Chapter 6 The influence of politics on girls’ education in Ethiopia

In this chapter we consider why education systems have not yet achieved equitable access and learning for all girls, despite high-level government commitment. Taking Ethiopia as a case study, we refer to the ‘domains of power’ framework (Hickey & Hossain, 2019) to explore the influence of politics on progress in girls’ education, focusing on the interaction between the political settlement and the education policy domain. The analysis draws on data from the Research on Improving Systems of Education (RISE) Ethiopia programme, including analysis of government documents, actor mapping and interviews with 150 key government stakeholders across seven regions and city administrations in Ethiopia. Adopting a gender lens, we take account of the influence and interaction of informal institutions within the education domain. We find that the education system cannot be considered to be a gender-neutral site given that women continue to be absent from positions of power. In addition, stakeholders’ ideas about the nature of gender roles influence their attitudes, behaviour and actions, holding back progress towards the high-level commitments

The effect of green waste composting on the concentration and composition of ambient bioaerosols

The emission and dispersal of bioaerosols from commercial composting facilities has become an issue of increasing concern over the past decade, as historical evidence links bioaerosol exposure to negative human health impacts. As a result, recommended concentrations and risk assessment limits were imposed in 2001. However, more recent research has suggested that these limits may be exceeded under certain circumstances. For example, underestimation of bioaerosol concentrations may occur through „snapshot‟ sampling, and the use of methods that may reduce culturability of bioaerosols. This study aimed to address several gaps in knowledge, including quantification of bioaerosol concentrations downwind from sites, analysis of the effect that operational and environmental influences have on emission and downwind concentrations, and investigation of methods for the enumeration of non-culturable bioaerosols. The concentrations of bioaerosols upwind, on-site and downwind from two open-air green waste windrow composting facilities were enumerated in extensive detail, producing the first detailed and validated database of bioaerosol concentrations at green-waste composting facilities. The effects of composting processing activities, season, and meteorological conditions on concentrations were also investigated utilising this dataset. Results from these studies suggested that bioaerosols are able to disperse in elevated concentrations to distances beyond the 250 m risk assessment limit. Downwind peaks in concentration were directly linked to compost processing activities on-site, with the risk of sensitive receptor exposure to bioaerosols during non-operational hours minimal. Further, it was found that patterns in downwind concentrations of bioaerosols are likely to be governed by buoyancy effects, as a second peak in concentrations was found at 100-150m downwind. This finding was further supported through the use of a novel direct counting method. Finally, molecular methods allowed the composition of bioaerosols emitted from composting to be determined and showed that composting significantly alters the aerobiotic community at distances downwind. The methods investigated provide the potential for detailed, continuous measurements of bioaerosols, alongside identification of potentially pathogenic microorganisms, and could ultimately lead to source apportionment of bioaerosols.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Microbiome diversity protects against pathogens by nutrient blocking

The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in gnotobiotic mice. Whereas single species alone had negligible effects, colonization resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explained these ecological patterns through the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Furthermore, we applied our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities

The intracellular chloride ion channel protein CLIC1 undergoes a redox-controlled structural transition.

Most proteins adopt a well defined three-dimensional structure; however, it is increasingly recognized that some proteins can exist with at least two stable conformations. Recently, a class of intracellular chloride ion channel proteins (CLICs) has been shown to exist in both soluble and integral membrane forms. The structure of the soluble form of CLIC1 is typical of a soluble glutathione S-transferase superfamily protein but contains a glutaredoxin-like active site. In this study we show that on oxidation CLIC1 undergoes a reversible transition from a monomeric to a non-covalent dimeric state due to the formation of an intramolecular disulfide bond (Cys-24-Cys-59). We have determined the crystal structure of this oxidized state and show that a major structural transition has occurred, exposing a large hydrophobic surface, which forms the dimer interface. The oxidized CLIC1 dimer maintains its ability to form chloride ion channels in artificial bilayers and vesicles, whereas a reducing environment prevents the formation of ion channels by CLIC1. Mutational studies show that both Cys-24 and Cys-59 are required for channel activity

