Nucleoside reverse transcriptase inhibitors (NRTIs) affect mitochondrial DNA polymerase gamma causing significant toxic effects, including fatal lactic acidosis. Little is known about mitochondrial DNA (mtDNA) in human immunodeficiency virus (HIV) infected children who face a lifetime exposure to these agents. We performed a cross sectional observation of mtDNA levels in whole blood in a pediatric population to ascertain the relationship between mtDNA, NRTI regimens and parameters of HIV-infection severity. Whole blood mitochondrial/nuclear DNA (mt:nDNA) ratios were determined by real-time PCR in three groups: 27 presumed HIV-negative, 89 HIV-infected, NRTI-treated and 62 HIV-infected treatment-naive children. Multivariate analysis was used to identify variables independently associated with mtDNA depletion. Mean mt: nDNA ratios were lower (p < 0.001) at 77% of control in the HIV-infected antiretroviral treatment (ART) naive group and 73% of control in the ART group, but not different between the two HIV-infected groups. Mt:nDNA ratios were negatively associated with age (p = 0.029), HIV status (p < 0.0001) and Log 10 of the HIV-1 viral load (p = 0.035) and positively associated with CD4 % (p = 0.032). A stavudine vs. zidovudine based regimen was associated with lower but not significant levels of mtDNA (p = 0.08). Depletion of whole blood mtDNA in children is associated independently with HIV-infection and markers of HIV infection severity, and does not improve with either stavudine or zidovudine based ART despite virological control, suggesting that these agents also deplete mtDNA. The long-term consequences of this potentially toxic effect remain a cause for concern

L-2 hydroxyglutaric aciduria is an autosomal recessive error of metabolism that manifests as an encephalopathy. The most common presenting signs are seizures, tremors, ataxia and/ or dementia. Some affected dogs show only subtle behavioural changes. Amongst canines, the condition has been best described in Staffordshire Bull Terriers. Although this is the first reported case in South Africa, at least three other affected dogs have been indentified by polmerase chain reaction (PCR) in this country. Affected dogs have normal haematology, serum biochemistry and routine urine analysis. This report discusses the advantages and limitations of the three main diagnostic modalities, namely: magnetic resonance imaging, urine gas chromatography-mass spectrometry and genetic testing. The aim of this report is to increase awareness of the condition, assist diagnosis in encephalopathic dogs and improve detection of carriers amongst breeding stock.

Complete complement component 6 deficiency (C6Q0) is a co-dominant genetic disease presenting as increased susceptibility to invasive Neisseria meningitidis infections. Affected individuals have two affected alleles which can be homozygous or compound heterozygous for the particular gene defects they carry. This disorder has been diagnosed relatively frequently in Western Cape South Africans. Affected patients are prescribed penicillin prophylaxis. In 2004 we commenced a clinical follow-up study of 46 patients. Of these, 43 had family age-matched C6 sufficient controls. Participants were classified as either (i) well, or (ii) having a serious illness (SI) or died (D). An SI was a long-term illness that did not allow the performance of normal daily activities. Among 43 patients, 21 were well and 22 were SI/D, while among 43 matched controls, 35 were well and eight were SI/D. This difference is highly significant. Among all 46 C6Q0 patients, those who had had recurrent infection had significantly more SI/D than those who had suffered none or one infection. Thus, this work demonstrates the long-term serious outcome of repeated meningococcal disease (MD) episodes. We investigated the frequencies of four C6Q0 pathogenic mutations known to affect Cape patients (828delG, 1138delC, 821delA and 1879delG) in 2250 newborns. A total of 103 defective alleles (2·28%) and three affected C6Q0 individuals were detected. For all defects combined, 5·24 affected subjects (C6Q0) are expected among 10,000 individuals. What is still unknown is the number of C6Q0 individuals who suffer MD or other infectious diseases.

