Modelling acute HIV infection using longitudinally measured biomarker data including informative drop-out.

Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2009.Background. Numerous methods have been developed to model longitudinal data. In HIV/AIDS studies, HIV markers, CD4+ count and viral load are measured over time. Informative drop-out and the lower detection limit of viral load assays can bias the results and influence assumptions of the models. Objective The objective of this thesis is to describe the evolution of HIV markers in an HIV-1 subtype C acutely infected cohort of women from the CAPRISA 002: Acute Infection Study in Durban, South Africa. They were HIV treatment naive. Methods. Various linear mixed models were fitted to both CD4+ count and viral load, adjusting for repeated measurements, as well as including intercept and slope as random effects. The rate of change in each of the HIV markers was assessed using weeks post infection as both a linear effect and piecewise linear effects. Left-censoring of viral load was explored to account for missing data resulting from undetectable measurements falling below the lower detection limit of the assay. Informative drop- out was addressed by using a method of joint modelling in which a longitudinal and survival model were jointly linked using a latent Gaussian process. The progression of HIV markers were described and the effectiveness and usefulness of each modelling procedure was evaluated. Results. 62 women were followed for a median of 29 months post infection (IQR 20-39). Viral load increased sharply by 2.6 log copies/ml per week in the first 2 weeks of infection and decreased by 0.4 log copies/ml per week the next fortnight. It decreased at a slower rate thereafter. Similarly CD4+ count fell in the first 2 weeks by 4.4 square root cells/ul per week then recovered slightly only to decrease again. Left-censoring was unnecessary in this acute infection cohort as few viral load measures were below the detection limit and provided no improvement on model fit. Conclusion. Piecewise linear effects proved to be useful in quantifying the degree at which the HIV markers progress during the first few weeks of HIV infection, whereas modelling time as a linear effect was not very meaningful. Modelling HIV markers jointly with informative drop-out is shown to be necessary to account for the missing data incurred from participants leaving the study to initiate ARV treatment. In ignoring this drop-out, CD4+ count is estimated to be higher than what it actually is

Cultivable microbiome of fresh white button mushrooms

Microbial dynamics on commercially grown white button mushrooms is of importance in terms of food safety assurance and quality control. The purpose of this study was to establish the microbial profile of fresh white button mushrooms, with the focus on potential presence of food-borne pathogens. The total microbial load was determined through standard viable counts. Presence and isolation of gram-negative bacteria including coagulase positive Staphylococci were performed using a selective enrichment approach. Dominant and presumptive organisms were confirmed using molecular methods. Total mushroom microbial counts ranged from 5.2 to 12.4 log cfu g-1, with the genus Pseudomonas being most frequently isolated (45.37% of all isolations). In total, 91 different microbial species were isolated and identified using Matrix assisted laser desorption ionisation time of flight mass spectrophotometry, PCR and sequencing. Considering current food safety guidelines in South Africa for ready-to-eat fresh produce, coliform counts exceeded the guidance specifications for fresh fruit and vegetables. Based on our research and similar studies, it is proposed that specifications for microbial loads on fresh, healthy mushrooms reflect a more natural microbiome at the pointof- harvest and point-of-sale.The National Research Foundation (NRF) and the Technology and Human Resources Industry Programme (THRIP), a partnership programme funded by the Department of Trade and Industry and managed by the NRF and the Department of Science and Technology-National Research Foundation funded Centre of Excellence in Food Security’s Food Safety Programme (Project 140701: Fresh Produce Safety).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1472-765X2018-02-28hb2017Plant Scienc

APOBEC3G expression is dysregulated in primary HIV-1 infection and polymorphic variants influence CD4+ T-cell counts and plasma viral load

OBJECTIVES: In the absence of HIV-1 virion infectivity factor (Vif), cellular cytosine deaminases such as apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) inhibit the virus by inducing hypermutations on viral DNA, among other mechanisms of action. We investigated the association of APOBEC3G mRNA levels and genetic variants on HIV-1 susceptibility, and early disease pathogenesis using viral load and CD4 T-cell counts as outcomes. METHODS: Study participants were 250 South African women at high risk for HIV-1 subtype C infection. We used real-time PCR to measure the expression of APOBEC3G in HIV-negative and HIV-positive primary infection samples. APOBEC3G variants were identified by DNA re-sequencing and TaqMan genotyping. RESULTS: We found no correlation between APOBEC3G expression levels and plasma viral loads (r = 0.053, P = 0.596) or CD4 T-cell counts (r = 0.030, P = 0.762) in 32 seroconverters. APOBEC3G expression levels were higher in HIV-negative individuals as compared with HIV-positive individuals (P < 0.0001), including matched pre and postinfection samples from the same individuals (n = 13, P < 0.0001). Twenty-four single nucleotide polymorphisms, including eight novel, were identified within APOBEC3G by re-sequencing and genotyping. The H186R mutation, a codon-changing variant in exon 4, and a 3' extragenic mutation (rs35228531) were associated with high viral loads (P = 0.0097 and P < 0.0001) and decreased CD4 T-cell levels (P = 0.0081 and P < 0.0001), respectively. CONCLUSION: These data suggest that APOBEC3G transcription is rapidly downregulated upon HIV-1 infection. During primary infection, APOBEC3G expression levels in peripheral blood mononuclear cells do not correlate with viral loads or CD4 T-cell counts. Genetic variation of APOBEC3G may significantly affect early HIV-1 pathogenesis, although the mechanism remains unclear and warrants further investigation

