The Impact of HIV/AIDS in the Context of Socioeconomic Stressors: an Evidence-Driven Approach

In this paper, we present an agent-based simulation model of the social impacts of HIV/AIDS in villages in the Sekhukhune district of the Limpopo province in South Africa. AIDS is a major concern in South Africa, not just in terms of disease spread but also in term of its impact on society and economic development. The impact of the disease cannot however be considered in isolation from other stresses, such as food insecurity, high climate variability, market fluctuations and variations in support from government and non-government sources. The model described in this paper focuses on decisions made at the individual and household level, based upon evidence from detailed case studies, and the different types of networks between these players that influence their decision making. Key to the model is that these networks are dynamic and co-evolving, something that has rarely been considered in social network analysis. The results presented here demonstrate how this type of simulation can aid better understanding of this complex interplay of issues. In turn, we hope that this will prove to be a powerful tool for policy development.Agent-Based Social Simulation, Evidence-Driven Modeling, Socioeconomic Stressors, HIV/AIDS Impact

Health Departments’ Engagement in Emergency Preparedness Activities: The Influence of Health Informatics Capacity

Background: Local health departments (LHDs) operate in a complex and dynamic public health landscape, with changing demands on their emergency response capacities. Informatics capacities might play an instrumental role in aiding LHDs emergency preparedness. This study aimed to explore the extent to which LHDs’ informatics capacities are associated with their activity level in emergency preparedness and to identify which health informatics capacities are associated with improved emergency preparedness. Methods: We used the 2013 National Profile of LHDs study to perform Poisson regression of emergency preparedness activities. Results: Only 38.3% of LHDs participated in full-scale exercises or drills for an emergency in the 12 months period prior to the survey, but a much larger proportion provided emergency preparedness training to staff (84.3%), and/or participated in tabletop exercises (76.4%). Our multivariable analysis showed that after adjusting for several resource-related LHD characteristics, LHDs with more of the 6 information systems still tend to have slightly more preparedness activities. In addition, having a designated emergency preparedness coordinator, and having one or more emergency preparedness staff were among the most significant factors associated with LHDs performing more emergency preparedness activities. Conclusion: LHDs might want to utilize better health information systems and information technology tools to improve their activity level in emergency preparedness, through improved information dissemination, and evidence collection

EXPLORATION OF REACTANT-PRODUCT LIPID PAIRS IN MUTANT-WILD TYPE LIPIDOMICS EXPERIMENTS

High-throughput metabolite analysis is very important for biologists to identify the functions of genes. A mutation in a gene encoding an enzyme is expected to alter the level of the metabolites which serve as the enzyme’s reactant(s) (also known as substrate) and product(s). To find the function of a mutated gene, metabolite data from a wild-type organism and a mutant are compared and candidate reactants and products are identified. The screening principle is that the concentration of reactants will be higher and the concentration of products will be lower in the mutant than in wild type. This is because the mutation reduces the reaction between the reactant and the product in the mutant organism. Based upon this principle, we suggest a method to screen metabolite pairs for candidate reactant-product pairs. Metrics are defined that quantify the effect of a mutation on each potential reaction, represented by a metabolite pair. For reactions catalyzed by well-characterized enzymes, one or more biologically functioning reactant-product pairs are known. Knowledge of the functional reactant-product pairs informs the development of the metrics. The goal is for ranking of the metrics for all possible pairs to reflect the likelihood that a particular metabolite pair is a functional reactant-product pair

Human neuronal LUHMES cell line as a model system for studying Rett syndrome

Rett syndrome (RTT) is a severe neurological disorder that affects approximately 1:10000 girls. Classical RTT is defined by a developmental regression phase and subsequent stabilisation of diagnostic criteria, which include partial or complete loss of spoken language, dyspraxic gait and stereotypic hand movements such as hand mouthing. RTT is a monogenic disorder, with the majority of cases being due to loss-of-function mutations in MeCP2 (methyl-CpG binding protein 2). Due to this clear genotype-phenotype link multiple RTT mouse models have been used to elucidate the molecular details, and consequent neuropathogenesis, of this complex neurological disease, as well as for the development of potential therapeutics for RTT. However, as the molecular details become clearer, the need for a simpler model system becomes evident. Human induced pluripotent stem cells (hiPSCs) generated from RTT patient fibroblasts are an option; however the handling of these cells is laborious, time-consuming and expensive and they often differentiate into a heterogeneous population of cells. To explore an alternative human model system I have been genetically engineering and experimenting with the human dopaminergic LUHMES cell line. LUHMES cells are an immortalised pre-neuronal cell line derived from an 8-week old, female foetus and can readily be differentiated into a homogeneous population of mature, electrically active neurons in just one week. In this thesis I have assessed the phenotypic properties of the wild-type cell line, demonstrated the ease of genetic manipulation of LUHMES cells by CRISPR/Cas9 approaches, generated seven mutant MECP2 LUHMES cell lines and explored the potential of protein therapy as a therapeutic approach for RTT. The LUHMES cell line proves to be extremely easy to handle and robust and has yielded novel molecular insights into the function of MeCP2 in human neurons. In particular, MeCP2-null cells show a striking relationship between the level of gene body methylation and the extent of transcriptional upregulation when compared to wild-type neurons. In contrast neurons that express a form of MeCP2 that can bind to DNA but cannot recruit a transcriptional corepressor complex (the R306C mutant) do not exhibit substantial gene expression alterations, yet do display a consistent decrease in total RNA amount. This decrease in total RNA is recapitulated in MeCP2-null LUHMES-derived neurons and in brain regions from MeCP2-R306C mice. The requirement for functional DNA binding for normal gene-body methylation dependent gene repression is demonstrated by assessing LUHMES cells that overexpress MeCP2-R111G, a protein that cannot bind to DNA. Furthermore, overexpression of the MeCP2-R306C protein highlights the importance of NCoR binding for normal gene repression, but also demonstrates that MeCP2-R306C protein retains some gene repression activity. Thinking more broadly, this cell line also has applications as a model system for a variety of other neurological disorders; as a simplified model system to elucidate molecular and neurological phenotypes, and as a relevant human system that can be cultured in a high-throughput manner for testing therapeutic strategies

Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

MeCP2 is an abundant protein in mature nerve cells, where it binds to DNA sequences containing methylated cytosine. Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome (RTT), provoking intensive study of the underlying molecular mechanisms. Multiple functions have been proposed, one of which involves a regulatory role in splicing. Here we leverage the recent availability of high-quality transcriptomic data sets to probe quantitatively the potential influence of MeCP2 on alternative splicing. Using a variety of machine learning approaches that can capture both linear and non-linear associations, we show that widely different levels of MeCP2 have a minimal effect on alternative splicing in three different systems. Alternative splicing was also apparently indifferent to developmental changes in DNA methylation levels. Our results suggest that regulation of splicing is not a major function of MeCP2. They also highlight the importance of multi-variate quantitative analyses in the formulation of biological hypotheses

Biochemical and Molecular-Genetic Characterization of SFD1’s Involvement in Lipid Metabolism and Defense Signaling

The Arabidopsis thaliana SFD1 (suppressor of fatty acid desaturase deficiency1) gene (also known as GLY1) is required for accumulation of 34:6 (i.e., 18:3–16:3) monogalactosyldiacylglycerol (MGDG) and for the activation of systemic acquired resistance (SAR), an inducible defense mechanism that confers resistance against a broad spectrum of pathogens. SFD1, which has been suggested to be involved in lipid-based signaling in SAR, contains a putative chloroplast transit peptide and has glycerol-3-phosphate synthesizing dihydroxyacetone phosphate (DHAP) reductase (also referred as glycerol-3-phosphate dehydrogenase) activity. The goals of this study were to determine if the DHAP reductase activity and chloroplast localization are required for SFD1’s involvement in galactolipid metabolism and SAR signaling. The crystal structure of a Leishmania mexicana glycerol-3-phosphate dehydrogenase was used to model SFD1 structure and identify Lys194, Lys279, and Asp332 as potential catalytic site residues in SFD1. Mutational analysis of SFD1 confirmed that Lys194, Lys279, and Asp332 are critical for SFD1’s DHAP reductase activity, and its involvement in SAR. SFD1 proteins with these residues individually substituted by Ala lacked DHAP reductase activity and were unable to complement the SAR defect of the sfd1 mutant. The SFD1–Ala279 protein was also unable to restore 34:6-MGDG content when expressed in the sfd1 mutant. In vivo imaging of a green fluorescent protein-tagged SFD1 protein demonstrated that SFD1 is targeted to the chloroplast. The N-terminal 43 amino acids, which are required for proper targeting of SFD1 to the chloroplast, are also required for SFD1’s function in lipid metabolism and SAR. Taken together, these results demonstrate that SFD1’s DHAP reductase activity is required in the chloroplast for lipid metabolism and defense signaling

Associations between diet, physical activity and body fat distribution: a cross sectional study in an Indian population.

BACKGROUND: Obesity is a growing health problem in India and worldwide, due to changes in lifestyle. This study aimed to explore the independent associations between dietary and physical activity exposure variables and total body fat and distribution in an Indian setting. METHODS: Individuals who had participated in the Indian Migration Study (IMS) or the Andhra Pradesh Children And Parents' Study (APCAPS), were invited to participate in the Hyderabad DXA Study. Total and abdominal body fat of study participants was measured using DXA scans. Diet and physical activity (PA) levels were measured using questionnaires. RESULTS: Data on 2208 participants was available for analysis; mean age was 49 yrs in IMS, 21 yrs in APCAPS. Total energy intake was positively associated with total body fat in the APCAPS sample: a 100 kcal higher energy intake was associated with 45 g higher body fat (95% CI 22, 68). In the IMS sample no association was found with total energy intake, but there was a positive association with percent protein intake (1% higher proportion of energy from protein associated with 509 g (95% CI 138,880) higher total body fat). Broadly the same pattern of associations was found with proportion of fat in the abdominal region as the outcome. PA was inversely associated with total body fat in both populations (in APCAPS, one MET-hour higher activity was associated with 46 g (95% CI 12, 81) less body fat; in the IMS it was associated with 145 g less body fat (95% CI 73, 218)). An inverse association was observed between PA and percentage abdominal fat in the IMS but no association was seen in the APCAPS population. CONCLUSIONS: In this Indian population, there was an inverse association between PA and body fat. Associations between body fat and dietary variables differed between the younger APCAPS population and older IMS population. Further longitudinal research is needed to elucidate causality and directions of these associations across the life course