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Investigating the role of PPE50 from mycobacterium tuberculosis. Insights into the evolution and pathogenesis of tuberculosis
No full textThis thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonTuberculosis, caused by M. tuberculosis, remains a significant global health challenge. This thesis explores the highly understudied member of the PE/PPE family of proteins in M. tuberculosis, PPE50, to elucidate its role in TB evolution, pathogenesis, and potential as a therapeutic candidate. Investigating the phylogenetics of PPE50 in a globally representative dataset of MTBC species and strains revealed PPE50 to exist as eight variants, with PPE50-381 as the ancestral variant. These variants also showed lineage specificity, indicating possible involvement in the host-pathogen co-evolution of TB, designating PPE50 as a phylogeographically associated protein. In silico characterisation of the identified PPE50 variants provided insights into their structure, subcellular localisation, and function. Significant structural variation was predicted between the variants, highlighting the importance of considering species, strain, and lineage-specific variation in the design of therapeutics. Recombinant PPE50-381 (rPPE50-381), the likely ancestral and progenitor variant, was expressed and purified for further experimental characterisations. Here, three approaches were explored: a maltose-binding protein (MBP) fusion, an intein fusion, and a histidine tag. The histidine tag was the most effective approach for obtaining soluble, stable, and functional rPPE50-381. Using PMA-differentiated THP-1 cells as a macrophage model, rPPE50-381 was shown to bind to these cells without causing cytotoxicity. RT-qPCR analysis then revealed that rPPE50-381 induces a dual-inflammatory response, defined by an initial upregulated pro-inflammatory phase, followed by a later upregulated pro- and anti-inflammatory phase. This highlights a function of PPE50-381 in modulating the host immune response.
Overall, this thesis furthers our understanding of the PE/PPE family protein PPE50 and provides insights into the evolution and pathogenesis of tuberculosis. The optimised methodologies herein provide a framework to recover and characterise not only the other variants, but also other complex PE/PPE family proteins in M. tuberculosis. The insights gained significantly inform the development of therapeutics with global efficacy, as well as highlight PPE50 as a potential therapeutic candidate
Influence of alluvial slope on avulsion in river deltas
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The morphometric variables and avulsion timescales observed from our models are available in Table S1. The datasets from natural and laboratory river deltas used in this study (Table S2) and model scenarios (Run a–f) are available on the Figshare repository (https://doi.org/10.6084/m9.figshare.20654037.v3, https://doi.org/10.6084/m9.figshare.23912625.v2; Prasojo et al., 2023a, b).The supplement related to this article is available online at https://doi.org/10.5194/esurf-13-349-2025-supplement.Video supplement:
Video S1 showing bed-level change as well as non-cohesive and cohesive sediment concentration distributions from Run a is available in the Figshare repository (Prasojo et al., 2024).Changing hydrological regimes, sea-level rise, and accelerated subsidence are all putting river deltas at risk across the globe. One mechanism by which deltas may respond to these stressors is that of avulsion. Decades of delta avulsion studies have resulted in conflicting hypotheses as to whether avulsion timing and location are primarily controlled by upstream (water and sediment discharge) or downstream (backwater and sea-level rise) drivers. Here we use Delft3D morphodynamic simulations to test the upstream-influence hypothesis by varying the initial alluvial slopes upstream of a self-formed delta plain within a range (1.13×10^−4 to 3.04×10^−3 m m^−1)) that is representative of global deltas, while leaving all other parameters constant. Avulsion timing and location were recorded in six scenarios modelled over a 400-year period. We measured independent morphometric variables including avulsion length, delta lobe width, bankfull depth, channel width at avulsion, delta topset slope, and sediment load and compare these to natural and laboratory deltas. We find that larger deltas take more time to avulse, as avulsion timing scales with avulsion length, delta lobe width, and bankfull depth. More importantly, we find strong negative correlations between sediment load avulsion timescale and sediment load initial alluvial slope. Sediment load is directly dependent on the upstream alluvial slope, and increases in this slope raise transport capacity and introduce more sediment into a delta plain, leading to higher aggradation rates and, consequently, more frequent avulsions. These results introduce further debate over the role of downstream controls on delta avulsion.This study was funded by an Indonesia Endowment Fund for Education (LPDP) awarded to Octria A. Prasojo (grant no. 201902220213875)
Quantifying riverbed surface roughness from point cloud data
