Biology subjects

Smith, H.

Publications and source records attributed to Smith, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Long-Term Surveillance Reveals Establishment of Aedes albopictus in Eastern Nebraska, USA

Aedes albopictus (Skuse), the Asian tiger mosquito, is a highly competent arboviral vector whose range has expanded substantially across the United States over the past four decades. Despite predictive models placing Nebraska within the species' climatically suitable range, its establishment status in the state has remained poorly characterized. Here, we report results from a nine-year mosquito surveillance program (2017-2025) conducted across 44 Nebraska counties in collaboration with the Nebraska Department of Health and Human Services. Ae. albopictus was detected in five counties, with sustained, annually increasing populations documented in Richardson, Douglas, and Lancaster counties. Richardson County recorded continuous detections during 2017-2025, with proportional representation rising to 60.50% of collected mosquitoes by 2025. In Douglas and Lancaster counties, temporal advancement of first seasonal detection in 2024 and 2025 provide evidence consistent with successful overwintering rather than annual reintroduction. A cumulative degree-day model predicted adult emergence in mid-May across all county-year combinations, consistently preceding trap deployment by two to seven weeks and revealing a systematic early-season surveillance gap. Generalized linear mixed-effects models indicated that trap-level detection persistence, rather than urban location, was the primary predictor of yearly Ae. albopictus positivity, suggesting that current invasion dynamics are driven by focal source populations. These findings provide strong evidence for the establishment of Ae. albopictus in eastern Nebraska and highlight the need for earlier seasonal surveillance and standardized criteria to define establishment in northward-expanding vector populations.

ecology↗

bioRxiv2026

A conserved vesicular circuit enables metabolic adaptation and maintains systemic heme homeostasis

Metabolic homeostasis depends on adaptive control of intracellular metabolite flux, yet how such control is reconfigured when canonical transport pathways fail is unknown. Here we define a conserved vesicular circuit that preserves systemic heme balance by rerouting intracellular heme flux. We show that loss of the intestinal heme exporter MRP-5 in Caenorhabditis elegans causes lethal heme sequestration within endolysosomal compartments. This defect is bypassed by disabling the vesicular adaptor AP-3, which stabilizes and reroutes the heme importer HRG-1, restoring heme export without increasing cytosolic heme. Unbiased genetics and transcriptomics identify two previously uncharacterized SLC49A family members, HRG-13 and HRG-14, as heme exporters with distinct affinities that engage in a vesicular importer-exporter handoff. Live imaging reveals heme-enhanced contacts between HRG-1 and SLC49A-containing vesicles, consistent with direct vesicular transfer. This circuitry extends to vertebrates as disruption of the SLC49A3 homolog impairs erythropoiesis in zebrafish and causes intracellular heme overload, premature hemoglobinization and apoptosis in differentiating human erythroid cells. Together, these findings establish SLC49A3 proteins as conserved heme exporters and uncover a general principle of metabolic adaptation in which reprogramming intracellular compartmentalization, rather than increasing nutrient supply, restores systemic homeostasis.

cell biology↗

bioRxiv2026

Infectious Disease Forecasting via Physics-Informed Machine Learning

Infectious disease transmission evolves as a dynamic process shaped by biological mechanisms, population behavior, and intervention policies, yet public health responses are often driven by lagging indicators. Accurate short- and long-term disease forecasting is essential for the timely deployment of intervention strategies, healthcare capacity planning, and uncertainty-aware, risk-informed decision-making. To address this challenge, three broad classes of forecasting models have traditionally been used: statistical, machine learning, and mechanistic approaches. However, each of these modeling paradigms faces fundamental limitations. In particular, traditional statistical models often lack the flexibility needed to capture complex disease dynamics, machine learning approaches require large, high-quality data streams, and mechanistic models are notoriously difficult to calibrate. To overcome these challenges, we propose a novel physics-informed machine learning (PIML) framework for forecasting infectious disease dynamics. Our approach simultaneously forecasts new case and hospitalization counts, along with other key epidemiological quantities such as the time-varying reproduction number. This is achieved through the design of a machine learning model and estimation strategy regularized by a system of differential equations that encode disease dynamics of the SIHR model, thereby bridging the gap between purely data-driven and mechanistic models. We demonstrate the proposed methodology through in-depth numerical studies and an application to COVID-19 data collected in the state of South Carolina.

