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  • Conference paper
    Ghani R, Mullish B, Ghazy A, Corbett R, Duncan N, Satta G, Gilchrist M, Williams H, Pavlu J, Innes A, MacDonald J, Miguens Blanco J, Danckert N, Davies F, Marchesi Jet al., 2024,

    P3438 – Intestinal microbiota transplantation for patients colonised with multidrug-resistant organisms have an improvement in clinical outcomes associated with a significant increase in alpha-diversity metrics of the gastrointestinal microbiota

    , ESCMID Global, Publisher: Elsevier
  • Journal article
    van Haaren C, Byrne B, Kazarian SG, 2024,

    Study of monoclonal antibody aggregation at the air-liquid interface under flow by ATR-FTIR spectroscopic imaging

    , Langmuir: the ACS journal of surfaces and colloids, Vol: 40, Pages: 5858-5868, ISSN: 0743-7463

    Throughout bioprocessing, transportation, and storage, therapeutic monoclonal antibodies (mAbs) experience stress conditions that may cause protein unfolding and/or chemical modifications. Such structural changes may lead to the formation of aggregates, which reduce mAb potency and may cause harmful immunogenic responses in patients. Therefore, aggregates need to be detected and removed or ideally prevented from forming. Air-liquid interfaces, which arise during various stages of bioprocessing, are one of the stress factors causing mAb aggregation. In this study, the behavior of an immunoglobulin G (IgG) at the air-liquid interface was investigated under flow using macro attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic imaging. This chemically specific imaging technique allows observation of adsorption of IgG to the air-liquid interface and detection of associated secondary structural changes. Chemical images revealed that IgG rapidly accumulated around an injected air bubble under flow at 45 °C; however, no such increase was observed at 25 °C. Analysis of the second derivative spectra of IgG at the air-liquid interface revealed changes in the protein secondary structure associated with increased intermolecular β-sheet content, indicative of aggregated IgG. The addition of 0.01% w/v polysorbate 80 (PS80) reduced the amount of IgG at the air-liquid interface in a static setup at 30 °C; however, this protective effect was lost at 45 °C. These results suggest that the presence of air-liquid interfaces under flow may be detrimental to mAb stability at elevated temperatures and demonstrate the power of ATR-FTIR spectroscopic imaging for studying the structural integrity of mAbs under bioprocessing conditions.

  • Journal article
    Joulia RPG, Puttur F, Stölting H, Traves W, Entwistle L, Voitovich A, Garcia Martín M, Al-Sahaf M, Bonner K, Scotney E, Molyneaux P, Hewitt R, Walker S, Yates L, Saglani S, Lloyd Cet al., 2024,

    Mast cell activation disrupts interactions between endothelial cells and pericytes during early life allergic asthma

    , Journal of Clinical Investigation, ISSN: 0021-9738
  • Journal article
    Jones MP, Bismarck A, 2024,

    Mycomining: perspective on fungi as scavengers of scattered metal, mineral, and rare earth element resources

    , RSC Sustainability, Vol: 2, Pages: 1350-1357

    Mining provides raw materials critical to our energy, agriculture, infrastructure, and technology but is associated with many environmental challenges. Resource recovery alternatives like urban mining rely on inconsistent supply streams and complicated disassembly and sorting, while extreme mining alternatives such as deep sea and space mining are potentially even less sustainable than traditional mining. This perspective investigates biological mining with emphasis on the potential of fungi for scavenging metals, minerals, and rare earth elements. “Mycomining” produces only biomass-based organic waste and can offer more versatile growth conditions than phytomining using hyperaccumulating plants including substrates ranging from soil, wood, water, and rock to living organisms and dark, space-restricted, or extreme i.e., pH levels, high salt, acidic, radioactive environments. This concept could represent a useful supplement to urban and phytomining to offset demand for traditional mining and is particularly viable when conventional mining may be inefficient or uneconomical i.e., with low-grade ores and sites unsuited to traditional mining for geographical, political, or social reasons.

  • Journal article
    Devoy E, Hughes D, Alharbi AF, Francis J, Davies JCet al., 2024,

    What is cystic fibrosis screen positive inconclusive diagnosis? And what is it not?

    , ARCHIVES OF DISEASE IN CHILDHOOD-EDUCATION AND PRACTICE EDITION, ISSN: 1743-0585
  • Journal article
    Thillai M, Oldham JM, Ruggiero A, Kanavati F, McLellan T, Saini G, Johnson SR, Ble F-X, Azim A, Ostridge K, Platt A, Belvisi M, Maher TM, Molyneaux PLet al., 2024,

    Deep Learning-based Segmentation of CT Scans Predicts Disease Progression and Mortality in IPF.

