Biodiversity and strain differentiation of cassava-infecting geminiviruses and Bemisa tabaci in southern Africa

Thesis (M.Sc.)--University of the Witwatersrand, Faculty of Science, School of Molecular and Cell Biology, 2001.Cassava mosaic disease is prevalent in Africa and significantly affects the growth and yield of cassava. This disease is caused by a number of whiteflytransmitted begomoviruses. The aims of this study were to establish the identity of cassava begomoviruses in southern Africa and to develop assays for their differentiation. Using primers that target the highly conserved core region of the coat protein gene it was possible to identify and establish the geographical distribution and relatedness of cassava begomoviruses in 6 countries within southern Africa. It was found that African cassava mosaic virus occurred in five countries (except Angola), East African cassava mosaic virus was present in all countries (except Zambia) and South African cassava mosaic virus was present in South Africa and Swaziland. In addition, this study reports for the first time in southern Africa, the Ugandan variant virus (UgV) which occurs frequently in mixed infections with other cassava-infecting begomoviruses. Bemisia tabaci (Gennadius) is the vector of begomoviruses that cause cassava mosaic disease (CMD) in Africa and India. The taxonomy of the B. tabaci complex is problematic, making it unclear whether more than one variant or 'type' of the vector is involved in the transmission of cassavainfecting begomoviruses. Phylogenetic analysis of mitochondrial COl gene sequences revealed that B. tabaci colonising cassava in Africa form 3 distinct clades (clade 1: Mozambique, South Africa, Swaziland, Zambia; clade 2: Cameroon; clade 3 : Zimbabwe). These results indicate that topotypes within B. tabaci vector populations from cassava exist and suggest a geographic basis for the separation of cassava-colonising B. tabaci in Africa. New cassava viruses and viral strains continue to be discovered and simple, rapid and sensitive techniques are needed for screening of cassava plantations. Here we report on the development of a heteroduplex mobility assay (HMA) for differentiating cassava-infecting begomoviruses. The HMA profiles were able to differentiate four different viral species and eleven different virus strains, and showed a good correlation with sequencing results and phylogenetic comparisons with other sequenced cassava viruses. This technique was found to be sensitive and rapid and had the added advantage of being able to detect mixtures of viruses in field-grown cassava. Current serological methods and antibodies are limited in their usefulness and specificity and new antibodies need to be developed to detect all the possible viral species. The viability of using phage antibodies to detect begomoviruses proved promising as a number of phage clones were isolated and characterised. These clones, when used in combination, were able to differentiate between several cassava-infecting begomoviruses. However a number of improvements on this technique would need to be implemented before it became an acceptable method for producing antibodies to identify and distinguish between cassava begomovirus species and strains

Process for a Reactive Monomer Alignment Layer for Liquid Crystals Formed on an Azodye Sublayer

In this work, the detailed studies of surface polymerization stabilizing liquid crystal formed on an azodye sublayer are presented. The surface localized stabilization is obtained by free-radical polymerization of a dilute solution of a bi-functional reactive monomer (RM) in a liquid crystal (LC) solvent. To optimize the process for surface localized stabilization, we investigate the effects of several process parameters including RM concentration in LC hosts, the types of materials (either RM or LC), the photo-initiator (PI) concentration, ultra-violet (UV) polymerization intensity, and the UV curing temperature. The quality of surface localized stabilization is characterized and/or evaluated by optical microscopy, electro-optical behavior (transmission/voltage curve), the life test, and photo-bleaching. Our results show that, by carefully selecting materials, formulating mixtures, and controlling the polymerizing variables, the RM polymerization can be realized either at the surface or through the bulk. Overall, the combination of surface localized stabilization and photo-alignment offers an elegant and dynamic solution for controlling the alignment for LC, which could play a profound role in almost all liquid crystal optical devices. Keywords: photoalignment; liquid crystals; reactive monomers; azo dyeUnited States. Army Research Office (Contract W911NF-14-1-0650

Improved control of Trialeurodes vaporariorum using mixture combinations of entomopathogenic fungi and the chemical insecticide spiromesifen