bioinformatics↗

bioRxiv2026

When clades collide: Genomic admixture in blacklegged ticks (Ixodes scapularis) from the Great Plains

Ixodes scapularis ticks transmit a number of pathogens important to human health, including Borrelia burgdorferi, the causative agent of Lyme disease. While I. scapularis is found across the Eastern United States, Lyme disease transmission is largely limited to the Northeast and Upper Midwest and is nearly absent in the South. This indicates that differences in northern versus southern clades of I. scapularis are associated with differences in Lyme disease transmission risk. I. scapularis is undergoing range expansion, including into the Great Plains region of the United States. Determining where I. scapularis populations in the Great Plains originated can inform future risk of Lyme disease transmission in this region. In this study, we use a population genomics framework to characterize diversity, structure, and B. burgdorferi infection rates of I. scapularis populations in the Great Plains region. We generated whole genome sequence data and single nucleotide polymorphism (SNP) datasets from I. scapularis ticks collected in Iowa, Kansas, Nebraska, and South Dakota to compare to publicly available data from across the species range. Our analysis of 200 I. scapularis SNP datasets indicated geographically well-defined populations that correspond to historical northern and southern ancestral clades of I. scapularis. Ticks from South Dakota, Iowa, and northeastern Nebraska are genetically similar populations from the Upper Midwest, while ticks from Kansas are more genetically similar to ticks from the Southeast. Ticks collected in the central eastern region of Nebraska, however, represent an evenly admixed population of both northern and southern genomic backgrounds. Analysis of B. burgdorferi reads from genomic datasets shows [~]50% infection rate in ticks from Iowa and northeastern Nebraska, whereas ticks from Kansas show no evidence of B. burgdorferi infection. Of note, evenly admixed ticks from the central eastern region of Nebraska also show no evidence of B. burgdorferi infection. These results provide further evidence that tick genomics may influence traits associated with B. burgdorferi infection status, and thus the potential for Lyme disease transmission. As the range of I. scapularis continues to expand, bringing historically isolated populations into contact, there is a clear need to understand the consequence of genomic admixture for B. burgdorferi transmission potential to inform future risk of Lyme disease in the United States.

genomics↗

bioRxiv2026

Stress-coping behavior during predator odor exposure is associated with differences in decision making

Post-traumatic stress disorder (PTSD) and alcohol use disorder (AUD) are chronic psychiatric disorders that have overlapping symptomology and risk factors, including altered motivation and impulsive behavior. Inescapable exposure to a predator odor stressor (2,3,5-Trimethyl-3-Thiazoline (TMT)) produces PTSD-like symptomology in rats. Individual differences in stress-coping behaviors such as freezing and defensive digging during TMT exposure can predict long-term differences in alcohol-related behaviors and altered neurobiology. Here, we sought to evaluate the relationship between stress coping behavior during TMT exposure and different aspects of decision making. In Experiment 1, male and female rats were trained on an adjusting-amounts delay discounting task, and delay discounting curves were established before and >2 weeks after TMT exposure. In Experiment 2, female rats were trained to self-administer alcohol and sucrose in a concurrent choice procedure. Lever responses and preference for alcohol over sucrose were evaluated before and >2 weeks after TMT exposure, and then motivation for competing reinforcers was evaluated using progressive ratios. Active coping (digging) during TMT exposure was correlated with increased post-TMT impulsive choice (Experiment 1), reduced sucrose lever responses both before and after TMT exposure (Experiment 2), and reduced sucrose lever breakpoint (Experiment 2). Additionally, TMT-exposed rats had increased motivation for both alcohol and sucrose self-administration when available concurrently (Experiment 2). Overall, these findings suggest that behavior prior to and during a stressful experience can predict susceptibility to negative effects on decision making, which may help future studies identify the neurobiology underlying risk for aberrant reward-related behaviors after a traumatic event.

neuroscience↗

bioRxiv2025

Mineralocorticoid and glucocorticoid receptor interaction drives TGFB1-induced triple-negative breast cancer progression to metastasis

