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D W Cox

Publications and source records attributed to D W Cox.

At least 109 records · Page 6Linked to original sources
PubMed1990

Physical mapping of probes within 14q32, a subtelomeric region showing a high recombination frequency.

The genetic linkage map of chromosome 14q32 contains 11 loci which span a distance of more than 60 cM. We have assigned 10 of these loci and the AKT1 proto-oncogene to segments of 14q32, using breakpoints derived from four independent chromosomal deletions or rearrangements. The most telomeric breakpoint was found in a proband (HSC 6) carrying a ring-14 chromosome. HSC 6 is monosomic for the distal part of 14q32, which contains the immunoglobulin heavy-chain locus (IGH), and random markers D14S20, D14S19, and D14S23. Two other chromosomal breakpoints, found in probands HSC 121 and HSC 981, could not be distinguished from each other using DNA probes, although the cytogenetic breakpoints appeared to be different at 14q32.32 and 14q32.31, respectively. The region between the breakpoints of HSC 6 and HSC 121 contains AKT1, D14S1, D14S17, and D14S16. The entire telomeric band 14q32 is assumed to contain about 10% of chromosome 14, or approximately 10 Mb. The 8 most telomeric loci, including D14S1, map to 14q32.32-qter, which measures only several megabases. However, these loci span a genetic distance of 23 cM. The high recombination frequency contrasts with the observation that two of the gamma genes in the IGH constant region show a high degree of linkage disequilibrium, though 180 kb apart. This finding suggests that a telomeric localization per se does not lead to a higher recombination frequency and favors the hypothesis that the higher recombination frequency at the telomeres may be due to specific "hot spots" for recombination.

Blotting, Southern↗
PubMed1990

A null deficiency allele of alpha 1-antitrypsin, QOludwigshafen, with altered tertiary structure.

The most common deficiency allele of the plasma protease inhibitor alpha 1-antitrypsin (alpha 1AT) is PI*Z. Some rare deficiency alleles of alpha 1AT produce low but detectable amounts of plasma alpha 1AT (1-20% of normal), which can be differentiated by isoelectric focusing. Others, designated null (QO) alleles, produce no alpha 1AT detectable by routine quantitative methods. We have previously described a method using DNA polymorphisms, haplotypes, and polyacrylamide isoelectric focusing gels, to differentiate various deficiency alleles. Based on haplotypes, we previously identified, in eight patients, five different null alleles, four of which had been previously sequenced. We have now analyzed all 12 null alleles in these eight patients, using allele-specific oligonucleotide probes, and have identified six different null alleles. We have cloned and sequenced one of these, PI*QOludwigshafen, which has a base substitution in exon II, replacing isoleucine 92 in the normal sequence with an asparagine. This substitution of a polar for a nonpolar amino acid occurs in one of the alpha-helices and is predicted to disrupt the tertiary structure. A total of 13 different alpha 1AT deficiency alleles, 6 of them null alleles, have been sequenced to date.

Alleles↗
PubMed1989

Deletion/frameshift mutation in the alpha 1-antitrypsin null allele, PI*QObolton.

The most common deficiency allele of the protease inhibitor (PI) alpha 1-antitrypsin (alpha 1AT) is PI*Z. Other rare deficiency alleles of alpha 1AT are of two types: those producing low but detectable amounts of alpha 1AT (less than 20% of normal serum concentrations), and null alleles producing less than 1% of normal alpha 1AT and therefore not detectable by routine quantitative methods. We have previously used DNA polymorphisms and family data to determine heterozygosity in an individual producing low levels of serum alpha 1AT (12% of normal) of PI type Mmalton. By DNA analysis we observed the typical haplotype associated with PI*Mmalton and a unique null haplotype associated with the allele PI*QObolton. The QObolton allele produces no detectable serum alpha 1AT. We have cloned and sequenced the QObolton allele from a phage genomic library. Deletion of a single cytosine residue near the active site of alpha 1 AT in exon V results in a frameshift causing an in-frame stop codon downstream of the deletion. This stop codon leads to premature termination of protein translation at amino acid 373, resulting in a truncated protein. The truncated protein is predicted to have an altered carboxy terminus (amino acids 363-372) and will lack structurally important amino acids.

