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Journal articlePeng H, Darlington APS, South EJ, et al., 2024,
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities
, Nature Reviews Microbiology, Vol: 9, Pages: 848-863, ISSN: 1740-1526Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model and key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic and overexpression yeast strains that can be used to create co-cultures through exchange of essential metabolites. Using these strains as modules, we engineered two- and three-member consortia using different cross-feeding architectures. Through a combination of ensemble modelling and experimentation, we explored how cellular (for example, metabolite production strength) and environmental (for example, initial population ratio, population density and extracellular supplementation) factors govern population dynamics in these systems. We tested the use of the toolkit in a division of labour biomanufacturing case study and show that it enables enhanced and tuneable antioxidant resveratrol production. We expect this toolkit to become a useful resource for a variety of applications in synthetic ecology and biomanufacturing.
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Journal articleDavies J, Mossop M, Jonathan I-H, et al., 2024,
Chronicity counts: the impact of P. aeruginosa, S. aureus, and co-infection in cystic fibrosis
, American Journal of Respiratory and Critical Care Medicine, ISSN: 1073-449X -
Journal articleEder T, Mautner A, Xu Y, et al., 2024,
Transparent PDMS Surfaces with Covalently Attached Lubricants for Enhanced Anti-adhesion Performance.
, ACS Appl Mater Interfaces, Vol: 16, Pages: 10942-10952Liquid-like surfaces featuring slippery, omniphobic, covalently attached liquids (SOCALs) reduce unwanted adhesion by providing a molecularly smooth and slippery surface arising from the high mobility of the liquid chains. Such SOCALs are commonly prepared on hard substrates, such as glass, wafers, or metal oxides, despite the importance of nonpolar elastomeric substrates, such as polydimethylsiloxane (PDMS) in anti-fouling or nonstick applications. Compared to polar elastomers, hydrophobic PDMS elastomer activation and covalent functionalization are significantly more challenging, as PDMS tends to display fast hydrophobic recovery upon activation as well as superficial cracking. Through the extraction of excess PDMS oligomers and fine-tuning of plasma activation parameters, homogeneously functionalized PDMS with fluorinated polysiloxane brushes could be obtained while at the same time reducing crack formation. Polymer brush mobility was increased through the addition of a smaller molecular silane linker to exhibit enhanced dewetting properties and reduced substrate swelling compared to functionalizations featuring hydrocarbon functionalities. Linear polymer brushes were verified by thermogravimetric analysis. The optical properties of PDMS remained unaffected by the activation in high-frequency plasma but were impacted by low-frequency plasma. Drastic decreases in solid adhesion of not just complex contaminants but even ice could be shown in horizontal push tests, demonstrating the potential of SOCAL-functionalized PDMS surfaces for improved nonstick applications.
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Journal articleYoon S, Bae HE, Hariharan P, et al., 2024,
Rational approach to improve detergent efficacy for membrane protein stabilization
, Bioconjugate Chemistry, Vol: 35, Pages: 223-231, ISSN: 1043-1802Membrane protein structures are essential for the molecular understanding of diverse cellular processes and drug discovery. Detergents are not only widely used to extract membrane proteins from membranes but also utilized to preserve native protein structures in aqueous solution. However, micelles formed by conventional detergents are suboptimal for membrane protein stabilization, necessitating the development of novel amphiphilic molecules with enhanced protein stabilization efficacy. In this study, we prepared two sets of tandem malonate-derived glucoside (TMG) variants, both of which were designed to increase the alkyl chain density in micelle interiors. The alkyl chain density was modulated either by reducing the spacer length (TMG-Ms) or by introducing an additional alkyl chain between the two alkyl chains of the original TMGs (TMG-Ps). When evaluated with a few membrane proteins including a G protein-coupled receptor, TMG-P10,8 was found to be substantially more efficient at extracting membrane proteins and also effective at preserving protein integrity in the long term compared to the previously described TMG-A13. This result reveals that inserting an additional alkyl chain between the two existing alkyl chains is an effective way to optimize detergent properties for membrane protein study. This new biochemical tool and the design principle described have the potential to facilitate membrane protein structure determination.
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Journal articleMurphy RA, Pizzato J, Cuthbertson L, et al., 2024,
Antimicrobial peptide glatiramer acetate targets Pseudomonas aeruginosa lipopolysaccharides to breach membranes without altering lipopolysaccharide modification
, npj Antimicrobials and Resistance, Vol: 2, ISSN: 2731-8745Antimicrobial peptides (AMPs) are key components of innate immunity across all domains of life. Natural and synthetic AMPs are receiving renewed attention in efforts to combat the antimicrobial resistance (AMR) crisis and the loss of antibiotic efficacy. The gram-negative pathogen Pseudomonas aeruginosa is one of the most concerning infecting bacteria in AMR, particularly in people with cystic fibrosis (CF) where respiratory infections are difficult to eradicate and associated with increased morbidity and mortality. Cationic AMPs exploit the negatively charged lipopolysaccharides (LPS) on P. aeruginosa to bind and disrupt bacterial membrane(s), causing lethal damage. P. aeruginosa modifies its LPS to evade AMP killing. Free-LPS is also a component of CF sputum and feeds pro-inflammatory cycles. Glatiramer acetate (GA) is a random peptide co-polymer—of glycine, lysine, alanine, tyrosine—used as a drug in treatment of multiple sclerosis (MS); we have previously shown GA to be an AMP which synergises with tobramycin against CF P. aeruginosa, functioning via bacterial membrane disruption. Here, we demonstrate GA’s direct binding and sequestration/neutralisation of P. aeruginosa LPS, in keeping with GA’s ability to disrupt the outer membrane. At CF-relevant LPS concentrations, however, membrane disruption by GA was not strongly inhibited. Furthermore, exposure to GA did not result in increased Lipid A modification of LPS or in increased gene expression of systems involved in AMP sensing and LPS modification. Therefore, despite the electrostatic targeting of LPS by GA as part of its activity, P. aeruginosa does not demonstrate LPS modification in its defence.
