Biology subjects

Thomas, K.

Publications and source records attributed to Thomas, K..

At least 19 recordsLinked to original sources

bioRxiv2026

A Neurotensin Brake on Exploratory Drive under Persistent Threat

Avoidance behavior is an adaptive response that delays exploration to promote survival. Avoidance is enhanced by psychological stress and is a hallmark of many neuropsychiatric disorders. Neural circuits that control avoidance by integrating stressful stimuli and modulating exploratory behavior remain underexplored. Elucidating the functional dynamics of this highly conserved phenomenon and the underlying neural mechanism of avoidance is an important open-ended question, with relevance to understanding both innate behaviors and neuropsychiatric disorders. Using predator odor as an innate, chronic stressor to increase avoidance behaviors in mice, we identified a neural population in the lateral septum (LS) that integrates threat information and modulates latency to explore. Calcium recordings in freely exploring mice combined with activity-based transcriptomics revealed that predator-responsive LS neurons are GABAergic and express neurotensin (LSNT). Further, single nuclei RNA-seq analysis revealed that among predator-responsive neurons, NT-enriched inhibitory clusters are predominant. Chronic activation of LSNT neurons induces avoidance behaviors in the absence of predator odor, while synaptic silencing of this population abrogates predator-enhanced avoidance. Using transgenic mouse models to indelibly tag predator-responsive neurons, we defined the downstream circuit that connects the encoding of predator odor information to the lateral hypothalamus. Projection-specific activation of LSNT[->]LHA neurons recapitulate stress-induced avoidance behaviors in mice. Finally, we showed that deletion of neurotensin from LS neurons prevented the effects of predator odor on exploration. Together, these findings offer a genetically-and projection-defined, top-down circuit linking the limbic neurotensinergic system to chronic psychological stress and avoidance behaviors in mice.

neuroscience↗

bioRxiv2026

Organoid-like Functional Adrenal Gland Cortex Derived From Human Pluripotent Stem Cells

The adrenal cortex is a critical for life endocrine system. It manages metabolic homeostasis, electrolyte balance, stress response, and sex development. This is accomplished through the release of various steroids from a dynamically changing landscape of concentric cellular zones/layers. Adrenocortical dysfunction is implicated in pathologies ranging from adrenal insufficiency to hypertension. The in-depth investigation of adrenal gland biology, pathology and drug discovery has been hampered by a lack of human, experimentally tractable models. Particularly missing are models that recapitulate the cellular diversity of the adrenal cortex with representation of all fetal and adult cell layers and the capsule. Here, we employ human pluripotent stem cells (hPSCs) to generate cells of all three cortex zones alongside capsular cells in a single 2D platform. This platform mimics the cellular diversity expected from an organoid, yet it provides the simplicity of monolayer cultures, that are better suited for drug discovery and high-throughput settings. These cultures secrete zone-specific steroids (cortisol, aldosterone, and DHEA-S) and exhibit robust, physiologically relevant ACTH stimulation responses. Transcriptomic analysis revealed sequential acquisition of profiles consistent with adrenocortical development, zonation, and signaling programs consistent with zone maintenance. Our platform is validated by a literature meta-analysis that defines transcriptomic signatures for each human cortical cell type, spanning fetal and adult stages. Together, this novel adrenocortical platform enables investigation of adrenal development, disease mechanisms, and therapeutic strategies. Significance StatementWe describe a hPSC-based 2D differentiation strategy with the cell type complexity of an organoid and the technical simplicity necessary for high-throughput assays. The platform contains all cortical subtypes that mediate electrolyte regulation, stress response, sex development and self-maintenance of the tissue. This co-differentiation offers a unique opportunity to study human adrenal development, biology, pathology and enables drug discovery.

developmental biology↗

bioRxiv2026

Single Platform Solution for Identity and Quantification of Influenza Hemagglutinin (HA) mRNA Constructs and Resulting Expressed Proteins for Application to Influenza mRNA Vaccines

