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Pretoria, South Africa

Wairuri C.K.,University of Pretoria | Van Der Waals J.E.,University of Pretoria | Van Schalkwyk A.,Inqaba Biotechnical Industries | Theron J.,University of Pretoria
Molecular Plant-Microbe Interactions | Year: 2012

Type IV pili are virulence factors in various bacteria. Several subclasses of type IV pili have been described according to the characteristics of the structural prepilin subunit. Although type IVa pili have been implicated in the virulence of Ralstonia solanacearum, type IVb pili have not previously been described in this plant pathogen. Here, we report the characterization of two distinct tad loci in the R. solanacearum genome. The tad genes encode functions necessary for biogenesis of the Flp subfamily of type IVb pili initially described for the periodontal pathogen Aggregatibacter actinomycetemcomitans. To determine the role of the tad loci in R. solanacearum virulence, we mutated the tadA2 gene located in the megaplasmid that encodes a predicted NTPase previously reported to function as the energizer for Flp pilus biogenesis. Characterization of the tadA2 mutant revealed that it was not growth impaired in vitro or in planta, produced wild-type levels of exopolysaccharide galactosamine, and exhibited swimming and twitching motility comparable with the wild-type strain. However, the tadA2 mutant was impaired in its ability to cause wilting of potato plants. This is the first report where type IVb pili in a phytopathogenic bacterium contribute significantly to plant pathogenesis. © 2012 The American Phytopathological Society.

Labuschagne C.D.J.,Inqaba Biotechnical Industries
Pharmacogenomics Journal | Year: 2015

The relationship between genetic variation in CYP2D6 and variable drug response represents a potentially powerful pharmacogenetic tool. However, little is known regarding this relationship in the genetically diverse South African population. The aim was therefore to evaluate the relationship between predicted and measured CYP2D6 phenotype. An XL-PCR+Sequencing approach was used to determine CYP2D6 genotype in 100 healthy volunteers and phenotype was predicted using activity scores. With dextromethorphan as the probe drug, metabolic ratios served as a surrogate measure of in vivo CYP2D6 activity. Three-hour plasma metabolic ratios of dextrorphan/dextromethorphan were measured simultaneously using semi-automated online solid phase extraction coupled with tandem mass spectrometry. Partial adaptation of the activity score system demonstrated a strong association between genotype and phenotype, as illustrated by a kappa value of 0.792, inter-rater discrepancy of 0.051 and sensitivity of 72.7%. Predicted phenotype frequencies using the modified activity score were 1.3% for poor metabolisers (PM), 7.6% for intermediate metabolisers (IM) and 87.3% for extensive metabolisers (EM). Measured phenotype frequencies were 1.3% for PM, 13.9% for IM and 84.8% for EM. Comprehensive CYP2D6 genotyping reliably predicts CYP2D6 activity in this South African cohort and can be utilised as a valuable pharmacogenetic tool.The Pharmacogenomics Journal advance online publication, 27 October 2015; doi:10.1038/tpj.2015.76. © 2015 Macmillan Publishers Limited

Van Aswegen E.,University of the Free State | Labuschagne C.,Inqaba Biotechnical Industries | Grobler J.P.,University of the Free State
Mammalian Biology | Year: 2012

The springbok (Antidorcas marsupialis) is a significant contributor to the economically important game ranching sector in Southern Africa. Phenotypic variation between springbok from the Karoo and Kalahari regions has been reported by several sources, with springbok from the Kalahari regarded as the larger form. There is no consensus on whether the two variants are determined by heredity, environment or a combination of the two. We studied variation in 80 individuals from four springbok populations using both a gene widely used for population studies (Cytb) and a gene that effects growth (BMP4). Results from Cytb haplotypes and BMP4 diploid gene sequences reveal moderate differentiation among springbok sampled from different regions. We also found a CA tandem repeat motive with high variability at the 3' end of the BMP4 gene region sequenced (the third exon). There is some support for a hypothesis that nominally short and long fragments at this BMP4 repeat are associated with different populations, which may indicate either neutral genetic differentiation between spatially isolated forms, or a relationship between phenotype and BMP4 genotype. We also present new primer sequences to amplify both a partial fragment of the BMP4 gene region and the complete BMP4 tandem repeat motive in springbok. © 2011 Deutsche Gesellschaft far Säugetierkunde.

Dodgen T.M.,University of Pretoria | Hochfeld W.E.,University of Pretoria | Fickl H.,University of Pretoria | Asfaha S.M.,University of Pretoria | And 10 more authors.
BMC Medical Genetics | Year: 2013

Background: Adverse drug reactions and lack of therapeutic efficacy associated with currently prescribed pharmacotherapeutics may be attributed, in part, to inter-individual variability in drug metabolism. Studies on the pharmacogenetics of Cytochrome P450 (CYP) enzymes offer insight into this variability. The objective of this study was to compare the AmpliChip CYP450 Test® (AmpliChip) to alternative genotyping platforms for phenotype prediction of CYP2C19 and CYP2D6 in a representative cohort of the South African population.Methods: AmpliChip was used to screen for thirty-three CYP2D6 and three CYP2C19 alleles in two different cohorts. As a comparison cohort 2 was then genotyped using a CYP2D6 specific long range PCR with sequencing (CYP2D6 XL-PCR + Sequencing) platform and a PCR-RFLP platform for seven CYP2C19 alleles.Results: Even though there was a low success rate for the AmpliChip, allele frequencies for both CYP2D6 and CYP2C19 were very similar between the two different cohorts. The CYP2D6 XL-PCR + Sequencing platform detected CYP2D6*5 more reliably and could correctly distinguish between CYP2D6*2 and *41 in the Black African individuals. Alleles not covered by the AmpliChip were identified and four novel CYP2D6 alleles were also detected. CYP2C19 PCR-RFLP identified CYP2C19*9,*15, *17 and *27 in the Black African individuals, with *2, *17 and *27 being relatively frequent in the cohort. Eliminating mismatches and identifying additional alleles will contribute to improving phenotype prediction for both enzymes. Phenotype prediction differed between platforms for both genes.Conclusion: Comprehensive genotyping of CYP2D6 and CYP2C19 with the platforms used in this study, would be more appropriate than AmpliChip for phenotypic prediction in the South African population. Pharmacogenetically important novel alleles may remain undiscovered when using assays that are designed according to Caucasian specific variation, unless alternate strategies are utilised. © 2013 Dodgen et al.; licensee BioMed Central Ltd.

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