Biology subjects

Thomson, R.

Publications and source records attributed to Thomson, R..

7 recordsLinked to original sources

bioRxiv2026

Standardized benthic imaging with small, modular ROVs: an open-source framework developed in temperate kelp forests

(1) Kelp forests support ecologically, commercially, and culturally important species, yet their benthic communities remain difficult to monitor consistently across space and time. Scientific SCUBA surveys provide valuable observations but can be constrained by safety, bottom time, depth, and the spatial extent that divers can efficiently cover, motivating complementary approaches for collecting standardized benthic imagery. (2) We developed and field-tested a standardized, open-source framework for benthic visual-imaging surveys using a small, modular remotely operated vehicle (ROV). Across four cost-scalable hardware configurations, we integrated navigation sensors, custom BlueOS Extensions, and our surftrak contribution to ArduSub, which enables fixed-altitude flight above the seafloor, and developed two open-source desktop applications that streamline field operations (rov_flight_ops) and imagery processing (rov_imagery_processing). We also evaluated power supplies, benthic lighting, camera settings, field protocols, and telemetry-processing workflows over 303 transects conducted on 64 survey days from 2022 to 2026. (3) The ROV operated across soft-sediment and rocky habitats, currents of 0-3 kt, and underwater visibility of 0-10 m. surftrak held the ROV within 0.2 m of its target altitude for 96% of 21 h of survey transects, producing an approximately 1 m^2 standardized image footprint. Sufficient illumination and optimized camera settings yielded high-resolution imagery in visibility below 2 m, while topside power increased endurance and operational flexibility. Combining Doppler velocity log and underwater acoustic positioning data through the vehicle's extended Kalman filter improved navigation and post hoc transect reconstruction. During 2026 surveys, rov_flight_ops and rov_imagery_processing automated flight logging, log retrieval, fault diagnosis, and the sorting, development, and telemetry annotation of survey imagery. Dense kelp canopies nevertheless constrained vehicle operation, and downward-facing imagery provided limited observations of cryptic or obscured organisms. (4) We provide configuration-specific bills of materials, hardware and wiring documentation, software and firmware inventories, camera settings, open-source field and imagery-processing software, step-by-step field protocols, and pre- and post-dive checklists to support replication and adaptation of the framework. Together, these resources provide a field-tested starting point for expanding standardized benthic imaging while complementing diver surveys across kelp forests and other shallow coastal ecosystems.

ecology↗

bioRxiv2026

Validation-free estimation of chronological age via close-kin

SO_SCPLOWUMMARYC_SCPLOWAge is a fundamental life-history parameter in animal ecology and wildlife management. Age informs key ecological characteristics including population age structure, recruitment strength, extinction risk, reproductive maturity, and mortality rates. This importance has necessitated the development of chronological age estimation methods for wild animals. However, estimating chronological age is challenging for wild species, with noisy and potentially biased measures typically gathered from morphometrics, physical characteristics or, more recently, molecular methods like DNA methylation. These measures of age require at least some initial validation set of known-age individuals, or known time intervals, which is difficult to obtain for many species. Here, we present a solution to inferring the relationship between chronological age and error-prone observed age that does not require known-age individuals. The model couples the formulae for occurrence rates of half-sibling pairs, which decrease as a function of the birth-year gap between two sampled individuals, with time of capture. A pseudo-likelihood framework is developed for parameter estimation that can resolve linear and non-linear relationships and provide variance parameter estimates. We explore the methods efficacy for estimating chronological age using forward-in-time simulation and validate prior estimates of the relationship between vertebral band counts and chronological age for 3,000 school shark (Galeorhinus galeus) from an Australian fishery.

ecology↗

bioRxiv2025

Germline Targeted Baboon Apolipoprotein L-1 Protects Mice Against African Trypanosomes

Certain primates are immune to infection by most African trypanosome parasites due to apolipoprotein L-1 (APOL1), a primate-specific ion channel-forming protein. To broaden our understanding of primate APOL1, we generated a panel of trypanosome-resistant murine models expressing various primate APOL1 proteins. We used these mice to investigate the role of APOL1 in trypanosome immunity in vivo by challenging them with various human and livestock trypanosome isolates. Baboon APOL1 provides partial protection to trypanosome isolates, though its protective capacity was limited by poor expression. A more highly expressed chimeric APOL1 encoding human APOL1 with the baboon APOL1 C-terminus was protective against human-infective trypanosomes, although with a fitness cost likely associated with high expression. We investigated the long-standing assumption that human resistance to Trypanosoma vivax is mediated by APOL1. Surprisingly, APOL1-expressing mice were fully susceptible to T. vivax infection, challenging this hypothesis. These model systems are useful tools for evaluating the possibility of generating genetic engineered livestock for disease control.

microbiology↗

bioRxiv2025

Dissecting Genotype-Environment interactions with functional implications for parental selection in Cannabis Breeding