I am not the kind of woman who complains of everything’: illness stories on self and shame in women with chronic pain. Soc Sci Med

Abstract In this study, we explore issues of self and shame in illness accounts from women with chronic pain. We focused on how these issues within their stories were shaped according to cultural discourses of gender and disease. A qualitative study was conducted with in-depth interviews including a purposeful sampling of 10 women of varying ages and backgrounds with chronic muscular pain. The women described themselves in various ways as &apos;strong&apos;, and expressed their disgust regarding talk of illness of other women with similar pain. The material was interpreted within a feminist frame of reference, inspired by narrative theory and discourse analysis. We read the women&apos;s descriptions of their own (positive) strength and the (negative) illness talk of others as a moral plot and argumentation, appealing to a public audience of health personnel, the general public, and the interviewer: As a plot, their stories attempt to cope with psychological and alternative explanations of the causes of their pain. As performance, their stories attempt to cope with the scepticism and distrust they report having been met with. Finally, as arguments, their stories attempt to convince us about the credibility of their pain as real and somatic rather than imagined or psychological. In several ways, the women negotiated a picture of themselves that fits with normative, biomedical expectations of what illness is and how it should be performed or lived out in &apos;storied form&apos; according to a gendered work of credibility as woman and as ill. Thus, their descriptions appear not merely in terms of individual behaviour, but also as organized by medical discourses of gender and diseases. Behind their stories, we hear whispered accounts relating to the medical narrative about hysteria; rejections of the stereotype medical discourse of the crazy, lazy, illness-fixed or weak woman.

Comparison of safe alternative dipping treatments to maintain quality of zucchini

Decay and quality loss severely affect the marketability of fresh zucchini. Zucchinis are easily damaged during harvesting, - handling and - storage and no commercial treatment is currently available that can protect the fruit from desiccation, quality loss and decay. The aim of this study was to compare different environmentally friendly dipping treatments (CaCl2, Aloe vera, warm water, chitosan, ascorbic- and citric acid) to retain quality of fresh zucchini. Treated fruit were evaluated for physiological, sensory and microbiological parameters after storage for seven and 14 days at 5.8°C and 85% relative humidity. The CaCl2, Aloe vera and warm water treatments were the most effective in maintaining firmness and preventing an increase in the total microflora of the fruit. The outcome of this study shows that alternative control methods have potential for effective quality maintenance of fresh zucchini. Future studies should focus on alternative packaging materials in combination with these treatments.The Gauteng Department of Agriculture and Rural Development (GDARD)http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1745-45572017-04-30hb2017Food ScienceMicrobiology and Plant Patholog

Drug concentrations after topical and oral antiretroviral pre-exposure prophylaxis: implications for HIV prevention in women

The early closure of a clinical trial assessing the effectiveness of oral antiretroviral pre-exposure prophylaxis (PrEP) in women, FEM-PrEP, is a substantial setback for HIV prevention. Expectations of this trial were high in view of favourable results from the pre-exposure prophylaxis initiative (iPrEX) trial, which studied the same drug and dosing strategy in men who have sex with men, and the Centre for the AIDS Programme of Research in South Africa (CAPRISA 004) trial,3 which tested tenofovir gel (a topical PrEP formulation) in heterosexual women. As a result, the interim FEM-PrEP trial results, announced on April 18, 2011, which showed no protection against HIV infection, were disappointing. Using publicly available information and data from other PrEP studies, we offer a potential explanation for the results of the FEM-PrEP trial