In triple-negative breast cancer (TNBC), p38 MAPK phosphorylates the glucocorticoid receptor (GR) at N-terminal Ser134 in response to cytokines, such as TGF{beta}1. Phospho-Ser134-GR (pSer134-GR) regulates genes that promote migratory/invasive behavior and altered metabolism. In addition to acting as ligands for GR, glucocorticoids also activate closely-related mineralocorticoid receptors (MR). Elevated MR activity via its physiological ligand aldosterone (aldo), mediates hypertension, inflammation and fibrosis. While GR/p-GR has been implicated in TNBC progression to metastasis, the contribution of MR remains unknown. The METABRIC dataset demonstrated significantly higher expression of MR transcripts in TNBC relative to luminal breast cancers. Further, high MR expression predicted worse overall survival in the KM-plotter database. We observed pSer134-GR- and p38-dependent association of cytoplasmic MR/p-GR complexes upon treatment of TNBC cells with TGF{beta}1, while nuclear MR-GR complexes predominated in response to dexamethasone (dex) and/or aldo. Cytoplasmic MR/p-GR complexes entered the nucleus within 4 hours. MR knockdown or inhibition with MR-selective antagonists (spironolactone, finerenone) significantly reduced aldo or TGF{beta}1-induced migratory and stemness properties. MR knockdown models exhibited reduced migration, attenuated stem cell expansion, and impaired metastasis to lungs following tail-vein injection, thereby phenocopying cells harboring phospho-mutant S134A-GR. MR activation by aldo or TGF{beta}1 transcriptionally upregulated both canonical MR-target genes (SGK1, ENaC1) and non-canonical target genes related to fibrosis (COL1A1, ICAM1 and CTGF). MR expression was essential for functionally intact p38 MAPK/p-Ser134-GR signaling downstream of TGF{beta}1 receptor activation. Our studies define a novel role of MR/p-GR complexes in regulation of TNBC cell migration, stemness potential, and metastasis. Pharmacological inhibition of MR with FDA-approved MR antagonists (MRAs) offers an exciting opportunity for improved clinical management of TNBC patients.

cancer biology↗

bioRxiv2025

Multiblock Integration and Modeling of Localized Microbiome, Metabolome, and Clinical Metadata to Identify Biomarkers Predictive of Outcome in Veterans with Non-Healing Wounds

The chronic wound microenvironment consists of a complex milieu of host cells, microbial species, and metabolites. While much is known about wound microbiomes, our knowledge of metabolic landscapes influencing wound healing is limited. Furthermore, integrating complex datasets into predictive models of wound healing is almost non-existent. Microbial rRNA and total metabolites were extracted from 45 diabetic foot ulcers (DFU) debridement samples from 13 patients, with 25 from non-healing wounds and 20 from healing wounds that remained closed for over 30 days. 16S rRNA sequencing and global metabolomics were performed and clinical metadata collected. Healing outcome was modeled as a function of three blocks of features (N = 21 clinical, 634 microbiome, and 865 metabolome) using DIABLO (Data Integration Analysis for Biomarker Discovery using Latent Components). The final model selected 176 features (N = 15 clinical, 8 microbiome, and 153 metabolome) and the correct clinical outcome was predicted with an accuracy of nearly 94%. These results indicate that integrating multi-omics data with clinical metadata can predict clinical wound healing with low error rates. Furthermore, the biomarkers selected within the model offer novel insights into wound microenvironment composition which may reveal innovative therapeutic approaches and improve treatment efficacy in difficult-to-heal wounds.

systems biology↗

bioRxiv2025

Genomic Characterization of a Severe West Nile Virus Transmission Season using a Single Reaction Amplicon Sequencing Approach

West Nile virus (WNV) is an endemic arthropod-borne virus that has routinely caused seasonal outbreaks in the United States since it was first detected in 1999. While phylogenetic studies have shown how WNV has diversified and undergone genotype replacement since introduction, more geographically focused studies are needed to understand intricate transmission dynamics at local and regional scales. In this study, we validate the IDT xGen WNV panel, a novel single reaction amplicon-based Next-Generation Sequencing approach, to generate high-quality WNV genomes and compare it to the "Primal Scheme" assay for WNV, a common amplicon sequencing strategy. We show that the IDT xGen WNV panel generated complete and accurate WNV genomes and was more robust to amplicon drop out compared to the current sequencing approaches. Additionally, we used this approach to generate 100 complete WNV genomes from surveillance pools of mosquitoes collected in Nebraska during the 2023 outbreak. Our discrete phylogeographic analysis revealed substantial genetic diversity in WNV genomes from 2023 with minimal clustering across the state. This study demonstrated the utility of a single reaction amplicon-based sequencing approach to generate quality WNV genomes from routine surveillance samples and characterize WNV transmission dynamics in a high-incidence setting.

