Rapid detection of a Mediterranean beta (0) beta-thalassemic splice junction mutation by DNA amplification and BsaB1 mapping.
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Child↗
Biomedical subjects
R Krishnamoorthy
Publications and source records attributed to R Krishnamoorthy.
Locus assignment of human alpha globin mutations by selective amplification and direct sequencing.
We describe a simple approach for molecular characterization and locus assignment of structural mutants by direct sequencing of enzymatically amplified DNA selective to alpha 1 and alpha 2 globin gene regions. Nucleotide substitution of two structural variants (Stanleyville II alpha 2(78Lys) and J Mexico alpha 2(54Glu) were determined and their encoding loci were specified. The amplified segment encompasses sequences upstream of the CAAT box to downstream of the Poly(A) addition signal. Hence all of the alpha globin structural variants and most of the nondeletion alpha thalassaemic mutants should be characterizable by this approach.
Africa↗
A simple, sensitive method of analyzing bacterial ribosomal DNA polymorphism.
A rapid DNA extraction procedure and random primer labelling of Escherichia coli ribosomal RNA with cloned reverse transcriptase have been used to establish a simple and highly sensitive method for studying ribosomal DNA polymorphism in bacteria. Examples of inter- and intraspecies differentiation of bacteria are given and potential applications in bacterial epidemiology and taxonomy are discussed.
Acinetobacter↗
Effect of ligand-affinity differences of human hemoglobin variants on electrophoretic behavior and their isolation and functional characterization.
A natural sulfated polysaccharide (agaropectin), contained in crude agar, can be used as a medium for electrophoretic separation of hemoglobin mutants, constituting a particular class of protein-ligand interactions. Mutations which either modify the electrostatic charge at the surface of the hemoglobin molecule or not, have been studied according to their putative interaction with the medium. Using conformational specificities of the hemoglobin molecule, we have also demonstrated that isoelectric focusing on a polyacrylamide gel in the absence of heme ligands represents a useful, convenient and rapid procedure for isolating silent Hb variants in their native form, provided that they exhibit an abnormal Bohr effect.
Calcium↗
The analysis of five carbenicillin-hydrolysing enzymes by electrophoretic methods.
Five carbenicillin-hydrolysing enzymes (carbenicillinases, or CARB), PSE-4 (CARB-1), PSE-1 (CARB-2), CARB-3, CARB-4 and CARB-5, and the beta-lactamase PSE-2 were compared by analysing their isoelectric points (pI), electrophoretic mobilities (mR) and titration curves (pH gradient electrophoresis). The pI determined by isoelectric focusing were 4.3 (CARB-4), 5.3 (PSE-4/CARB-1), 5.7 (PSE-1/CARB-2), 5.75 (CARB-3), 6.1 (PSE-2) and 6.35 (CARB-5). Their mR were estimated by zone electrophoresis as congruent to 26 for PSE-1 (CARB-2), CARB-3 and CARB-5, congruent to 30 for PSE-2, congruent to 33 for PSE-4 (CARB-1) and congruent to 61 for CARB-4. Titration curve analyses indicated that (1) PSE-4 (CARB-1), PSE-1 (CARB-2), CARB-3 and CARB-5 are closely related variants differing by a few amino acid substitutions; (2) the qualitative titration curve of CARB-4 is different from those of PSE-4 (CARB-1), PSE-1 (CARB-2), CARB-3 and CARB-5, although their patterns are somewhat similar; and (3) PSE-2 has no structural relationship with any of the other carbenicillin-hydrolysing enzymes or carbenicillinases (CARB) studied. Electrophoretic methods, and in particular titration curve determination combined with other physicochemical and enzymatic data, allowed a rapid comparison of the molecular structures of the beta-lactamases, and hence their classification.
Acinetobacter↗
Analysis of the molecular relatedness of four extended spectrum beta-lactamases (SHV-2, SHV-3, SHV-4 and SHV-5) by comparative protein titration curves.
