Biology subjects

Wood, C. M.

Publications and source records attributed to Wood, C. M..

8 recordsLinked to original sources

bioRxiv2026

Passive acoustic monitoring of the rare orange-bellied parrot: automated detection using BirdNET-based transfer learning

Efficiently finding rare species is a perennial challenge in conservation science. The orange-bellied parrot Neophema chrysogaster is a rare mobile bird that is difficult to locate using traditional field survey techniques with human observers. We harnessed recent advances in bioacoustic technology to create a survey framework that integrates passive acoustic surveys and semi-automated detection to increase monitoring capacity for the orange-bellied parrot. We developed a custom BirdNET classifier for the orange-bellied parrot and compared efficacy of acoustic and field surveys using an occupancy framework. We deployed autonomous recording units across the orange-bellied parrots breeding range in southwest Tasmania and concurrently undertook between three and six repeated point-count surveys at the same 48 sites using human observers. Our custom BirdNET classifier had high accuracy and discrimination abilities. Validation of model scores across a week (5,712 hours of audio) required 60 hours reviewing time and yielded a 95% confidence of a correct BirdNET prediction at scores over 0.998. Occupancy analysis showed that the detection probability of acoustic surveys (p = 0.80) was more than eleven times greater than field surveys by skilled ecologists familiar with the species (p = 0.07). We provide a template for how to implement monitoring of the orange-bellied parrot and recommendations for how our methods can be improved to optimise the classifier to account for other species and locations.

ecology↗

bioRxiv2026

Overcoming software bottlenecks for scalable passive acoustic monitoring: insights from a global expert assessment

1.Passive acoustic monitoring (PAM) enables non-invasive sampling of wildlife across broad spatial, temporal and taxonomic scales. Its ongoing and widespread use has generated unprecedented volumes of acoustic data, shifting the primary bottleneck from data collection to the storage, processing, integration, and interpretation of PAM outputs. Although many software tools exist to address these challenges, differences in their design, scope, and usability often create fragmented and complex analytical workflows. To identify the key barriers and opportunities shaping the implementation of PAM surveys, we conducted a structured expert solicitation involving 30 international practitioners working across terrestrial and aquatic ecosystems. Experts identified and ranked their most critical pain points in current PAM workflows, spanning data storage, processing, and interpretation. The top challenge identified related to accurate species identification using deep learning and artificial intelligence (AI) models, especially in noisy soundscapes or for underrepresented taxa. Eight additional priority challenges included workflow fragmentation, limited availability of user-friendly analytical and visualisation tools, uneven access to software, manual validation bottlenecks, computational constraints, and difficulties in data handling, standardisation, and sharing. Participants also proposed practical mitigation strategies for these priority challenges, supported by step-by-step guidance to help overcome key barriers. Together, these insights provide a roadmap toward more scalable, open-access, and collaborative software systems, which are increasingly essential to realise the full potential of PAM in global biodiversity monitoring.

ecology↗

bioRxiv2026

A Course-Undergraduate Research Experience (CURE) to explore the effect of structural variants on gene expression in C. elegans balancers

Bioinformatics, a discipline at the crossroads of Biology and Computational Sciences, also referred to as Computational Biology, is nowadays widely spread in research programs. However, implementing any Bioinformatics projects requires the ability to comprehend biological concepts and apply computational approaches, and rare are the undergraduate programs offering such multi-disciplinary training. In addition, understanding the dynamic between Biology research projects and Bioinformatics analyses is challenging with no real-life experience. Course-based undergraduate research experience (CURE) courses are innovative programs that allow more students to acquire research experience and provide the perfect setting to introduce students to applied bioinformatics. As a part of the Bachelor of Health Sciences of the Cumming School of Medicine at the University of Calgary (Canada), a CURE applied bioinformatics was implemented in the Winter of 2023 to 2025. Students investigated the effect of structural variants (SVs, genetic variants larger than 50 bp) on gene expression in the model organism Caenorhabditis elegans (a hermaphrodite 1-mm long roundworm). The students detected and characterized SVs by analyzing genome and transcriptome sequencing data of C. elegans strains called balancers, as they are known to carry large genomic variations balancing regions of the genome by limiting recombination and allowing maintenance of lethal mutations. They used Galaxy, a public web-based supercomputing resource, but also a local High-Performance computing system, and R, to report different effects of SVs on gene expression and splicing. Students research explained the molecular mechanism behind the uncoordinated phenotype caused by the reciprocal translocation eT1(III;V) and uncovered unexpected effects on gene expression on an understudied gene. We evaluated the courses impact on student learning journeys and showed that the CURE favored students understanding of the Bioinformatics field and fostered their research interest. We provide here guidelines to facilitate the CURE implementations to improve access for undergraduate students to bioinformatics research experiences.

bioinformatics↗

bioRxiv2025

The pore-forming protein APOL7C ruptures Leishmania major-containing parasitophorous vacuoles in dendritic cells to promote IL-12 production and the induction of T helper type 1 immunity

Classical dendritic cells (cDCs) are required for the efficient priming of T helper type 1 (Th1) immunity against Leishmania major infections in mice. They do so by producing large quantities of IL-12 in response to L. major infection. IL-12 in turn supports the generation of protective CD4+ Th1 cells. However, the mechanism(s) by which L. major instigates robust IL-12 production by cDCs has not been addressed. Here we show that expression of a pore-forming protein called APOL7C is induced in cDCs by L. major infection. APOL7C is expressed in the cytosol of host cells and, remarkably, upon infection is recruited to L. major parasitophorous vacuoles (PVs) where it induces PV rupture. PV rupture leads to the exposure of L. major-derived pathogen-associated molecular patterns (PAMPs) to cytosolic pattern recognition receptors (PRRs). Cytosolic PRR signaling then drives IL-12 production by cDCs. Consequently, L. major challenge of APOL7C-deficient mice results in reduced numbers of IL-12 producing cDCs as well as a diminished Th1 response. In sum, our data indicate the presence of pore-forming proteins in the cytosol of cDCs that interfere with the intracellular niche of Leishmania to modulate immunity to these parasites.

