Biology subjects

Carroll, S.

Publications and source records attributed to Carroll, S..

9 recordsLinked to original sources

bioRxiv2026

The novel viper FETUA-3 protein evolved a unique mode of inhibiting snake venom metalloproteinases

Molecular innovation and coevolution play major roles in the evolution of biological diversity, yet we have relatively few instances in which we understand the biological and molecular bases of coevolution. Rattlesnakes and other vipers have evolved resistance to their own novel venom metalloproteinase (MP) toxins through the invention and coevolution of serum-borne inhibitors (FETUAs) derived from the ancestral, non-inhibitory, serum glycoprotein Fetuin-A. However, how FETUAs acquired their function and their mechanism of action are unknown. Here, we use a combination of structure prediction, site-directed mutagenesis, functional analyses, and molecular dynamics to elucidate how the rattlesnake FETUA-3 protein evolved to inhibit three classes of venom MP toxins. We show that FETUA-3 uses a combination of structural motifs to bind multiple MPs with high-affinity and acts as a potent noncompetitive inhibitor by inserting its N-terminus into MP active sites and directly disrupting substrate cleavage. We also find strong selective constraints on key N-terminal residues that maintain FETUA-3 specificity for multiple MP targets. These results reveal that FETUA-3 evolved a unique mechanism of action distinct from other vertebrate metalloproteinase inhibitors and how a small number of FETUA proteins controls the activities of a large family of venom toxins.

evolutionary biology↗

bioRxiv2026

The genomic origins and evolutionary path to a key innovation in the world's most venomous snakes

Evolutionary innovation is a key driver of the colonization of new environments and the adaptive radiations of major groups. Novel traits typically evolve through the modification of pre-existing characters but the genetic paths underlying their origin have been challenging to trace, and the general requirements for and relative order of different kinds of gene mutations have been difficult to assess. Here, we trace the genomic origins of four procoagulant venom toxins (factor X, factor V, group I phospholipase A2, and Kunitz-type toxins) that collectively underlie a novel, especially potent blood-clotting venom type in the recently evolved Australian brown snake and taipan clade. We discover evidence for a previously unknown fifth toxin, coagulation factor VII, and show that the toxins evolved through two distinct genetic paths. The factor X and factor V toxins evolved through the sequential de novo co-option of ancestral clotting factor proteins that entailed their heterotopic expression in the venom gland, the fixation of segmental duplications containing each locus, and subsequent gain-of-function mutations that rendered factor X and factor V constitutively active. In contrast, the phospholipase A2 and Kunitz-type toxins evolved by modifying the functions of neurotoxins that were part of the venom arsenal. Our findings support models in which innovative mutations in single-copy genes precede gene duplication in the evolution of novel proteins and offer a rare view into the genesis of a complex trait that has played a central role in a major adaptive radiation. Significance StatementThis study investigates how an entirely new blood-clotting venom type evolved during the recent radiation of Australias iconic venomous snakes. We traced the key genetic events that occurred on the evolutionary path to one of the worlds most potent venoms. We found that the novel venom activity evolved through the sequential co-option of multiple proteins of the snakes own blood-clotting system, followed by the modification of two venom neurotoxins into proteins with procoagulant activities. We suggest that these unique de novo gene co-options are seminal events that can unlock new ecological strategies, which in turn, may enable major adaptive radiations.

evolutionary biology↗

bioRxiv2026

Nature's antivenom: Combinations of conserved rattlesnake serum metalloproteinase inhibitors block the lethal action of viper venoms

Snakebite maims or kills several hundred thousand people each year. For more than a century, treatment has relied on antivenoms derived from animals immunized with whole venoms, but their efficacy, safety, and availability are highly variable, and it is often not well understood which specific venom components must be inhibited to prevent mortality and major morbidities. New therapeutic approaches are needed. Here, we take an evolutionary approach to antivenom design inspired by the longstanding observation that vipers have evolved serum-borne toxin inhibitors that confer resistance to their own venoms. We have investigated the abilities of a family of four rattlesnake metalloproteinase (MP) inhibitors derived from the ancestral serum glycoprotein Fetuin-A (FETUAs) to neutralize the enzymatic, hemorrhagic, and lethal activities of viper venoms. We find that while certain individual FETUA proteins are able to inhibit enzymatic or hemorrhagic activity, they are unable or only partially able to inhibit venom lethality. However, we show that specific combinations of FETUA proteins complement one anothers activities and are sufficient to fully neutralize rattlesnake venom lethality with approximately 10 times greater potency than commercial antivenom. Moreover, we demonstrate that FETUA proteins are well-conserved among viper subfamilies and that rattlesnake FETUAs are able to inhibit the MPs and neutralize the lethality of several evolutionarily distant pit viper or true viper venoms. Our results highlight the critical importance of inhibiting MPs in hemorrhagic venoms and the potential general utility of combinations of naturally evolved, recombinant MP inhibitors in the treatment of viper snakebite. Significance StatementSnakebite remains an undertreated tropical disease that affects over one million people annually, and new therapeutic approaches are needed. Here, we develop a novel approach to viper antivenoms inspired by the observations that these snakes are typically resistant to the hemorrhagic and lethal effects of their own venoms and that this resistance can be transferred to experimental animals through snake sera. We show that a small set of serum metalloproteinase inhibitors from the Western Diamondback rattlesnake are potent inhibitors of the lethality of its own venom, and able to block the lethality of other rattlesnakes and evolutionarily distant vipers. Recombinant natural antitoxins offer a promising approach for formulating more potent viper antivenoms.

