Biology subjects

Young, A. M.

Publications and source records attributed to Young, A. M..

5 recordsLinked to original sources

bioRxiv2025

A Machine Learning Approach Reveals CRISPR-Cas I-F as a Genomic Marker of Antibiotic Susceptibility in Uropathogenic E. coli

BackgroundAntimicrobial resistance (AMR) in Escherichia coli is a critical global health challenge, particularly in urinary tract infections, where first-line treatments are increasingly compromised. While horizontal gene transfer (HGT) via mobile genetic elements is a major driver of AMR, the genomic factors that may constrain resistance gene acquisition remain underexplored. CRISPR-Cas systems, which provide adaptive immunity against foreign DNA, could influence AMR dynamics, but their role in E. coli remains incompletely understood. MethodsWe conducted a comprehensive whole-genome analysis of uropathogenic E. coli isolates, including a newly sequenced collection from Australian clinical samples and an independent, globally sourced validation cohort. Antimicrobial susceptibility profiles were integrated with CRISPR-Cas subtype classification, resistance gene burden, and mobile element content. Elastic net regression, adaptive lasso, and tree-based machine learning models were used to identify genomic predictors of resistance, with performance validated across both datasets. ResultsCRISPR-Cas subtype I-F was consistently associated with susceptibility to antibiotics commonly acquired through HGT, including trimethoprim and ampicillin, and linked to lower ARG and MGE burden. In contrast, Type I-E arrays, especially when co-occurring with orphan I-F arrays, were associated with increased resistance. These associations remained robust after adjusting for phylogroup, plasmid content, and genomic background, and were validated across datasets. ConclusionsSubtype-specific CRISPR-Cas systems shape antibiotic resistance profiles in E. coli, with Type I-F functioning as a potential genomic barrier to ARG acquisition. These findings highlight CRISPR array typing as a novel biomarker for AMR risk prediction and surveillance, and suggest new opportunities for leveraging CRISPR-based mechanisms to limit resistance propagation in clinical contexts.

genomics↗

bioRxiv2021

Coevolution of brain size and longevity in parrots

Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the Cognitive Buffer Hypothesis, which proposes that increased cognitive abilities enable longer life spans, and the Expensive Brain Hypothesis, which holds that increases in life span are caused by prolonged developmental time of, and increased parental investment in, large brained offspring. We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using a principled Bayesian approach that addresses data uncertainty and imputation of missing values, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction. Our results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans.

evolutionary biology↗

bioRxiv2020

Distracting stimuli evoke ventral tegmental area responses in rats during ongoing saccharin consumption

Disruptions in attention, salience and increased distractibility are implicated in multiple psychiatric conditions. The ventral tegmental area (VTA) is a potential site for converging information about external stimuli and internal states to be integrated and guide adaptive behaviours. Given the dual role of dopamine signals in both driving ongoing behaviours (e.g. feeding) and monitoring salient environmental stimuli, understanding the interaction between these functions is crucial. Here we investigate VTA neuronal activity during distraction from ongoing feeding. We developed a task to assess distraction exploiting self-paced licking in rats. Rats trained to lick for saccharin were given a distraction test, in which three consecutive licks within 1 second triggered a random distractor (e.g. light and tone stimulus). On each trial they were quantified as distracted or not based on the length of their pauses in licking behaviour. We expressed GCaMP6s in VTA neurons and used fibre photometry to record calcium fluctuations during this task as a proxy for neuronal activity. Distractor stimuli caused rats to interrupt their consumption of saccharin, a behavioural effect which quickly habituated with repeat testing. VTA neural activity showed consistent increases to distractor presentations and, furthermore, these responses were greater on distracted trials compared to non-distracted trials. Interestingly, neural responses show a slower habituation than behaviour with consistent VTA responses seen to distractors even after they are no longer distracting. These data highlight the complex role of the VTA in maintaining ongoing appetitive and consummatory behaviours while also monitoring the environment for salient stimuli.

neuroscience↗

bioRxiv2020

BAF facilitates interphase nuclear envelope repair through recruitment of nuclear transmembrane proteins.