Get PDFMeeting abstract presented at EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, Session GM2.2: Novel data, methods and applications in Geomorphometry. Convener: Giulia Sofia | Co-conveners: David Mair, Mathilde LetardECS, Stuart Grieve, Massimiliano Alvioli. Orals | Mon, 28 Apr, 08:30–10:15 (CEST) Room -2.21. Posters on site | Attendance Mon, 28 Apr, 16:15–18:00 (CEST) | Display Mon, 28 Apr, 14:00–18:00. Posters virtual | Attendance Mon, 28 Apr, 14:00–15:45 (CEST) | Display Mon, 28 Apr, 08:30–18:00 (CEST).Surface roughness is an important control on a wide range of Earth surface processes. The increasing spatiotemporal availability of topographic point cloud data provides scope for advances in quantifying geomorphic surfaces and topography. Here, bedrock riverbed point clouds were obtained from dry riverbeds using terrestrial laser scanning (TLS) and Structures from Motion (SfM) photogrammetry. These data were processed using a unified workflow to extract the channel morphology and multiple different surface roughness. Metrics were calculated based on vertical and horizontal point spacings, cell area and slope, and incorporated multiscale analysis methods. Principal component analysis and hierarchical clustering revealed the concurrent use of multiple metrics is required to comprehensively describe the diversity in bed topographic characteristics. Multiple metrics are required as riverbed characteristics and features are shown to be represented by differing surface roughness metrics. This work further explores the applications of these metrics to advance the understanding of geomorphic and Earth surface processes, including sediment transport processes and hydrodynamics. It is proposed these metrics and analysis approaches can be applied more widely to landscapes beyond riverbeds, yet the most appropriate metric likely depends on the process that is of interest
An investigation of the potential side effects of adeno-associated virus as a vector for gene therapy and methods to improve its gene transfer
No full textThis thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonGene therapy offers a promising strategy to deliver functional genes that can correct mutations causing genetic diseases. Among viral vectors, Adeno-associated virus (AAV) is commonly used as a safe and efficient vector for gene transfer of genetic material. Even though recombinant AAV (rAAV) has long been considered a non-integrative vector, in recent years it has been found to integrate into the genome, raising concerns about the potential safety of using AAV in humans. Nevertheless, variations exist in AAV integration profile between different animal models suggesting integration site selection in animals may not be predictive of insertion site choice by AAV in humans. Human studies are very limited in providing enough data to predict AAV safety and therefore human-based models are needed to understand risk of adverse effects by AAV before moving to clinical trials.
To overcome this limitation, the hIngetox model was developed in our lab as the first induced pluripotent stem cell (iPSCs)-derived liver model for genotoxicity studies. This model has been shown that hepatocyte-like cells (HLCs) derived from iPSCs closely mimic human primary hepatocytes, enhancing the likelihood that results from this model will be translatable to predict clinical outcome following AAV gene transfer. The hIngetox model was used to investigate four main genotoxicity hallmarks associated with gene therapy safety and cancer. These are insertion site (IS) selection, gene splicing between the vector and the host genome, gene expression changes caused by the vector following insertion close to a cancer gene and clonal tracking to identify proliferating cells in bulk infected populations. Both iPSCs and iPSCs-derived HLCs were transduced with AAV vectors carrying either a weak Apolipoprotein (ApoE) promoter or a strong Chicken β-actin (CB7) promoter to drive green fluorescence protein (GFP) reporter gene expression to investigate the association of promoter strength on genotoxicity. Integration events and fusion genes were identified in both iPSCs and HLCs after viral transduction and these events were found to be associated with biological pathways and gene expression changes. Contrary to expectations, the ApoE promoter, appeared with the highest level of integration as measured by q-PCR for vector copy number, suggesting vector integration is not dependent on promoter strength. In this study, to provide a positive control for genotoxicity for the hInGetox model, a nucleic sequence previously identified associated with AAV induced hepatocellular carcinoma was cloned into a rAAV vector. This vector was used to transduce HLCs and compared to rAAV vectors not carrying this sequence in this study.
To understand further AAV IS selection and the potential for vector tethering to sites within the host genome, AAV IS were used to investigate the presence of transcription factor binding sites (TFBS) on the vector and human genome. It was identified that all TFBS found in rAAV were also present at IS in host genome, suggesting these sites were used by the vector for tethering to the host transcription factors. Also, in attempt to understand whether viral tethering and integration causes damage to the host DNA, the H2A histone family member (γH2AX) on Ser139 protein, which become phosphorylated in the presence of double strand breaks was measured during and after viral integration. In collaboration with Vidiia Ltd, γH2AX was quantified using a newly developed AI-driven diagnostic device that can detect DNA damage in a fast, affordable and sensitive manner. In line with integration site quantification, AAV carrying the ApoE promoter appeared associated with the highest level of DNA damage and, therefore, higher potential for genotoxicity.
Viral vector toxicity has also been associated with the level of vector dose required for successful gene transfer. To determine whether vector dose could be reduced yet achieve high gene transfer efficacy by enhancement of transduction, in collaboration with N4Pharma Ltd, the potential of Nuvec® silica nanoparticles (SiNPs) to encapsulate and deliver viral vectors was investigated. By this study, it was found that Nuvec® SiNPs can enhance viral efficiency at low dose compared to the vector alone. Also, the potential of Nuvec® to enhance viral stability at temperatures other than storage at -80°C was explored. It was demonstrated that Nuvec® can enhance vector stability at room temperature (RT) and 4°C up to 30 days post complexing vectors with Nuvec®.