molecular biology↗

bioRxiv2025

Sustainable cattle management by communities supports African wildlife

Community-based conservation (CBC) initiatives aim to reconcile biodiversity protection with local livelihoods, yet their effectiveness in protecting wildlife remains uncertain, often hinging on local management1,2. We evaluated a globally significant CBC model in Kenyas Greater Maasai Mara Ecosystem (GME), where conservancies, run jointly by Maasai landowners and the tourism sector, employ rotational cattle grazing to support both wildlife and pastoralism3,4. Using a [~]1200 km2 grid of 180 camera traps across gradients of livestock pressure in Maasai Mara National Reserve and three conservancies in 2018, we collected and analysed over 2 million images with a customised AI-powered pipeline. We found a positive impact of observed cattle pressure on mammal community occupancy and species richness, except for at the highest levels of cattle grazing. However, sheep and goat grazing and proximity to infrastructure had a negative impact. These results provide evidence that wildlife and pastoralism can coexist under community-led stewardship5, but only with active management and targeted control of emerging threats. AI tools such as our image classifier may contribute to more adaptive community-led management of these areas6. As conservation policy shifts beyond formal protected areas, our findings support CBC as a scalable model for conserving biodiversity within working landscapes, offering a pathway to meet global targets while maintaining local livelihoods7.

ecology↗

bioRxiv2025

Multiscale Segmentation using Hierarchical Phase-contrast Tomography and Deep Learning

Biomedical systems span multiple spatial scales, encompassing tiny functional units to entire organs. Interpreting these systems through image segmentation requires the effective propagation and integration of information across different scales. However, most existing segmentation methods are optimised for single-scale imaging modalities, limiting their ability to capture and analyse small functional units throughout complete human organs. To facilitate multiscale biomedical image segmentation, we utilised Hierarchical Phase-Contrast Tomography (HiP-CT), an advanced imaging modality that can generate 3D multiscale datasets from high-resolution volumes of interest (VOIs) at ca. 1 {micro}m/voxel to whole-organ scans at ca. 20 {micro}m/voxel. Building on these hierarchical multiscale datasets, we developed a deep learning-based segmentation pipeline that is initially trained on manually annotated high-resolution HiP-CT data and then extended to lower-resolution whole-organ scans using pseudo-labels generated from high-resolution predictions and multiscale image registration. As a case study, we focused on glomeruli in human kidneys, benchmarking four 3D deep learning models for biomedical image segmentation on a manually annotated high-resolution dataset extracted from VOIs, at 2.58 to ca. 5 {micro}m/voxel, of four human kidneys. Among them, nnUNet demonstrated the best performance, achieving an average test Dice score of 0.906, and was subsequently used as the baseline model for multiscale segmentation in the pipeline. Applying this pipeline to two low-resolution full-organ data at ca. 25 {micro}m/voxel, the model identified 1,019,890 and 231,179 glomeruli in a 62-year-old donor without kidney diseases and a 94-year-old hypertensive donor, enabling comprehensive morphological analyses, including cortical spatial statistics and glomerular distributions, which aligned well with previous anatomical studies. Our results highlight the effectiveness of the proposed pipeline for segmenting small functional units in multiscale bioimaging datasets and suggest its broader applicability to other organ systems.