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Journal articleCuthbertson L, Löber U, Ish-Horowicz JS, et al., 2024,
Genomic attributes of airway commensal bacteria and mucosa
, Communications Biology, Vol: 7, ISSN: 2399-3642Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.
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Journal articleWoubshete M, Cioccolo S, Byrne B, 2024,
Advances in membrane mimetic systems for manipulation and analysis of membrane proteins; detergents, polymers, lipids and scaffolds
, ChemPlusChem, ISSN: 2192-6506Extracting membrane proteins from the hydrophobic environment of the biological membrane, in a physiologically relevant and stable state, suitable for downstream analysis remains a challenge. The traditional route to membrane protein extraction has been to use detergents and the last 15 years or so have seen a veritable explosion in the development of novel detergents with improved properties, making them more suitable for individual proteins and specific applications. There have also been significant advances in the development of encapsulation of membrane proteins in lipid based nanodiscs, either directly from the native membrane using polymers allowing effective capture of the protein and protein-associated membrane lipids, or via reconstitution of detergent extracted and purified protein into nanodiscs of defined lipid composition. All of these advances have been successfully applied to the study of membrane proteins via a range of techniques and there have been some spectacular membrane protein structures solved. In addition, the first detailed structural and biophysical analyses of membrane proteins retained within a biological membrane have been reported. Here we summarise and review the recent advances with respect to these new agents and systems for membrane protein extraction, reconstitution and analysis.
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Journal articleGuder F, Coatsworth P, Bozkurt O, et al., 2024,
Time-resolved chemical monitoring of whole plant roots with printed electrochemical sensors and machine learning
, Science Advances, Vol: 10, ISSN: 2375-2548Traditional single-point measurements fail to capture dynamic chemical responses of plants, which are complex, nonequilibrium biological systems. We report TETRIS (time-resolved electrochemical technology for plant root environment in situ chemical sensing), a real-time chemical phenotyping system for continuously monitoring chemical signals in the often-neglected plant root environment. TETRIS consisted of low-cost, highly scalable screen-printed electrochemical sensors for monitoring concentrations of salt, pH, and H2O2 in the root environment of whole plants, where multiplexing allowed for parallel sensing operation. TETRIS was used to measure ion uptake in tomato, kale, and rice and detected differences between nutrient and heavy metal ion uptake. Modulation of ion uptake with ion channel blocker LaCl3 was monitored by TETRIS and machine learning used to predict ion uptake. TETRIS has the potential to overcome the urgent “bottleneck” in high-throughput screening in producing high-yielding plant varieties with improved resistance against stress.
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Journal articleMayer F, Prado-Roller A, Mautner A, et al., 2024,
Retain strength, gain ductility: tough and transparent nanopapers by mercerisation
, Cellulose, Vol: 31, Pages: 1533-1544, ISSN: 0969-0239Nanocellulose papers offer high tensile strength and modulus but suffer from drawbacks such as their brittle nature. We show that mercerisation of cellulose nanopapers in strong alkaline media for 2 min to 24 h results in the (partial) transformation of native cellulose I into the more ductile cellulose II allomorph. The strain to failure of mercerised nanopapers tripled compared to the original nanopapers while retaining their tensile strength in excess of 100 MPa at the expense of a slight drop in modulus resulting in a significant increase in toughness (total work of fracture). An additional advantage of mercerisation is a reduction in porosity of the nanopapers and increased transparency.
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Journal articleVerster R, Ghosh PN, Sewell TR, et al., 2024,
Environment predicts Batrachochytrium dendrobatidis lineage distribution and zones of recombination in South Africa
, Ecology and Evolution, Vol: 14, ISSN: 2045-7758The amphibian-infecting chytrid fungus, Batrachochytrium dendrobatidis (Bd), is widespread throughout Africa and is linked to declines of populations and species across the continent. While it is well established that the lineage of Bd encodes traits which determine disease severity, knowledge around how lineages are distributed according to environmental envelope is unclear. We here studied the distribution of Bd in South Africa based on the two lineages found, BdGPL and BdCAPE, in terms of their genome and environmental envelope statistically associated with their distribution. We used Bd surveillance data from published studies, as well as data collected during fieldwork from across South Africa, Lesotho, and eSwatini with samples collected along a transect spanning most of South Africa from Lesotho to the west coast. We utilized lineage-typing qPCR to resolve the spatial distribution of BdGPL and BdCAPE across South Africa and used the resulting surveillance data to create a predictive ecological niche model for Bd lineages in South Africa. Phylogenomic analyses were performed on isolates sourced from across the transect. We show that BdGPL demonstrates a strong isolation by distance suggestive of stepping-stone dispersal, while BdCAPE showed two distinct clusters within their genomic structure that appear geographically and temporally clustered, indicating two separate invasions. Our predictive niche model revealed that the two lineages tended to occur in different ecotypes; BdGPL was associated with lower altitude, arid regions while BdCAPE occurred across cooler, higher altitude environs. Niche predictions identified a zone of lineage contact, where genomics identified inter-lineage recombinants. We argue that this zone of recombination should be prioritized for disease surveillance as it is a potential hotspot for the evolution of variants of amphibian chytrid with novel traits that may be epidemiologically relevant.
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