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N Davidson

Publications and source records attributed to N Davidson.

At least 217 records · Page 12Linked to original sources
PubMed1982

Identification of the class I genes of the mouse major histocompatibility complex by DNA-mediated gene transfer.

DNA-mediated gene transfer was used to identify cloned class I genes from the major histocompatibility complex of the BALB/c mouse. Three genes encoding the transplantation antigens H-2 Kd, Dd and Ld were identified as well as genes encoding the Qa-2,3 and two TL differentiation antigens. As many as 10 putative novel class I genes were detected by the association of their gene products with beta 2-microglobulin. Alloantiserum prepared to one of the novel antigens was used to demonstrate the expression of the previously undetected antigen on spleen cells of various inbred, congeneic, and recombinant congeneic strains of mice.

Animals↗
PubMed1982

Identification of a BALB/c H-2Ld gene by DNA-mediated gene transfer.

Gene transfer and immunoselection were used in the identification of a BALB/c genomic clone containing an H-2Ld gene (clone 27.5). Transformation of thymidine kinase-negative C3H mouse L cells with the cloned 27.5 DNA together with the herpes simplex virus tk gene produced transformants expressing Ld molecules detected by radioimmune assay with monoclonal hybridoma antibodies to Ld antigens. The foreign Ld gene products expressed by cloned mouse L cell transformants were shown to be virtually indistinguishable from BALB/c spleen Ld molecules by two-dimensional electrophoretic analysis of H-2Ld immunoprecipitates. These results indicate that the genomic clone 27.5 contains a functional BALB/c H-2Ld gene and demonstrate the usefulness of this approach for identifying the gene products encoded by cloned genes which are members of a multigene family. Furthermore, the ability to place cell-surface recognition molecules on the surfaces of foreign cells provides a powerful opportunity for functional analyses of these molecules.

Animals↗
PubMed1982

Cuticle protein genes of Drosophila: structure, organization and evolution of four clustered genes.

Most of a 9 kb region of the Drosophila genome containing genes for several cuticle proteins has been sequenced. Five cuticle-gene-like sequences have been identified and mapped. Amino acid sequences of four of the five major third instar cuticle proteins have been determined. These four sequences are identical with those predicted from the sequences of four of the five genes. Two cuticle genes are transcribed in one direction and two in the opposite direction. The fifth cuticle-like gene is judged to be a pseudogene because several features of its structure and the absence of detectable transcripts suggest it is nonfunctional. Sequence comparisons indicate that it arose by an unequal crossing-over event involving two closely related and adjacent cuticle genes. Each of the four cuticle genes contains a signal peptide coding sequence interrupted by a short intervening sequence (about 60 bp) at a conserved site. Conserved sequences occur in the 5' mRNA untranslated region, in the adjacent 35 bp of upstream flanking sequence and at -200 bp from the mRNA start position in each of the cuticle genes. We discuss the structure, organization and evolution of these cuticle genes as a model small gene family.

Amino Acid Sequence↗
PubMed1982

Representation of DNA sequences in recombinant DNA libraries prepared by restriction enzyme partial digestion.

We present a theoretical study of the fraction of sequences incorporated in a recombinant DNA partial digest library as a function of the size of the library. The fraction incorporated depends on the degree of restriction enzyme partial digestion. If all restriction sites in the target DNA can be cleaved with the same rate, optimum incorporation of sequences is observed when the number average length of the digested DNA equals the desired average length of the cloned insert. Overdigestion severely reduces the fraction of sequences present in a sample of clones. Heterogeneity in restriction enzyme cleavage rates also reduces the fraction incorporated, and underdigestion improves sequence representation in the face of cleavage rate heterogeneity. Practical methods for determining the number average length of partially digested DNAs are also presented.

Base Composition↗
PubMed1982

A transposable element that splits the promoter region inactivates a Drosophila cuticle protein gene.

Two mutations that affect larval cuticle protein gene expression in the 2/3 variant Drosophila melanogaster strain were investigated. We demonstrate that this strain synthesizes an electrophoretic variant, fast 2 (CPf2), of wild-type cuticle protein 2(CP2). It also lacks detectable amounts of cuticle protein 3 (CP3). The other major cuticle proteins are still present. Protein and DNA sequence analyses indicate that point mutations cause two amino acid substitutions that change the electrophoretic mobility of CPf2 relative to that of CP2. The mutation abolishing the expression of CP3 was found to be a 7.3-kilobase DNA insertion located within the T-A-T-A box region of this gene, at -31 base pairs from the mRNA start site. This DNA insertion, called H.M.S. Beagle, belongs to a conserved family of repeated DNA elements that have characteristics similar to those of previously characterized Drosophila transposable elements. H.M.S. Beagle elements are repeated approximately 50 times in the haploid genome and exhibit restriction fragment-length polymorphisms around points of insertion between Canton S, Oregon R, and 2/3 Drosophila strains. Sequence analysis indicates that H.M.S. Beagle contains 266-base-pair direct repeats at its termini and is flanked by a duplication of 4 base pairs of target DNA sequence, T-A-T-A, in the CP3 gene insertion. Thus, insertion of a transposable element into the putative promoter region of the CP3 gene is evidently responsible for inactivating CP3 gene expression.