The rapid response to the Coronavirus Disease (COVID-19) pandemic highlighted mRNA as an attractive modality for vaccines and therapeutics to address infectious diseases, cancer, and other diseases. The current analytical methods for identification and quantification of both the mRNA construct as well as the resulting expressed protein(s) relevant to mRNA vaccines are inherently singleplex and usually labor and time intensive, presenting a bottleneck as these vaccines become increasing multivalent. Here, we first present performance data from an approximately 2-hour DNA microarray assay developed specifically to provide identity and quantity measurements for the mRNA constructs present in an influenza virus hemagglutinin (HA)-encoding multivalent mRNA vaccine regardless of the specific strain or codon optimization strategy utilized. The assay functions on both naked and lipid nanoparticle (LNP)-encapsulated mRNAs without the requirement of an upfront mRNA extraction or amplification. Second, we show that a separate [~]2-hour multiplexed immunoassay executed on the same VaxArray Platform can be utilized to measure the expressed proteins produced from these influenza HA mRNAs post-transfection as an in vitro potency assay readout. Both assays provide the necessary specificity for each component present in a multivalent mixture and represent new tools in the analytical toolbox for multiplexed mRNA vaccine analytics.

molecular biology↗

bioRxiv2026

Dysregulation of xenobiotic metabolism and mitochondrial dysfunction exacerbate acetaminophen-induced hepatotoxicity in human antigen R-deficient male mice

Acetaminophen (APAP) overdose is a leading cause of acute liver failure worldwide. The RNA-binding protein Human antigen R (HuR) is a multifunctional post-transcriptional regulator that plays a pivotal role in cellular stress responses, including those triggered by APAP toxicity. This study investigated the mechanisms by which HuR protects against APAP-induced hepatotoxicity in male mice. Hepatocyte-specific HuR-deficient (HuRHep-/-) male mice on a C57BL/6N background and wild-type (WT) littermates were treated with 200 mg/kg APAP, and liver tissues were collected at 2, 6, and 24 hours post-treatment. APAP administration increased hepatic HuR mRNA expression and induced HuR cleavage and the formation of a higher-molecular weight HuR-immunoreactive band, with the latter two correlating with injury severity. Compared with WT controls, HuRHep-/- mice exhibited markedly increased susceptibility to hepatotoxicity at both 2 and 6 hours. Metabolite profiling revealed altered APAP metabolism and reduced glutathione S-transferase (Gst) expression in HuRHep-/- livers, consistent with impaired APAP detoxification and increased APAP-protein adduct formation. Fourier-transform infrared (FTIR) spectroscopy further identified early biochemical differences between WT and HuRHep-/- livers as early as 2 hours after APAP exposure. Additionally, HuR deficiency resulted in pronounced mitochondrial structural abnormalities and dysfunction at 2 and 6 hours, accompanied by reduced expression of the mitochondrial fission and fusion proteins Drp1 and Mfn2, increased mitochondrial protein release, and enhanced hepatocyte death. Although pro-inflammatory cytokine levels were elevated in HuRHep-/- mice relative to WT controls at 24 hours, hepatocyte proliferation was similarly blunted in both genotypes, consistent with severe liver injury and delayed recovery. Collectively, these findings identify hepatocyte HuR as a critical regulator of xenobiotic metabolism and mitochondrial integrity and establish its essential role in early protection against APAP-induced hepatotoxicity in male mice.

pharmacology and toxicology↗

bioRxiv2025

Pre-Human Immunodeficiency Virus (HIV) infection Th17 CD4+ T cells as predictors of early HIV disease progression

