Browsing by Subject "DNA"

Now showing 1 - 6 of 6
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    Open Access
    Circular dichroism as a means to follow DNA gymnastics:on the shoulders of giants
    (2009) Mills, M; Lin, C; Chauhan, M; Klump, H H
    This is the first report of DNA stem-loops self-assembled by 'foot-loop' interactions into either two-dimensional strings or three-dimensional spirals, distinguished by circular dichroism spectroscopy. All subunits are linked by cooperative Watson-Crick hydrogen bonds
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    Open Access
    DNA repair in Bacteroides fragilis Bf-2
    (1987) Abratt, Valerie Rose; Woods, David R; Jones, David T
    Repair deficient mutants of Bacteroides fragilis have been isolated in order to study the responses of this organism to various DNA damaging agents at the physiological and molecular levels. Two types of mutants were isolated by ethyl methane sulphonate mutagenesis of B.fragilis followed by selection for sensitivity to mitomycin C. One mutant (UVS9) showed sensitivity to both mitomycin C and far-UV irradiation. The other (MTC25) was more sensitive to mitomycin C than UVS9, but showed wild-type resistance to UV radiation. Both mutant strains had wild-type resistance to methyl methane sulphonate.
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    Open Access
    DNA-mediated biomineralization of a new planar Pt-complex
    (2006) Klump, H H; Koch, K; Lin, C T
    The crystal growth morphology of a coordination complex of Pt(II) that crystallizes from solution can be controlled by using a second molecular species such as peptides or other organic compounds. Examples of crystal growth controlled by nucleic acids are few. In this article we describe the use of branched three-way junction (3WJ) DNA to influence the crystal growth of a planar platinum compound, cis-[(2, 2′-bipyridyl)N,N-di(2-hydroxyethyl)-N′-benzoylthioureatoplatinum(II)]chloride. Platinum complexes with extended planar aromatic residues are capable of stacking in the absence as well as in the presence of linear DNA double helices. This feature is based on the interaction of the compound with DNA through intercalation, resulting in the prevention of binding of DNA polymerase. Microscopic one-dimensional crystals were observed under these conditions. In the presence of the branched 3WJ DNA, however, additional nucleation sites are present, resulting in extended crystal growth of unique Pt compounds. At least two different crystal modifications were observed using transmission electron microscopy.
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    Fat mass and obesity associated (FTO) gene influences skeletal muscle phenotypes in non-resistance trained males and elite rugby playing position
    (2017) Heffernan, S M; Stebbings, G K; Kilduff, L P; Erskine, R M; Day, S H; Morse, C I; McPhee, J S; Cook, C J; Vance, B; Ribbans, W J; Raleigh, S M; Roberts, C; Bennett, M A; Wang, G; Collins, M; Pitsiladis, Y P; Williams, A G
    Abstract Background FTO gene variants have been associated with obesity phenotypes in sedentary and obese populations, but rarely with skeletal muscle and elite athlete phenotypes. Methods In 1089 participants, comprising 530 elite rugby athletes and 559 non-athletes, DNA was collected and genotyped for the FTO rs9939609 variant using real-time PCR. In a subgroup of non-resistance trained individuals (NT; n = 120), we also assessed structural and functional skeletal muscle phenotypes using dual energy x-ray absorptiometry, ultrasound and isokinetic dynamometry. In a subgroup of rugby athletes (n = 77), we assessed muscle power during a countermovement jump. Results In NT, TT genotype and T allele carriers had greater total body (4.8% and 4.1%) and total appendicular lean mass (LM; 3.0% and 2.1%) compared to AA genotype, with greater arm LM (0.8%) in T allele carriers and leg LM (2.1%) for TT, compared to AA genotype. Furthermore, the T allele was more common (94%) in selected elite rugby union athletes (back three and centre players) who are most reliant on LM rather than total body mass for success, compared to other rugby athletes (82%; P = 0.01, OR = 3.34) and controls (84%; P = 0.03, OR = 2.88). Accordingly, these athletes had greater peak power relative to body mass than other rugby athletes (14%; P = 2 x 10 -6 ). Conclusion Collectively, these results suggest that the T allele is associated with increased LM and elite athletic success. This has implications for athletic populations, as well as conditions characterised by low LM such as sarcopenia and cachexia.
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    Maternal blood contamination of collected cord blood can be identified using DNA methylation at three CpGs
    (2017) Jones, Meaghan J
    Abstract Background Cord blood is a commonly used tissue in environmental, genetic, and epigenetic population studies due to its ready availability and potential to inform on a sensitive period of human development. However, the introduction of maternal blood during labor or cross-contamination during sample collection may complicate downstream analyses. After discovering maternal contamination of cord blood in a cohort study of 150 neonates using Illumina 450K DNA methylation (DNAm) data, we used a combination of linear regression and random forest machine learning to create a DNAm-based screening method. We identified a panel of DNAm sites that could discriminate between contaminated and non-contaminated samples, then designed pyrosequencing assays to pre-screen DNA prior to being assayed on an array. Results Maternal contamination of cord blood was initially identified by unusual X chromosome DNA methylation patterns in 17 males. We utilized our DNAm panel to detect contaminated male samples and a proportional amount of female samples in the same cohort. We validated our DNAm screening method on an additional 189 sample cohort using both pyrosequencing and DNAm arrays, as well as 9 publically available cord blood 450K data sets. The rate of contamination varied from 0 to 10% within these studies, likely related to collection specific methods. Conclusions Maternal blood can contaminate cord blood during sample collection at appreciable levels across multiple studies. We have identified a panel of markers that can be used to identify this contamination, either post hoc after DNAm arrays have been completed, or in advance using a targeted technique like pyrosequencing.
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    No evidence for association of insulin receptor substrate-1 Gly972Arg variant with type 2 diabetes mellitus in a mixed-ancestry population of South Africa
    (2014) Vergotine, Zelda; Kengne, André Pascal; Erasmus, Rajiv Timothy; Matsha, Tandi Edith
    BACKGROUND: The most common single-nucleotide polymorphism in the insulin receptor substrate-1 (IRS1) gene is Gly972Arg, which is associated with a 25% increased risk of developing diabetes. The mixed-ancestry population of South Africa (SA) has one of the highest prevalences of type 2 diabetes mellitus (T2DM) in Africa. OBJECTIVE: To report the frequency of IRS1 Gly972Arg and investigate its associations with cardiometabolic traits. METHODS: DNA from 856 mixed-ancestry adults drawn from an urban community of Bellville South, Cape Town, SA, was genotyped by two independent laboratories. Oral glucose tolerance tests were performed and cardiometabolic risk factors measured. RESULTS: A total of 237 (24.7%) participants had T2DM. The IRS1 Gly972Arg variant was present in 7.9% of the individuals studied and only one participant (non-diabetic) carried the homozygous A/A variant. In linear and logistic regression analyses, Gly972Arg was not associated with obesity, insulin resistance/sensitivity or T2DM. CONCLUSIONS: The prevalence of the Gly972Arg variant in the mixed-ancestry population of SA is comparable to that reported in African Americans, but its presence is not associated with cardiometabolic traits. This suggests that the Gly972Arg variant may not aid diabetes risk evaluation in this setting, nor can such information help explain the high prevalence of diabetes previously reported in this population.