cell biology↗

bioRxiv2025

A decision matrix to better identify repeatable physiological variation within individuals

The performance of an individual has remained at the heart of evolutionary biology since the time of Darwin. Physiologists are equally drawn to the implications of individual variation for health and sporting endeavours, and specifically, whether or not a physiological trait is repeatable within an individual. Experimental biologists are especially interested in temporally stable physiological traits that are relevant to an individuals lifetime fitness for natural selection to act upon. Experimental noise, however, confounds the measurement of such repeatability, even though validated protocols exist for measuring many meaningful physiological performance traits. Missing is a decision matrix that helps distinguish individual variation from experimental noise. We propose a precision-&-repeatability assessment matrix (PRAM) that integrates established assessments of individual variability and repeatability. This matrix places metrics that are more repeatable and precise in the quadrant closest to the origins of Cartesian coordinates; those farthest away are less acceptable in terms of both repeatability and precision. As a case study, PRAM is applied to whole-organism aerobic and non-aerobic metabolic performance metrics from fish that were measured with the same protocols. The analysis illustrates that aerobic metabolic metrics can be more repeatable and precise than non-aerobic ones. Consequently, PRAM helps physiologists to better understand whether the observed variability is due to non-repeatable metrics or true individual variation.

physiology↗

bioRxiv2023

Subcallosal area 25: its responsivity to the stress hormone cortisol and its opposing effects on appetitive motivation in marmosets

Aberrant activity in caudal subcallosal anterior cingulate cortex (scACC) is implicated in depression and anxiety symptomatology, with its normalisation a putative biomarker of successful treatment response. The function of scACC in emotion processing and mental health is not fully understood despite its known influence on stress-mediated processes through its rich expression of mineralocorticoid and glucocorticoid receptors. Here we examine the causal interaction between area 25 within scACC (scACC-25) and the stress hormone, cortisol, in the context of anhedonia and anxiety-like behaviour. Moreover, the overall role of scACC-25 in hedonic capacity and motivation is investigated under transient pharmacological inactivation and overactivation. The results suggest that a local increase of cortisol in scACC-25 shows a rapid induction of anticipatory anhedonia and increased responsiveness to uncertain threat. Separate inactivation and overactivation of scACC-25 increased and decreased motivation and hedonic capacity, respectively, likely through different underlying mechanisms. Together, these data show that area scACC-25 has a causal role in consummatory and motivational behaviour and produces rapid responses to the stress hormone cortisol, that mediates anhedonia and anxiety-like behaviour.

animal behavior and cognition↗

bioRxiv2023

The pore-forming apolipoprotein APOL7C drives phagosomal rupture and antigen cross-presentation by dendritic cells

Type I conventional dendritic cells (cDC1s) are essential for the generation of protective cytotoxic T lymphocyte (CTL) responses against many types of viruses and tumours. They do so by internalizing antigens from virally infected or tumour cells and presenting them to CD8+ T cells in a process known as cross-presentation (XP). Despite the obvious biological importance of XP, the molecular mechanism(s) driving this process remain unclear. Here, we show that a cDC-specific pore-forming protein called apolipoprotein 7C (APOL7C) is upregulated in response to innate immune stimuli and is recruited to phagosomes. Strikingly, the association of APOL7C with phagosomes leads to phagosomal rupture, which in turn allows for the escape of engulfed protein antigens to the cytosol where they can be processed via the endogenous major histocompatibility complex (MHC) class I antigen processing pathway. We show that APOL7C recruitment to phagosomes is voltage-dependent and occurs in response to NADPH oxidase-induced depolarization of the phagosomal membrane. Our data indicate the presence of dedicated pore-forming apolipoproteins that mediate the delivery of phagocytosed proteins to the cytosol of activated cDC1s to facilitate MHC class I presentation of exogenous antigen and to regulate adaptive immunity.

cell biology↗

bioRxiv2022

DNA metabarcoding reveals the threat of rapidly expanding barred owl populations to native wildlife in western North America

Invasive predators can have detrimental impacts on native species and biological communities through direct consumptive effects and indirect effects on trophic interactions. As an invasive, apex predator achieving high densities, barred owls (Strix varia) may pose a substantial threat to native wildlife in western North American forests. Studies of the trophic ecology of barred owls in their invasive range, however, have involved morphological examinations of prey remains with limited taxonomic resolution. We conducted DNA metabarcoding using intestinal samples collected from barred owls at the leading edge of their range expansion in northeastern California. Using customized primers, we screened the intestinal contents of 124 barred owls and detected a broad diet of 78 unique prey types (48 vertebrates and 30 invertebrates), including many previously undetected prey types. Mammals were the most consumed vertebrate class (frequency of occurrence = 65%), followed by amphibians (32%), birds (22%), and reptiles (19%). Diets differed regionally but were similar among ages and sexes and exhibited limited variation in response to local environmental conditions. Our work highlights the generalist predatory strategy of invasive barred owls, indicates that they will not serve as ecological replacements for the congeneric spotted owls (S. occidentalis) they displace, and identifies numerous native species potentially threatened by their range expansion. Expanding currently limited barred owl removals could benefit native species and wildlife communities in western North America. More broadly, DNA metabarcoding provides a powerful tool for conducting detailed assessments of species consumed by invasive predators, potentially incentivizing conservation actions and improving outcomes.

ecology↗