Interleukin-17-producing T helper (Th17) CD4+ T cells are highly susceptible to HIV infection and are depleted early in people living with HIV. Here, we investigated whether systemic Th17 cell levels prior to HIV infection are associated with subsequent HIV disease progression. We analyzed archived cryopreserved peripheral blood mononuclear cells (PBMCs) collected within one year prior to HIV acquisition from participants enrolled in a South African cohort (HIV Vaccine Trials Network [HVTN] 503; n = 35) and an East African cohort (Partners Pre-exposure Prophylaxis/Couples Observational Study [PP/COS]; n = 32). Th17 cell frequencies were quantified by flow cytometry. In HVTN 503, higher pre-HIV IL-17+ CD4+ T cell frequencies were inversely correlated with CD4/CD8 ratio measured both within 180 days (Spearman rank R = -0.42, p = 0.012) and beyond 180 days (R = -0.55, p = 0.001) after HIV infection, and were associated with faster CD4+ T cells decline (adjusted hazard ratio [aHR] = 3.5, 95% CI: 1.2-9.9, p = 0.020). In contrast, no significant association with CD4 decline was observed in the PP/COS cohort (HR = 1.2, 95% CI: 0.4-3.4, p = 0.795). Sex-stratified analyses in HVTN 503 indicated a more pronounced association between pre-HIV IL-17+ CD4+ T cells and faster CD4 decline in males than females. In analyses combining all cohorts, higher pre-HIV IL-17+ CD4+ T cell frequencies remained associated with faster CD4 decline, particularly among younger participants (HR = 3.5; 95% CI: 1.35-9.22, p = 0.010). Pre-HIV IL-17+ CD4+ T cell frequencies were not associated with peak or set-point viral load in either cohort. Together, these findings suggest that pre-HIV Th17 cells abundance may influence subsequent HIV disease progression independently of early viral replication. Author SummaryHIV infection leads to progressive damage of the immune system, but the rate at which this damage occurs varies widely between individuals. Understanding the factors that influence HIV disease progression is essential for improving prevention and treatment strategies. Previous studies have suggested that immune characteristics present before infection may shape disease outcomes after HIV acquisition. In this study, we examined whether the abundance of IL-17-producing CD4+ T cells, known as Th17 cells, measured prior to HIV acquisition, were associated with markers of disease progression after infection. We analyzed blood samples from individuals who were HIV-negative at the time of sampling and later acquired HIV during follow-up. We found that individuals with higher pre-infection levels of Th17 cells experienced faster immune decline after HIV infection, including more rapid loss of CD4+ T cells and lower CD4/CD8 ratios. These associations were observed independently of viral load and varied by cohort, age and sex. Our findings indicate that immune conditions present before HIV infection can influence subsequent disease progression and suggest that Th17 cells may serve as biomarkers to identify individuals at higher risk of rapid HIV-related immune damage.

immunology↗

bioRxiv2025

Sex Dependent Effects of Minocycline on Contextual Fear Memory

Recent studies have highlighted the crucial role of microglia in fear learning and memory. This supports the potential therapeutic value of the anti-inflammatory agent minocycline, which regulates microglial activity, in psychiatric disorders involving dysregulated emotional memory. To assess the impact of minocycline during a tractable intervention window, we examined its acute systemic effects on the reconsolidation, extinction, and forgetting of contextual fear memory (CFM) in rats. Our findings show that the effects of minocycline on fear memory and anxiety-like behaviours depend on sex, memory activation (i.e., whether it was retrieved), and memory age. In males with recently acquired CFM, minocycline given before retrieval enhanced extinction and reduced fear expression. When administered without retrieval, it disrupted passive forgetting, increasing evoked fear behaviour. This extinction-enhancing effect did not occur with older (28-day) memories rather it strengthened CFM through enhancing reconsolidation. In contrast, in females, minocycline increased the expression of recent fear memories regardless of retrieval, without affecting extinction or forgetting. This elevated fear expression appeared linked to heightened anxiety-like behaviour. These findings suggest that minocycline, or other microglia-targeting agents, would need to be used in a highly selective and targeted manner to therapeutically modulate pathological fear memories. Minocycline may be beneficial as an adjunct to exposure therapy in men explicitly retrieving recent fear or trauma-related memories, but outside these conditions, it may worsen fear expression. These results help explain the mixed findings from therapeutic trials using minocycline in psychiatry and support the application of a more precision approach in any future applications.

animal behavior and cognition↗

bioRxiv2025

Ascl3+ ionocytes in murine salivary gland ducts are innervated sensory cells that display unique calcium signaling characteristics and contribute to the composition of saliva