Without intervention, classic galactosemia is a potentially fatal disorder in infancy. With the benefit of early diagnosis and dietary restriction of galactose, the acute sequelae of classic galactosemia can be prevented or reversed. However, despite early and lifelong dietary treatment, many galactosemic patients go on to experience serious long-term complications including cognitive disability, speech problems, neurological and/or movement disorders and, in girls and women, ovarian dysfunction. Further, there remains uncertainty surrounding what constitutes a 'best practice' for treating this disorder. To explore the extent and implications of this uncertainty, we conducted a small but global survey of healthcare providers who follow patients with classic galactosemia, seeking to compare established protocols for diagnosis, intervention, and follow-up, as well as the outcomes and outcome frequencies seen in the patient populations cared for by these providers. We received 13 survey responses representing five continents and 11 countries. Respondents underscored disparities in approaches to diagnosis, management and follow-up care. Notably, we saw no clear relationship between differing approaches to care and long-term outcomes in the populations studied. Negative outcomes occurred in the majority of cases regardless of when treatment was initiated, how tightly galactose intake was restricted, or how closely patients were monitored. We document here what is, to our knowledge, the first global comparison of healthcare approaches to classic galactosemia. These data reinforce the idea that there is currently no one best practice for treating patients with classic galactosemia, and underscore the need for more extensive and statistically powerful comparative studies to reveal potential positive or negative impacts of differing approaches.

Glutaric Aciduria type 1 (GA 1) is an inherited disorder of lysine and tryptophan catabolism that typically manifests in infants with acute cerebral injury associated with intercurrent illness. We investigated the clinical, biochemical and molecular features in 14 known GA 1 patients in South Africa, most of whom were recently confirmed following the implementation of sensitive urine organic acid screening at our laboratory. Age at diagnosis ranged from 3days to 5years and poor clinical outcome reflected the delay in diagnosis in all but one patient. Twelve patients were unrelated black South Africans of whom all those tested (n=11) were found homozygous for the same A293T mutation in the glutaryl-CoA dehydrogenase (GCDH) gene. Excretion of 3-hydroxyglutarate (3-OHGA) was >30.1μmol/mmol creatinine (reference range <2.5) in all cases but glutarate excretion varied with 5 patients considered low excretors (glutarate <50μmol/mmol creatinine). Fibroblast GCDH activity was very low or absent in all of five cases tested. Heterozygosity for the A293T mutation was found 1 in 36 (95% CI; 1/54 - 1/24) unrelated black South African newborns (n=750) giving a predicted prevalence rate for GA 1 of 1 in 5184 (95% CI; 1/11664 - 1/2304) in this population. GA 1 is a treatable but often missed inherited disorder with a previously unrecognised high carrier frequency of a single mutation in the South African black population.

Host recognition of mycobacterial surface molecules occurs through toll like receptors (TLR) 2 and 6. The adaptor protein TIRAP mediates down stream signalling of TLR2 and 4, and polymorphisms in the TIRAP gene (TIRAP) have been associated with susceptibility and resistance to tuberculosis (TB) in adults. In order to investigate the role of polymorphic variation in TIRAP in childhood TB in South Africa, which has one of the highest TB incidence rates in the world, we screened the entire open reading frame of TIRAP for sequence variation in two cohorts of childhood TB from different ethnic groups (Xhosa and mixed ancestry). We identified 13 SNPs, including seven previously unreported, in the two cohorts, and found significant differences in frequency of the variants between the two ethnic groups. No differences in frequency between individual SNPs or combinations were found between TB cases and controls in either cohort. However the 558C-->T SNP previously associated with TB meningitis (TBM) in a Vietnamese population was found to be associated with TBM in the mixed ancestry group. Polymorphisms in TIRAP do not appear to be involved in childhood TB susceptibility in South Africa, but may play a role in determining occurrence of TBM.