genomics↗

bioRxiv2025

Exercise serum promotes DNA damage repair and upregulates DNA repair gene PNKP in colon cancer cells

Exercise protects against colon cancer progression, but the underlying biological mechanisms remain incompletely understood. One proposed mechanism is the release of bioactive molecules into the interstitium and systemic circulation during exercise, which may act directly on precancerous or tumour cells to suppress DNA damage, inhibit proliferation, and preserve genomic stability. Here, we evaluated the effects of exercise-conditioned human serum on DNA damage kinetics and transcriptomic signatures in colon cancer cells. Blood samples were collected from 30 participants (age 50-78 years, body mass index [≥]25 kg/m2) before and immediately after a maximal incremental cycling test. LoVo cells were exposed to pre- or post-exercise serum, treated with 2 Gy irradiation, and assessed for {gamma}-H2AX foci over 24 hours. Compared to pre-exercise serum, post-exercise serum significantly reduced {gamma}-H2AX foci at 6 hours (p=0.024) and decreased the area under the curve (AUC, p=0.014), indicating accelerated DNA repair. Post-exercise serum also increased expression of the DNA repair protein PNKP in LoVo cells, both with and without irradiation (p=0.007 and p=0.029, respectively). Transcriptomic analysis revealed upregulation of mitochondrial energy metabolism and downregulation of cell cycle and proteasome-related pathways. These findings suggest that acute exercise elicits systemic responses that enhance DNA repair and shift colon cancer cells towards a less proliferative transcriptomic state under sublethal genotoxic stress, offering a potential mechanistic explanation for the protective effects of exercise against colorectal carcinogenesis.

cancer biology↗

bioRxiv2025

Molecular Insights into the Production of Extracellular Vesicles by Plants

Extracellular vesicles (EVs) produced by Arabidopsis are highly heterogeneous in protein content. Specific EV subpopulations have been proposed to participate in plant immunity, particularly during plant-fungal interaction. To understand the origins of plant EV heterogeneity, we used a proximity labeling approach to identify proteins and pathways involved in the secretion of distinct EV subpopulations. Proximity labeling, co-immunoprecipitation, and fluorescence microscopy in Nicotiana benthamiana all indicated a general role in EV secretion for EXO70 proteins (a subunit of the exocyst complex) and the immune-related protein RPM1-INTERACTING PROTEIN 4 (RIN4), while the ER-localized VAMP-ASSOCIATED PROTEIN 27(VAP27) was specifically associated with the EV marker protein TETRAPSANIN8 (TET8). Despite being secreted in separate EV populations, we found that TET8 and PENETRATION 1 (PEN1) co-localized in multivesicular body-like subcellular structures. Based on these results, we tested Arabidopsis mutants and identified several proteins involved in EV secretion, including members of the exo70 family, rin4, rabA2a, scd1 (a GTP-exchange factor for RabE GTPases), and vap27. We also uncovered a possible connection between trichomes and EVs, as the trichomeless mutant glabrous1 secreted approximately half the number of EVs as wild type. Furthermore, PEN1 MVB-like structures were prevalent in guard cells, suggesting that guard cells may contribute to secretion of PEN1+ EVs on the leaf surface. Lastly, we found that exo70 family mutants are more susceptible to infection with the fungal pathogen Colletotrichum higginsianum, underlining the importance of secretion for plant immunity. Together, our results unravel some of the complex mechanisms that give rise to EV subpopulations in plants.

plant biology↗

bioRxiv2025

Intestinal Stem Cells Retain an Epigenetic Memory of Prior Inflammation

Intestinal epithelial damage and impaired repair are hallmarks of ulcerative colitis (UC), even after inflammation resolves. Intestinal stem cells (ISCs) can retain stable epigenetic changes after inflammation, highlighting the potential for long-lived epithelial memory in the gut. Inflammatory injury in barrier tissues induces epigenetic memory in epithelial stem cells, and the tendency of UC to relapse at previously inflamed sites led us to hypothesize that ISCs from IBD patients acquire lasting memory of prior inflammation. To test this, we derived colonic organoids from inflamed and uninflamed regions of the same UC patients and propagated in long-term culture. Chromatin profiling revealed 2,252 accessible regions unique to prior-inflamed (PI) organoids, associated with stress response, repair, and inflammatory genes. Although these regions remained accessible, [~]95% of associated genes were not upregulated in PI organoids, indicating a primed state. Upon inflammatory or injury re-challenge, PI organoids exhibited heightened transcriptional responses and accelerated wound closure, despite reduced clonogenicity and impaired barrier function, indicating a retained inflammatory memory program. Our findings demonstrate that human ISCs retain a chromatin-based memory of inflammation that persists in the absence of immune cues and shapes future responses to injury. While this may support epithelial adaptation to secondary insults, it may predispose tissue to relapse in patients with UC.