Greenhouse whitefly (Trialeurodes vaporariorum) is a major global pest, causing direct damage to plants and transmitting viral plant diseases. Management of T. vaporariorum is problematic because of widespread pesticide resistance, and many greenhouse growers rely on biological control agents to regulate T. vaporariorum populations. However, these are often slow and vary in efficacy, leading to subsequent application of chemical insecticides when pest populations exceed threshold levels. Combining chemical and biological pesticides has great potential but can result in different outcomes, from positive to negative interactions. In this study, we evaluated co-applications of the entomopathogenic fungi (EPF) Beauveria bassiana and Cordyceps farinosa and the chemical insecticide spiromesifen in laboratory bioassays. Complex interactions between the EPFs and insecticide were described using an ecotoxicological mixtures model, the MixTox analysis. Depending on the EPF and chemical concentrations applied, mixtures resulted in additivity, synergism, or antagonism in terms of total whitefly mortality. Combinations of B. bassiana and spiromesifen, compared to single treatments, increased the rate of kill by 5 days. Results indicate the potential for combined applications of EPF and spiromesifen as an effective integrated pest management strategy and demonstrate the applicability of the MixTox model to describe complex mixture interactions

Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria

The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence

Population Health Surveillance Using Mobile Phone Surveys in Low- and Middle-Income Countries: Methodology and Sample Representativeness of a Cross-sectional Survey of Live Poultry Exposure in Bangladesh

Background: Population-based health surveys are typically conducted using face-to-face household interviews in low- and middle-income countries (LMICs). However, telephone-based surveys are cheaper, faster, and can provide greater access to hard-to-reach or remote populations. The rapid growth in mobile phone ownership in LMICs provides a unique opportunity to implement novel data collection methods for population health surveys. Objective: This study aims to describe the development and population representativeness of a mobile phone survey measuring live poultry exposure in urban Bangladesh. Methods: A population-based, cross-sectional, mobile phone survey was conducted between September and November 2019 in North and South Dhaka City Corporations (DCC), Bangladesh, to measure live poultry exposure using a stratified probability sampling design. Data were collected using a computer-assisted telephone interview platform. The call operational data were summarized, and the participant data were weighted by age, sex, and education to the 2011 census. The demographic distribution of the weighted sample was compared with external sources to assess population representativeness. Results: A total of 5486 unique mobile phone numbers were dialed, with 1047 respondents completing the survey. The survey had an overall response rate of 52.2% (1047/2006) and a co-operation rate of 89.0% (1047/1176). Initial results comparing the sociodemographic profile of the survey sample to the census population showed that mobile phone sampling slightly underrepresented older individuals and overrepresented those with higher secondary education. After weighting, the demographic profile of the sample population matched well with the latest DCC census population profile. Conclusions: Probability-based mobile phone survey sampling and data collection methods produced a population-representative sample with minimal adjustment in DCC, Bangladesh. Mobile phone–based surveys can offer an efficient, economic, and robust way to conduct surveillance for population health outcomes, which has important implications for improving population health surveillance in LMICs

Frequency and patterns of exposure to live poultry and the potential risk of avian influenza transmission to humans in urban Bangladesh

Avian influenza is endemic in Bangladesh, where greater than 90% of poultry are marketed through live poultry markets (LPMs). We conducted a population-based cross-sectional mobile telephone survey in urban Dhaka, Bangladesh to investigate the frequency and patterns of human exposure to live poultry in LPMs and at home. Among 1047 urban residents surveyed, 74.2% (95% CI 70.9-77.2) reported exposure to live poultry in the past year, with the majority of exposure occurring on a weekly basis. While visiting LPMs was less common amongst females (40.3%, 95% CI 35.0-45.8) than males (58.9%, 95% CI 54.0-63.5), females reported greater poultry exposure through food preparation, including defeathering (13.2%, 95% CI 9.5-17.9) and eviscerating (14.8%, 95% CI 11.2-19.4) (p < 0.001). A large proportion of the urban population is frequently exposed to live poultry in a setting where avian influenza viruses are endemic in LPMs. There is thus not only ample opportunity for spillover of avian influenza infections into humans in Dhaka, Bangladesh, but also greater potential for viral reassortment which could generate novel strains with pandemic potential

Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic

Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett Syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here we integrate quantitative, multidimensionalexperimental analysis and mathematical modelling to indicate that MeCP2 is a novel type of global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. We hypothesise that waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shock waves in non-equilibrium physics transport models. This mechanism differs from conventional gene regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene expression patterns are choreographed

Very early invasive angiography versus standard of care in higher-risk non-ST elevation myocardial infarction: study protocol for the prospective multicentre randomised controlled RAPID N-STEMI trial

Background: There are a paucity of randomised data on the optimal timing of invasive coronary angiography (ICA) in higher-risk patients with non-ST elevation myocardial infarction (N-STEMI). International guideline recommendations for early ICA are primarily based on retrospective subgroup analyses of neutral trials. Aims: The RAPID N-STEMI trial aims to determine whether very early percutaneous revascularisation improves clinical outcomes as compared with a standard of care strategy in higher-risk N-STEMI patients. Methods and analysis: RAPID N-STEMI is a prospective, multicentre, open-label, randomised-controlled, pragmatic strategy trial. Higher-risk N-STEMI patients, as defined by Global Registry of Acute Coronary Events 2.0 score ≥118, or &gt;90 with at least one additional high-risk feature, were randomised to either: very early ICA±revascularisation or standard of care timing of ICA±revascularisation. The primary outcome is the proportion of participants with at least one of the following events (all-cause mortality, non-fatal myocardial infarction and hospital admission for heart failure) at 12 months. Key secondary outcomes include major bleeding and stroke. A hypothesis generating cardiac magnetic resonance (CMR) substudy will provide mechanistic data on infarct size, myocardial salvage and residual ischaemia post percutaneous coronary intervention. On 7 April 2021, the sponsor discontinued enrolment due to the impact of the COVID-19 pandemic and lower than expected event rates. 425 patients were enrolled, and 61 patients underwent CMR. Ethics and dissemination: The trial has been reviewed and approved by the East of England Cambridge East Research Ethics Committee (18/EE/0222). The study results will be submitted for publication within 6 months of completion. Trial registration number: NCT03707314; Pre-results

Very early invasive strategy in higher risk non-ST-elevation acute coronary syndrome: the RAPID NSTEMI trial

Objective To investigate whether a very early invasive strategy (IS)±revascularisation improves clinical outcomes compared with standard care IS in higher risk patients with non-ST-elevation acute coronary syndrome (NSTE-ACS). Methods Multicentre, randomised, controlled, pragmatic strategy trial of higher risk patients with NSTE-ACS, defined by Global Registry of Acute Coronary Events 2.0 score of ≥118, or ≥90 with at least one additional high-risk feature. Participants were randomly assigned to very early IS±revascularisation (<90 min from randomisation) or standard care IS±revascularisation (<72 hours). The primary outcome was a composite of all-cause mortality, new myocardial infarction or hospitalisation for heart failure at 12 months. Results The trial was discontinued early by the funder due to slow recruitment during the COVID-19 pandemic. 425 patients were randomised, of whom 413 underwent an IS: 204 to very early IS (median time from randomisation: 1.5 hours (IQR: 0.9–2.0)) and 209 to standard care IS (median: 44.0 hours (IQR: 22.9–72.6)). At 12 months, there was no significant difference in the primary outcome between the early IS (5.9%) and standard IS (6.7%) groups (OR 0.93, 95% CI 0.42 to 2.09; p=0.86). The incidence of stroke and major bleeding was similar. The length of hospital stay was reduced with a very early IS (3.9 days (SD 6.5) vs 6.3 days (SD 7.6), p<0.01). Conclusions A strategy of very early IS did not improve clinical outcomes compared with a standard care IS in higher risk patients with NSTE-ACS. However, the primary outcome rate was low and the trial was underpowered to detect such a difference