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N Davidson

Publications and source records attributed to N Davidson.

At least 325 records · Page 18Linked to original sources
PubMed1976

Electron microscope study of a plasmid chimera containing the replication region of the Escherichia coli F plasmid.

pML31, a plasmid chimera constructed to contain the replication genes of an Flac plasmid, has been studied by electron microscope methods. Heteroduplex analysis shows that the only F sequence present in pML31 is that with corrdinates 40.3-49.3F. This region has previously been identified as essential for plasmid maintenance. The sequence of pML31, which was derived originally from R6-5, carries the km gene(s) and an inverted duplication of a 1.0-kilobase sequence. On the basis of length measurements, the repeated sequence is different from IS1, IS2, IS3, and an inverted repeat associated with the km gene(s) of plasmid JR67.

Base Sequence↗
PubMed1976

Size, subunit composition, and secondary structure of the Friend virus genome.

Electron microscope and gel electrophoresis studies show that the high-molecular-weight (50 to 70S) RNA extract from Friend virus (FV) is a dimer with the same basic structure previously observed for the RNAs from RD-114 virus, baboon virus, and woolly monkey virus. This observation greatly strengthens the inference that the dimer structure is a general characteristic of the RNAs of all mammalian type C viruses. The FV dimer is slightly less stable than the RNA dimer of woolly monkey virus, which is, in turn, much less stable than those of RD-114 and baboon virus. There are three FV monomer components, small (S), medium (M), and large (L), with molecular lengths of 6.7 +/- 0.6, 7.7 +/- 0.6, and 9.5 +/- 0.6 kilobases, respectively. There are approximately equal amounts of the S and M components and much less of the L component. Most of the dimers are homodimers (SS, MM, and LL). The frequency of heterodimers (SM, SL, ML) is much less than expected for a random assortment model.

Friend murine leukemia virus↗
PubMed1975

A new method of in situ hybridization.

A new method for gene mapping at the chromosome level using in situ hybridization and scanning electron microscopy is described and has been applied to mapping the rRNA genes of Drosophila melanogaster. Biotin is covalently attached to Drosophila rRNA via a cytochrome c bridge at a ratio of one cytochrome-biotin per 130 nucleotides by a chemical procedure. Polymethacrylate spheres with a diameter of ca. 60 nm are prepared by emulsion polymerization and are covalently attached to the protein avidin at a ratio of 5-20 avidins per sphere. The biotin-labeled rRNA is hybridized to denatured DNA in a chromosome squash. Upon incubation with a sphere solution, some of the biotin sites become labeled with spheres because of the strong non-covalent interaction between biotin and avidin. The chromosome squash is examined in the scanning electron microscope (SEM). Polymer spheres, which are visible in the SEM, are observed to label the nucleolus, where the rRNA genes are located.

Animals↗
PubMed1975

Meningococcal antigen in diagnosis and treatment of group A meningococcal infections.

Meningococcal antigen was measured by countercurrent immunoelectrophoresis in the blood and cerebrospinal fluid of 200 patients with group A meningococcal meningitis. Antigen was detected in the blood of 27 (13.5 per cent) patients. These patients had a worse prognosis and a higher incidence of allergic complications, such as arthritis and vasculitis, about 5 days after the start of antibiotic treatment. Antigen was found in the CSF of 129 (67.5 per cent) patients); antigen often persisted in the cerebrospinal fluid despite antibiotic treatment before admission. A combination of immunoelectrophoresis and routine bacteriologic study was used in the diagnosis of 162 (84.8 per cent) patients with meningococcal meningitis. High levels of antigen and a slow antigen disappearance were associated with neurologic damage. The antigen is stable and may be detected from specimens of cerebrospinal fluid dried on filter paper.

Antigens, Bacterial↗
PubMed1975

Inverted repeat sequences in the Drosophila genome.

The properties of inverted repeat (foldback) sequences in Drosophila melanogaster DNA have been studied by HAP chromatography and electron microscope methods. Electron microscope observations show that there is a broad distribution of lengths of the duplex regions of the inverted repeats from very short to greater than 15 kb, with number and weight average values of 1.35 kb and 5.0 kb respectively. About 20% of the inverted repeats are separated by a single-strand spacer with lengths too short to observe, but the other 80% have spacers, P, with lengths ranging from 0.5 kb to greater than 30 kb. The number average and weight average spacer lengths for the total sample are 2.7 kb and 6.1 kb. With respect to the lengths of the spacers, P, between inverted repeats, the Drosophila genome differs from that of most organisms which have been studied where the spacers P are mostly too short to be measured. EM and HAP studies suggest that the average center-to-center spacing between sets of inverted repeats is 40-80 kb. The HAP studies show that there is a broad range of thermal stabilities for the duplexes formed by reassociation of inverted repeat sequences. Kinetic analysis shows that all of the frequency components of the Drosophila genome are present in the inverted repeats, the loops P, and the flanking sequences. There is a somewhat larger proportion of middle repetitive DNA in those inverted repeat duplexes which are resistant to digestion by Mung Bean Endonuclease I. These enzyme resistant duplexes comprise about 3% of the entire genome. It is estimated that there are approximately 2000-4000 inverted repeat pairs in the entire genome.

