Biology subjects

Griffiths, D.

Publications and source records attributed to Griffiths, D..

5 recordsLinked to original sources

bioRxiv2026

An Automated HDX-MS Platform for in situ characterisation of Membrane Proteins

The structural study of membrane proteins has traditionally relied on detergent-based extraction from cellular membranes. Although native-like reconstitution approaches have advanced, fully understanding membrane protein dynamics requires examining them within their native membrane environment. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful method for probing structural dynamics in reconstituted systems, but the presence of the lipid bilayer introduces considerable complexity, limiting broader adoption under physiological conditions. Here, we present the first fully automated HDX-MS platform incorporating a two-stage delipidation workflow. We applied this approach to monitor the dynamics of the ABC transporter MsbA in isolated inner membrane vesicles (IIMVs) from Escherichia coli through its ATPase cycle. IIMVs revealed distinct dynamic features within the nucleotide binding domains and substrate binding cavity, highlighting physiologically relevant motions not observed with detergent solubilised MsbA. This platform significantly advances HDX-MS and underscores the importance of studying membrane proteins in native lipid environments.

biochemistry↗

bioRxiv2019

No evidence for motion dazzle in an evolutionary citizen science game

The motion dazzle hypothesis posits that high contrast geometric patterns can cause difficulties in tracking a moving target, and has been argued to explain the patterning of animals such as zebras. Research to date has only tested a small number of patterns, offering equivocal support for the hypothesis. Here, we take a genetic programming approach to allow patterns to evolve based on their fitness (time taken to capture) and thus find the optimal strategy for providing protection when moving. Our Dazzle Bug citizen science game tested over 1.5 million targets in a touch screen game at a popular visitor attraction. Surprisingly, we found that targets lost pattern elements during evolution and became closely background matching. Modelling results suggested that targets with lower motion energy were harder to catch. Our results indicate that low contrast, featureless targets offer the greatest protection against capture when in motion, challenging the motion dazzle hypothesis.

evolutionary biology↗

bioRxiv2019

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide a more reliable assessment of susceptibility than traditional methods, we predicted resistance from WGS for 976 E. coli bloodstream infection isolates from Oxfordshire, UK, comparing against phenotypes from the BD Phoenix (calibrated against EUCAST guidelines). 339/976 (35%) isolates were amoxicillin-clavulanate resistant. Predictions based solely on beta-lactamase presence/absence performed poorly (sensitivity 23% (78/339)) but improved when genetic features associated with penicillinase hyper-production (e.g. promoter mutations, copy number estimates) were considered (sensitivity 82% (277/339); p<0.0001). Most discrepancies occurred in isolates with peri-breakpoint MICs. We investigated two potential causes; the phenotypic reference and the binary resistant/susceptible classification. We performed reference standard, replicated phenotyping in a random stratified subsample of 261/976 (27%) isolates using agar dilution, following both EUCAST and CLSI guidelines, which use different clavulanate concentrations. As well as disagreeing with each other, neither agar dilution phenotype aligned perfectly with genetic features. A random-effects model investigating associations between genetic features and MICs showed that some genetic features had small, variable and additive effects, resulting in variable resistance classification. Using model fixed-effects to predict MICs for the non-agar dilution isolates, predicted MICs were in essential agreement ({+/-}1 doubling dilution) with observed (BD Phoenix) MICs for 691/715 (97%) isolates. This suggests amoxicillin-clavulanate resistance in E. coli is quantitative, rather than qualitative, explaining the poorly reproducible binary (resistant/susceptible) phenotypes and suboptimal concordance between different phenotypic methods and with WGS-based predictions.

microbiology↗

bioRxiv2018

Generalisation behaviour of predators toward warning signals displayed by harmful prey: answers from a video-game played by humans.

The persistence of several warning signals in sympatry is a puzzling evolutionary question because selection favours convergence of colour patterns among toxic species. Such convergence is shaped by predators reaction to similar but not identical stimulus, i.e. generalisation behaviour. However, studying generalisation behaviour in complex natural communities of predators is challenging, and is thus generally limited to simple variations of prey colour patterns. Here, we used humans as surrogate predators to investigate generalisation behaviours on two prey communities with different level of warning signals complexity. Humans generalisation capacities were estimated using a computer game simulating a simple (4 morphs) and a complex (10 morphs) community of defended (associated with a penalty) and palatable butterflies. Colour patterns used in the game are actually observed in natural populations of the defended butterflies H. numata, and generalisation behaviour of natural predators communities on these colour patterns have previously been investigated in the wild, allowing direct comparison with human behaviour. We investigated human predation behaviour by recording attack rates on the different defended and palatable colour patterns, as well as player survival time (i.e. score). Phenotypic similarity among the different colour patterns was precisely quantified using a custom algorithm accounting for both colour and pattern variations (CPM method). By analysing attack behaviours of 491 game players, we found that learning was more efficient in the simple prey community. Additionally, profitable prey gained protection from sharing key visual features with unprofitable prey in both communities while learning, in accordance with natural predator behaviours. Moreover, other behaviours observed in natural predators, such as colour neophobia, were detected in humans and shaped morph vulnerability during the game. Similarities between our results in humans and the reaction of natural predator communities to the same colour patterns validate our video-game as a useful proxy to study predator behaviour. This experimental set-up can thus be compared to natural systems, enabling further investigations of generalisation on mimicry evolution.

evolutionary biology↗

bioRxiv2017

Sonic Kayaks: Environmental monitoring and experimental music by citizens

The Sonic Kayak is a musical instrument with which to investigate nature, developed during open hacklab events. Kayaks rigged with underwater environmental sensors allow paddlers to hear real-time water temperature sonifications and underwater sounds, generating live music from the marine world. Sensor data is also logged every second with GPS, time and date, allowing fine scale mapping of water temperatures and underwater noise that was previously unattainable using standard research equipment. The system provides the paddler with an extra dimension of senses with which to explore the underwater climate, while enabling citizens to gather data for scientific research. The system can be used as a citizen-science data-collection device, research equipment for professional scientists, or a sound-art installation in its own right, and has been implemented in a public setting at the British Science Festival 2016, demonstrating the considerable advantages of adopting transdisciplinary approaches during project development. Here we present instructions for building the open-hardware and open-source software, tests of the sensors used, and preliminary data demonstrating applications for the Sonic Kayak in marine climate and noise-pollution research.

ecology↗