Lipoprotein lipase deficiency causes severe hypertriglyceridaemia due to chylomicronaemia, and leads to recurrent and potentially life-threatening pancreatitis. This disorder can only be managed by dietary fat restriction as drugs are ineffective.We review the experience with familial chylomicronaemia in patients who attended the lipid clinics at Groote Schuur Hospital and Red Cross Children's War Memorial Hospital in Cape Town. Criteria for inclusion were an initial plasma triglyceride concentration of >15 mmol/l and a typical type I Fredrickson hyperlipidaemia pattern on plasma lipoprotein electrophoresis. A total of 29 patients were seen over 25 years. The mean age of presentation was 10 years, but ranged from 0 to 43 years. The modes of presentation differed: pancreatitis (N=16), eruptive xanthomata (N=2), coincidental detection of hypertriglyceridaemia (N=2), screening relatives (N=7), and after death from pancreatitis (N=1). Plasma triglycerides responded rapidly and dramatically to dietary fat restriction, and some patients sustained good control of the hyperlipidaemia. The onset of pancreatitis was earlier in patients of Indian ancestry, suggesting a genotype/phenotype interaction within this disorder. Genetic work-up indicated founder effects in the Afrikaner and Indian patients.Lipaemic plasma should be taken seriously at all ages, and necessitates work-up at specialised clinics where the diagnosis of chylomicronaemia or type I hyperlipidaemia facilitates appropriate dietary management that can prevent pancreatitis.

The prevalence of the common mutations in the surfactant protein-B (121ins2), surfactant protein-C (I73T), and ATP-binding cassette member A3 (E292V) genes in population-based or case-control cohorts of newborn respiratory distress syndrome (RDS) is unknown. We determined the frequencies of these mutations in ethnically diverse population and disease-based cohorts using restriction enzyme analysis (121ins2 and E292V) and a 5′ nuclease assay (I73T) in DNA samples from population-based cohorts in Missouri, Norway, South Korea, and South Africa, and from a case–control cohort of newborns with and without RDS (n = 420). We resequenced the ATP-binding cassette member A3 gene (ABCA3) in E292V carriers and computationally inferred ABCA3 haplotypes. The population-based frequencies of 121ins2, E292V, and I73T were rare (<0.4%). E292V was present in 3.8% of newborns with RDS, a 10-fold greater prevalence than in the Missouri cohort (p < 0.001). We did not identify other loss of function mutations in ABCA3 among patients with E292V that would account for their RDS. E292V occurred on a unique haplotype that was derived from a recombination of two common ABCA3 haplotypes. E292V was over-represented in newborns with RDS suggesting that E292V or its unique haplotype impart increased genetic risk for RDS.

Objective: To determine haplotype background of common mutations in the genes encoding surfactant proteins B and C (SFTPB and SFTPC) and to assess recombination in SFTPC. Study Design: Using comprehensive resequencing of SFTPC and SFTPB, we assessed linkage disequilibrium (LD) (D'), and computationally inferred haplotypes. We computed average recombination rates and Bayes factors (BFs) within SFTPC in a population cohort and near SFTPC ( +/- 50 kb) in HapMap cohorts. We then biochemically confirmed haplotypes in families with sporadic SFTPC mutations (n = 11) and in individuals with the common SFTPB mutation (121ins2, n = 30). Results: We detected strong evidence (weak LD and BFs > 1,400) for an intragenic recombination hot spot in both genes. The 121 ins2 SFTPB mutation occurred predominantly (89%) on 2 common haplotypes. In contrast, no consistent haplotypes were associated with mutated SFTPC alleles. Sporadic SFTPC mutations arose on the paternal allele in four of five families; the remaining child had evidence for somatic recombination on the mutated allele. Conclusions: In contrast to SFTPB, disease alleles at SFTPC do not share a common haplotype background. Most sporadic mutations in SFTPC occurred on the paternal allele, but somatic recombination may be an important mechanism of mutation in SFTPC.