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near point of care. We demonstrate a low-cost DNA extraction method for TB WGS direct from patient samples. We initially evaluated the method using the Illumina MiSeq sequencer (40 smear-positive respiratory samples, obtained after routine clinical testing, and 27 matched liquid cultures). M. tuberculosis was identified in all 39 samples from which DNA was successfully extracted. Sufficient data for antibiotic susceptibility prediction was obtained from 24 (62%) samples; all results were concordant with reference laboratory phenotypes. Phylogenetic placement was concordant between direct and cultured samples. Using an 70 Illumina MiSeq/MiniSeq the workflow from patient sample to results can be completed in 44/16 hours at a reagent cost of £96/£198 per sample. We then employed a non-specific PCR-based library preparation method for sequencing on an Oxford Nanopore Technologies MinION sequencer. We applied this to cultured Mycobacterium bovis BCG strain (BCG), and to combined culture negative sputum DNA and BCG DNA. For flowcell version R9.4, the estimated turnaround time from patient to identification of BCG, detection of pyrazinamide resistance, and phylogenetic placement was 7.5 hours, with full susceptibility results 5 hours later. Antibiotic susceptibility predictions were fully concordant. A critical advantage of the MinION is the ability to continue sequencing until sufficient coverage is obtained, providing a potential solution to the problem of variable amounts of M. tuberculosis in direct samples

Population genomics of <i>Escherichia coli</i> in livestock-keeping households across a rapidly developing urban landscape

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package ('Mykrobe predictor') that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes

The Effect of Green Waste Composting on the Concentration and Composition of Ambient Bioaerosols

The emission and dispersal of bioaerosols from commercial composting facilities has become an issue of increasing concern over the past decade, as historical evidence links bioaerosol exposure to negative human health impacts. As a result, recommended concentrations and risk assessment limits were imposed in 2001. However, more recent research has suggested that these limits may be exceeded under certain circumstances. For example, underestimation of bioaerosol concentrations may occur through „snapshot‟ sampling, and the use of methods that may reduce culturability of bioaerosols. This study aimed to address several gaps in knowledge, including quantification of bioaerosol concentrations downwind from sites, analysis of the effect that operational and environmental influences have on emission and downwind concentrations, and investigation of methods for the enumeration of non-culturable bioaerosols. The concentrations of bioaerosols upwind, on-site and downwind from two open-air green waste windrow composting facilities were enumerated in extensive detail, producing the first detailed and validated database of bioaerosol concentrations at green-waste composting facilities. The effects of composting processing activities, season, and meteorological conditions on concentrations were also investigated utilising this dataset. Results from these studies suggested that bioaerosols are able to disperse in elevated concentrations to distances beyond the 250 m risk assessment limit. Downwind peaks in concentration were directly linked to compost processing activities on-site, with the risk of sensitive receptor exposure to bioaerosols during non-operational hours minimal. Further, it was found that patterns in downwind concentrations of bioaerosols are likely to be governed by buoyancy effects, as a second peak in concentrations was found at 100-150m downwind. This finding was further supported through the use of a novel direct counting method. Finally, molecular methods allowed the composition of bioaerosols emitted from composting to be determined and showed that composting significantly alters the aerobiotic community at distances downwind. The methods investigated provide the potential for detailed, continuous measurements of bioaerosols, alongside identification of potentially pathogenic microorganisms, and could ultimately lead to source apportionment of bioaerosols

Chapter 6 The influence of politics on girls’ education in Ethiopia

In this chapter we consider why education systems have not yet achieved equitable access and learning for all girls, despite high-level government commitment. Taking Ethiopia as a case study, we refer to the ‘domains of power’ framework (Hickey & Hossain, 2019) to explore the influence of politics on progress in girls’ education, focusing on the interaction between the political settlement and the education policy domain. The analysis draws on data from the Research on Improving Systems of Education (RISE) Ethiopia programme, including analysis of government documents, actor mapping and interviews with 150 key government stakeholders across seven regions and city administrations in Ethiopia. Adopting a gender lens, we take account of the influence and interaction of informal institutions within the education domain. We find that the education system cannot be considered to be a gender-neutral site given that women continue to be absent from positions of power. In addition, stakeholders’ ideas about the nature of gender roles influence their attitudes, behaviour and actions, holding back progress towards the high-level commitments

Endotoxin emissions from commercial composting activities

This paper describes an exploratory study of endotoxin emissions and dispersal from a commercial composting facility. Replicated samples of air were taken by filtration at different locations around the facility on 10 occasions. Measurements were made of endotoxin and associated culturable microorganisms. The inflammatory response of cell cultures exposed to extracts from the filters was measured. Endotoxin was detected in elevated concentrations close to composting activities. A secondary peak, of lesser magnitude than the peak at source was detected at 100-150 m downwind of the site boundary. Unexpectedly high concentrations of endotoxin were measured at the most distant downwind sampling point. Extracted endotoxin was found to stimulate human monocytes and a human lung epithelial cell line to produce significant amounts of pro- inflammatory cytokines. On a weight basis, endotoxin extracted from the composting source has a greater inflammatory cytokine inducing effect than commercial E. coli endotoxin