Ionocytes are distinct epithelial sensory cells scattered throughout the ductal system of the salivary glands. These cells are distinguished by their unusual morphology, as well as by a specific transcriptomic signature that includes expression of the Foxi1 and Ascl3 transcription factors. Currently, little is known about the biology or function of ionocytes in the salivary glands. To facilitate characterization of these cells, we generated an inducible Cre mouse allele driven by the Ascl3 promoter. This strain was crossed with a reporter to fluorescently label Ascl3+ ionocytes, highlighting that they are the site of enriched CFTR expression in the salivary glands, and demonstrating the proximity of these cells to neurons. Conditional Cre-mediated cell ablation, using diphtheria toxin (DTA), removed Ascl3+ ionocytes from the salivary glands and resulted in an altered pH of total saliva, supporting a function for ionocytes in transepithelial ion flow. Finally, Cre-mediated expression of the calcium indicator GCaMP6f revealed that Ascl3+ ionocytes exhibit unique properties not observed in acinar or surrounding duct cells, including elevated basal [Ca2+]I, spontaneous blinking in the absence of stimulation, and a rapid loss of [Ca2+]I following nerve stimulation. These unique properties distinguish ionocytes as a specialized subset of salivary gland duct cells.

physiology↗

bioRxiv2025

A Microphysiologic Model of the Cervical Epithelium Recapitulates Microbial, Immunologic, and Pathogenic Properties of Sexually Transmitted Infections

Sexually transmitted infections (STIs) of the cervicovaginal mucosa are among the most common global infections. Clinical studies have revealed that susceptibility to STIs and the subsequent host responses they elicit are frequently associated with vaginal microbiota compositions that facilitate infection. Current monolayer cell culture and animal models fail to reproduce the multilevel complexity required to investigate these relationships simultaneously and/or with sufficient physiological relevance. To address this limitation, we have developed a microphysiologic system (MPS) that models human cervical tissue, its microbiota, and is susceptible to infection by two prominent genital pathogens, Chlamydia trachomatis and Neisseria gonorrhoeae. Significantly, this MPS platform recapitulates essential dynamic, polymicrobial, immune, and pathogenic features of chlamydial and gonococcal infections as they occur in humans. The lowcost MPS device requires no specialized equipment or specific expertise and was experimentally validated for both chlamydial and gonococcal infections across multiple nonengineering, remotely located laboratories, demonstrating its transferability and reproducibility. The MPS platform described herein provides a novel tool for expanded research into genital infections in a reconstituted system that closely mimics the cervical epithelium, a significant advance over existing models.

bioengineering↗

bioRxiv2025

XPC loss-of-function triggers melanomagenesis through CDKN2A downregulation

We identified a novel XPC variant, c.2420+5G>A (XPCvar), in siblings with multiple melanomas, inherited alongside c.779+1G>T, which results in an absent or disrupted protein. However, they did not exhibit significantly higher nucleotide excision repair (NER) deficits compared to their unaffected parents, suggesting an NER-independent tumor suppressor function for XPC. XPC knockdown increased cell proliferation and tumorigenicity in vitro without affecting NER. Single-cell RNA sequencing revealed lower Cdkn2a in Xpcvar/var mouse melanocytes. Additionally, XPC knockdown downregulated CDKN2A in vitro. Furthermore, patient fibroblasts showed decreased p16INK4a, which was rescued by XPC overexpression. ChIP-PCR and luciferase assays confirmed XPC binding to the CDKN2A promoter, initiating transcription. Premature stop codon read-through, with gentamicin, restored XPC and p16INK4A in patient fibroblasts. These suggest that XPC regulates CDKN2A and XPC loss might promote melanomagenesis by downregulating CDKN2A, independent of its NER function. We provide preclinical evidence for potential preventive and/or therapeutic strategies for similarly affected individuals. STATEMENT OF SIGNIFICANCECharacterizing a novel XPC variant identified in patients with melanoma revealed a non-canonical role for XPC in regulating CDKN2A transcription. XPC binding to the CDKN2A promoter is crucial for CDKN2A expression and might suppress melanomagenesis. This expands our understanding of melanomagenesis and suggests potential therapies targeting XPC-mediated regulation of CDKN2A.

cancer biology↗

bioRxiv2025

Mature neutrophils promote long-term functional recovery after spinal cord injury in a sex-dependent manner

