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It is the purpose of this study to ascertain what environmental factors might cause morphological changes exhibited by certain algae, also to determine if this variation in morphology is vegetative, reproductive, or artifactual in nature, and to show what effects these changes in morpohology might have on classification of the organisms in question.

A Thesis Submitted to the School of Public Health, Faculty of Health Sciences University of the Witwatersrand, Johannesburg, South Africa, in fulfilment of the requirements for the Degree of Doctor of Philosophy 15 June 2017 / Background HIV infection has remained a major global health burden since its discovery in 1983 and Sub-Saharan Africa remains the region hardest hit by the HIV/AIDS pandemic. The HIV pandemic continues to ravage most parts of Southern African countries, current prevalence between 10-20%. Individuals worldwide differ in their degree of susceptibility to HIV infection and genetic polymorphisms play a major role. Mannose Binding Lectin (MBL) is one such immunological factor found in serum/plasma, it is a normal liver-derived protein and is a key component of the innate immune defence system. MBL deficiency, due to mutations in the MBL2 gene and promoter region, leading to decreased plasma/serum MBL concentration, characterised by defective opsonisation activities of the innate immune system and increased susceptibility to infections including HIV-1 and schistosomiasis. Rationale While there is a lot of advancement in HIV prevention and treatment in Southern African countries, there is still need to investigate host genetic molecules in adults and mother-baby pairs that could be playing a role in HIV-1 transmission/acquisition, disease progression and survival. It was imperative to carry out this study because of the need to quantify the burden of MBL deficiency in this Zimbabwean adult and PMTCT study populations. Alsoto contribute to the knowledge gap on the role of MBL deficiency in HIV-1 transmission, disease progression and survival in African populations in adults and children. The available literature shows that the majority of studies on the association of MBL deficiency and HIV-1 infection in adults and children have been done on populations outside the African continent. There is dearth of information on the role of MBL in this era when access to ART has greatly improved even in developing countries like Zimbabwe. This will be the second study that will assess MBL2 genes and promoter typing in mother-infant pairs in HIV vertical transmission/acquisition. This study aimed to identify and explore potential biomarkers for susceptibility to HIV infection and disease progression. We assessed role of MBL deficiency in HIV-1 and schistosoma infections in Zimbabwean adults enrolled in the Mupfure Schistosomiasis and HIV Cohort (MUSH Cohort) (Paper 1).We also assessed the role of MBL deficiency on HIV progression and survival in this African adult population. We hypothesized that MBL deficiency has a role to play in HIV infection by increasing HIV disease progression and decreasing survival (Paper 2). We also determined prevalence of MBL deficiency, as estimated by MBL2 haplotypes among Zimbabwean mothers and their children aged 9-18 months old as well as its association with risk of HIV-1 infection and vertical transmission from their HIV positive mothers (Paper 3). Main Aim The broad objective of this study was to determine the relationship between MBL deficiency and HIV infection in an adult population of males and females and among mother-infant pairs in Zimbabwe. Study Specific Objectives 1. To determine the prevalence of MBL deficiency among the Zimbabwean adult population. 2. To determine the relationship of MBL deficiency with HIV infection among the Zimbabwean adult population. 3. To determine the effect of MBL deficiency on disease progression and survival among the Zimbabwean adult population. 4. To determine prevalence of MBL deficiency among mothers and their infants in a Zimbabwean population. 5. To determine the relationship between MBL deficiency and HIV transmission from mother to child in a Zimbabwean population. Methods DNA and plasma samples for MBL and HIV analysis were collected from the 379 adult males and females from the MUSH cohort and stored dried blood samples from 622 mother infant pairs from a national PMTCT survey. HIV-1, S. haematobium and S. mansoni infections were determined at baseline using HIV commercial kits and parasitologically respectively. Plasma MBL concentration was measured by ELISA and MBL2 genotypes determined by PCR. We calculated and compared the proportions of plasma MBL deficiency, MBL2 structural variant alleles B (codon 54A>G), C (codon 57A>G), and D (codon 52T>C) as well as MBL2 promoter variants -550(H/L), -221(X/Y) and +4(P/Q) between HIV-1 and schistosoma co-infection and control groups using Chi Square test (Paper 1). We also assessed the role of MBL deficiency on HIV disease progression and survival inthe adult (MUSH) cohort.We analysed blood samples for MBL levels, MBL2 genotypes, HIV-1 status, viral load and CD4+ T cell counts (Paper 1). Participants were followed up for 3 years wherein the endpoints were measured at baseline, 6 weeks, 3, 6, 12, 24 and 36 months. Disease progression was measured as the rate of decline in CD4+ T cell counts and the rate of increase in HIV viral load (Paper 2). Generalised Estimating Equations (GEE) models were used to compare rates of change of the CD4+ T cell count and viral load measurements over the three-year follow-up period. The role of plasma MBL deficiency