Biology subjects

Cole, G.

Publications and source records attributed to Cole, G..

3 recordsLinked to original sources

bioRxiv2025

Animal tracking with particle algorithms for conservation

The movements of aquatic animals affect their exposure to threats and the efficacy of conservation measures, such as Marine Protected Areas (MPAs). However, many species movements remain poorly understood and difficult to reconstruct from available datasets, hampering conservation efforts. This is especially the case for species that rarely surface, for which data are often limited to observations from acoustic telemetry (detections) and ancillary sensors, such as archival tags. Here, we pioneer the use of state-of-the-art particle algorithms to model animal movement, integrate datasets and assess MPA design, using a case study of the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. Our algorithms led to 5-fold improvements in maps of space use and 30-fold improvements in residency estimates (lower mean error) compared to prevailing heuristic methods. By formally integrating tracking datasets, we were uniquely able to examine movements beyond receivers into fished zones, MPA-scale residency and specific habitats beyond protected areas that may warrant protection. This work showcases a probabilistically sound modelling framework that is sufficiently fast, flexible and accessible to meet the demands of modern animal-tracking datasets in acoustic telemetry systems. This represents a marked advance for analyses of animal movements and MPA efficacy worldwide.

ecology↗

bioRxiv2024

Analysis of protein levels and solubility in distinct brain regions reveals several elements of the protein homeostasis network that are impacted by aging

The onset of protein conformation diseases is inextricably linked to aging. During aging, cellular protein quality control declines which results in diminished protein homeostasis (proteostasis). In model organisms, such as C. elegans and killifish, proteostatic decline with age has been linked to the onset of aggregation of proteins in wild-type animals, observed through detergent-insoluble fractionation. Analysis of studies applying detergent-insoluble fractionation in mice revealed that the composition of detergent-insoluble proteins changes with age. However, these individual fractionation studies have generally been limited to small numbers of mice. Herein, we expand on our previous analysis by extending the experiments to a larger cohort of mice and to two brain regions implicated in neurodegenerative diseases, the cortex and hippocampus. These experiments unveil insights into alterations in the abundance and solubility of proteins involved in protein quality control and in inflammation. For example, ribosomal proteins and many chaperone proteins are downregulated with age. Consistent enrichment of subunits of the extracellular C1q complex was also observed in both brain regions alongside an increase in immunoglobulin signal indicating that markers of increased inflammation may also become insoluble during aging. More generally, insoluble proteins share features observed in datasets of impaired protein degradation indicating that the loss of activity of cellular protein degradation machinery may contribute to the specific aggregation of these proteins.

cell biology↗

bioRxiv2022

Shift of the insoluble content of the proteome in aging mouse brain

Aging and protein aggregation diseases are inextricably linked. During aging, cellular response to unfolded proteins are believed to decline which results in diminished protein homeostasis (proteostasis). Indeed, in model organisms, such as C. elegans, proteostatic decline with age has even been linked to the onset of aggregation of proteins in wild-type animals. However, this correlation has not been extensively characterized in aging mammals. To reveal the insoluble portion of the proteome, we analyzed the detergent-insoluble fraction of mouse brain tissues after high-speed centrifugation by quantitative mass spectrometry. We identified a cohort of 171 proteins enriched in the pellet fraction of older mice including the alpha crystallin small heat shock protein. We then performed a meta-analysis to compare features among distinct groups of detergent-insoluble proteins reported in the literature. Surprisingly, our analysis revealed that features associated with proteins found in the pellet fraction differ depending on the ages of the mice. In general, insoluble proteins from young models (<15 weeks) were more likely to be RNA-binding, more disordered and more likely to be found in membraneless organelles. These traits become less prominent with age within the combined dataset, as proteins with more structure enter the pellet fraction. This analysis suggests that age-related changes to proteome organization lead a specific group of proteins to enter the pellet fraction as a result of loss of proteostasis.

cell biology↗