Late-onset urea cycle disorder in a 20-month-old boy is unusually associated with Klinefelter syndrome with a 47XXY karyotype. We record the typical clinical and biochemical findings of ornithine transcarbamylase (OTC) deficiency in a young boy with a short history of recurrent vomiting, self mutilating behaviour, lethargy, ataxia and seizures. Laboratory studies showed hyperammonaemia and orotic aciduria, with normal citrulline and other urea cycle amino acids. Unfortunately, a liver biopsy for OTC activity measurement was refused by the parents. A rapid reversal of phenotype was seen on the introduction of a low-protein diet with accompanying benzoate and phenylbutyrate administration. Linkage studies suggested the inheritance of two X chromosomes, which was confirmed by karyotype analysis. Sequencing of all exons and immediate splice site regions revealed no sequence alterations in these sections of the OTC gene. A search for skewing of X-inactivation in the liver was not possible but we did show a random pattern of X-inactivation in leukocytes. The possibility of maternal X chromosome iso-disomy in our patient was discounted by microsatellite analysis, which revealed the inheritance of two independent X chromosomes. Mutation analysis in the OTC gene has shown that approximately 20% of patients with liver biopsy confirmed OTC deficiency do not have mutations in the coding or immediate splice-site sequences of this gene. Their classification as OTC phenocopies remains speculative, awaiting clarification of the underlying DNA alteration. We report on the novel association of OTC deficiency and Klinefelter syndrome with the additional interest of a probable unusual genetic defect underlying the OTC abnormality.

Background: Phenocopies of homozygous familial hypercholesterolemia (hoFH) having autosomal recessive inheritance, were recently found to arise from defects in the LDL receptor (LDLR) adapter protein, called ARH, which facilitates the clearance of circulating LDL. Discrimination between the two causes of the phenotype at a clinical level may not be possible when parents display moderate hypercholesterolaemia. An effective strategy is thus required to identify the appropriate mechanism for the disorder.Methods: Fibroblast LDL uptake studies were coupled with Western blotting for ARH protein in cell extracts, to identify the defective gene before DNA studies were initiated. Two subjects with the hoFH phenotype, but with indeterminate dyslipidaemia in their parents, were fully worked up.Results: Defective LDL metabolism was established in both patients by functional and protein studies and farther confirmed by detecting deleterious mutations, in the LDLR and ARH genes. The ARH patient is the first subject of Negroid identity to be described and records a specific mutation in this racial grouping.Conclusion: This study highlights the occasional complexity and uncertainty of a clinical diagnosis of hoFH and presents Western blotting of leucocyte extracts for ARH protein, as a rapid strategy for the detection of ARH before sequencing the gene for mutation(s). This strategy may be particularly useful in populations where founder mutations for ARH and LDLR defects are rare or co-exist. (c) 2006 Elsevier B.V. All rights reserved.

Complement component C6 is one of five terminal complement components incorporated into the membrane attack complex. Complete deficiency of C6 (C6Q0) leads to an increased susceptibility to Neisseria meningitidis infections, and affected individuals typically present with recurrent meningococcal disease. There is a relatively high prevalence of C6Q0 in the Western Cape, South Africa and three frameshift mutations have previously been described to be responsible for C6Q0 in this area-879delG, 1195delC, and 1936delG (current nomenclature). We have now genotyped a further nine genetically independent individuals with C6Q0, confirming previous reports that the most common defect in the Western Cape is 879delG. Moreover, we report the first identification of the 878delA mutation within the Western Cape, which has previously only been reported in individuals of African descent living in the United States or Europe. We also investigated the genotype of an Irish C6Q0 individual and her sibling, and report two previously undescribed mutations. One mutation alters a tyrosine codon to a stop codon within exon 10. The second mutation is within the 5' donor splice site of intron 3, and would, in all probability, disrupt splicing. These two mutations were shown to segregate independently. We also discuss the nomenclature for reporting C6 and C7 gene mutations, as the current nomenclature does not follow the recognised guidelines.

