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• Journal article
  Fleming A, Galey M, Briggs L, Edwards M, Hogg C, John S, Wilkinson S, Quinn E, Rai R, Burgoyne T, Rogers A, Patel MP, Griffin P, Muller S, Carr SB, Loebinger MR, Lucas JS, Shah A, Jose R, Mitchison HM, Shoemark A, Miller DE, Morris-Rosendahl DJet al., 2024,

  Combined approaches, including long-read sequencing, address the diagnostic challenge of <i>HYDIN</i> in primary ciliary dyskinesia

  , EUROPEAN JOURNAL OF HUMAN GENETICS, ISSN: 1018-4813
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• Journal article
  Richter F, Calonne-Salmon M, van der Heijden MGA, Declerck S, Stanley CEet al., 2024,

  AMF-SporeChip provides new insights into arbuscular mycorrhizal fungal asymbiotic hyphal growth dynamics at the cellular level

  , Lab on a Chip: miniaturisation for chemistry, physics, biology, materials science and bioengineering, Vol: 24, Pages: 1930-1946, ISSN: 1473-0189

  Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants and deliver a wide range of soil-based ecosystem services. Due to their conspicuous belowground lifestyle in a dark environment surrounded by soil particles, much is still to be learned about the influence of environmental (i.e., physical) cues on spore germination, hyphal morphogenesis and anastomosis/hyphal healing mechanisms. To fill existing gaps in AMF knowledge, we developed a new microfluidic platform – the AMF-SporeChip – to visualise the foraging behaviour of germinating Rhizophagus and Gigaspora spores and confront asymbiotic hyphae with physical obstacles. In combination with timelapse microscopy, the fungi could be examined at the cellular level and in real-time. The AMF-SporeChip allowed us to acquire movies with unprecedented visual clarity and therefore identify various exploration strategies of AMF asymbiotic hyphae. We witnessed tip-to-tip and tip-to-side hyphal anastomosis formation. Anastomosis involved directed hyphal growth in a “stop-and-go” manner, yielding visual evidence of pre-anastomosis signalling and decision-making. Remarkably, we also revealed a so-far undescribed reversible cytoplasmic retraction, including the formation of up to 8 septa upon retraction, as part of a highly dynamic space navigation, probably evolved to optimise foraging efficiency. Our findings demonstrated how AMF employ an intricate mechanism of space searching, involving reversible cytoplasmic retraction, branching and directional changes. In turn, the AMF-SporeChip is expected to open many future frontiers for AMF research.

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• Journal article
  Budden KF, Shukla SD, Bowerman KL, Vaughan A, Gellatly SL, Wood DLA, Lachner N, Idrees S, Rehman SF, Faiz A, Patel VK, Donovan C, Alemao CA, Shen S, Amorim N, Majumder R, Vanka KS, Mason J, Haw TJ, Tillet B, Fricker M, Keely S, Hansbro N, Belz GT, Horvat J, Ashhurst T, van Vreden C, McGuire H, Fazekas de St Groth B, King NJC, Crossett B, Cordwell SJ, Bonaguro L, Schultze JL, Hamilton-Williams EE, Mann E, Forster SC, Cooper MA, Segal LN, Chotirmall SH, Collins P, Bowman R, Fong KM, Yang IA, Wark PAB, Dennis PG, Hugenholtz P, Hansbro PMet al., 2024,

  Faecal microbial transfer and complex carbohydrates mediate protection against COPD.

  , Gut, Vol: 73, Pages: 751-769

  OBJECTIVE: Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear. DESIGN: Using an in vivo mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation. RESULTS: FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of Muribaculaceae, Desulfovibrionaceae and Lachnospiraceae family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes. CONCLUSION: The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.

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• Journal article
  Wu Y, Li Y, Liu Y, Xiu X, Liu J, Zhang L, Li J, Du G, Lv X, Chen J, Ledesma-Amaro R, Liu Let al., 2024,

  Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor

  , Nucleic Acids Research, Vol: 52, Pages: 4739-4755, ISSN: 0305-1048

  Mutagenesis driving genetic diversity is vital for understanding and engineering biological systems. However, the lack of effective methods to generate in-situ mutagenesis in multiple genomic loci combinatorially limits the study of complex biological functions. Here, we design and construct MultiduBE, a dCas12a-based multiplexed dual-function base editor, in an all-in-one plasmid for performing combinatorial in-situ mutagenesis. Two synthetic effectors, duBE-1a and duBE-2b, are created by amalgamating the functionalities of cytosine deaminase (from hAPOBEC3A or hAID*Δ ), adenine deaminase (from TadA9), and crRNA array processing (from dCas12a). Furthermore, introducing the synthetic separator Sp4 minimizes interference in the crRNA array, thereby facilitating multiplexed in-situ mutagenesis in both Escherichia coli and Bacillus subtilis. Guided by the corresponding crRNA arrays, MultiduBE is successfully employed for cell physiology reprogramming and metabolic regulation. A novel mutation conferring streptomycin resistance has been identified in B. subtilis and incorporated into the mutant strains with multiple antibiotic resistance. Moreover, surfactin and riboflavin titers of the combinatorially mutant strains improved by 42% and 15-fold, respectively, compared with the control strains with single gene mutation. Overall, MultiduBE provides a convenient and efficient way to perform multiplexed in-situ mutagenesis.

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• Journal article
  Ellis T, Walker K, 2024,

  Genetically encoding colors and images into bioengineered microbial materials

  , NATURE BIOTECHNOLOGY, ISSN: 1087-0156
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• Journal article
  Walker K, Li IS, Lee K, Ellis Tet al., 2024,

  Self-pigmenting textiles grown from cellulose-producing bacteria with engineered tyrosinase expression

  , Nature Biotechnology, ISSN: 1087-0156

  Environmental concerns are driving interest in postpetroleum synthetic textiles produced from microbial and fungal sources. Bacterial cellulose (BC) is a promising sustainable leather alternative, on account of its material properties, low infrastructure needs and biodegradability. However, for alternative textiles like BC to be fully sustainable, alternative ways to dye textiles need to be developed alongside alternative production methods. To address this, we genetically engineer Komagataeibacter rhaeticus to create a bacterial strain that grows self-pigmenting BC. Melanin biosynthesis in the bacteria from recombinant tyrosinase expression achieves dark black coloration robust to material use. Melanated BC production can be scaled up for the construction of prototype fashion products, and we illustrate the potential of combining engineered self-pigmentation with tools from synthetic biology, through the optogenetic patterning of gene expression in cellulose-producing bacteria. With this study, we demonstrate that combining genetic engineering with current and future methods of textile biofabrication has the potential to create a new class of textiles.

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• Journal article
  Agarwal R, Sehgal IS, Muthu V, Denning DW, Chakrabarti A, Soundappan K, Garg M, Rudramurthy SM, Dhooria S, Armstrong-James D, Asano K, Gangneux J-P, Chotirmall SH, Salzer HJF, Chalmers JD, Godet C, Joest M, Page I, Nair P, Arjun P, Dhar R, Jat KR, Joe G, Krishnaswamy UM, Mathew JL, Maturu VN, Mohan A, Nath A, Patel D, Savio J, Saxena P, Soman R, Thangakunam B, Baxter CG, Bongomin F, Calhoun WJ, Cornely OA, Douglass JA, Kosmidis C, Meis JF, Moss R, Pasqualotto AC, Seidel D, Sprute R, Prasad KT, Aggarwal ANet al., 2024,

  Revised ISHAM-ABPA working group clinical practice guidelines for diagnosing, classifying and treating allergic bronchopulmonary aspergillosis/mycoses

  , EUROPEAN RESPIRATORY JOURNAL, Vol: 63, ISSN: 0903-1936
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• Journal article
  Sinanaj B, Pressel S, Bidartondo MI, Field KJet al., 2024,

  Fungal symbiont diversity drives growth of <i>Holcus lanatus</i> depending on soil nutrient availability

  , FUNCTIONAL ECOLOGY, Vol: 38, Pages: 984-997, ISSN: 0269-8463
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• Journal article
  Wu Z, Spencer LG, Banya W, Westoby J, Tudor VA, Rivera-Ortega P, Chaudhuri N, Jakupovic I, Patel B, Thillai M, West A, Wijsenbeek M, Maher TM, Smith JA, Molyneaux PLet al., 2024,

  Morphine for treatment of cough in idiopathic pulmonary fibrosis (PACIFY COUGH): a prospective, multicentre, randomised, double-blind, placebo-controlled, two-way crossover trial

  , LANCET RESPIRATORY MEDICINE, Vol: 12, Pages: 273-280, ISSN: 2213-2600
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• Journal article
  Yim SHL, Li Y, Huang T, Lim JT, Lee HF, Chotirmall SH, Dong GH, Abisheganaden J, Wedzicha JA, Schuster SC, Horton BP, Sung JJYet al., 2024,

  Global health impacts of ambient fine particulate pollution associated with climate variability

  , ENVIRONMENT INTERNATIONAL, Vol: 186, ISSN: 0160-4120
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