Nuclear membrane rupture during interphase occurs in a variety of cell contexts, both healthy and pathological. Membrane ruptures can be rapidly repaired, but these mechanisms are still unclear. Here we show BAF, a nuclear envelope protein that shapes chromatin and recruits membrane proteins in mitosis, also facilitates nuclear membrane repair in interphase, in part through recruitment of the nuclear membrane proteins emerin and LEMD2 to rupture sites. Characterization of GFP-BAF accumulation at nuclear membrane rupture sites confirmed BAF is a fast, accurate, and persistent mark of nucleus rupture whose kinetics are partially dictated by membrane resealing. BAF depletion significantly delayed nuclear membrane repair, with a larger effect on longer ruptures. This phenotype could be rescued by GFP-BAF, but not by a BAF mutant lacking the LEM-protein binding domain. Depletion of the BAF interactors LEMD2 or emerin, and to a lesser extent lamin A/C, increased the duration of nucleus ruptures, consistent with LEM-protein binding being a key function of BAF during membrane repair. Overall our results suggest a model where BAF is critical for timely repair of large ruptures in the nuclear membrane, potentially by facilitating membrane attachment to the rupture site.

cell biology↗

bioRxiv2018

Polymerization Kinetics Stability, Volumetric Changes, Apatite Precipitation, Strontium Release and Fatigue of Novel Bone Composites for Vertebroplasty

PurposeThe aim was to determine effects of diluent monomer and monocalcium phosphate monohydrate (MCPM) on polymerization kinetics and volumetric stability, apatite precipitation, strontium release and fatigue of novel dual-paste composites for vertebroplasty.\n\nMaterials and methodsPolypropylene (PPGDMA) or triethylene (TEGDMA) glycol dimethacrylates (25 wt%) diluents were combined with urethane dimethacrylate (70 wt%) and hydroxyethyl methacrylate (5 wt%). 70 wt% filler containing glass particles, glass fibers (20 wt%) and polylysine (5 wt%) was added. Benzoyl peroxide and MCPM (10 or 20 wt%) or N-tolyglycine glycidyl methacrylate and tristrontium phosphate (15 wt%) were included to give initiator or activator pastes. Commercial PMMA (Simplex) and bone composite (Cortoss) were used for comparison.\n\nATR-FTIR was used to determine thermal activated polymerization kinetics of initiator pastes at 50-80 {degrees}C. Paste stability, following storage at 4-37 {degrees}C, was assessed visually or through mixed paste polymerization kinetics at 25 {degrees}C. Polymerization shrinkage and heat generation were calculated from final monomer conversions. Subsequent expansion and surface apatite precipitation in simulated body fluid (SBF) were assessed gravimetrically and via SEM. Strontium release into water was assessed using ICP-MS. Biaxial flexural strength (BFS) and fatigue properties were determined at 37 {degrees}C after 4 weeks in SBF.\n\nResultsPolymerization profiles all exhibited an inhibition time before polymerization as predicted by free radical polymerization mechanisms. Initiator paste inhibition times and maximum reaction rates were described well by Arrhenius plots. Plot extrapolation, however, underestimated lower temperature paste stability. Replacement of TEGDMA by PPGDMA, enhanced paste stability, final monomer conversion, water-sorption induced expansion and strontium release but reduced polymerisation shrinkage and heat generation. Increasing MCPM level enhanced volume expansion, surface apatite precipitation and strontium release. Although the experimental composite flexural strengths were lower compared to those of commercially available Simplex, the extrapolated low load fatigue lives of all materials were comparable.\n\nConclusionsIncreased inhibition times at high temperature give longer predicted shelf-life whilst stability of mixed paste inhibition times is important for consistent clinical application. Increased volumetric stability, strontium release and apatite formation should encourage bone integration. Replacing TEGDMA by PPGDMA and increasing MCPM could therefore increase suitability of the above novel bone composites for vertebroplasty. Long fatigue lives of the composites may also ensure long-term durability of the materials.

bioengineering↗