bioinformatics↗

bioRxiv2025

Loss of a major venom toxin gene in a Western Diamondback rattlesnake population

The biochemical complexity and evolutionary diversity of snake venom composition reflects adaptation to the diversity of prey in their diets. However, the genetic mechanisms underlying the evolutionary diversity of venoms are not well understood. Here, we explored the potential extent of and genetic basis for venom protein variation in the widely-distributed Western Diamondback rattlesnake (Crotalus atrox). As in many rattlesnake venoms, metalloproteinases (SVMPs) are the major component of C. atrox venom, with three proteins belonging to three distinct major structural SVMP classes, MDC4, MAD3a, and MPO1, constituting the most abundant SVMPs. We found that while most venom proteins, including MDC4 and MAD3a, vary little among individuals, the MPO1 protein is completely absent from some animals, most commonly those from the western part of the species geographic range. This distribution correlates with the previous finding of two distinct lineages within C. atrox and indicates that different ecological factors have shaped venom composition across the species range. We further show that the loss of MPO1 expression is not due to transcriptional down-regulation, but to several independent inactivating mutations at the locus, including whole gene deletion. The recurrent inactivation of a major toxin gene within a C. atrox population may reflect relaxed selection on the maintenance of MPO1 function, but we also raise the possibility that the loss of venom components may be favored if there is a cost to producing a less effective toxin in protein-rich venoms.

evolutionary biology↗

bioRxiv2021

An extended amygdala-midbrain circuit controlling cocaine withdrawal-induced anxiety and reinstatement

While midbrain dopamine (DA) neuronal circuits are central to motivated behaviors, much remains unknown about our knowledge of how these circuits are modified over time by experience to facilitate selective aspects of experience-dependent plasticity. Most studies of the DA system in drug addiction focus on the role of the mesolimbic DA pathway from the ventral tegmental area (VTA) to the nucleus accumbens (NAc) in facilitating drug-associated reward. In contrast, less is known about how midbrain DA cells and associated circuits contribute to negative affective states including anxiety that emerge during protracted withdrawal from drug administration. Here, we demonstrate the selective role of a midbrain DA projection to the amygdala (VTADA[->]Amygdala) for anxiety that develops during protracted withdrawal from cocaine administration but does not participate in cocaine reward or sensitization. Our rabies virus-mediated circuit mapping approach revealed a persistent elevation in spontaneous and task-related activity of GABAergic cells from the bed nucleus of the stria terminals (BNST) and downstream VTADA[->]Amygdala cells that could be detected even after a single cocaine exposure. Activity in BNSTGABA cells was related to cocaine-induced anxiety but not reward or sensitization, and silencing the projection from these cells to the midbrain was sufficient to prevent the development of anxiety during protracted withdrawal following cocaine administration. We observed that VTADA[->]Amygdala cells, but not other midbrain DA cells, were strongly activated after a challenge exposure to cocaine, and found that activity in these cells was necessary for the expression of reinstatement of cocaine place preference. Lastly, the importance of activity in VTADA[->]Amygdala cells extends beyond cocaine, as these cells mediate the development of anxiety states triggered by morphine and a predator odor. Our results provide an exemplar for how to identify key circuit substrates that contribute to behavioral adaptations and reveal a critical role for BNSTGABA[->]VTADA[->]Amygdala pathway in anxiety states induced by drugs of abuse or natural experiences as well as cocaine-primed reinstatement of conditioned place preference.

neuroscience↗

bioRxiv2020

Development and validation of the Irish Science Self-Efficacy Children's Questionnaire to assess the short-term influence of scientists facilitating outreach

Despite the positive relationship between science self-efficacy and science motivation, and the prevalence of scientist-led outreach programs, there is limited research on the effect of scientists on childrens science self-efficacy beliefs. Furthermore, there is no extant science self-efficacy research on primary pupils in Ireland, possibly due to the absence of a suitable and valid assessment instrument. This multi-study research aimed to develop and validate a questionnaire suitable for investigating the effect of scientist-facilitated science outreach on the science self-efficacy of children aged 11-12 years old. In Study 1 the first version of the Irish Science Self-Efficacy Childrens Questionnaire (IS-SEC-Q) was developed and tested with 92 primary school students. In Study 2, the revised questionnaire was re-tested with 282 students. For both studies, construct validity was examined through factor analysis. Questionnaire interpretation and comprehension were investigated via interviews (N=4 and 25 respectively). In Study 2, convergent and criterion validity of the scales was also examined. The final IS-SEC-Q contained 5 scales (63 items), including an adaptation of Usher and Pajares Sources of Self-Efficacy in Mathematics scale. Study 2 interviews indicated possible misinterpretations of the Emotional State subscale. The questionnaire demonstrated good psychometric properties and should serve well for informal science education practitioners endeavouring to assess their impact on primary childrens science self-efficacy.

scientific communication and education↗

bioRxiv2019

Systematic comparative analysis of single cell RNA-sequencing methods

A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic advances in scale and power, and enabling major discoveries and large scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single cell and/or single nucleus profiling from three types of samples - cell lines, peripheral blood mononuclear cells and brain tissue - generating 36 libraries in six separate experiments in a single center. To analyze these datasets, we developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method. We evaluated the methods for both basic performance and for their ability to recover known biological information in the samples. Our study will help guide experiments with the methods in this study as well as serve as a benchmark for future studies and for computational algorithm development.

genomics↗