Overall, this research provides an analysis of rAAV genotoxicity in a human derived liver model and identifies potential mechanisms of AAV associated genotoxicity. By exploring strategies to mitigate genotoxicity risks, using a genotoxicity model or ways of improving vector transduction to reduce vector dose vector, this thesis aims to provide information that can be used to identify and improve rAAV risk and safety for gene therapy
Assessing the feasibility and impact of clinical trial trustworthiness checks via an application to Cochrane Reviews: Stage 2 of the INSPECT-SR project
Get PDFThis is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Background:
The aim of the INSPECT-SR project is to develop a tool to identify problematic RCTs in systematic reviews. In Stage 1 of the project, a list of potential trustworthiness checks was created. The checks on this list must be evaluated to determine which should be included in the INSPECT-SR tool.
Methods:
We attempted to apply 72 trustworthiness checks to RCTs in 50 Cochrane Reviews. For each, we recorded whether the check was passed, failed or possibly failed, or whether it was not feasible to complete the check. Following application of the checks, we recorded whether we had concerns about the authenticity of each RCT. We repeated each meta-analysis after removing RCTs flagged by each check, and again after removing RCTs where we had concerns about authenticity, to estimate the impact of trustworthiness assessment. Trustworthiness assessments were compared to Risk of Bias and GRADE assessments in the reviews.
Results:
95 RCTs were assessed. Following application of the checks, assessors had some or serious concerns about the authenticity of 25% and 6% of the RCTs, respectively. Removing RCTs with either some or serious concerns resulted in 22% of meta-analyses having no remaining RCTs. However, many checks proved difficult to understand or implement, which may have led to unwarranted scepticism in some instances. Furthermore, we restricted assessment to meta-analyses with no more than 5 RCTs (54% contained only 1 RCT), which will distort the impact on results. No relationship was identified between trustworthiness assessment and Risk of Bias or GRADE.
Conclusions:
This study supports the case for routine trustworthiness assessment in systematic reviews, as problematic studies do not appear to be flagged by Risk of Bias assessment. The study produced evidence on the feasibility and impact of trustworthiness checks. These results will be used, in conjunction with those from a subsequent Delphi process, to determine which checks should be included in the INSPECT-SR tool.This study/project is funded by the NIHR Research for Patient Benefit programme (NIHR203568). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care
Machinery Multimodal Uncertainty-Aware RUL Prediction: A Stochastic Modeling Framework for Uncertainty Quantification and Informed Fusion
Get PDFAccurate prediction of machinery’sremaining useful life (RUL) is essential for preventing catastrophic breakdowns and supporting predictive maintenance. Although RUL prediction has been extensively studied, most literature develops on unimodal data, which providesa limited and often biased perspective. Multimodal monitoring, which collects multiple sensor data, enables a more comprehensive understanding of degradation processes. While promising, significant challenges are encountered in existing methods: 1) point yet deterministic predictions are predominantly produced which, while potentially erroneous, tend to exhibit overconfidence, thereby lacking the dynamic uncertainty informing; 2) the processing of heterogeneous data and the achievement of physically interpretable fusion remain challenging; and 3) anomalies in the operation process are not appropriately identified. To address these issues, a new multimodal uncertainty-aware RUL prediction framework is proposed, grounded in stochastic modeling. Fractional stochastic differential equation-controlled subnets process each modality independently, wherein layer-wise transformations are modeled as state evolution in stochastic dynamical systems, allowing modality-specific uncertainty to be quantified without requiring parameter priors. A Lagrange multiplier-based fusion module is subsequently employed to perform explicit uncertainty-based fusion, enabling an interpretable and synergistic integration. Validation on harmonic drive reducers for robots demonstrates the superiority of the proposed framework, achieving an average improvement of 26.6% in RMSE and a 16.6% reduction in MAPE compared to state-of-the-art benchmarks. Furthermore, the method significantly reduces prediction uncertainty variance by 21.3%, offering more reliable insights into system degradation.National Science Fund for Distinguished Young Scholars of China (Grant Number: 52025056);
10.13039/501100001809-National Natural Science Foundation of China (Grant Number: 52375121 and 52435003);
Fundamental Research Funds for the Central Universities of China
PISCES Living Labs: Co-creating solutions to tackle plastic pollution in Indonesia