We present an equation of state that can represent within experimental error most individual sets of published PVT data for most fluids, whether in the range of vapor at moderate pressures, or compressed liquids, or gases at very high temperatures and densities, any region in fact except the vicinity of the critical point. In terms of pressure the equation is P = DRT [1 + (D/T) (c1T + c2D - 1) / (c3 + c4Tsol12 + c5D + c6D2)] where D = 1/V, the density in mole 1−1. The coefficients are readily determined by a least squares fit of the data. An additional term is sometimes needed if the D range is very wide, say several times Dc. Different fluids can be simultaneously represented over a limited range, such as the compressed liquid region, by a single reduced form of the equation in which all but three of the constants are the same for all, and these three (a reducing T, 1/c1, a reducing D, 1 / c2, and a dimensionless parameter) are characteristic of each individual fluid. The equation can also simultaneously represent many data sets for a single fluid from many labs and covering various T and D ranges. From this, a consistent representation of its thermodynamic properties can be derived.

BACKGROUND:The objective of this study was to describe the clinical and molecular features of the first South African family with X-linked hyper-IgM syndrome (HIGM1).METHODS:Diagnoses were based on immunoglobulin results and the absence of CD40 ligand (CD40L) expression on activated T-cells. Complete molecular characterisation involved CD40L cDNA sequencing, and genomic DNA analysis by polymerase chain reaction amplification, restriction enzyme digestion and sequencing. A PCR-based diagnostic assay was established for carrier detection and prenatal diagnosis in this family.RESULTS:There were originally six children, three males and three females. The eldest boy died after being diagnosed with hypogammaglobulinaemia, before HIGM1 was considered. This disorder was diagnosed in the second eldest boy at the age of 5 years, after failing to detect CD40L expression on his activated T-cells. A deficiency of CD40L was also confirmed in the youngest male at the age of 5 years. Both younger brothers have since died of infections relating to HIGM1. Molecular investigation showed that exon 3 was deleted from the CD40L mRNA of the affected males. Genomic DNA analysis identified a 1.5 kilobase deletion, spanning exon 3 and including extended flanking intronic sequence. Carrier status in the mother was confirmed by RT-PCR of her CD40L mRNA. Genetic analysis of the three female children was deferred because they were below the legal consenting age of 18 years. A PCR-based assay for genomic DNA was established for easy identification of female carriers and affected males in the future.CONCLUSIONS:This study confirmed the diagnosis of HIGM1 in the first South African family to be investigated and identified a novel mutation in the CD40L gene.

BACKGROUND:The objective of this study was to document the clinical, laboratory and genetic features of galactosemia in patients from the Cape Town metropolitan region.METHODS:Diagnoses were based on thin layer chromatography for galactosuria/galactosemia and assays of erythrocyte galactose-1-phosphate uridyltransferase (GALT) and galactokinase activities. Patients were screened for the common S135L and Q188R transferase gene mutations, using PCR-based assays. Screening for the S135L mutation in black newborns was used to estimate the carrier rate for galactosemia in black South Africans.RESULTS:A positive diagnosis of galactosemia was made in 17 patients between the years 1980 to 2001. All had very low or absent galactose-1-phosphate uridyltransferase (GALT) activity, and normal galactokinase levels. The mean age at diagnosis was 5.1 months (range 4 days to 6.5 months). A review of 9 patients showed that hepatomegaly (9/9), and splenomegaly, failure to thrive, developmental delay, bilateral cataracts (6/9) were the most frequent features at diagnosis. Six had conjugated hyperbilirubinemia. Four experienced invasive E. coli infection before diagnosis. Ten patients were submitted to DNA analysis. All 4 black patients and 2 of mixed extraction were homozygous for the S135L allele, while all 3 white patients were homozygous for the Q188R allele. The remaining patient of mixed extraction was heterozygous for the Q188R allele. The estimated carrier frequency of the S135L mutation in 725 healthy black newborns was 1/60.CONCLUSIONS:In the absence of newborn screening the delay in diagnosis is most often unacceptably long. Also, carrier frequency data predict a galactosemia incidence of approximately 1/14 400 for black newborns in the Cape Metropole, which is much higher than the current detection rate. It is thus likely that many patients go undetected.

