Biology subjects

Thomas, J. L.

Publications and source records attributed to Thomas, J. L..

5 recordsLinked to original sources

bioRxiv2026

Description of Alternaria kierstenii sp. nov. from invasive garlic mustard highlights agricultural biosecurity risks of foreign weeds as pathogen reservoirs

Invasive weeds can increase agricultural biosecurity risks by serving as reservoirs for emerging or undercharacterized plant pathogens. Garlic mustard (Alliaria petiolata), an invasive brassicaceous weed in North America, occurs near agricultural landscapes and is susceptible to multiple crop pathogens. A previously undescribed Alternaria species was isolated from a diseased garlic mustard population in Maryland, USA, prompting investigation of its taxonomy, origins, and host range. De novo genome sequencing produced a near-chromosome scale assembly of 35.8 Mb comprising 17 contigs. Comparative genomic analyses with other crucifer-infecting Alternaria species revealed expanded repertoires of predicted CAZymes and peptidases, as well as unique effectors and biosynthetic gene clusters. Phylogenetic and comparative analyses supported recognition of this fungus as Alternaria kierstenii sp. nov., representing a distinct lineage within section Sonchi. Host range assays demonstrated that A. kierstenii was highly aggressive on diverse hosts in the Brassicaceae, including vegetable, ornamental, cover crop, and invasive species. The disease caused by this new pathogen manifested as foliar and stem lesions, chlorosis, necrosis, leaf death, and, in several hosts, rapid plant mortality. Amplicon sequence data from a nationwide garlic mustard microbiome study detected closely related taxa only in the plants from the eastern states of Maryland, Pennsylvania, and New York, suggesting a geographically restricted population consistent with expectations for a potentially emerging pathogen. The description of this phylogenetically unique, broad host range pathogen demonstrates the potential for widespread invasive weeds to harbor pathogens and pathogen genomic diversity with agricultural relevance, underscoring the hidden biosecurity risk of understudied invasive weeds.

microbiology↗

bioRxiv2026

Resolving platypus behaviour from accelerometry: frequency-domain features improve detection of rhythmic behaviours in hydrodynamically challenging aquatic environments

Developing robust methods to quantify how animals allocate time across behaviours is essential for understanding energy use, habitat requirements, and responses to environmental change. For cryptic, semi-aquatic mammals such as the platypus, direct observation is difficult, creating a reliance on remote biologging approaches that can reliably infer behaviour in the wild. However, aquatic environments can both smooth acceleration signals through hydrodynamic damping and introduce noise from water movement, turbulence, and drag, potentially obscuring behavioural differences of similar magnitudes. We tested whether progressively incorporating biomechanical and frequency-domain (FFT-derived) predictors improved behavioural classification in hydrodynamically challenging aquatic environments. Tri-axial accelerometers were deployed on four ex situ platypuses, with synchronised video observations used to validate behaviour. From the acceleration data, we derived three predictor classes of increasing complexity: summary statistics describing activity level, engineered biomechanical variables capturing posture and body orientation, and FFT-derived features describing movement rhythm. These predictors were progressively incorporated into Random Forest models to classify five behaviours: burrow resting, surface resting, grooming, travelling/foraging, and diving. Model performance improved with increasing predictor complexity, although gains were behaviour specific. FFT-derived features substantially improved classification of rhythmic behaviours such as diving and foraging, while engineered biomechanical predictors improved grooming detection. In contrast, resting behaviours, particularly surface resting, showed little improvement. Overall accuracy increased from [~]75% to [~]88% when frequency-domain features were included. Misclassification was greatest among behaviours with overlapping or low-amplitude signals, and cross-individual validation revealed reduced model generalisability, indicating that individual variation in movement patterns constrained transferability. Incorporating frequency-domain features substantially improved behavioural classification in platypuses, particularly for rhythmic behaviours such as diving and foraging. This study provides the first validated accelerometry-based behavioural classification framework for the species and highlights the importance of matching predictor selection to behavioural mechanics. More broadly, the approach offers a transferable framework for aquatic and semi-aquatic taxa.

animal behavior and cognition↗

bioRxiv2025

IN4MER Bioink: A Phosphorescent Biosensing Bio-ink for Multiple Analytes (Glucose, Lactate, Oxygen) Measurements and Temperature Sensing Applications

3D bioprinting has revolutionized tissue engineering by enabling researchers to create much more complex structures than was practical with earlier techniques. Bioprinting uses computer-controlled layer-by-layer deposition of a mixture of hydrogels and living cells and the resulting structures can mimic the complex geometries of many living tissues by incorporating multiple bioinks with varied material properties and cell populations, allowing researchers to design structures that vary not only in shape, but also in mechanical, chemical, and biological properties throughout the bioprinted construct. However, techniques for evaluating these living constructs and monitoring them over time have not yet caught up to these innovations. Here we describe a novel approach to reporting nutrient values in real-time throughout the scaffold itself, accomplished by dispersing oxygen, glucose, and lactate sensitive microspheres within bioinks. These can be noninvasively interrogated using low-cost phosphorescence lifetime readers to determine and track nutrient concentrations across our bioprinted constructs in real time. The wealth of information this technique produces suggests this may provide a powerful new tool for evaluating and designing future bioprinted constructs.

bioengineering↗

bioRxiv2023

Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status: implications for conservation and management

The duck-billed platypus (Ornithorhynchus anatinus) is currently listed as Near-Threatened under the International Union for Conservation of Nature (IUCN) Red List based on observed population declines and local extinctions. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often undergo significant changes in their gut microbiome. The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high-throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with twenty-one core bacteria identified. Captive individuals did not differ in their microbial -diversity compared to wild platypus but had significantly different community composition ({beta}-diversity) and exhibited higher abundances of Enterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, including Rickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.

microbiology↗

bioRxiv2022

Connexin 43-mediated Neurovascular Interactions Regulate Neurogenesis in the Adult Brain Subventricular Zone

The subventricular zone (SVZ) is the largest neural stem cell (NSC) niche in the adult brain; herein, the blood-brain barrier is leaky, allowing direct interactions between NSCs and endothelial cells (ECs). Mechanisms by which direct NSC-EC interactions in the SVZ control NSC behavior are unclear. We found Cx43 to be highly expressed by both NSCs and ECs in the SVZ, and its deletion in either cell type leads to increased NSC proliferation and neuroblast generation, suggesting that Cx43-mediated NSC-EC interactions maintain NSC quiescence. This is further supported by in vitro studies showing co-culture with ECs decreases NSC proliferation and increases their expression of genes associated with quiescence in a Cx43-dependent manner. Cx43 mediates these effects in a channel-independent manner involving its cytoplasmic tail and ERK activation. Such insights further advance our understanding of NSC regulation in vivo and may inform NSC maintenance ex vivo for stem cell therapies for neurodegenerative disorders.

neuroscience↗