Porifera Lectins: diversity, physiological roles and biotechnological potential

An overview on the diversity of 39 lectins from the phylum Porifera is presented, including 38 lectins, which were identified from the class of demosponges, and one lectin from the class of hexactinellida. Their purification from crude extracts was mainly performed by using affinity chromatography and gel filtration techniques. Other protocols were also developed in order to collect and study sponge lectins, including screening of sponge genomes and expression in heterologous bacterial systems. The characterization of the lectins was performed by Edman degradation or mass spectrometry. Regarding their physiological roles, sponge lectins showed to be involved in morphogenesis and cell interaction, biomineralization and spiculogenesis, as well as host defense mechanisms and potentially in the association between the sponge and its microorganisms. In addition, these lectins exhibited a broad range of bioactivities, including modulation of inflammatory response, antimicrobial and cytotoxic activities, as well as anticancer and neuromodulatory activity. In view of their potential pharmacological applications, sponge lectins constitute promising molecules of biotechnological interest

Stabilizing HIV prevalence masks high HIV incidence rates amongst rural and urban women in KwaZulu-Natal, South Africa

Background: In mature generalized human immunodeficiency virus (HIV) epidemics, as survival from accessing antiretroviral treatment (ART) increases, HIV prevalence data may be suboptimal and difficult to interpret without HIV incidence rates. Objective: To determine the HIV incidence rate among rural and urban women in KwaZulu-Natal, South Africa. Methods: We conducted a prospective cohort study from March 2004 to May 2007. Volunteers were recruited from a rural family-planning clinic and an urban clinic for sexually transmitted infections. Consenting, HIV-uninfected women aged 14-30 years were enrolled. Demographic, clinical, sexual and behavioural data were collected using standardized questionnaires with HIV risk reduction counselling and HIV testing. Pelvic examinations were completed at quarterly visits. Results: The HIV prevalence at screening was 35.7% [95% confidence interval (CI) 32.7-38.8] amongst rural women and 59.3% (95% CI 56.5-62.0) amongst urban women. A total of 594/2240 (26.5%) enrolled women contributed to 602 person-years (PYs) of follow-up. The median age was 22 years [inter-quartile range 18-23 years]. HIV incidence rate was 6.5/100 PY (95% CI 4.4-9.2) amongst rural women and 6.4/100 PY (95% CI 2.6-13.2) amongst urban women. HIV incidence rate of 17.2/100 PY (95% CI 2.1-62.2) was highest amongst urban women <20 years of age and 10.2/100 PY (95% CI 4.1-20.9) amongst rural women ≥25 years of age. Conclusion: HIV incidence rates are devastatingly high in young women in rural and urban KwaZulu-Natal, despite reports of stabilized HIV prevalence observed in current surveillance data. The diffuse nature of the HIV epidemic underscores the urgent need to enhance HIV prevention and treatment modalities

Adherence in the treatment of patients with extensively drug-resistant tuberculosis and HIV in South Africa: a prospective cohort study.

CAPRISA, 2014.Abstract available in pdf

Association of polymorphisms in the LEDGF/p75 gene (PSIP1) with susceptibility to HIV-1 infection and disease progression

OBJECTIVE: LEDGF/p75, encoded by the PSIP1 gene, interacts with HIV-1 integrase and targets HIV-1 integration into active genes. We investigated the influence of polymorphisms in PSIP1 on HIV-1 acquisition and disease progression in black South Africans. METHODS: Integrase binding domain of LEDGF/p75 was sequenced in 126 participants. Four haplotype tagging SNPs rs2277191, rs1033056, rs12339417 and rs10283923 referred to as SNP1, SNP2, SNP3 and SNP4, respectively, and one exonic SNP rs61744944 (SNP5, Q472L) were genotyped in 195 HIV-1 seronegative, 52 primary and 403 chronically infected individuals using TaqMan assays. LEDGF/p75 expression was quantified by real-time RT-PCR. The impact of Q472L mutation on the interaction with HIV_1 IN was measured by AlphaScreen. RESULTS: rs2277191 (SNP1) A was more frequent among seropositives (P = 0.06, Fisher's exact test). Among individuals followed longitudinally SNP1A trended towards association with higher likelihood of HIV-1 acquisition [relative hazard (RH) = 2.21, P = 0.08; Cox model] and it was also associated with rapid disease progression (RH = 5.98, P = 0.04; Cox model) in the recently infected (primary infection) cohort. rs12339417 (SNP3)C was associated with slower decline of CD4(+) T cells (P = 0.02) and lower messenger RNA (mRNA) levels of LEDGF/p75 (P < 0.01). Seroconverters had higher preinfection mRNA levels of LEDGF/p75 (P < 0.01) and these levels decreased after HIV-1 infection (P = 0.02). CONCLUSIONS: Genetic variants of PSIP1 may affect HIV-1 outcomes. Further studies are needed to confirm the effect of genetic variation of PSIP1 on HIV-1 pathogenesis in different cohorts