Get PDFBrunel Policy Brief.Policy Context: Indonesia, one of the world's largest contributors to marine plastic pollution, has taken significant steps towards improving its plastic waste management. Landmark initiatives such as the National Action Plan on Marine Debris and the Extended Producer Responsibility (EPR) Regulation signal a strong commitment to change. However, achieving the ambitious target of a 70% reduction in marine plastic debris by 2025 requires political will, strong regulatory enforcement, targeted investment and cross-sectoral engagement. Key Findings: The PISCES Living Lab, an infrastructure and hands-on space for developing and testing design solutions to the plastic packaging problem provided valuable insights into drivers and barriers to adopting innovative plastic waste reduction and management solutions. Advice: Policymakers should finance the creation of PISCES Living Labs in diverse socio-economic contexts. These Labs can support the development of upstream (e.g. alternative packaging designs) and downstream solutions (e.g. improved waste sorting and collection systems) specifically tailored to the needs of different contexts, as well as incentivising businesses to make use of these labs.Natural Environment Research Council grant ref. NE/V006428/1 [Plastics in Indonesian Societies (PISCES): Systems Analytics Approach to Reduce Plastic Pollution]
Dysregulated SASS6 expression promotes increased ciliogenesis and cell invasion phenotypes
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Microarray data have been deposited in the EMBL European Bioinformatics Institute database repository (https://www.ebi.ac.uk/biostudies/) with the accession number E-MTAB-13783. Additional data generated or analyzed in this study will be made available upon request.Centriole and/or cilium defects are characteristic of cancer cells and have been linked to cancer cell invasion. However, the mechanistic bases of this regulation remain incompletely understood. Spindle assembly abnormal protein 6 homolog (SAS-6) is essential for centriole biogenesis and cilium formation. SAS-6 levels decrease at the end of mitosis and G1, resulting from APCCdh1-targeted degradation. To examine the biological consequences of unrestrained SAS-6 expression, we used a nondegradable SAS-6 mutant (SAS-6ND). This led to an increase in ciliation and cell invasion and caused an up-regulation of the YAP/TAZ pathway. SAS-6ND expression resulted in cell morphology changes, nuclear deformation, and YAP translocation to the nucleus, resulting in increased TEAD-dependent transcription. SAS-6-mediated invasion was prevented by YAP down-regulation or by blocking ciliogenesis. Similarly, down-regulation of SAS-6 in DMS273, a highly invasive and highly ciliated lung cancer cell line that overexpresses SAS-6, completely blocked cell invasion and depleted YAP protein levels. Thus, our data provide evidence for a defined role of SAS-6 in cell invasion through the activation of the YAP/TAZ pathway.BE Tanos is funded by a Kidney Research UK Senior Fellowship and a June Hancock Mesothelioma Research Fund. TCGA results reported here are based, in part, upon data generated by The Cancer Genome Atlas pilot project established by the NCI and NHGRI; Centre for Cell Imaging (CCI), University of Liverpool, for their help with image acquisition on the CD7 (grant code: MR/X013502/1
Decomposition for Large-Scale Optimization Problems: An Overview
Get PDFFormalizing complex processes and phenomena of a real-world problem may require a large number of variables and constraints, resulting in what is termed a large-scale optimization problem. Nowadays, such large-scale optimization problems are solved using computing machines, leading to an enormous computational time being required, which may delay deriving timely solutions. Decomposition methods, which partition a large-scale optimization problem into lower-dimensional subproblems, represent a key approach to addressing time-efficiency issues. There has been significant progress in both applied mathematics and emerging artificial intelligence approaches on this front. This work aims at providing an overview of the decomposition methods from both the mathematics and computer science points of view. We also remark on the state-of-the-art developments and recent applications of the decomposition methods, and discuss the future research and development perspectives.10.13039/501100000923-The Australian Research Council (Grant Number: DP200101197,DP230101107
Institutional Quality and Sustainable Firm Growth: Evidence from North African Countries
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The data that support the findings of this study are available from the corresponding author upon reasonable request.JEL classification: C23, G38, Q56.This study investigates the relationship between institutional quality (IQ) and sustainable firm growth (SFG) in North African countries, focusing on Egypt, Morocco, and Tunisia. Utilizing panel data from 155 non-financial firms over the period 2007–2020, we employ a system generalized method of moments (GMM) approach to analyze this relationship. Our findings reveal a significant U-shaped relationship between IQ and SFG, indicating that both very low and very high levels of IQ are associated with limited firm growth, while an optimal level of IQ promotes substantial growth. This suggests that firms in low-IQ environments struggle due to weak regulatory frameworks and corruption, whereas those in high-IQ environments benefit from better governance and transparency, leading to enhanced growth. The study makes several contributions by providing empirical evidence from an underexplored region, highlighting the complex dynamics between institutional quality and firm growth, and offering robust methodological insights. Policy implications underscore the need for balanced regulation and long-term investment in institutional quality, education, and infrastructure.The authors received no specific funding for this work
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