Six beta-lactamases from Klebsiella pneumoniae, five of which (SHV-1, SHV-2, SHV-3, SHV-4 and SHV-5) were plasmid-encoded and one which (beta 1a GN 11-03) was chromosomally-encoded, were compared by analysis of their isoelectric points (pI), electrophoresis mobilities (MF) and titration curves or pH gradient electrophoresis. Four groups were defined by their pI and MF, namely SHV-1 and SHV-2 (pI = 7.6, MF approximately 14), SHV-3 and beta 1a GN 11-03 (pI = 7.0, MF approximately 20), SHV-4 (pI = 7.8 MF approximately 12) and SHV-5 (pI = 8.2, MF approximately 5). The titration curves of SHV-1 and SHV-2 enzymes on the one hand, and SHV-3 and beta 1a GN 11-03 on the other were completely superimposable for the whole of the pH gradient (3.5-10), indicating strongly similarity. Conservative amino-acid substitutions could account for the differences in the substrate spectra of the purified enzymes. The differences observed between the titration curves of the enzymes SHV-1/SHV-3, SHV-1/beta 1a GN 11-03, SHV-2/SHV-3 and SHV-5/SHV-4 pairs were consistent with the replacement of a basic amino-acid residue in the former enzyme of each pair by an acidic residue in the latter. Similarly, the titration curves of SHV-1/SHV-4 and of SHV-2/SHV-4 pairs may suggest the replacement of an acidic amino-acid in the former beta-lactamases by a neutral amino-acid in the latter of each pair. However, the presence of several self-cancelling or neutral substitutions is also possible. In contrast, when SHV-1 and TEM-1 (pI = 5.4 MF approximately 45) were titrated together, no structural relationship could be inferred.
Chromosomes, Bacterial↗
A gene conversion located 5' to the A gamma gene in linkage disequilibrium with the Bantu haplotype in sickle cell anemia.
Cloning and sequencing of the gamma-globin gene of a sickle cell anemia patient homozygous for the Bantu haplotype has revealed a gene conversion that involves the replacement of an A gamma sequence by a G gamma sequence in the promoter area of the A gamma gene. This event is similar to another gene conversion believed to be responsible for the very high homology between gamma-globin genes, suggesting that the promoter area of these genes is prone to this type of genetic rearrangement. Further analysis demonstrated that the chromosome bearing this gene conversion has a very high frequency among Bantu chromosomes and a very low or nil frequency in other haplotypes linked to the beta s gene. No correlation was found between the G gamma/A gamma ratio and the presence of the gene conversion among Bantu haplotype patients, thus excluding a portion of the gamma gene sequence in the determination of this ratio.
Anemia, Sickle Cell↗
Nucleotide variations in the 3' A gamma enhancer region are linked to beta-gene cluster haplotypes and are unrelated to fetal hemoglobin expression.
Molecular cloning and sequence analysis of a nondeletion form of Sicilian beta o hereditary persistence of fetal hemoglobinemia (HPFH) (mutation in IVS2 nt1 position) homozygous for haplotype III revealed the presence of four sequence variations: C----T at -158 5' to G gamma, T----C at +2285, C----A at +2476, and A----G at +2676, all 3' to A gamma. The latter three variations in the putative A gamma enhancer are identical to those observed in the case of Seattle HPFH. However, a severe beta o-thalassemia case from Algeria (mutation in IVS1 nt1 position), also homozygous for haplotype III, revealed the same nucleotide variation, albeit an inefficient HbF production. We conclude that the variations in the A gamma enhancer element do not play a role in the regulation of HbF production. To assess both the linkage of these sites with the beta-cluster haplotype and the extent of the polymorphism, we examined several black and Mediterranean chromosomes, by PCR amplification followed by both EspI digestion and oligonucleotide hybridization. Our data indicate that these sequence variations in the enhancer element are absent in Mediterranean haplotypes I, V, and VII but are consistently associated with Mediterranean haplotypes II, III, and IX, as well as with the black beta c-associated haplotype. The common feature of all the latter haplotypes is the presence of a polymorphic PvuII site between A gamma and psi beta, which is thus in linkage disequilibrium with the variations in the A gamma enhancer.(ABSTRACT TRUNCATED AT 250 WORDS)
Base Sequence↗
Sequence variations in the 3' A gamma enhancer are silent polymorphisms.