Neutrophils are abundant and complex innate immune cells that act as first responders to tissue injury, with critical roles in combating infection and initiating would healing. Following spinal cord injury (SCI), neutrophils are the first peripheral immune cells to infiltrate the injured spinal cord in large numbers. Despite the growing body of evidence demonstrating sex differences in neutrophil function, sex as a biological variable in neutrophil responses following SCI has yet to be thoroughly investigated. Here we provide novel evidence that neutrophil responses differ by sex following SCI with divergent effects on long-term outcomes. We show substantial sex-dependent shifts in the phenotype of circulating and intraspinal neutrophils across time following SCI. Depletion of neutrophils immediately after SCI reveals a previously unidentified role for mature neutrophils in promoting long-term functional recovery in a sex-dependent manner. Mechanistically, mature neutrophils acquire an inflammation-resolving phenotype in the acutely injured spinal cord and depletion of mature neutrophils exacerbates long-term macrophage accumulation following SCI in a sex-dependent manner. Collectively, our findings provide the first account of marked sex differences in the response of neutrophils to SCI and elucidate a novel and sex-dependent role for mature neutrophils in promoting resolution of inflammation and long-term recovery following SCI.

neuroscience↗

bioRxiv2025

Corticospinal, reticulospinal, and motoneuronal contributions to fatigability during a sustained contraction of the elbow flexors

Synaptic input to the motoneuron pool is altered during fatiguing muscle contractions. In humans, the corticospinal tract is often studied, with equivocal findings regarding its role in the reduction of force. To date, the involvement of the reticulospinal tract during states of fatigue has not been explored. Fourteen participants (28{+/-}6 years, nine males) visited the laboratory twice, first for a familiarisation, then an experimental trial. Participants completed a 5-min sustained elbow flexor contraction at an intensity eliciting 40% of the EMG recorded during a maximal isometric voluntary contraction (MVC). Before, during, and after the contraction, transcranial magnetic stimulation and electrical cervicomedullary stimulation were used to elicit motor evoked potentials (MEPs) and cervicomedullary evoked potentials during the silent period (SP-CMEPs) respectively, with CMEPs also being evoked in combination with a startling acoustic sound (CMEPcon). Electrical stimulation of the brachial plexus was used to evoke maximal compound action potentials of the elbow flexors (Mmax). The 5-min contraction induced a 53% loss of force (p<0.001), with no change in background EMG ([~]4% Mmax, p=0.293). Neither MEP amplitude (p=0.246) nor CMEPcon ratio (p=0.489) were altered during the contraction. Whereas CMEP and SP-CMEP amplitudes were reduced by [~]20 and 50%, respectively (p<0.001) and remained depressed post-task. The results suggest that neither corticospinal nor reticulospinal tract excitability was altered during a 5-min constant-EMG task at 40% maximal EMG. Instead, the aetiology of the neural contribution to fatigability appeared to be primarily related to the loss of motoneuron excitability.

neuroscience↗

bioRxiv2024

Motor unit mechanisms of speed control in mouse locomotion

During locomotion, the coordinated activity of dozens of muscles shapes the kinematic features of each stride, including systematic changes in limb movement across walking speed. Motor units, each of which consists of a single motor neuron and the muscle fibers it innervates, contribute to the total activation of each muscle through their recruitment and firing rate when active. However, it remains unknown how the nervous system controls locomotor speed by changing the firing of individual motor units. To address this, we combined quantitative behavioral analysis of mouse locomotion with single motor unit recordings from the lateral and long heads of the triceps brachii, which drive monoarticular extension of the elbow and biarticular movements of the elbow and shoulder, respectively. In contrast to prior studies employing bulk EMG to examine muscle activity, our recordings revealed the diversity of spike patterning across motor units as well as systematic differences in motor unit activity across muscles and locomotor speeds. First, motor unit activity differed significantly across the lateral and long heads, suggesting differential control of these two closely apposed elbow extensor muscles. Second, we found that individual units were recruited probabilistically (during only a subset of strides), showing that the highly repeatable bulk EMG signals observed across strides in fact reflect varying subsets of individual motor units. Finally, although recruitment probability and firing rate both increased at faster walking speeds, increases in recruitment were proportionally larger than rate changes, and recruitment of individual units accompanied changes in limb kinematics. Together, these results reveal how the firing of individual motor units varies systematically across muscles and walking speeds to produce flexible locomotor behavior.