molecular biology↗

bioRxiv2025

Tracking Conditioned Fear in Pair-Housed Mice Using Deep Learning and Real-Time Cue Delivery

Post-traumatic stress disorder (PTSD) is a complex and prevalent neuropsychiatric condition that arises in response to exposure to a traumatic event. A common diagnostic criterion for PTSD includes heightened physiological reactivity to trauma-related sensory cues, in safe or familiar environments. Understanding complex PTSD criteria requires new pre-clinical paradigms and technologies that integrate sensory physiology (e.g., auditory, visual, olfactory) with behavior. Here we present a novel Pavlovian-based paradigm using an open-source software plus deep learning-based pose estimation to investigate the effects of a recurrent conditioned stimulus (CS) on fear behaviors in pair-housed mice within the home cage. Simultaneous home cage video recording and analysis of CS-evoked freezing behaviors were performed using a deep learning model, with consideration for light-dark circadian cycles. Fear- conditioned dyad mice exhibited high CS-evoked freezing, with evidence of extinction learning (characterized by low freezing) during the mid-phase of the 2-week paradigm. Females exhibited reduced CS-evoked home cage freezing compared to males with circadian differences between the light (low freezing) and dark (high freezing) periods. Following the 2-week paradigm, fear-conditioned mice, compared to controls, exhibited heightened context-dependent freezing, while males but not females showed heightened startle reactivity. Taken together, these results demonstrate a novel software application for examining conditioned defensive and fear behaviors over time in mouse dyads within an ethologically relevant environment. Future applications could be used for more integrative analysis and understanding of neural circuits and heightened sensory threat reactivity, potentially improving the understanding and treatment of PTSD.

animal behavior and cognition↗

bioRxiv2025

Distinct impacts of sodium channel blockers on the strength-duration properties of human motor cortex neurones

Voltage-gated sodium channels (VGSCs) are essential for regulating axonal excitability in the human brain. While sodium channel blockers are known to modulate neuronal excitability, their in vivo effects on the human cortex remain poorly understood. Here, we employed novel transcranial magnetic stimulation (TMS) measures to investigate the effects of sodium channel blockers, carbamazepine and lacosamide, on the strength-duration behaviour of human cortical neurones, serving as an index of sodium channel function. Our data showed that single doses of both medications elevated resting motor thresholds compared to placebo, indicating reduced excitability; however, their impacts varied according to TMS pulse width. Carbamazepine raised thresholds proportionally across all pulse widths, whereas lacosamide disproportionately influenced thresholds for long-duration pulses. Crucially, lacosamide reduced the strength-duration time constant and increased rheobase, while carbamazepine had minimal effects on both. These results reveal subtle and unexpected differences in cortical neurone behaviour following VGSC-blocking medication administration. Lacosamides response aligns with the proposed mechanism of sodium conductance blockade, while carbamazepines effects suggest distinct VGSC interactions or potential off-target effects. Our findings advance the understanding of VGSC-blocking medication interactions in the human cortex and underscore the importance of employing specific TMS measures to gain deeper insights into medication mechanisms of action in vivo. Such measures could serve as valuable adjuncts in medication development and patient monitoring, enhancing understanding of medication action in clinical settings.