Alleles↗
PubMed1989

A method for two-dimensional DNA electrophoresis (2D-DE): application to the immunoglobulin heavy chain variable region.

The scarcity of single-copy probes creates difficulty in the generation of large-scale physical maps of mammalian gene families. A simple method of two-dimensional DNA electrophoresis (2D-DE) has been developed to overcome this problem. DNA (2 micrograms) is digested with a rare-cutting restriction endonuclease and size separated by pulsed-field gel electrophoresis (PFGE). The DNA, still contained within the lane of the PFGE gel, is digested with a second frequent-cutting restriction enzyme and is subjected to an electrical field perpendicular to that of the PFGE. 2D-DE allows the simultaneous mapping, to large restriction fragments, of all the genes detected by a particular probe. The human immunoglobulin variable region was used as an example for this procedure. Two VH5 genes, on 8- and 9-kb EcoRI fragments, were mapped to 200- and 65-kb SfiI fragments, respectively, by 2D-DE. This technique will be particularly useful in the generation of physical maps of complex human gene families and of repeat families.

Chromosome Mapping↗
PubMed1989

Complete physical map of the human immunoglobulin heavy chain constant region gene complex.

We have found by pulsed-field gel electrophoresis that the human immunoglobulin heavy chain constant region gene complex maps entirely to a 350-kilobase (kb) Mlu I fragment. The enzyme Eag I was used with pulsed-field gel electrophoresis alone and in double digests with Spe I to map the region. C gamma 3, of the C gamma 3-C gamma 1-C psi epsilon 1-C alpha 1 cluster, maps 60 kb to the 3' side of C delta; C gamma 2 of the C gamma 2-C gamma 4-C epsilon-C alpha 2 cluster maps 80 kb to the 3' side of C alpha 1, where C gamma 3 encodes the constant region of the immunoglobulin gamma 3 chain, C gamma 1 encodes the constant region of the immunoglobulin gamma 1 chain, etc. C psi gamma maps 35 kb to the 3' side of C alpha 1 and is in the same transcriptional orientation as the other genes. Although in the cloned DNA many CpG-containing restriction sites were identified, most of these were methylated in peripheral blood leukocytes. The sites that were not methylated were predominantly found in three clusters, or Hpa I tiny fragment islands. One was found on the 5' side of C mu; the other two lie 30 kb to the 3' side of each of the C alpha genes and could indicate the presence of regulatory sequences or genes. A region showing strong linkage disequilibrium between all C gamma genes spans at least 160 kb. The 70-kb C mu-C gamma 3 region, however, shows no linkage disequilibrium, possibly indicating a recombination hot spot. The immunoglobulin heavy chain constant region has been almost entirely cloned and mapped, and thus most rearrangements occurring in this region should be detectable.

Blotting, Southern↗
PubMed1989

Polymorphisms of the immunoglobulin heavy-chain delta gene and association with other constant-region genes.

Polymorphisms have previously been reported for the C mu, C alpha, C epsilon, and C gamma genes of the immunoglobulin heavy-chain (IGH) gene cluster. Here we report polymorphisms of the IGH C delta gene region, observed using the enzymes ApaI, AvaII, TaqI, and XbaI. The TaqI and XbaI polymorphisms were used in an investigation of linkage disequilibrium throughout the cluster of constant-region genes. The TaqI polymorphism, located 5' to the C delta gene, is in linkage disequilibrium with a polymorphism of the C mu switch region. The XbaI polymorphism, which is in the vicinity of the C delta 2 exon, is not strongly associated with any other polymorphisms, including the TaqI polymorphism and the Gm polymorphism of C gamma 3. Although there is a high degree of association between most genes of the IGH region, there is a lack of association between C delta and C gamma 3, which may indicate a hot spot for recombination.

DNA↗
PubMed1989

Rare deficiency types of alpha 1-antitrypsin: electrophoretic variation and DNA haplotypes.

