Biology subjects

Evans, I.

Publications and source records attributed to Evans, I..

3 recordsLinked to original sources

bioRxiv2025

Hunger, displacement, or play? Object manipulation behaviour in Asian small-clawed otters (Aonyx cinereus)

Asian small-clawed otters (Aonyx cinereus) engage in intricate activities using their paws for purposes such as food extraction, exploration, and tactile communication within their social group. However, some expressions of these behaviours do not appear to be immediately functional in captive populations. Here, we explore the expression of object manipulation behaviours (OMBs), such as rock manipulation (or juggling); the factors that may be driving their expression; and what OMBs may represent. A troop of six otters was observed at Lincolnshire Wildlife Park (United Kingdom) using camera-traps placed at three key locations in their enclosure: outside of their den, at the main feeding area, and at a rock-garden foraging area. A total of 2895 video clips were analysed using a hierarchical ethogram consisting of the behavioural categories of locomotion, stationary, vocalisation, physical affiliative, sustenance, and OMBs. The most commonly observed behaviours were walking (21.5%), lying (20.8%) and feeding (12.2%). OMBs were observed in 3.9% of total observations. Otters performed OMBs significantly more often outside their den than at the other locations. Grooming was also more frequent at this location. There was a negative association between the expression of OMBs and air temperature. Results suggest that in this otter population, OMBs were more likely an expression of play behaviour, contrasting findings reported elsewhere that rock juggling may be driven by hunger.

animal behavior and cognition↗

bioRxiv2023

Technical and biological sources of unreliability of Infinium type II probes of the Illumina MethylationEPIC BeadChip microarray

The Illumina Methylation array platform has facilitated countless epigenetic studies on DNA methylation (DNAme) in health and disease, yet relatively few studies have so studied its reliability, i.e., the consistency of repeated measures. Here we focus on the reliability of both type I and type II Infinium probes. We propose a method for excluding unreliable probes based on dynamic thresholds for mean intensity (MI) and unreliability, estimated by probe-level simulation of the influence of technical noise on methylation {beta}-values using the background intensities of negative control probes. We validate our method in several datasets, including Illumina MethylationEPIC BeadChip v1.0 data from paired whole blood samples taken six weeks apart. Our analysis revealed that specifically probes with low MI exhibit higher {beta}-value variability between repeated samples. MI was associated with the number of C-bases in the respective probe sequence and correlated negatively with unreliability scores. The unreliability scores were substantiated through validation in a new EPIC v1.0 (blood and cervix) and a publicly available 450k (blood) dataset, as they effectively captured the variability observed in {beta}-values between technical replicates. Finally, despite promising higher robustness, the newer version v2.0 of the MethylationEPIC BeadChip retained a substantial number of probes with poor unreliability scores. To enhance current pre-processing pipelines, we developed an R package to calculate MI and unreliability scores and provide guidance on establishing optimal dynamic score thresholds for a given data set.

genomics↗

bioRxiv2022

Ionic control of porin permeability in bacteria.

Bacterial porins permit permeation of hydrophilic nutrients and antibiotics across the outer membrane but also contribute to proton leak from the periplasmic space, suggesting that their activity might be dynamically regulated. Here we show, in Escherichia coli, that porin permeability is controlled by changes in periplasmic ions, inhibited by periplasmic acidification, thereby limiting proton loss during electron transport chain activity, and enhanced during starvation, promoting nutrient uptake. Growth in glucose increases periplasmic potassium through activating the voltage-gated channel Kch, triggering enhanced porin permeation and membrane action potentials. This metabolic control of porin permeability explains the recognized decrease in antibiotic susceptibility when bacteria are grown in lipid media and the impact of mutations in central metabolism genes on drug resistance, identifying Kch as a therapeutic target to improve bacterial killing by antibiotics. One sentence summaryThe permeability of bacterial porin is dynamically regulated by periplasmic pH and potassium levels, altering antibiotic resistance.

microbiology↗