neuroscience↗

bioRxiv2025

TOWARDS CLIMATE-SMART REWILDING: AN INTEGRATED FRAMEWORK FOR BIODIVERSITY, CLIMATE CHANGE, AND SOCIETY

The UN Decade on Ecosystem Restoration and the Kunming-Montreal Global Biodiversity Framework aim to restore 30% of degraded ecosystems. Both the IPCC and IPBES highlight the crucial role of ecosystem restoration in addressing the interconnected crises of climate change and biodiversity loss. One key restoration strategy is rewilding, which enhances ecosystem complexity with minimal human intervention. While traditional rewilding strategies often focus on benefits for biodiversity, we propose a climate-smart rewilding framework as a new approach designed to deliver climate benefits alongside biodiversity restoration. This framework seeks to integrate biodiversity, climate change adaptation and mitigation, as well as socio-economic benefits and trade-offs. We illustrate how this framework can be utilized to identify areas across Europe where rewilding could increase carbon sequestration, enhance species abilities to adapt to the velocity of climate change, and maximize wildlife-watching benefits while minimizing the costs associated with livestock-wildlife conflict. Finally, we acknowledge some limitations of climate-smart rewilding, but we argue that its adaptability and low cost render it a promising solution to the challenges facing Europe and beyond.

ecology↗

bioRxiv2025

Sex-specific human electromechanical multiscale in-silico models for virtual therapy evaluation

Background and AimWomen are significantly under-represented in cardiovascular research and in the evaluation of treatment safety and efficacy, leading to poorer patient outcomes. Quantification and investigation of sex differences in human electromechanical function and underlying mechanisms is crucial. To address this, we present sex-specific human cellular and biventricular electromechanical models for mechanistic investigations into sex-differences in therapy evaluation through simulations. MethodsProtein genomic expression data from healthy human myocytes were used to calibrate sex-specific models of human cellular electrophysiology, subsequently integrated in biventricular electromechanical models with male and female anatomies. A validation, verification and uncertainty evaluation were implemented at the cellular and biventricular level, including validation using sex-specific datasets from randomised controlled trials for Dofetilide and Verapamil, with known sex-differences. Ionic mechanisms underlying sex-differences in drug response were mechanistically investigated. ResultsSex-specific electromechanical models recapitulate sex-differences from ionic currents to ECG biomarkers including QTc interval (Male: 312ms; Female: 339ms; 9% difference), T-wave amplitude (6-9% difference) and ST-steepness through electrophysiological changes alone. Sex-specific simulations demonstrate both ECG biomarkers and mechanical biomarkers (Female LVEF: 68%, Male LVEF: 50%) within healthy ranges in clinical data for male and female population in the UK Biobank (n= 806, 46% Male). ECGs sex-differences are primarily explained by ionic currents, whereas mechanical sex-differences are driven by anatomical differences, and secondarily through more robust calcium function in females. Under Dofetilide, simulations show exacerbated QT prolongation in women compared to men (54-78% increase in effect), and a T-wave amplitude decrease in males (up to 0.25 mV), consistent with clinical data. This is explained in simulations by lower repolarisation reserve in women (due to low potassium and high calcium currents) than men. Verapamil shows no effect on simulated QT in either sex, and divergent T-wave modulation (increased amplitude in females, decreased in males) consistent with clinical trial data. Simulations identify enhanced contractile reservoir in female compared to male, with lesser decreases to ejection fraction with calcium current block. ConclusionSimulations using novel, sex-specific cellular and biventricular electromechanical models reveal the primary role of ionic currents sex-differences in ECG and drug response, whereas mechanical sex-differences are also underpinned by anatomical differences. Main ContributionsO_LIDevelopment, calibration and validation of sex-specific human ventricular electromechanical, multiscale models. C_LIO_LIAn analysis of clinical randomised trial data in the context of sex-specific effects of multi-channel blockers on the ECG by dosage, where previous analysis focused on pharmacokinetics. C_LIO_LIConsideration of both sex-specific electrophysiology and anatomy explains sex-specific differences on the impact of drugs on ECG and mechanics. C_LIO_LISimulations demonstrate that the reduced repolarisation reserve in females increases the susceptibility to QTc prolongation via potassium channel block compared to males, and more robust calcium dynamics protect against t-wave amplitude reduction and the more severe contractility loss through L-type calcium inhibition observed in males. C_LI

physiology↗

bioRxiv2024

Comparing efficiencies of population control methods for responding to foreign animal disease threats in wild pigs

