Using Modelling to Optimise the Use of Biological Control Agents Against Soil-Borne Plant Pathogens

There is considerable interest in the use of biological control agents as a control strategy against plant pathogens. However, significant variability in their success at pathogen suppression across field trials has resulted in them often not being seen as commercially viable. This thesis uses mathematical modelling to explore the interactions between a soil- borne biocontrol agent, a soil-borne pathogen, and the roots of a host plant. Understanding the dynamics of these organisms in more detail can allow us to optimise the use of biological control agents. We construct a model that focuses on the roots of a plant and whether they are infected by a pathogen or colonised by a biocontrol agent, as well as including any free-living pathogen and biocontrol agent in the surrounding soil. Although this model can be used across multiple systems, this thesis focuses on modelling the infection of winter wheat by Gaeumannomyces graminis var. tritici and suppression by the biocontrol agent 2,4-DAPG fluorescent Pseudomonas spp. Parameter values are obtained for the model through fitting it to data from this system. Application timing and amount of application were both found to affect the ability for a biocontrol agent to suppress a pathogen. Including a break crop into a simulation had a negative impact on both the pathogen and biocontrol agent, suggesting that combining multiple strategies for epidemic suppression may not always be effective. Planting a crop with even spaces between plants, or in rows with 12cm between each row, was found to reduce epidemic severity more than if rows were spaced further apart for the first year of an epidemic. However, large-scale dispersal of free-living material between growing seasons from agricultural machinery reduced any benefit of specific spatial arrangements of a crop in the second year of an epidemic. Aggregation of the pathogen and biocontrol agent were found to affect epidemic severity, with the greatest reduction from a highly aggregated pathogen and a uniformly distributed biocontrol agent. We suggest that a greater focus on optimising application, as well as a detailed understanding of how the spatial dynamics of a biocontrol agent and pathogen can affect this application, may enhance the success of biocontrol agents and allow them to be seen as a viable control strategy.BBSR

A proteomic approach to identify endosomal cargoes controlling cancer invasiveness

We have previously shown that Rab17 - a small GTPase associated with epithelial polarity - is specifically suppressed by ERK2 signalling to promote an invasive phenotype. However, the mechanisms through which Rab17 loss permits invasiveness, and the endosomal cargoes that are responsible for mediating this are not known. Using quantitative mass spectrometry-based proteomics, we have found that knockdown of Rab17 leads to highly selective reduction in the cellular levels of a v-SNARE (Vamp8). Moreover, proteomics and immunofluorescence indicate that Vamp-8 is associated with Rab17 at late endosomes. Reduced levels of Vamp8 promote transition between ductal carcinoma in situ (DCIS) and a more invasive phenotype. We developed an unbiased proteomic approach to elucidate the complement of receptors that redistributes between endosomes and the plasma membrane, and have pin-pointed neuropilin-2 (NRP2) as a key pro-invasive cargo of Rab17/Vamp8-regulated trafficking. Indeed, reduced Rab17 or Vamp8 levels lead to increased mobilisation of NRP2-containing late endosomes and upregulated cell surface expression of NRP2. Finally, we show that NRP2 is required for the basement membrane disruption which accompanies transition between DCIS and a more invasive phenotype

An analysis of the construct validity and responsiveness of the ICECAP-SCM capability wellbeing measure in a palliative care hospice setting

Background For outcome measures to be useful in health and care decision-making, they need to have certain psychometric properties. The ICECAP-Supportive Care Measure (ICECAP-SCM), a seven attribute measure (1. Choice, 2. Love and affection, 3. Physical suffering, 4. Emotional suffering, 5. Dignity, 6. Being supported, 7. Preparation) developed for use in economic evaluation of end-of-life interventions, has face validity and is feasible to use. This study aimed to assess the construct validity and responsiveness of the ICECAP-SCM in hospice inpatient and outpatient settings. Methods: A secondary analysis of data collated from two studies, one focusing on palliative care day services and the other on constipation management, undertaken in the same national hospice organisation across three UK hospices, was conducted. Other quality of life and wellbeing outcome measures used were the EQ-5D-5L, McGill Quality of Life Questionnaire – Expanded (MQOL-E), Patient Health Questionnaire-2 (PHQ-2) and Palliative Outcomes Scale Symptom list (POS-S). The construct validity of the ICECAP-SCM was assessed, following hypotheses generation, by calculating correlations between: (i) its domains and the domains of other outcome measures, (ii) its summary score and the other measures’ domains, (iii) its summary score and the summary scores of the other measures. The responsiveness of the ICECAP-SCM was assessed using anchor-based methods to understand change over time. Statistical analysis consisted of Spearman and Pearson correlations for construct validity and paired t-tests for the responsiveness analysis. Results Sixty-eight participants were included in the baseline analysis. Five strong correlations were found with ICECAP-SCM attributes and items on the other measures: four with the Emotional suffering attribute (Anxiety/depression on EQ-5D-5L, Psychological and Burden on MQOL-E and Feeling down, depressed or hopeless on PHQ-2), and one with Physical suffering (Weakness or lack of energy on POS-S). ICECAP-SCM attributes and scores were most strongly associated with the MQOL-E measure (0.73 correlation coefficient between summary scores). The responsiveness analysis (n = 36) showed the ICECAP-SCM score was responsive to change when anchored to changes on the MQOL-E over time (p Conclusions This study provides initial evidence of construct validity and responsiveness of the ICECAP-SCM in hospice settings and suggests its potential for use in end-of-life care research