A deficiency of the plasma protease inhibitor alpha 1-antitrypsin (alpha 1AT), is usually associated with the deficiency allele PI*Z. However, other alleles can also produce a deficiency. Some of these rare deficiency alleles produce a low concentration (3%-15% of normal) of alpha 1AT and include Mmalton, Mduarte, Mheerlen, and Mprocida. Null, or nonproducing, alleles are associated with trace amounts (less than 1%) of plasma alpha 1AT. We have identified, using isoelectric focusing, the deficiency alleles in 222 patients (68 children and 154 adults) with alpha 1AT deficiency. In addition to PI*Z, we found low-producing alleles PI*Mmalton and PI*Mcobalt and four null (PI*QO) alleles. On the basis of a population frequency of .0122 for PI*Z, frequencies for other deficiency alleles are 1.1 x 10(-4) for PI*Mmalton, 2.5 x 10(-5) for PI*Mcobalt (which may be the same as that for PI*Mduarte, and 1.4 x 10(-4) for all null alleles combined. Using 12 polymorphic restriction sites with seven different restriction enzymes, we have obtained DNA haplotypes for each of the rare deficiency types. All of the rare deficiency alleles can be distinguished from PI*Z by their DNA haplotype, and most can be distinguished from each other. DNA haplotypes are useful to indicate the presence of new types of null alleles, to identify genetic compounds for rare deficiency alleles, and to identify the original normal allele from which each deficiency allele is derived.

Adult↗
PubMed1989

In-frame single codon deletion in the Mmalton deficiency allele of alpha 1-antitrypsin.

A deficiency of the plasma protease inhibitor alpha 1-antitrypsin (alpha 1AT) is usually a consequence of the PI*Z allele. Mmalton is another deficiency allele which, like Z alpha 1AT, is associated with hepatocyte inclusions and impaired secretion. We report here the sequence of the PI Mmalton allele, which contains a 3-bp deletion coding for one of two adjacent phenylalanine residues (amino acid 51 or 52 of the mature protein). Using oligonucleotide hybridization of polymerase chain reaction-amplified DNA, we have demonstrated cosegregation of the PI Mmalton protein and the 3-bp deletion in the family in which this allele was originally described and in three other, unrelated kindreds. This deletion is found exclusively in PI Mmalton alleles and not in the normal M2 alleles from which, to judge on the basis of haplotype data, the Mmalton mutation must have been derived. In polyacrylamide isoelectric focusing (PIEF) gels, the isoelectric point of Mmalton is only slightly more cathodal than M2, a finding consistent with the loss of a single uncharged amino acid. To judge on the basis of X-ray crystallography data for the normal alpha 1AT protein, the deletion of aa 51/52 would shorten one strand of the beta sheet, B6, apparently preventing normal processing and secretion.

Amino Acid Sequence↗
PubMed1988

Kinetic analysis of the cerebral creatine kinase reaction under hypoxic and hypoglycaemic conditions in vitro. A 31P-n.m.r. study.

1. The tissue concentration of phosphocreatine (PCr) and the pseudo-first-order rate constant of creatine kinase (kf) were monitored in superfused guinea-pig brain slices in vitro by using 31P-n.m.r. techniques. 2. Superfusion of slices in low oxygen partial pressure (pO2 approx. 16 kPa) decreased tissue PCr concentrations by 48% but ATP concentrations were unchanged. Regression analysis revealed a significant negative correlation between the PCr concentration in hypoxic tissue and the increase in the rate constant, kf. Nevertheless the forward flux through the enzyme (Jf = kf.[PCr]) declined under these conditions. 3. Lowering the glucose concentration to 0.2 or 0.1 mM decreased PCr concentrations by 29% and 48% respectively; here ATP concentrations as well as PCr concentrations also decreased. Only in the presence of the lower glucose concentration (0.1 mM) was kf increased. However, unlike the situation in hypoxic tissue, Jf was maintained at control rates. 4. In spectra obtained in the presence of low oxygen or low glucose concentrations, a resonance attributable to tissue inorganic phosphate became dectectable. This observation is discussed in terms of known changes in tissue phosphate concentrations and possible alterations in cytoplasmic pH.

Animals↗
PubMed1988

On the relationship between the excitability of dentate granule cell field potentials and their sensitivity to low glucose.