    , Am J Respir Crit Care Med

    RATIONALE: Despite evidence demonstrating a prognostic role for CT scans in IPF, image-based biomarkers are not routinely used in clinical practice or trials. OBJECTIVES: Develop automated imaging biomarkers using deep learning based segmentation of CT scans. METHODS: We developed segmentation processes for four anatomical biomarkers which were applied to a unique cohort of treatment-naive IPF patients enrolled in the PROFILE study and tested against a further UK cohort. The relationship between CT biomarkers, lung function, disease progression and mortality were assessed. MEASUREMENTS AND MAIN RESULTS: Data was analysed from 446 PROFILE patients. Median follow-up was 39.1 months (IQR 18.1-66.4) with cumulative incidence of death of 277 over 5 years (62.1%). Segmentation was successful on 97.8% of all scans, across multiple imaging vendors at slice thicknesses 0.5-5mm. Of 4 segmentations, lung volume showed strongest correlation with FVC (r=0.82, p<0.001). Lung, vascular and fibrosis volumes were consistently associated across cohorts with differential five-year survival, which persisted after adjustment for baseline GAP score. Lower lung volume (HR 0.98, CI 0.96-0.99, p=0.001), increased vascular volume (HR 1.30, CI 1.12-1.51, p=0.001) and increased fibrosis volume (HR 1.17, CI 1.12-1.22, p=<0.001) were associated with reduced two-year progression-free survival in the pooled PROFILE cohort. Longitudinally, decreasing lung volume (HR 3.41; 95% CI 1.36-8.54; p=0.009) and increasing fibrosis volume (HR 2.23; 95% CI 1.22-4.08; p=0.009) were associated with differential survival. CONCLUSIONS: Automated models can rapidly segment IPF CT scans, providing prognostic near and long-term information, which could be used in routine clinical practice or as key trial endpoints. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

  • Journal article
    Chotirmall SH, Sung JJY, 2024,

    Opening a new chapter in health care: reporting on the inauguration of the International Conference on AI in Medicine.

    , Singapore Med J, Vol: 65, Pages: 176-178
  • Journal article
    King FJ, Yuen ELH, Bozkurt TO, 2024,

    Border control: manipulation of the host-pathogen interface by perihaustorial oomycete effectors

    , Molecular Plant-Microbe Interactions, Vol: 37, Pages: 220-226, ISSN: 0894-0282

    Filamentous plant pathogens, including fungi and oomycetes, cause some of the most devastating plant diseases. These organisms serve as ideal models for understanding the intricate molecular interplay between plants and the invading pathogens. Filamentous pathogens secrete effector proteins via haustoria, specialized structures for infection and nutrient uptake, to suppress the plant immune response and to reprogram plant metabolism. Recent advances in cell biology have provided crucial insights into the biogenesis of the extrahaustorial membrane and the redirection of host endomembrane trafficking toward this interface. Functional studies have shown that an increasing number of oomycete effectors accumulate at the perihaustorial interface to subvert plant focal immune responses, with a particular convergence on targets involved in host endomembrane trafficking. In this review, we summarize the diverse mechanisms of perihaustorial effectors from oomycetes and pinpoint pressing questions regarding their role in manipulating host defense and metabolism at the haustorial interface. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

  • Journal article
    Sole A, Davies JC, Quintana-Gallego E, 2024,

    Cystic Fibrosis: From Salty Malediction to Possible Cure

    , ARCHIVOS DE BRONCONEUMOLOGIA, Vol: 60, Pages: 129-130, ISSN: 0300-2896
  • Journal article
    King FJ, Yuen ELH, Bozkurt O, 2024,

    Border control: manipulation of the host–pathogeninterface by perihaustorial oomycete effectors

    , Molecular Plant-Microbe Interactions, Vol: 37, Pages: 220-226, ISSN: 0894-0282

    Filamentous plant pathogens, including fungi and oomycetes, cause some of the most devastating plant diseases. These organisms serve as ideal models for understanding the intricate molecular interplay between plants and the invading pathogens. Filamentous pathogens secrete effector proteins via haustoria, specialized structures for infection and nutrient uptake, to suppress the plant immune response and to reprogram plant metabolism. Recent advances in cell biology have provided crucial insights into the biogenesis of the extrahaustorial membrane and the redirection of host endomembrane trafficking toward this interface. Functional studies have shown that an increasing number of oomycete effectors accumulate at the perihaustorial interface to subvert plant focal immune responses, with a particular convergence on targets involved in host endomembrane trafficking. In this review, we summarize the diverse mechanisms of perihaustorial effectors from oomycetes and pinpoint pressing questions regarding their role in manipulating host defense and metabolism at the haustorial interface.

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