Animals↗
PubMed1975

Interspersion of repetitive and nonrepetitive DNA sequences in the Drosophila melanogaster genome.

Cot analysis shows that the haploid Drosophila genome contains 12 percent rapidly reassociating, highly reiterated DNA, 12 percent middle repetitive DNA with an average reiteration frequency of 70, and 70 percent single-copy DNA. The distribution of the middle repetitive sequences in the genome has been studied by an examination in the electron microscope of the structures obtained when middle repetitive sequences present on large DNA strands reassociate and by the hydroxyapatite binding methods developed by Davidson et al. (1973). At least one third by weight of the middle repetitive sequences are interspersed in single-copy sequences. These interspersed middle repetitive sequences have a fairly uniform distribution of lengths from less than 0.5 to 13 kb, with a number average value of 5.6 kb. The average distance between middle repetitive sequences is greater than 13 kb. The data do not exclude the possibility that essentially all of the middle repetitive sequences have the interspersion pattern described above; however, it is possible that some of the middle repetitive sequences of Drosophila are clustered in stretches of length much greater than 13 kb. The interspersion pattern of the middle repetitive sequences in Drosophila is quite different from that which occurs in the sea urchin, in Xenopus, in rat, and probably many other higher eucaryotes.

Animals↗
PubMed1975

Use of gene 32 protein staining of single-strand polynucleotides for gene mapping by electron microscopy: application to the phi80d3ilvsu+7 system.

A method for visualizing RNA-DNA duplex regions along a single strand of DNA in the electron microscope is described. A preparation of RNA molecules is hybridized to a long DNA strand containing the coding sequences (genes) for some of the RNAs. T4 gene 32 protein, which binds selectively and cooperatively only to the single-strand regions, is added, followed by glutaraldehyde. The resulting nucleic acid-gene 32 complex is adsorbed to the surface of an electron microscope grid in the presence of ethidium bromide. The single-strand regions are relatively thick (8.5 nm) compared to the duplex (RNA-DNA hybrid) regions (3.5 nm), so that the two kinds of regions are readily recognized by electron microscopy. In favorable cases, tRNA-DNA hybrids of length about 80 nucleotide pairs can be recognized (although with difficulty). The positions of a number of interesting genetic sequences on the DNA of the transducing phage phi80d3ilvsu+7 have been mapped. The r strand contains 16S, 23S, and 5S rRNA coding sequences in that order. The spacer between 16S and 23S genes has a length of 500 nucleotides and contains the coding sequence for a tRNA2Glu gene in agreement with previous biochemical observations. The spacer between the 23S and 5S genes has a length of 180 nucleotides. The su+7 tRNATrp coding sequence has been mapped on the l strand at a position just to the left of the ilv genes. Secondary structure loops due to short inverted repeat sequences flanking the 16S, 23S, tRNATrp, and F sequences in the DNA have been observed.

Chromosome Mapping↗
PubMed1975

Electron microscopic heteroduplex studies of sequence relations among plasmids of Escherichia coli: structure of F13 and related F-primes.

The structure of F13, a plasmid containing lac, purE, and proC, has been determined by heteroduplex analysis. As expected for an F-prime formed by a type II excision event, it contains all the sequences of F plus a large segment of Escherichia coli chromosomal deoxyribonucleic acid. There is a sequence of F with coordinates 16.3-17.6F which has been shown in other studies to be the insertion sequence IS2. This IS2 occurs twice on F13, once at each of the two junctions of F deoxyribonucleic acid with chromosomal deoxyribonucleic acid. The sequence alpha beta which occurs twice on F with coordinates 93.2-94.5/OF and 13.7-15.0F occurs an additional three times, twice in an inverted order relative to the alpha beta sequences of F, on the chromosomal sequences of F13. The structures of the plasmids F13-4 and F210 have been determined. The common sequences of F13 with F152-1 (a derivative of F152, the classical F2gal) and with F13-4 and F210 have been mapped. These results partially map lac, proC, tsx, and purE on F13. On the basis of all of these results, it is proposed that Hfr 13 (the parent of F13) was formed by recirpocal recombination between IS2 on F and an IS2 resident at a point between lac and proC on the chromosome of the F+ parent of Hfr 13. It is proposed that this IS2 and the several alpha beta sequences on the chromosomal part of F13 are hot spots for recombination with F, i.e., for Hfr formation. The point of origin and direction of transfer of many Hfr's can be explained by this hypothesis. In particular, the sequence relations of F42-1 (Flac) and of F152-1 (F 2gal) with F13 are completely consistent with this model.