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Adolescent↗
The enhancer-like sequence 3' to the A gamma gene is polymorphic in human populations.
Cloning and sequencing of the enhancer 3' of the A gamma globin gene of a particularly low G gamma and HbF sickle cell anemia (SCA) patient unexpectedly revealed three base changes (T----C, C----A, and A----G at sites +2285, +2460, and +2676) previously associated with the Seattle-type HPFH, thus leading the authors to suspect that the three mutations were polymorphic. The determination of the incidence of the mutations among various ethnic groups allowed the authors to conclude that this is a widely spread polymorphism, thus excluding any role of these base changes in the determination of the hereditary persistence of fetal hemoglobin (HPFH) phenotype. The origin of these three mutations is not clear because they appear linked, and the same bases (C, A, G) are found in homologous position in the 3' of the normal G gamma gene. As C, A, G at positions +2285, +2460, and +2676 are found with a 100% frequency in African SS patients and presumably among normal Africans (to explain the extremely high frequency among normal American blacks), it is likely that this was the sequence preceding the division of races. The presence of T, C, and A at the same positions apparently occurred after the divergence between blacks and the other races, that is, within the last 1 million years.
Base Sequence↗
Retrieval of precursors for white-type adipose conversion in brown adipose tissue.
A cellular compartment from brown adipose tissue (BAT) of newborn rats was isolated by Percoll-density-gradient centrifugation and was shown to proliferate and to undergo adipose conversion in vitro in primary culture. The features of the effector requirement for adipose conversion as well as the differentiated morphological and biochemical phenotype are almost identical with that of a compartment designated HCF, from white adipose tissue (WAT). A possible role for these precursors from BAT and WAT in the involution of BAT into WAT, on the one hand, and in the development of brown adipose cells among typical WAT deposits, on the other, is discussed.
Adipose Tissue, Brown↗
A simple strategy to amplify specifically the HLA-DQ beta gene region with genomic DNA as template.
The nature of codon 57 in the HLA-DQ beta gene was recently reported as a potential marker of genetic susceptibility to insulin-dependent diabetes mellitus. When exploring the relevance of this marker by using genomic DNA amplification, we encountered difficulties resulting from the coamplification of the homologous DX beta region. A simple strategy is proposed to amplify the DQ beta region exclusively. It involves the preliminary digestion of genomic DNA with a restriction enzyme which cleaves DX beta specifically, leaving intact the DQ beta sequence. The amplified material is suitable for dot blot analysis and restriction enzyme digestion. This strategy is of general interest when homologous sequences impair the specificity of enzymatic DNA amplification.
DNA↗
A novel beta thalassemia gene with a single base mutation in the conserved polypyrimidine sequence at the 3' end of IVS 2.
An adult Algerian patient with homozygous beta thalassemia was found to have a unique beta thalassemia gene. Cloning and sequencing revealed that the only abnormality present in this beta gene is a transversion in the polypyrimidine stretch at the 3' end of the large intervening sequence (IVS 2) six bases 5' to the consensus AG dinucleotide sequence (CCGCCCACAG instead of CCTCCCACAG). In addition, digestion of the cloned fragment by the enzyme Mnl I demonstrates the disappearance of a restriction site as expected. This is the first example of a defect in the consensus sequence at the 3' end of an IVS leading to a thalassemia phenotype presumably due to decreased splicing.
Adult↗
Atypical haplotypes linked to the beta S gene in Africa are likely to be the product of recombination.
