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Antibiotic efficacy testing in an ex vivo model of Pseudomonas aeruginosa and Staphylococcus aureus biofilms in the Cystic Fibrosis lung

JoVeHarrington Niamh, Sweeney Esther, Alav Ilyas, Allen Freya, Moat John and Harrison Freya

The effective prescription of antibiotics for the bacterial biofilms present within the lungs of individuals with cystic fibrosis (CF) is limited by a poor correlation between antibiotic susceptibility testing (AST) results using standard diagnostic methods and clinical outcomes after antibiotic treatment. Attempts to improve AST by the use of off-the-shelf biofilm growth platforms show little improvement in results. The limited ability of in vitro biofilm systems to mimic the physicochemical environment of the CF lung and, therefore bacterial physiology and biofilm architecture, also acts as a brake on the discovery of novel therapies for CF infection. Here, we present a protocol to perform AST of CF pathogens grown as mature, in vivo-like biofilms in an ex vivo CF lung model comprised of pig bronchiolar tissue and synthetic CF sputum (ex vivo pig lung, EVPL).

Journal of Visualized Experiments. January 2021

Fri 26 Feb 2021, 08:49

Richard Napier publications

RSC Chem Bio jan21Hyaluronan (HA)-inspired glycopolymers as molecular tools for studying HA functions

Dominic W. P. Collis, Gokhan Yilmaz, Yichen Yuan, Alessandra Monaco, Guy Ochbaum, Yejiao Shi, Clare O’Malley, Veselina Uzunova, Richard Napier, Ronit Bitton, C. Remzi Becer, Helena S. Azevedo

Whilst the physicochemical and biological properties of Hyaluronic acid have been widely studied for decades, the exact mechanisms by which HA exerts its multiple functions are not completely understood. Glycopolymers offer a simple and precise synthetic platform for the preparation of glycan analogues, being an alternative to the demanding synthetic chemical glycosylation. These studies revealed potential structure-binding relationships between HA monosaccharides and HA receptors and novel HA binders, such as Dectin-1 and DEC-205 lectins. The inhibitory effect of HA glycopolymers on hyaluronidase (HAase) activity was also investigated suggesting GlcNAc- and GlcA-based glycopolymers as potential HAase inhibitors.

RSC Chemical Biology January 21

New Phytologist jan21 smNew fluorescent auxin probes visualize tissue-specific and subcellular distributions of auxin in Arabidopsis

Staniszewska, Sophie, Hill, Edward M., Grant, Richard, Grove, Peter, Porter, Jarina, Shiri, Tinevimbo, Tulip, Sue, Whitehurst, Jane, Wright, Claire, Datta, Barbora Pařízková, Asta Žukauskaitė, Thomas Vain, Peter Grones, Sara Raggi, Martin F. Kubeš, Martin Kieffer, Siamsa M. Doyle, Miroslav Strnad, Stefan Kepinski, Richard Napier, Karel Doležal, Stéphanie Robert and Ondřej Novák

In a world that will rely increasingly on efficient plant growth for sufficient food, it is important to learn about natural mechanisms of phytohormone action. In this work, the introduction of a fluorophore to an auxin molecule represents a sensitive and non‐invasive method to directly visualize auxin localization with high spatiotemporal resolution. Our work provides powerful tools to visualize auxin distribution within different plant tissues at cellular or subcellular levels and in response to internal and environmental stimuli during plant development.

Wed 24 Feb 2021, 08:55

Structural basis of trehalose recognition by the mycobacterial LpqY-SugABC transporter

J.Biological Chem jan1`Christopher M Furze, Ignacio Delso, Enriqueta Casal, Jesus Angulo, Alexander D Cameron, Elizabeth Fullam

The Mycobacterium tuberculosis ( Mtb) LpqY-SugABC ATP-binding cassette transporter is a recycling system that imports trehalose released during remodelling of the Mtb cell-envelope. As this process is essential for the virulence of the Mtb pathogen it may represent an important target for tuberculosis drug and diagnostic development, but the transporter specificity and molecular determinants of substrate recognition are unknown. To address this, we have determined the structural and biochemical basis of how mycobacteria transport trehalose using a combination of crystallography, STD NMR, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays and the synthesis of trehalose analogues. Our findings provide critical insights into how the essential Mtb LpqY-SugABC transporter reuses trehalose and modified analogues, and specifies a framework that can be exploited for the design of new anti-tubercular agents and/or diagnostic tools.