Introductions of foreign animal diseases (FADs) into free-ranging wildlife can be difficult to control and devastating for domestic livestock trade. Combating a new FAD introduction in wildlife with an emergency response requires quickly limiting spread of the disease by intensely removing wild animals and recovering their carcasses for proper disposal. In the case of African swine fever virus (ASFv) in wild pigs (Sus scrofa), which has been spreading in many regions of the world, there is little information on the time- and cost-efficiency of methods for intensively and consistently removing wild pigs and recovering carcasses in an emergency response scenario. We compared the efficiencies of aerial operations, trapping, an experimental toxic bait, and ground shooting in northcentral Texas, USA during two months in 2023. Removing and recovering carcasses of wild pigs averaged a rate of 0.15 wild pigs/person hour and cost an average of $233.04/wild pig ($USD 2023) across all four methods. Aerial operations required the greatest initial investment but subsequently was the most time- and cost-efficient, costing an average of $7,266 to incrementally reduce the population by 10% including recovering carcasses. Aerial operations required a ground crew of [~]7 people/helicopter to recover carcasses. Costs for reducing the population of wild pigs using trapping were similar, although took 13.5 times longer to accomplish. A benefit of trapping was carcass recovery was incorporated. Toxic baiting was less efficient because carcass recovery required substantial time, and we removed very few wild pigs with ground shooting in this landscape. We recommend combining aerial and trapping methodologies to remove wild pigs and their carcasses efficiently and effectively during a FAD response. Overall, our findings can inform the preparation of resources, personnel needs, and deployment readiness for FAD responses involving wild pigs.

ecology↗

bioRxiv2024

Operational lessons learned from simulating an elimination response to a transboundary animal disease in wild animals

Transboundary animal disease (TAD) introductions can have myriad economic, ecological, and societal impacts. When TADs are introduced into wild species, rapid and intense control efforts to reduce wild animal host populations are sometimes needed to eliminate the disease and prevent endemicity and spillover to domestic animal populations. Yet, such intensive efforts are non-trivial, and the rarity of TAD introductions means that personnel rarely have direct experience with these types of operations. Thus, explicit assessments of operational challenges for these kinds of efforts can provide direction to build emergency response preparedness capacity. Here, we simulated a TAD control effort in response to initial detection of a hypothetical index case of a TAD in wild pigs (Sus scrofa) (e.g., African swine fever; ASF). We used three removal methods (aerial control, trapping, and an experimental toxic bait). Then, we conducted an after-action assessment to identify operational challenges for rapidly reducing a population of invasive wild pigs within a simulated outbreak zone. We also simulated carcass recoveries of dispatched pigs, similar to what might be conducted during a response to a TAD with carcass-based transmission (e.g., ASF virus). Here, we describe operational challenges identified during our effort, alongside technological development solutions and a priori strategy needs to improve TAD response operation outcomes.

ecology↗

bioRxiv2024

Appearance of green tea compounds in plasma following green tea consumption is modulated by the gut microbiome in mice

Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to differential metabolism of phytochemicals resulting from variation in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea. A total of 20 LCM mice received 10 distinct human fecal slurries for an n=2 mice per human gut microbiome; 9 LCM mice remained un-colonized with human slurries throughout the experiment. We performed untargeted metabolomics on green tea and plasma to identify green tea compounds that were found in plasma of LCM and HU mice that had consumed green tea. 16S ribosomal RNA gene sequencing was performed on feces of all mice at study end to assess microbiome composition. We found multiple green tea compounds in plasma associated with microbiome presence and diversity (including acetylagmatine, lactiflorin, and aspartic acid negatively associated with diversity). Additionally, we detected strong associations between bioactive green tea compounds in plasma and specific gut bacteria, including associations between spiramycin and Gemmiger, and between wildforlide and Anaerorhabdus. Additionally, some of the physiologically relevant green tea compounds are likely derived from plant-associated microbes, highlighting the importance of considering foods and food products as meta-organisms. Overall, we describe a novel workflow for discovering relationships between individual food compounds and composition of the gut microbiome. ImportanceFoods contain thousands of unique and biologically important compounds beyond the macro- and micro-nutrients listed on nutrition facts labels. In mammals, many of these compounds are metabolized by the community of microbes in the colon. These microbes may impact the thousands of biologically important compounds we consume; therefore, understanding microbial metabolism of food compounds will be important for understanding how foods impact health. We used metabolomics to track green tea compounds in plasma of mice with and without complex microbiomes. From this, we can start to recognize certain groups of green tea-derived compounds that are impacted by mammalian microbiomes. This research presents a novel technique for understanding microbial metabolism of food-derived compounds in the gut, which can be applied to other foods.

systems biology↗