We report here the haplotypes of 10 MstII-defined SS patients and a S/beta o thalassemia from the Central African Republic, exhibiting 7 different atypical haplotypes that are different from the typical Bantu haplotype that characterize over 93% of the beta s bearing chromosomes in that region of Africa. Of the seven atypical haplotypes, six can be easily interpreted as the result of recombination around the "hot spot" 5' of the beta gene, between a typical Bantu haplotype and other haplotypes available in the normal population. Except for one case that requires further study, this result demonstrates that the main mutational event leading to sickle hemoglobin in Bantu-speaking Africa was the mutation of the beta gene in a Bantu haplotype background.
Africa↗
DNA haplotype distribution in Algerian beta thalassaemia patients. An extended evaluation by family studies and representative molecular characterization.
An evaluation of beta thalassaemia mutations and the associated chromosomal haplotypes has been made among Algerian thalassaemic patients in this extended series. The major features of our findings are: (i) due to elevated proportion of consanguinity, the frequency of true homozygotes for a defect is high; (ii) Despite this high homozygosity within families, the number of molecular defects resulting in beta thalassaemia are very heterogeneous within this population. This is exemplified not only by the high heterogeneity of haplotypes and associated mutations, but also by the definition of several new haplotypes, among which two of them were found to be associated with novel mutations. Family studies have been performed in parallel to evaluate the degree of feasibility of antenatal diagnosis in this population.
Algeria↗
Electrophoretic data in designing strategies for purification and identification of a highly polymorphic bacterial esterase.
We have purified a bacterial enzyme, designated esterase M, by tailoring an efficient and rapid strategy with information derived from titration curves of proteins in crude extract. The pH-dependent stability of the enzyme activity observed by titration pattern allowed an acidic pH treatment of extract and a cationic exchange chromatography at pH 4.1. These two steps were followed by an anionic exchange chromatography and a preparative electrophoresis. Thus, the enzyme was purified about 2000-fold within two days with a recovery of 13.3%. The electrophoretic variants of esterase M were investigated for their molecular relationship through the specific effect of antibodies on esterase electrophoretic pattern (immunosubtractive electrophoresis) which is applicable to large series of samples. By this process, we have demonstrated the presence of common antigenic determinants among the electromorphs of esterase M produced by the three species of motile Aeromonas.
Aeromonas↗
Interaction of deletional alpha-thalassaemia with sickle cell beta-thalassaemia and its influence on foetal haemoglobin expression.
A rare association of three haemoglobin defects, viz: traits for deletion form of alpha-thalassaemia, beta-thalassaemia, and sickle cell gene, in a family of French West Indies origin, was studied both at phenotype and genotype levels. In this sickle cell beta-thalassaemia, interacting alpha-thalassaemia is shown to influence the foetal haemoglobin expression. A reverse relationship between the foetal haemoglobin level and the number of alpha genes was observed.
Anemia, Sickle Cell↗
Characterization of rat preadipocytes from normal rat adipose tissue by their effector response.
We isolated from normal rat adipose tissue, by a Percoll-density-gradient procedure, two populations of adipocyte precursors. These preadipocytes undergo morphological and biochemical adipose conversion in primary culture. For full adipose conversion, these precursor cells, in addition to the adipogenic factor present in fetal-calf serum, require other effectors differentially. One population completes terminal differentiation in the presence of physiological concentrations of insulin. The second population requires a pre-sensitization with isobutylmethylxanthine at a critical period of the culture in order to respond to insulin. The fact that dibutyryl cyclic AMP could not be substituted for isobutylmethylxanthine suggests that the effect of the latter agent is not through its inhibition of particulate phosphodiesterase activity. These two populations further differ in their response to exogenously added haemin. Thus the existence of at least two developmentally regulated rat adipose-precursor compartments is demonstrated.
1-Methyl-3-isobutylxanthine↗