Journal of Biological Chemistry. January 2021

Sun 21 Feb 2021, 16:21

Matt Keeling publications

PLoS Computational BiologyQuantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo

Crump, Ronald E., Huang, Ching-I, Knock, Edward, Spencer, Simon E. F., Brown, Paul E., Mwamba Miaka, Erick, Shampa, Chansy, Keeling, Matthew James and Rock, Kat S

Gambiense human African trypanosomiasis (gHAT) is a virulent disease declining in burden but still endemic in West and Central Africa. In this study we focus on the Democratic Republic of Congo (DRC), which accounted for 84% of the global case burden in 2016, to explore changes in transmission across the country and elucidate factors which may have contributed to the persistence of disease or success of interventions in different regions.. Previously, it was not clear whether a fall in active case finding in the period contributed to the declining case numbers. The modelling here accounts for variable screening and suggests that underlying transmission has also reduced greatly-on average 96% in former Equateur, 93% in former Bas Congo and 89% in former Bandundu-Equateur and Bandundu having had the highest case burdens in 2000. This analysis also sets out a framework to enable future predictions for the country.

PLoS Computational Biology. January 2021

The Patient PCR jan21Developing a framework for public involvement in mathematical and economic modelling : bringing new dynamism to vaccination policy recommendations

Staniszewska, Sophie, Hill, Edward M., Grant, Richard, Grove, Peter, Porter, Jarina, Shiri, Tinevimbo, Tulip, Sue, Whitehurst, Jane, Wright, Claire, Datta, Samik, Petrou, Stavros and Keeling, Matthew James

The Mathematical and Economic Modelling for Vaccination and Immunisation Evaluation (MEMVIE) programme aimed to explore, capture and support the potential contribution of the public to mathematical and economic modelling, in order to identify the values that underpin public involvement (PI) in modelling and co-produce a framework that identifies the nature and type of PI in modelling and supports its implementation. PI in modelling is in its infancy. The MEMVIE Framework is the first attempt to identify potential points of collaborative public contribution to modelling, but it requires further evaluation and refinement that we are undertaking in a subsequent study.

The Patient -Patient Centred Outcome Research. January 2021

Fri 19 Feb 2021, 09:17

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Nucleic Acids ResearchL Garczarek, U Guyet, H Doré, GK Farrant, M Hoebeke, L Brillet-Guéguen, A Bisch, M Ferrieux, J Siltanen, E Corre, G Le Corguillé, M Ratin, FD Pitt, M Ostrowski, l Conan, A Siegel, K Labadie, J-M Aury, P Wincker, DJ Scanlan, F Partensky

Cyanorak v2.1 is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.

Nucleic Acids Research. January 2021

Wed 17 Feb 2021, 08:47 | Tags: Environmental Bioscience

The white-rot fungus, Phanerochaete chrysosporium, under combinatorial stress produces variable oil profiles following analysis of secondary metabolites

J.Applied Microbiology jan21Whiteford, Rory; Nurika, Irnia; Schiller, Tara; Barker, Guy

The effects of combinatorial stress on lipid production in Phanerochaete chrysosporium remains understudied. This species of white‐rot fungi was cultivated on solid‐state media whilst under variable levels of known abiotic and biotic stressors to establish the effect upon fungal oil profiles. Interspecies competition produced the most notable impact on lipid production for solid‐state media cultivated fungi whilst the addition of nitrogen supplementation presented growth and lipid accumulation to be uncorrelated. Combinatorial stress therefore influences the yield of overall lipid production as well as the number of intermediate fatty acids produced, deriving similar oil profiles to the composition of vegetable and fish oils.

Journal of Applied Microbiology. January 2021

Mon 15 Feb 2021, 08:10

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