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Biomedical subjects

D N Cooper

Publications and source records attributed to D N Cooper.

At least 163 records · Page 9Linked to original sources
PubMed1989

Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes.

The dinucleotide CpG is a "hotspot" for mutation in the human genome as a result of (1) the modification of the 5' cytosine by cellular DNA methyltransferases and (2) the consequent high frequency of spontaneous deamination of 5-methyl cytosine (5mC) to thymidine. DNA methylation thus contributes significantly, albeit indirectly, to the incidence of human genetic disease. We have attempted to estimate for the first time the in vivo rate of deamination of 5mC from the measured rate of 5mC deamination in vitro and the known error frequency of the cellular G/T mismatch-repair system. The accuracy and utility of this estimate (md) was then assessed by comparison with clinical data, and an improved estimate of md (1.66 X 10(-16) s-1) was derived. Comparison of the CpG mutation rates exhibited by globin gene and pseudogene sequences from human, chimpanzee and macaque provided further estimates of md, all of which were consistent with the first. Use of this value in a mathematical model then permitted the estimation of the length of time required to produce the level of "CpG suppression" currently found in the "bulk DNA" of vertebrate genomes. This time span, approximately 450 million years, corresponds closely to the estimated time since the emergence and adaptive radiation of the vertebrates and thus coincides with the probable advent of heavily methylated genomes. An accurate estimate of the 5mC deamination rate is important not only for clinical medicine but also for studies of gene evolution. Our data suggest both that patterns of vertebrate gene methylation may be comparatively stable over relatively long periods of evolutionary time, and that the rate of CpG deamination can, under certain limited conditions, serve as a "molecular clock".

Animals↗
PubMed1989

Diagnosis of genetic disease using recombinant DNA. Second edition.

Recombinant DNA methodology has greatly increased our knowledge of the molecular pathology of the human genome at the same time as providing the means to diagnose inherited disease at the DNA level. Direct detection and analysis of a range of genetic defects are now possible using cloned gene or oligonucleotide probes or by direct sequencing of the disease gene(s). In addition, the use of restriction fragment length polymorphism (RFLPs) within and around these genes as indirect genetic markers has now potentiated the tracking of disease alleles in affected pedigrees in cases where direct analysis was not feasible. RFLPs associated with linked anonymous segments may also be used not only to diagnose hitherto undetectable disease states, but also for chromosomal localization of the loci responsible. We present here an up-to date list of reports describing both the direct and the indirect analysis/diagnosis of human inherited disease, which is intended to serve as a guide to current molecular genetic approaches in diagnostic medicine.

DNA, Recombinant↗
PubMed1989

A comprehensive list of cloned human DNA sequences.

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements.

Base Sequence↗
PubMed1988

The CpG dinucleotide and human genetic disease.

Reports of single base-pair mutations within gene coding regions causing human genetic disease were collated. Thirty-five per cent of mutations were found to have occurred within CpG dinucleotides. Over 90% of these mutations were C----T or G----A transitions, which thus occur within coding regions at a frequency 42-fold higher than that predicted from random mutations. These findings are consistent with methylation-induced deamination of 5-methyl cytosine and suggest that methylation of DNA within coding regions may contribute significantly to the incidence of human genetic disease.

5-Methylcytosine↗
PubMed1988

DNA polymorphism and the study of disease associations.

Recombinant DNA approaches to disease analysis may be as applicable to studies of disease association as they are to the analysis and diagnosis of single-gene defects. Population and/or family association analyses, using restriction fragment length polymorphisms around candidate genes as markers, have been employed to study conditions such as atherosclerosis and disease with an HLA-association. Progress made to date in disease-association studies using recombinant DNA methodology is reviewed, the rationale behind such studies is examined and associated problems and pitfalls discussed.

Alleles↗
PubMed1988

Multiple soluble vertebrate galactoside-binding lectins.

