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antimicrobial resistance clinical microbiology publication research tuberculosis

New preprint: Predicting pyrazinamide resistance by machine learning

Usually, the protein that an antibiotic binds is essential for bacterial survival, which is how the drug has its effect. In this case, relatively few protein mutations arise that confer resistance, they are often subtle in nature and one can try to predict the phenotype of a protein mutation by considering how it affects the […]

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antimicrobial resistance citizen science clinical microbiology publication tuberculosis

New publication: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of M. tuberculosis

In this Microbiology paper we show how a Python package, called the Automated Mycobacterial Detection Growth Algorithm (AMyDGA for short), can be used to independently read a 96-well plate designed for determining the minimum inhibitory concentration of 14 different anti-tubercular drugs. AMyGDA is reproducible and shows promising levels of accuracy. Where it fails, it does in […]

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antimicrobial resistance citizen science clinical microbiology publication tuberculosis

New publication: Assessing Drug Susceptibility in Tuberculosis

A paper was published in the New England Journal of Medicine earlier this week by the CRyPTIC project, of which I am part, with help from the 100,000 genomes project. It demonstrates how whole genome sequencing can be used to accurately predict drug susceptibility for the four first-line anti-tubercular drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) […]

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antimicrobial resistance clinical microbiology publication tuberculosis

New publication: Validating a bespoke 96-well plate for high-throughput drug susceptibility testing of M. tuberculosis

This paper, published in Antimicrobial Agents and Chemotherapy, determines the reproducibility and accuracy of minimum inhibitory concentrations for a panel of 14 different anti-TB compounds using a specifically designed 96-well plate (called UKMYC5) manufactured by Thermo Fisher.

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antimicrobial resistance molecular dynamics publication research

New Publication: Predicting whether mutations confer resistance to an antibiotic

Due to the rise of antibiotic resistance, it is increasingly important that your clinician knows which antibiotics will work (and which will not). Traditionally, this is done in hospital microbiology labs by growing a sample taken from the infection site, and then testing how a range of antibiotics affect its growth, or, ideally, kill it. […]

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publication research

New Publication: Protein crowding affects the organisation of ion channels

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes It is difficult to look at the dynamic spatial organisation of ion channels in cell membranes, but this is something coarse-grained molecular dynamics simulations can offer insights. This work, led by Anna Duncan, shows how altering the lipid composition of […]

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publication research

New Publication: Effect of SAO mutation on Band 3

There is a lovely story behind this paper just published earlier this week in Biochemistry. Reinhart Reithmeier came to visit Mark Sansom in Oxford whilst on sabbatical back in 2002. Now Reinhart, if you don’t know, is a world-expert on Band 3 which is the transmembrane protein in the membrane of red blood cells that […]

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publication research

New Publication: Lipids can form anti-registered phases

When we think of lipids phase separating in a cell membrane we usually think of this process occurring symmetrically, i.e. with like on top of like (this is described as a registered phase). If we consider the simplest case of two lipids, one saturated (A), one unsaturated (B), then if their lengths are sufficiently different […]

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publication research

New Publication: Proteins Alter the Stiffness of Membranes

Although there have been many studies of proteins whose primary function is to ‘sculpt’ the surface of membranes e.g. BAR domains, there have been very few investigations of what effect regular membrane proteins have on the stiffness of membranes. Here we show via very large simulations, using the MARTINI coarse-grained forcefield, that ‘regular’ integral membrane […]

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publication research

New Publication: Membrane Compartmentalization Reduces the Mobility of Lipids.

Lipids are not free to diffuse around the cell membrane. Rather they are constrained not just by all the embedded proteins but also by the cytoskeleton, which, it has been suggested, corral the lipids. In this paper, we show by very large coarse-grained simulations of a realistic model of the plasma membrane how compartmentalisation leads […]