Economic Analysis Shows Value of Volunteering in Palliative Care Day Services

This is the final version. Available on open access from SAGE Publications via the DOI in this recordPublic Health Research in Palliative Care: Towards Solutions for Global Challenges seminar. Hosted online by All-Ireland Institute of Hospice and Palliative Care (AIIHPC), 17-18 November 2020Background: Research shows that people living with severe economic disadvantage are less likely to access palliative care services in the United Kingdom and that funeral poverty is growing. However, little is understood about the ways in which the structural, social, and economic aspects of poverty impact upon preparing for end of life, and experiences of dying and bereavement. While public health approaches to palliative care and ‘death awareness’ initiatives encourage wider acceptance of the need to prepare for end of life, there is a need to examine the relevance of these approaches to people struggling to live well. Aims: This study examines the notion of ‘a good death’ within low-income communities, and the ways in which poverty affects attitudes towards, and experiences of, death and dying. Methods: Taking a qualitative and engaged approach, exploratory workshops were held bringing together health care professionals, voluntary organisations, and community groups to share existing knowledge and identify research priorities. Qualitative interviews were then carried out with 10 professionals supporting individuals through end-of-life and bereavement in low-income communities (e.g. funeral directors, faith leaders, advice workers) and 10 bereaved individuals with experience of funeral poverty. Interviews were conducted via phone/video call and data include experiences of end of life and bereavement both before and during the pandemic. Results: This article will present early findings and provide evidence of the impact of poverty on experiences of death and dying at different stages of the life course; including concerns around preparing for death, experiences of end of life, and bereavement. Discussion: This paper will consider whether some public health approaches to palliative care might inadvertently increase inequalities in access to care and support, and whether specific approaches may be needed to address the concerns of people on a low income in relation to a ‘good death’.Wellcome Trus

Cucurbitacins elicit anti-platelet activity via perturbation of the actin cytoskeleton and integrin function

Cucurbitacins are dietary compounds that have been shown to elicit a range of anti-tumour, anti-inflammatory and anti-atherosclerotic activities. Originally identified as STAT inhibitors, a variety of mechanisms of action have since been described, including dysregulation of the actin cytoskeleton and disruption of integrin function. Integrin outside-in signalling and cytoskeletal rearrangements are critical for the propagation of stable thrombus formation and clot retraction following platelet adhesion at the site of vessel damage. The effects of cucurbitacins on platelet function and thrombus formation are unknown. We report for the first time anti-platelet and anti-thrombotic effects of cucurbitacins B, E and I in human platelets. Treatment of platelets with cucurbitacins resulted in attenuation of platelet aggregation, secretion and fibrinogen binding following stimulation by ADP, TRAP6, collagen and CRP-XL. Cucurbitacins were also found to potently inhibit other integrin- and cytoskeleton-mediated events, including adhesion, spreading and clot retraction. Further investigation of cytoskeletal dynamics found treatment with cucurbitacins altered cofilin phosphorylation, enhanced activation, and increased F actin polymerisation and microtubule assembly. Disruption to cytoskeletal dynamics has been previously shown to impair integrin activation, platelet spreading and clot retraction. Anti-platelet properties of cucurbitacins were found to extend to a disruption of stable thrombus formation, with an increase in thrombi instability and de-aggregation under flow. Our research identifies novel, anti-platelet and anti-thrombotic actions of cucurbitacins that appear to be linked to dysregulation of cytoskeletal dynamics and integrin function

Multi-site genetic analysis of diffusion images and voxelwise heritability analysis : a pilot project of the ENIGMA–DTI working group

The ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium was set up to analyze brain measures and genotypes from multiple sites across the world to improve the power to detect genetic variants that influence the brain. Diffusion tensor imaging (DTI) yields quantitative measures sensitive to brain development and degeneration, and some common genetic variants may be associated with white matter integrity or connectivity. DTI measures, such as the fractional anisotropy (FA) of water diffusion, may be useful for identifying genetic variants that influence brain microstructure. However, genome-wide association studies (GWAS) require large populations to obtain sufficient power to detect and replicate significant effects, motivating a multi-site consortium effort. As part of an ENIGMA–DTI working group, we analyzed high-resolution FA images from multiple imaging sites across North America, Australia, and Europe, to address the challenge of harmonizing imaging data collected at multiple sites. Four hundred images of healthy adults aged 18–85 from four sites were used to create a template and corresponding skeletonized FA image as a common reference space. Using twin and pedigree samples of different ethnicities, we used our common template to evaluate the heritability of tract-derived FA measures. We show that our template is reliable for integrating multiple datasets by combining results through meta-analysis and unifying the data through exploratory mega-analyses. Our results may help prioritize regions of the FA map that are consistently influenced by additive genetic factors for future genetic discovery studies. Protocols and templates are publicly available at (http://enigma.loni.ucla.edu/ongoing/dti-working-group/)

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis

Osteoarthritis is one of the most frequent and disabling diseases of the elderly. Only few genetic variants have been identified for osteoarthritis, which is partly due to large phenotype heterogeneity. To reduce heterogeneity, we here examined cartilage thickness, one of the structural components of joint health. We conducted a genome-wide association study of minimal joint space width (mJSW), a proxy for cartilage thickness, in a discovery set of 13,013 participants from five different cohorts and replication in 8,227 individuals from seven independent cohorts. We identified five genome-wide significant (GWS, P≤5·0×10−8) SNPs annotated to four distinct loci. In addition, we found two additional loci that were significantly replicated, but results of combined meta-analysis fell just below the genome wide significance threshold. The four novel associated genetic loci were located in/near TGFA (rs2862851), PIK3R1 (rs10471753), SLBP/FGFR3 (rs2236995), and TREH/DDX6 (rs496547), while the other two (DOT1L and SUPT3H/RUNX2) were previously identified. A systematic prioritization for underlying causal genes was performed using diverse lines of evidence. Exome sequencing data (n = 2,050 individuals) indicated that there were no rare exonic variants that could explain the identified associations. In addition, TGFA, FGFR3 and PIK3R1 were differentially expressed in OA cartilage lesions versus non-lesioned cartilage in the same individuals. In conclusion, we identified four novel loci (TGFA, PIK3R1, FGFR3 and TREH) and confirmed two loci known to be associated with cartilage thickness.The identified associations were not caused by rare exonic variants. This is the first report linking TGFA to human OA, which may serve as a new target for future therapies

BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration

BRF1 is a rate-limiting factor for RNA Polymerase III-mediated transcription and is elevated in numerous cancers. Here, we report that elevated levels of BRF1 associate with poor prognosis in human prostate cancer. In vitro studies in human prostate cancer cell lines demonstrated that transient overexpression of BRF1 increased cell proliferation whereas the transient downregulation of BRF1 reduced proliferation and mediated cell cycle arrest. Consistent with our clinical observations, BRF1 overexpression in a Pten-deficient mouse (Pten BRF1 ) prostate cancer model accelerated prostate carcinogenesis and shortened survival. In Pten BRF1 tumours, immune and inflammatory processes were altered, with reduced tumoral infiltration of neutrophils and CD4 positive T cells, which can be explained by decreased levels of complement factor D (CFD) and C7 components of the complement cascade, an innate immune pathway that influences the adaptive immune response. We tested if the secretome was involved in BRF1-driven tumorigenesis. Unbiased proteomic analysis on BRF1-overexpresing PC3 cells confirmed reduced levels of CFD in the secretome, implicating the complement system in prostate carcinogenesis. We further identify that expression of C7 significantly correlates with expression of CD4 and has the potential to alter clinical outcome in human prostate cancer, where low levels of C7 associate with poorer prognosis

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis

Osteoarthritis is one of the most frequent and disabling diseases of the elderly. Only few genetic variants have been identified for osteoarthritis, which is partly due to large phenotype heterogeneity. To reduce heterogeneity, we here examined cartilage thickness, one of the structural components of joint health. We conducted a genome-wide association study of minimal joint space width (mJSW), a proxy for cartilage thickness, in a discovery set of 13,013 participants from five different cohorts and replication in 8,227 individuals from seven independent cohorts. We identified five genome-wide significant (GWS, P≤5·0×10−8) SNPs annotated to four distinct loci. In addition, we found two additional loci that were significantly replicated, but results of combined meta-analysis fell just below the genome wide significance threshold. The four novel associated genetic loci were located in/near TGFA (rs2862851), PIK3R1 (rs10471753), SLBP/FGFR3 (rs2236995), and TREH/DDX6 (rs49654