and MBL2 genetic variants on survival over the 3-year period were estimated using the Cox proportional hazard models. Regression analysis was used to test for interaction and confounding between MBL deficiency, MBL2 genetic variance, age and sex. We used the Wald Chi-square statistic to choose between full and nested models. We also assessed MBL2 polymorphisms in Zimbabwean HIV positive mothers and their children enrolled in a national PMTCT survey carried out in 2012. MBL deficiency was defined as presence of A/O and O/O genotypes in the mothers and their children. We extracted DNA from two dried blood spots for 622 mothers and infant pairs using the Gene Extract and Amp kit reagents. MBL2 Exon 1 genotypes and promoter region alleles -221(X/Y) and -550(H/L) SNP were detected by pyrosequencing. Differences in distribution frequency between HIV infected and uninfected children, of the MBL2 genotypes, promoter region variants and MBL2 haplotypes, were determined by the Chi square test or Fisher’s exact tests (Paper 3). Key findings For specific objective number 1, we assessed 379 adults, 80% females, median age (IQR) 30 (17-41) years. HIV-1, S. haematobium and S. mansoni prevalence were 26%, 43% and 18% respectively in the MUSH baseline survey. Median (IQR) plasma MBL concentration was 800μg/L (192-1936μg/L). Prevalence of plasma MBL deficiency was 18% with high frequency of the C (codon 57G>A) mutant allele (20%). For specific objective number 2, we found no significant difference in median plasma MBL levels between HIV negative (912μg/L) and HIV positive (688μg/L), p=0.066. However plasma MBL levels at the assay detection limit of 20μg/L were more frequent among the HIV-1 infected (p=0.007). S. haematobium andS. mansoni infected participants had significantly higher MBL levels than uninfected. All MBL2 variants were not associated with HIV-1 infection but promoter variants LY and LL were significantly associated with S. haematobium infection (Paper 1). For specific objective number 3, we assessed 197 HIV positive adults where 83% (164) were women with a median age of 31 years old. Prevalence of plasma MBL deficiency (less than 100μg/L) and MBL2 deficient genetic variants (A/O and O/O genotypes) was 21% (42 out of 197) and 39% (74 out of 190), respectively. We did not observe a significant role to explain individual variation in mortality, change of CD4+ T cell count and viral load by MBL plasma deficiency or MBL2 genetic variants from baseline to 3 years follow up period in this adult population (Paper 2). For specific objective number 4, from the PMTCT study, the median age (IQR) of the mothers was 30(26 - 34) years and the children mean age (IQR) was 12 (11-15) months old at the time of enrolment. All 622 mothers were HIV-1 infected, 574 babies were HIV negative and 48 were HIV-1 positive babies. MBL2 normal structural allele A and variants B (codon 5A>G), C (codon 57 A>G) and promoter region SNPs -550(H/L) and -221(X/Y) were detected. Prevalence of MBL deficiency was 34% among the mothers and 32% among the children. For specific objective number 5, we found no association between maternal MBL2 deficiency and HIV-1 transmission to their children. We found no difference in the distribution of HIV-1 infected and uninfected children between the MBL2 genotypes of the mothers and those of the children (Paper 3). Conclusions The results from our study indicate high prevalence of MBL deficiency but we found no evidence of association between MBL deficiency and HIV-1 infection. However, lower plasma MBL levels were associated with reduced prevalence of both S. haematobium and S. mansoni infections and MBL2 promoter and variants LY and LL were associated with increased susceptibility to S. haematobium infection (Paper 1). Our findings attest to the large between-population variability in a host of factors that can predispose individuals susceptible to HIV progression and mortality. We therefore cannot recommend at this time the use of plasma MBL levels or MBL2 genetic variants as a prognostic marker in HIV infection, disease progression and survival in this adult population in Africa (Paper 2). MBL deficiency was not associated with HIV-1 infection among the children nor was it associated with HIV-1 vertical transmission in this study population (Paper 3). / MT2017

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science 6 February 2017, Johannesburg. / Polymorphism is not only limited to single component systems. Co-crystals have exhibited polymorphism and various polymorphic co-crystals have been reported. Polymorphism in co-crystals presents an expansion of the optimization space around a pharmaceutical compound and also offers the opportunity to develop novel patentable material. Polymorphism of pharmaceutical co-crystals was investigated by means of an exhaustive data mining survey and the formation of polymorphic co-crystals. The search was performed using the Cambridge Structural Database (CSD). The search aimed to find and tally neutral pharmaceutical co-crystals which are polymorphic. The survey of the CSD showed that 14% of the pharmaceutical co-crystals were polymorphic. The co-crystal of theophylline and 3,4-dihydroxybenzoic acid was found to be polymorphic and the novel polymorph was synthesized and characterized. The co-crystals were characterized by x-ray crystallographic techniques and Differential Scanning Calorimetry. The single crystals of carbamazepine and cinnamic acid was grown and characterized by SCXRD for the first time. The single crystal data was able to show that the hydrogen bonding packing that was modelled in the literature is incorrect. / MT2017