Animals↗
PubMed1981

The cuticle genes of drosophila: a developmentally regulated gene cluster.

A 36 kilobase (kb) DNA segment of the Drosophila genome that contains several larval cuticle protein genes has been cloned and characterized. This segment maps at chromosomal locus 44D. It contains five genes, all of which are expressed at the same time of Drosophila development. Four of the genes are clustered within 7.9 kb of DNA and are abundantly expressed as poly(A)RNA in the epidermis of late third instar larvae but are not abundantly expressed in other developmental stages. A fifth gene lies 8 kb away from this cluster and is expressed at a much lower level in late third instar larval poly(A) RNA. Three of the four abundantly expressed genes have been shown to code for larval cuticle proteins; less decisive evidence indicates that the fourth gene also probably codes for a larval cuticle protein. Some of the genes are related in DNA sequence, and the proteins encoded in the cluster are related immunologically. Thus the cuticle genes encoded by the segment at 44D are members of a family of genes of common ancestry, which share the same pattern of developmental expression and reside in a small segment of the Drosophila genome.

Animals↗
PubMed1981

Analysis of a drosophila tRNA gene cluster: two tRNALeu genes contain intervening sequences.

A recombinant DNA phage containing a cluster of Drosophila melanogaster tRNA genes has been isolated and analyzed. The insert of this phage has been mapped by in situ hybridization to chromosomal region 50AB, a known tRNA site. Nucleotide sequencing of the entire Drosophila tRNA coding region reveals seven tRNA genes spanning 2.5 kb of chromosomal DNA. This cluster is separated from other tRNA regions on the chromosome by at least 2.7 kb on one side, and 9.6 kb on the other. Two tRNA genes are nearly identical and contain intervening sequences of length 38 and 45 bases, respectively, in the anticodon loop. These two genes are assigned to be tRNALeu genes because of significant sequence homology with yeast tRNA3Leu, and secondary structure homology with yeast tRNA3Leu intervening sequence. In addition, an 8 base sequence (AAAAUCUU) is conserved in the same location in the intervening sequences of Drosophila tRNALeu genes and a yeast tRNA3Leu gene. Similar sequenes occur in all other tRNAs containing intervening sequences. The remaining five genes are identical tRNAIle genes, which are also identical to a tRNAIle gene from chromosomal region 42A. The 5' flanking regions are only weakly homologous, but each set of isoacceptors contains short regions of strong homology approximately 20 nucleotides preceding the tRNA coding sequences: GCNTTTTG preceding tRNAIle genes; and GANTTTGG preceding tRNALeu genes. The genes are irregularly distributed on both DNA strands; spacing regions are divergent in sequence and length.

Base Sequence↗
PubMed1981

The actin genes of Drosophila: protein coding regions are highly conserved but intron positions are not.

The entire set of six closely related Drosophila actin genes was isolated using recombinant DNA methodology, and the structures of the respective coding regions were characterized by gene mapping techniques and by nucleotide sequencing of selected portions. Structural comparisons of these genes have resulted in several unexpected findings. Most striking is the nonconservation of the positions of intervening sequences within the protein-encoding regions of these genes. One of the Drosophila actin genes, DmA4, is split within a glycine codon at position 13; none of the remaining five genes is interrupted in the analogous position. Another gene, DmA6, is split within a glycine codon at position 307; at least two of the Drosophila actin genes are not split in the analogous position. Additionally, none of the Drosophila actin genes is split within codon four, where the yeast actin gene is interrupted. The six Drosophila actin genes encode several different proteins, but the amino acid sequence of each is similar to that of vertebrate cytoplasmic actins. None of the genes encodes a protein comparable in primary sequence to vertebrate skeletal muscle actin. Surprisingly, in each of these derived actin amino acid sequences in the initiator methionine is directly followed by a cysteine residue, which in turn precedes the string of three acidic amino acids characteristic of the amino termini of mature vertebrate cytoplasmic actins. We discuss these findings in the context of actin gene evolution and function.

Actins↗
PubMed1981

Transmission electron microscopic method for gene mapping on polytene chromosomes by in situ hybridization.