All vertebrates synthesize soluble galactoside-binding lectins. Many are expressed at high levels in the embryo and at lower levels in the adult, whereas others show an inverse pattern of expression. Most lectins tend to be concentrated in one or a number of specific cell types. In the past few years, the multiplicity of these lectins has become more apparent. For example, in Xenopus laevis 3 galactoside-binding lectins, 2 with a preference for alpha-galactosides, have been purified and partially characterized. They have subunit molecular weights ranging from 16,000 to 69,000. More detailed studies have been done in mammals. For example, rat lung contains 3 soluble beta-galactoside-binding lectins, RL-14.5, RL-18 and RL-29, with subunit molecular weights, respectively, of 14,500, 18,000 and 29,000. A notable feature of these lectins is that, although they all bind lactose about equally well, their carbohydrate-binding sites are actually quite different, as shown by competitive binding studies with a range of complex mammalian glycoconjugates. Human lung also contains several beta-galactoside-binding lectins, including HL-14, HL-22 and HL-29 with subunit molecular weights, respectively, of 14,000, 22,000 and 29,000. They too show significant differences in their carbohydrate-binding sites when analyzed with naturally occurring mammalian glycoconjugates. Sequencing of purified lectins and cDNA clones indicates that at least 4 distinct genes code for what appears to be a family of HL-14. Heterogeneity is also indicated from isoelectric focusing studies which resolve at least 6 acidic forms of HL-14 and 5 acidic forms of HL-29.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1988

A comprehensive list of cloned human DNA sequences.

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements.

Cloning, Molecular↗
PubMed1987

Precursor-product relationship between vitellogenin and the yolk proteins as derived from the complete sequence of a Xenopus vitellogenin gene.

In Xenopus laevis four estrogen-responsive genes are expressed simultaneously to produce vitellogenin, the precursor of the yolk proteins. One of these four genes, the gene A2, was sequenced completely, as well as cDNAs representing 75% of the coding region of the gene. From this data the exon-intron structure of the gene was established, revealing 35 exons that give a transcript of 5,619 bp without the poly A-tail. This A2 transcript encodes a vitellogenin of 1,807 amino acids, whose structure is discussed with respect to its function. At the nucleic acid as well as at the protein level no extensive homologies with any sequences other than vitellogenin were observed. Comparison of the amino acid sequence of the vitellogenin A2 molecule with biochemical data obtained from the different yolk proteins allowed us to localize the cleavage products on the vitellogenin precursor as follows: NH2 - lipovitellin I - phosvitin (or phosvette II - phosvette I) - lipovitellin II - COOH.

Amino Acid Sequence↗
PubMed1987

Expression and developmental regulation of two unique mRNAs specific to brain membrane-bound polyribosomes.

Translation in vitro of membrane-bound polyribosomal mRNAs from rat brain has shown several to be developmentally regulated [Hall & Lim (1981) Biochem. J. 196, 327-336]. Here we describe the isolation and characterization of cDNAs corresponding to two such brain mRNAs. One cDNA (M444) hybrid-selected a 0.95 kb mRNA directing the synthesis in vitro of a 21 kDa pI-6.3 polypeptide, which was processed in vitro by microsomal membranes. A second cDNA (M1622) hybridized to a 2.2 kb mRNA directing the synthesis of a 55 kDa pI-5.8 polypeptide. Both mRNAs were specific to membrane-bound polyribosomes. Restriction maps of the corresponding genomic DNA sequences are consistent with both being single copy. The two mRNAs were present in astrocytic and neuronal cultures, but not in liver or spleen or in neuroblastoma or glioma cells. The two mRNAs were differently regulated during brain development. In the developing forebrain there was a gradual and sustained increase in M444 mRNA during the first 3 weeks post partum, whereas M1622 mRNA appeared earlier and showed no further increase after day 10. In the cerebellum the developmental increase in M444 mRNA was biphasic. After a small initial increase there was a decrease in this mRNA at day 10, coincident with high amounts of M1622 mRNA. This was followed by a second, larger, increase in M444 mRNA, when amounts of M1622 mRNA were constant. The contrasting changes in these two mRNAs in the developing cerebellum are of particular interest, since they occur during an intensive period of cell proliferation, migration and altering neural connectivity. As these mRNAs are specific to differentiated neural tissue, they represent useful molecular markers for studying brain differentiation.