As climate variability continues to impact agricultural systems, identifying genetic factors that contribute to environmental adaptation will be essential for optimizing breeding strategies for the development of climate resilient varieties. Through human cultivation and naturalization, Cannabis sativa has dispersed globally, adapting to a range of environmental conditions across various climates and latitudes. We combined raw data from multiple public sources to conduct an Environmental Genomic Selection (EGS) analysis on 149 Cannabis sativa samples, to assess how different populations of Cannabis relate to their environmental conditions. Exploring Genomic Estimated Adaptive Values (GEAVs) across bioclimatic variables can facilitate the selection of parental material adapted for a specific condition. We further explore potential mechanisms of local adaptation by characterizing the individual marker effects which underlie these GEAV scores. To facilitate interpretation, we used previously described genetic groupings (Basal, Hemp-type, Drug-type feral, Drug-type). Distinct patterns emerged across population groups with the drug-type (Type I) group showing consistently narrow GEAV ranges, whereas the drug-type feral group showed a broader distribution, often having high GEAVs for precipitation variables. A key climate variable difference was seen in monthly average values, revealing a seasonal response to precipitation in drug-type feral samples. Exploring marker-effect differences between seasonal GEAVs indicated a response to seasonal precipitation in drug-type feral samples. As this samples are sourced from geographic regions that have seasonal monsoons, they may have traits conferring flood tolerance (water logging) that could be introgressed into other backgrounds. The basal group also exhibited broad GEAV ranges across several bioclimatic traits, indicating they may be a valuable genetic resource for introgression to enhance environmental resilience. These findings underscore the importance of incorporating diverse germplasm into breeding programs to improve Cannabis resilience to changing environmental conditions. EGS provides a fast method to enable climate-conscious parental selection while gaining mechanistic information. Ultimately, we hope that such a strategy could support the development of climate-resilient Cannabis varieties tailored to both current and future environmental challenges.

plant biology↗

bioRxiv2024

Antibiotic lethality dictates mycobacterial infection outcomes

Antibiotic development and treatment focus on bacterial growth inhibition, often with limited success. Here, we introduce Antimicrobial Single-Cell Testing (ASCT), an advanced imaging strategy to assess bacterial killing in real-time. By tracking 140 million bacteria and generating over 20,000 in vitro time-kill curves, we can predict Mycobacterium tuberculosis treatment outcomes in mice and humans and link strain-specific survival (drug tolerance) in Mycobacterium abscessus to clinical responses. Using ASCT, we reveal drug tolerance as a distinct genetically encoded bacterial trait conserved across drugs with similar targets and, via genome-wide associations, uncover molecular mechanisms that govern bacterial killing. This study establishes the technical framework and in vivo validation for large-scale bacterial killing assessments to advance our understanding of bacterial survival, antibiotic development and clinical decision-making.

microbiology↗

bioRxiv2018

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

Genome mining has become a key technology to explore and exploit natural product diversity through the identification and analysis of biosynthetic gene clusters (BGCs). Initially, this was performed on a single-genome basis; currently, the process is being scaled up to large-scale mining of pan-genomes of entire genera, complete strain collections and metagenomic datasets from which thousands of bacterial genomes can be extracted at once. However, no bioinformatic framework is currently available for the effective analysis of datasets of this size and complexity. Here, we provide a streamlined computational workflow, tightly integrated with antiSMASH and MIBiG, that consists of two new software tools, BiG-SCAPE and CORASON. BiG-SCAPE facilitates rapid calculation and interactive visual exploration of BGC sequence similarity networks, grouping gene clusters at multiple hierarchical levels, and includes a glocal alignment mode that accurately groups both complete and fragmented BGCs. CORASON employs a phylogenomic approach to elucidate the detailed evolutionary relationships between gene clusters by computing high-resolution multi-locus phylogenies of all BGCs within and across gene cluster families (GCFs), and allows researchers to comprehensively identify all genomic contexts in which particular biosynthetic gene cassettes are found. We validate BiG-SCAPE by correlating its GCF output to metabolomic data across 403 actinobacterial strains. Furthermore, we demonstrate the discovery potential of the platform by using CORASON to comprehensively map the phylogenetic diversity of the large detoxin/rimosamide gene cluster clan, prioritizing three new detoxin families for subsequent characterization of six new analogs using isotopic labeling and analysis of tandem mass spectrometric data.

bioinformatics↗

bioRxiv2017

Demonstration of short-term plasticity in the dorsolateral prefrontal cortexwith theta burst stimulation: A TMS-EEG study

ObjectivesTo examine the effects of intermittent TBS (iTBS) and continuous TBS (cTBS) on cortical reactivity in the dorsolateral prefrontal cortex.\n\nMethods10 healthy participants were stimulated with either iTBS, cTBS or sham at F3 electrode. Single- and paired-pulse TMS and concurrent electroencephalography (EEG) were used to assess change in cortical reactivity and long-interval intracortical inhibition (LICI) via TMS-evoked potentials (TEPs) and TMS-evoked oscillations.\n\nResultsSignificant increases in N120 amplitudes (p < 0.01) were observed following iTBS over prefrontal cortex. Changes in TMS-evoked theta oscillations and LICI of theta oscillations were also observed following iTBS (increase) and cTBS (decrease). Change in LICI of theta oscillations correlated with change in N120 amplitude following TBS (r = -0.670, p = 0.001).\n\nConclusionsThis study provides preliminary evidence that TBS produces direct changes in cortical reactivity in the prefrontal cortex. Combining TBS with TMS-EEG may be a useful approach to optimise stimulation paradigms prior to the conduct of clinical trials.\n\nSignificanceTBS is able to modulate cortical reactivity and cortical inhibition in the prefrontal cortex.\n\nHighlightsO_LIEffects of iTBS and cTBS were studied in the DLPFC using TMS-EEG\nC_LIO_LIiTBS increased N120 amplitude, theta power and LICI of theta\nC_LIO_LIcTBS decreased theta power alone\nC_LI

neuroscience↗