An in vitro study was conducted to investigate whether the sensitivity to low glucose (0.5 mM) of dentate granule cell evoked activity was increased in more excitable tissue preparations. Four different measures of granule cell excitability were made under control conditions in the presence of 10 mM glucose. Three showed a positive correlation between excitability of populations of cells and the sensitivity of their population spikes to low glucose. There was a particularly strong correlation between the latency of the population spike and the period of superfusion in low glucose medium required to depress the amplitude of the spike by 25%. The data suggest that increased excitability of dentate granule cells is associated with an increased vulnerability to low glucose.

Animals↗
PubMed1988

Partial attenuation of dentate granule cell evoked activity by the alternative substrates, lactate and pyruvate: evidence for a postsynaptic action.

Granule cell field potentials were evoked by stimulation of the perforant path of superfused hippocampal slices. Replacing the glucose in the superfusion medium with pyruvate (10 mM) or lactate (10 mM) attenuated the field potentials, significant decreases occurring in both the population spike and the population EPSP. Usually, a new steady state level of evoked activity was established which could be maintained for at least 20 min. Input-output analyses (EPSP vs stimulus strength, population spike vs EPSP) were performed using variable stimulus strengths on slices superfused with control or test media (under steady state conditions). At higher stimulus strengths the rate of rise of population EPSP was significantly lower for a given stimulus strength when pyruvate or lactate replaced glucose. However, the threshold stimulus intensity required to evoke a population EPSP was the same under all conditions. EPSP/population spike relationships were also analyzed under control and test conditions. Pyruvate, but not lactate, increased the threshold EPSP required to generate a population spike. Neither substrate significantly affected the incremental change in EPSP associated with a given increase in the population spike. It is argued that lactate and pyruvate attenuate granule cell evoked activity solely by postsynaptic actions. Lactate and pyruvate both appear to affect the summation of EPSPs; pyruvate may also affect the process of granule cell discharge.

Action Potentials↗
PubMed1988

Physical linkage of a human immunoglobulin heavy chain variable region gene segment to diversity and joining region elements.

Antibody genes are assembled from a series of germ-line gene segments that are juxtaposed during the maturation of B lymphocytes. Although diversification of the adult antibody repertoire results in large part from the combinatorial joining of these gene segments, a restricted set of antibody heavy chain variable (VH), diversity (DH), and joining (JH) region gene segments appears preferentially in the human fetal repertoire. We report here that one of these early-expressed VH elements (termed VH6) is the most 3' VH gene segment, positioned 77 kilobases on the 5' side of the JH locus and immediately adjacent to a set of previously described DH sequences. In addition to providing a physical map linking human VH, DH, and JH elements, these results support the view that the programmed development of the antibody VH repertoire is determined in part by the chromosomal position of these gene segments.

B-Lymphocytes↗
PubMed1988

Brain levels of NADH and NAD+ under hypoxic and hypoglycaemic conditions in vitro.

The effects of hypoxia and hypoglycaemia on the redox state in vitro have been studied. NADH and NAD+ were extracted simultaneously from superfused cerebral cortex slices and assayed by bioluminescence. The results show a nonsignificant increase in NADH and the redox ratio in "mild hypoxia," whereas "severe hypoxia" produced an increase of over 200% in NADH and in the NADH/NAD+ ratio. When the glucose in the incubation medium was reduced from its control value of 10 mM to 0.5 mM, significant decreases in NADH and the redox ratio to 60% of control value were observed. Further decreasing the glucose to 0.2 mM gave lower levels of NADH and the redox ratio (40% of control). The effects on the redox state of alternative substrates to glucose were also tested. Replacement of glucose by 10 mM pyruvate decreased the NADH by 77% and the NADH/NAD+ ratio by 79%. Replacement of glucose with 10 mM lactate gave decreases of 70% and 71%, respectively, whereas in the presence of 15 mM 2-deoxyglucose and 5 mM glucose, the NADH was decreased by 56% and the ratio by 50%. The results are discussed in relation to levels of creatine phosphate and ATP, as well as evoked action potentials, observed from parallel studies.

Adenosine Triphosphate↗