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Biology subjects

Galloway, J.

Publications and source records attributed to Galloway, J..

8 recordsLinked to original sources

BehaveAI: a framework for rapidly detecting and classifying objects and behaviour from motion

Here we introduce BehaveAI, a biologically inspired video analysis framework that integrates static and motion information through a novel colour-from-motion encoding strategy. This method translates object movement - direction, speed, and acceleration - into colour gradients, enabling both human annotators and pre-trained convolutional neural networks (CNNs) to infer motion patterns while retaining high-resolution spatial detail. Using a range of case studies, we demonstrate how the increased salience of motion information allows for the robust detection of objects that are challenging or impossible to identify reliably from static frames alone, particularly in complex natural scenes. We further demonstrate the reliable classification of different behaviours in animals and single-celled organisms. Additionally, the framework supports flexible hierarchical model structures that can separate the tasks of detection and classification for optimal efficiency, and provide individual tracking data that specifies what is present where and what it is doing in each frame. The framework makes use of the latest deep learning architecture (YOLO), combined with a semi-supervised annotation workflow. Together with salient motion information, these features can dramatically reduce the effort required for dataset annotation such that reliable models can often be made within an hour. Moreover, smaller annotation datasets mean that model training can be achieved on conventional computers without dedicated hardware, thereby improving accessibility. The motion encoding approach is also computationally lightweight, and can run in real-time on low-end edge devices such as a Raspberry Pi. We release the framework as a free, open source, and user-friendly package.

ecology↗

Inference of germinal center evolutionary dynamics via simulation-based deep learning

B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (GCs) from which mature B cells arise. It is known that B cells with higher affinity for their cognate antigen (Ag) will, on average, tend to have more offspring. However, the exact form of this relationship between affinity and fecundity, which we call the "affinity-fitness response function", is not known. Here we use deep learning and simulation-based inference to learn this function from a unique experiment that replays a particular combination of GC conditions many times. All code is freely available at https://github.com/matsengrp/gcdyn, while datasets and inference results can be found at https://doi.org/10.5281/zenodo.15022130.

evolutionary biology↗

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

ABSTRACTHuman influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.

microbiology↗

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.

immunology↗

Epitope profiling reveals binding signatures of SARS-CoV-2 immune response and cross-reactivity with endemic HCoVs

A major goal of current SARS-CoV-2 vaccine efforts is to elicit antibody responses that confer protection. Mapping the epitope targets of the SARS-CoV-2 antibody response is critical for innovative vaccine design, diagnostics, and development of therapeutics. Here, we developed a phage display library to map antibody binding sites at high resolution within the complete viral proteomes of all human-infecting coronaviruses in patients with mild or moderate/severe COVID-19. The dominant immune responses to SARS-CoV-2 were targeted to regions spanning the Spike protein, Nucleocapsid, and ORF1ab. Some epitopes were identified in the majority of samples while others were rare, and we found variation in the number of epitopes targeted by different individuals. We also identified a set of cross-reactive sequences that were bound by antibodies in SARS-CoV-2 unexposed individuals. Finally, we uncovered a subset of enriched epitopes from commonly circulating human coronaviruses with significant homology to highly reactive SARS-CoV-2 sequences.

immunology↗

The role of conidia in the dispersal of Ascochyta rabiei

Ascochyta rabiei asexual spores (conidia) were assumed to spread over short distances ([~]10 m) in a combination of rain and strong wind. The potential distance of conidial spread was investigated in three rainfall and three sprinkler irrigation events. Chickpea trap plants were distributed at the distances of 0, 10, 25, 50 and 75 m from infected chickpea plots before scheduled irrigation and forecast rainfall events. Trap plants were transferred to a controlled temperature room (20 {degrees}C) for 48 h (100% humidity) after being exposed in the field for 2-6 days for rainfall events, and for one day for irrigation events. After a 48 h incubation period, trap plants were transferred to a glasshouse (20 {degrees}C) to allow lesion development. Lesions on all plant parts were counted after two weeks, which gave an estimate of the number of conidia released and the distance travelled. Trap plants at all distances were infected in all sprinkler irrigation and rainfall events. The highest number of lesions on trap plants were recorded closest to the infected plots - the numbers decreased as the distance from the infected plots increased. There was a positive relationship between the amount of rainfall and the number of lesions recorded. A generalised additive model was developed that efficiently described spatial patterns of conidial spread. With further development, the model can be used to predict the spread of A. rabiei. This is the first systematic study to show that conidia distribute A. rabiei over longer distances than previously reported.

plant biology↗

A few stickleback suffice for the transport of alleles to new lakes

Threespine stickleback populations provide a striking example of local adaptation to divergent habitats in populations that are connected by recurrent gene flow. These small fish occur in marine and freshwater habitats throughout the Northern Hemisphere, and in numerous cases the smaller freshwater populations have been established \"de novo\" from marine colonists. Independently evolved freshwater populations show similar phenotypes that have been shown to derive largely from the same standing genetic variants. Geographic isolation prevents direct migration between the freshwater populations, strongly suggesting that these shared locally adaptive alleles are transported through the marine population. However it is still largely unknown how gene flow, recombination, and selection jointly impact the standing variation that might fuel this adaptation. Here we use individual-based, spatially explicit simulations to determine the levels of gene flow that best match observed patterns of allele sharing among habitats in stickleback. We aim to better understand how gene flow and local adaptation in large metapopulations determine the speed of adaptation and re-use of standing genetic variation. In our simulations we find that repeated adaptation uses a shared set of alleles that are maintained at low frequency by migration-selection balance in oceanic populations. This process occurs over a realistic range of intermediate levels of gene flow that match previous empirical population genomic studies in stickleback. Examining these simulations more deeply reveals how lower levels of gene flow leads to slow, independent adaptation to different habitats, whereas higher levels gene flow leads to significant mutation load - but an increased probability of successful population genomic scans for locally adapted alleles. Surprisingly, we find that the genealogical origins of most freshwater adapted alleles can be traced back to the original generation of marine individuals that colonized the lakes, as opposed to subsequent migrants. These simulations provide deeper context for existing studies of stickleback evolutionary genomics, and guidance for future empirical studies in this model. More broadly, our results support existing theory of local adaptation but extend it by more completely documenting the genealogical history of adaptive alleles in a metapopulation.

evolutionary biology↗

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher et al., 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using \"recapitation\"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a populations genealogy that can be analyzed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modeling and exploration of evolutionary processes.

evolutionary biology↗