Objective: Molecular analysis of the Bruton's tyrosine kinase (Btk) gene in two unrelated families, with a combined total of seven boys, affected by X-linked agammaglobulinaemia (XLA).Methods: Protein electrophoresis and western blotting were used for the examination of Btk protein synthesis in blood leucocytes. Isolation of the coding sequence of the Btk gene was performed by amplification using the reverse transcription-polymerase chain reaction (RT-PCR) technique. Sequence alterations were screened for by the single-stranded conformation polymorphism (SSCP) method and characterized by standard sequencing protocols.Results: Western blotting revealed Btk protein to be absent in leucocytes of affected males from both families. A novel 3 b.p. deletion in exon 3 of the Btk gene was found to be responsible for the XLA phenotype in the affected proband in one family (kindred I). A diagnostic PCR assay was established to detect this mutation in other affected male siblings and carrier females. For the second family (kindred II), the coding sequence of the Btk gene and the promoter region were found to be normal.Conclusions: The present study has demonstrated genetic heterogeneity in the Btk gene in South African XLA patients and has identified a novel mutation in this gene in the largest of the affected kindreds. The gene mutation in the second kindred was undetermined and may be indicative of a defect in some other gene associated with Btk function or stability. Western blotting was found to be informative in establishing a deficiency of Btk protein in both probands and is recommended as a frontline procedure in the molecular diagnosis and work-up of XLA.

Lipoprotein lipase (LPL) interaction with membrane-associated polyanions is a critical component of normal catalytic function. Two strong candidate binding regions, rich in arginine and lysine residues, have been defined in the N-terminal domain (aa279-282 and aa292-304) that show homology to the heparin-binding consensus sequences -X-B-B-X-B-X- and -X-B-B-B-X-X-B-X-, respectively. Additional candidate regions appear in the C-terminal domain, (residues 390-393), which are homologous to the thrombospondin heparin-binding repeat, and the positively charged terminal decapeptide (residues 439-448). To determine residues and domains critical to heparin binding, we have generated different LPL mutants that have alanine substitutions of single arginine and lysine residues and sequence interchanges with the homologous hepatic (HL) and pancreatic (PL) lipases. The mutant cDNAs were expressed in COS-1 cells and catalytically active mutants were assessed for binding to heparin-Sepharose. All the alanine substitutions within the two regions homologous to the heparin-binding consensus sequences in the N-terminal domain either abolished activity or produced a lowering of heparin binding affinity. None of the mutants in the C-terminal domain of LPL showed a loss of activity or a reduction in heparin binding affinity. These data demonstrate that charged residues at positions 279-282 and 292-304 of LPL are important for heparin binding affinity whereas the residues 390-393 and 439-448 in the C-terminal domain are not involved in heparin binding.

Lipoprotein lipase (LPL) plays a crucial role in the hydrolysis of the triglyceride core of circulating chylomicrons and very low density lipoproteins (VLDL) and also has a major effect on the levels and lipid composition of high density lipoproteins (HDL). LPL deficiency is inherited as an autosomal recessive trait and most commonly presents with chylomicronaemia, abdominal pain, and eruptive xanthomata. We have previously described a mutation in exon 5 of the LPL gene which results in a substitution of glutamic acid for glycine at amino acid 188. We have now assessed 16 South African LPL deficient patients from nine separate kindreds for this mutation. Nine of these probands were homozygous for the mutation and were from four families, all of Indian descent. The ancestors of these probands have their origins in villages close to Bombay, India, which suggests a common ancestral mutation for the four Indian kindreds, particularly as the mutant allele in each family carried the identical restriction fragment length polymorphism (RFLP) haplotype. The presence of at least nine affected subjects in this small community around Cape Town is evidence for a higher than expected gene frequency for LPL deficiency in this population.