in atherosclerosis, because its product, nitric oxide, possesses antiatherogenic properties. Recent reports of molecular genetic analysis have suggested that genetic polymorphisms of the eNOS gene may be associated with coronary artery disease (CAD) or myocardial infarction (MI). However, some studies have reported discrepant results. The aims of this study were to assess whether any association exists between the Glu298Asp variant of the eNOS gene and the risk of CAD and/or MI among Taiwanese. METHODS: The subjects included 218 CAD patients and the same number of age- and sex-matched control subjects from Taiwan. Subjects' DNA was extracted from their blood and genotypes were determined by polymerase chain reaction and restriction mapping using the restriction enzyme MboI. The alleleic and genotypic frequencies were analyzed. RESULTS: The frequencies of the eNOS genotypes were similar for CAD patients (GG:GT:TT = 81.7%:17.4%:0.9%) and controls (81.2%:17.4%:1.4%; p = 0.904). No evidence of difference was found in the frequency of the T allele between CAD patients (9.6%) and controls (10.1%; p = 0.822), or between MI patients (7.5%) and controls (p = 0.322). Subjects with the GT or TT genotype did not demonstrate an increased risk of CAD compared with those with a GG genotype (p = 0.89; OR = 0.98; 95% confidence interval, CI, 0.76-1.27) in multivariate logistic regression, or when different subgroups of age, sex, or risk factors were analyzed. CONCLUSIONS: In the present case-control study, we found no evidence of an association between the Glu298Asp variant of the eNOS gene and CAD/MI among Taiwanese.

Coronary Disease↗

[Plasmid-encoded antibiotic resistance in Staphylococcus hyicus].

A total of 33 Staphylococcus hyicus-cultures from piglets with exudative epidermatitis were analyzed for the presence of antibiotic resistance plasmids. Four small plasmids encoding resistances to chloramphenicol, macrolide-lincosamide-antibiotics, streptomycin or tetracyclines could be identified in plasmid-curing and plasmid-transformation experiments. For further characterization these plasmids were digested with restriction endonucleases. This led to the construction of a specific restriction map for each of the 4 plasmids. On the basis of their restriction maps, these 4 antibiotic resistance plasmids from "porcine" S. hyicus-cultures were compared with the respective resistance plasmids of other staphylococcal species from infections of humans and animals.

Animals↗