Animals↗
PubMed1987

Diagnosis of genetic disease using recombinant DNA. Supplement.

Recombinant DNA methodology has greatly increased our knowledge of the molecular pathology of the human genome at the same time as providing the means to diagnose inherited disease as the DNA level. We present here a list of recent reports of both direct and indirect analysis of human inherited disease which is intended to serve as a guide to current molecular genetic approaches to diagnostic medicine.

DNA, Recombinant↗
PubMed1987

Localization of a human heat-shock HSP 70 gene sequence to chromosome 6 and detection of two other loci by somatic-cell hybrid and restriction fragment length polymorphism analysis.

The human 70 kdalton heat-shock protein (HSP 70) is a member of a multigene family which is expressed in response to various physiological stresses including elevated temperatures. Using a cloned genomic HSP 70 DNA sequence we demonstrate by somatic cell hybrid and restriction fragment length polymorphism (RFLP) analyses that there are a minimum of three distinct HSP 70 loci in the human genome, one of which is located on chromosome 6.

Animals↗
PubMed1987

Regional localization and characterization of a DNA segment on the long arm of chromosome 21.

A human genomic DNA fragment, pAM37 (HGM8; D21S22), was mapped to chromosome 21q2.1-q2.21 by in situ hybridization. This segment is therefore situated on the boundary of the "pathological region" of Down syndrome. A genomic restriction map encompassing 35 kb of chromosome 21 was derived and two restriction fragment length polymorphisms (RFLPs) were mapped and characterized. A homologous sequence was detected in the mouse genome but no homologous RNA was detected in a range of human tissues. This DNA segment will contribute to the linkage mapping of chromosome 21 and will facilitate delineation of the pathological region of Down syndrome.

Chromosome Banding↗
PubMed1987

The distribution of the dinucleotide CpG and cytosine methylation in the vitellogenin gene family.

Sequence data from regions of five vertebrate vitellogenin genes were used to examine the frequency, distribution, and mutability of the dinucleotide CpG, the preferred modification site for eukaryotic DNA methyltransferases. The observed level of the CpG dinucleotide in all five genes was markedly lower than that expected from the known mononucleotide frequencies. CpG suppression was greater in introns than in exons. CpG-containing codons were found to be avoided in the vitellogenin genes, but not completely despite the redundancy of the genetic code. Frequency and distribution patterns of this dinucleotide varied dramatically among these otherwise closely related genes. Dense clusters of CpG dinucleotides tended to appear in regions of either functional or structural interest (e.g., in the transposon-like Vi-element of Xenopus) and these clusters contained 5-methylcytosine (5 mC). 5 mC is known to undergo deamination to form thymidine, but the extent to which this transition occurs in the heavily methylated genomes of vertebrates and its contribution to CpG suppression are still unclear. Sequence comparison of the methylated vitellogenin gene regions identified C----T and G----A substitutions that were found to occur at relatively high frequencies. The predicted products of CpG deamination, TpG and CpA, were elevated. These findings are consistent with the view that CpG distribution and methylation are interdependent and that deamination of 5 mC plays an important role in promoting evolutionary change at the nucleotide sequence level.

Animals↗
PubMed1987

Molecular genetic approaches to the analysis of human ophthalmic disease.

In this review of the recent literature, the contribution that the new techniques of molecular genetics has made in the analysis and diagnosis of human ophthalmic conditions is presented and discussed. Among the disorders reviewed are X-linked retinitis pigmentosa, Norrie's disease, gyrate atrophy and retinoblastoma, and there are also sections on crystallins and visual pigments.

Chromosome Mapping↗
PubMed1987

A comprehensive list of cloned human DNA sequences.

A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterized DNA segments and repetitive DNA elements.

Base Sequence↗