A transmission electron microscope method for gene mapping by in situ hybridization to Drosophila polytene chromosomes has been developed. As electron-opaque labels, we use colloidal gold spheres having a diameter of 25 nm. The spheres are coated with a layer of protein to which Escherichia coli single-stranded DNA is photochemically crosslinked. Poly(dT) tails are added to the 3' OH ends of these DNA strands, and poly(dA) tails are added to the 3' OH ends of a fragmented cloned Drosophila DNA. These probe--dA strands are hybridized in situ to polytene chromosome squashes. Gold spheres are linked to the hybridized probe--dA strands by A.T base pairing. The sphere positions relative to the chromosome bands can be observed by transmission electron microscopy. The method shows low background and high resolution.

Animals↗
PubMed1981

The U3 portion of feline leukemia virus DNA identifies horizontally acquired proviruses in leukemic cats.

The presence and location of DNA sequences related to the U3 and U5 portions of the infectious exogenous feline leukemia virus (FeLV) long terminal repeat (LTR) in various cat DNAs have been determined by hybridization experiments. In uninfected cat DNAs, the U5 LTR segment from the Gardner-Arnstein strain B virus is present at approximately 150 copies per cell. This level is approximately 10-fold greater than that of endogenous internal FeLV sequences. The U5 sequences differ in copy number and, to some extent, in location from one animal to another. For any one animal, the sequence organization of the U5 segments is the same among different tissues, showing that the pattern is inherited through the germ line. Most importantly, the viral U3 LTR probe hybridizes only very weakly with uninfected cat DNAs. Both the U3 and the U5 regions of the LTR from the Gardner-Arnstein strain of virus cross-hybridize with DNA derived from four other infectious FeLVs representing A, B, and C subtypes. Thus, the C3 region may be used as a probe for studying the number and location of exogenously acquired FeLV proviruses in infected cat tissues. In some cases exogenously acquired proviruses are present in unique sites in the genome of virus-positive cat lymphosarcomas, indicating a monoclonal origin for the tumor. In other tumors, the proviral sequences are randomly distributed over many sites. Lymphosarcomas of virus-negative cats have no exogenous U3 sequences despite epidemiological evidence of an association of virus-negative leukemia with exposure to FeLV.

Animals↗
PubMed1981

Determination of cellular RNA concentrations by electron microscopy of R loop-containing DNA.

R loop hybridizations and electron microscopy have been used to determine cellular RNA concentrations for cloned genes. In plasmid DNA sequence excess, all the complementary RNA is driven into R loop structures that can be assayed by electron microscopy. To determine the concentration of a particular poly(A)+ RNA, plasmid DNA crosslinked once every 2000-5000 base pairs with trioxsalen and UV light is hybridized in DNA sequence excess to various known amounts of total poly(A)+ RNA, and the R loops are stabilized by treatment with glyoxal. If necessary, excess nonhybridized RNA is removed by Sepharose 2B chromatography, which enables the visualization of less abundant transcripts. Reconstruction experiments demonstrated that electron microscopic determination of the fraction of plasmid DNA molecules containing specific RNA loops gives accurate values of specific RNA weight fractions or concentrations in the total poly(A)+ RNA populations. These methods were also used to determine the concentrations of five RNA species complementary to sequences on TRT3, a recombinant DNA plasmid containing yeast histone 2A and 2B genes and three other nonhistone genes. The methods described allow one to visualize the R loop structures for both abundant and nonabundant transcripts and to estimate concentrations of these RNA species simply by determining the fraction of DNA containing R loops.

Animals↗
PubMed1981

Baboon endogenous virus genome: molecular cloning and structural characterization of nondefective viral genomes from DNA of a baboon cell strain.

Several heterogeneities in the baboon endogenous virus (BaEV) genomes that are present in the DNA of normal baboon tissues and the baboon cell strain BEF-3 have been described previously. To study these genomes, we cloned BaEV proviruses from BEF-3 cellular DNA into the lambda vector Charon 4A. Of the four full-length clones isolated, one was nondefective as determined by transfection. The sequence of a portion of this clone was found to code for amino acids 61-91 in the p30 region of the gag gene. This identification allowed us to align the restriction map with the BaEV genetic map. One heterogeneity, a BamHI site 2.4 kilobases (kb) from the proviral 5' end, was located close to the gag-pol junction; another, a BamHI site 1.4 kb from the 5' end of the genome, corresponded to the gag p30 coding sequence for amino acids 32-34; and a third, a Xho I site, was near the 3' end of the pol gene. To select the nondefective BaEV genomes from BEF-3 cells, we infected permissive cells with virus produced by BEF-3 cells and also transfected BEF-3 cellular DNA into permissive cells. The BaEV genomes in the permissive recipient cultures were then analyzed by restriction enzyme analysis. These nondefective genomes were found to be heterogeneous with respect to the gag-pol BamHI site and the Xho I site, but all were found to contain the BamHI site 1.4 kb from the 5' end of the genome.

Animals↗