Base Sequence↗
PubMed1975

Electron microscope heteroduplex studies of sequence relations among bacterial plasmids: identification and mapping of the insertion sequences IS1 and IS2 in F and R plasmids.

Heteroduplex experiments between the plasmid R6 and one strand of the deoxyribonucleic acid (DNA) of a lambda phage carrying the insertion sequence IS1 show that IS1 occurs on R6 at the two previously mapped junctions of resistance transfer factor (RTF) DNA with R-determinant DNA. From previous heteroduplex experiments, it then follows that IS1 occurs at the same junctions in R6-5, R100-1, and R1 plasmids. Heteroduplex experiments with the DNA from a lambda phage carrying the insertion sequence IS2 show that one copy of IS2 occurs in R6, R6-5, and R100-1 (but not R1) at a point within the RTF with coordinates 67.5 TO 68.9 kilobase units (kb). In an accompanying paper, Ptashne and Cohen (1975) show that the insertion sequence IS3 occurs on R6 and R6-5. R100-25, a traC mutant, differs from its parent R100-1 only in that it contains an additional copy of IS1 inserted within the tra gene region of 82.1 kb. R100-31, atraX, TC-s mutant of R100-1, is deleted in R100-1 sequences starting at one of the IS3 termini (46.9 kb) and extending with RTF to 61.0 kb. Heteroduplex studies of F plasmids with the DNA of a lambda phage bearing insertion sequence IS2 show that the sequence of F with coordinates 16.3-17.6F is IS2. The occurrence of IS1 at the two junctions of R-determinant DNA and RTF DNA in R plasmids provides a structural basis to explain the mechanism of the previously observed formation of molecules containing one RTF unit and several tandem copies of the R-determinant unit, when R plasmids in Proteus mirabilis are grown in the presence of antibiotics, and the segregation of an R plasmid into an RTF unit and an R-determinant unit. In general, correlation of our results with previous studies shows that insertion sequences play a role in a variety of F- and R-related intra- and intermolecular recombination phenomena.

Base Sequence↗
PubMed1975

alphabeta sequence of F is IS31.

Previous studies have shown that there is a deoxyribonucleic acid (DNA) segment, of length 1.3 kb and denoted as the alphabeta sequence, which occurs twice on the F plasmid at corrdinates 93.2 to 94.5/OF kb and 13.7 to 15.0F kb. In the present investigation, heteroduplexes were prepared between a phage DNA carrying the insertion sequence IS3 and suitable F-prime DNAs. The hybrids formed show that IS3 is the same as alphabeta. This result plus previous studies support the view that: (i) the insertion sequence IS2 and IS3 occur on F and, in multiple copies, on the main bacterial chromosome of Escherichia coli K-12; and (ii)these IS sequences on the main bacterial chromosomes are hot spots for Hfr formation by reciprocal recombination with the corresponding sequences of F.

Base Sequence↗
PubMed1975

Structure, subunit composition, and molecular weight of RD-114 RNA.

The properties and subunit composition of the RNA extracted from RD-114 virions have been studied. The RNA extracted from the virion has a sedimentation coefficient of 52S in a nondenaturing aqueous electrolyte. The estimated molecular weight by sedimentation in nondenaturing and weakly denaturing media is in the range 5.7 X 10(6) to 7.0 X 10(6). By electron microscopy, under moderately denaturing conditions, the 52S molecule is seen to be an extended single strand with a contour length of about 4.0 mum corresponding to a molecular weight of 5.74 X 10(6). It contains two characteristic secondary structure features: (i) a central Y- or T-shaped structure (the rabbit ears) with a molecular weight of 0.3 X 10(6), (ii) two symmetreically disposed loops on each side of and at equal distance from the center. The 52S molecule consists of two half-size molecules, with molecular weight 2.8 X 10(6), joined together within the central rabbit ears feature. Melting of the rabbit ears with concomitant dissociation of the 52S molecule into subunits, has been caused by either one of two strongly denaturing treatments: incubation in a mixture of CH3HgOH and glyoxal at room temperature, or thermal dissociation in a urea-formamide solvent. When half-size molecules are quenched from denaturing temperatures, a new off-center secondary structure feature termed the branch-like structure is seen. The dissociation behavior of the 52S complex and the molecular weight of the subunits have been confirmed by gel electrophoresis studies. The loop structures melt at fairly low temperatures; the dissociation of the 52S molecule into its two subunits occurs at a higher temperature corresponding to a base composition of about 63% guanosine plus cytosine. Polyadenylic acid mapping by electron microscopy shows that the 52S molecule contains two polyadenylic acid segments, one at each end. It thus appears that 52S RD-114 RNA consists of two 2.8 X 10(6) dalton subunits, each with a characteristic secondary structure loop, and joined at the 5' ends to form the rabbit ears secondary structure feature. The observations are consistent with but do not require the conclusion that the two 2.8 X 10(6) dalton subunits of 52S RD-114 RNA are identical.

Animals↗