neuroscience↗

bioRxiv2024

Simulating Offshore Oilfield Conditions: Insights into Microbiologically Influenced Corrosion from a Dual Anaerobic Biofilm Reactor

Oilfield systems are a multifaceted ecological niche which consistently experience microbiologically influenced corrosion. However, simulating environmental conditions of an offshore system within the laboratory is notoriously difficult. A novel dual anaerobic biofilm reactor protocol allowed a complex mixed-species marine biofilm to be studied. Interestingly, electroactive corrosive bacteria and fermentative electroactive bacteria growth was supported within the biofilm microenvironment. Critically, the biotic condition exhibited pits with a greater average area which is characteristic of microbiologically influenced corrosion. This research seeks to bridge the gap between experimental and real-world scenarios, ultimately enhancing the reliability of biofilm management strategies in the industry. ImportanceIt is becoming more widely understood that any investigation of microbiologically influenced corrosion requires a multidisciplinary focus on multiple lines of evidence. While there are numerous standards available to guide specific types of testing, there are none that focus on integrating biofilm testing. By developing a novel dual anaerobic reactor model to study biofilms, insights into the different abiotic and biotic corrosion mechanisms under relevant environmental conditions can be gained. Using multiple lines of evidence to gain a holistic understanding, more sustainable prevention and mitigation strategies can be designed. To our knowledge, this is the first time all these metrics have been combined in one unified approach. The overall aim for this paper is to explore recent advances in biofilm testing and corrosion research, to provide recommendations for future standards being drafted. However, it is important to note that this article itself is not intending to serve as a standard.

microbiology↗

bioRxiv2024

REDUCED CACNA1C EXPRESSION PRODUCES ANHEDONIC REACTIONS TO PALATABLE SUCROSE IN RATS: NO INTERACTIONS WITH JUVENILE OR ADULT STRESS

Genetic variation in CACNA1C, which encodes the alpha-1 subunit of Cav1.2 L-type voltage-gated calcium channels, is strongly linked to risk for psychiatric disorders including schizophrenia, bipolar disorder, and major depression. Here we investigated the impact of mutations of one copy of Cacna1c on rats hedonic responses to palatable sucrose (assessed using the analysis of consumption microstructure). In addition, we also investigated the effects of combining either juvenile or adult stress with the manipulation of Cacna1c. Across three experiments Cacna1c+/- rats displayed attenuated hedonic reactions to sucrose compared to WT littermate controls, despite the Cacna1c+/- rats retaining sensitivity to sucrose concentration in terms of the amount of consumption. Unexpectedly, juvenile stress enhanced rather than reduced hedonic reactions to sucrose, while adult stress did not have clear hedonic effects. The effects of Cacna1c manipulation did not interact with either juvenile or adult stress. The fact that Cacna1c+/- rats display a clear analogue of anhedonia - a reduction in the positive hedonic reactions normally elicited by highly palatable sucrose - a symptom observed transdiagnostically across psychiatric disorders linked to CACNA1C, suggests this model may play a valuable role in the translational fiinvestigation of anhedonia.

genetics↗

bioRxiv2024

Birds affected by a 2021 avian mortality event are strongly associated with supplemental feeding and ground foraging behaviors

In 2021, news outlets and state natural resources agencies reported a large number of avian deaths across several states in the eastern and midwestern USA. This event fomented a rapid and robust response from animal health experts from across the country. Given the clustered pattern of disease and death, an infectious etiology was rigorously investigated. No single causative pathogen was identified, leaving the cause and thus epidemiology of the mortality event unex-plained. In this study, we attempted to hone in on potential causes or contributors to this event by constructing a dataset on affected birds life history, phylogeny, and ecology. After a preliminary analysis of these features, we developed a statistical pipeline to test two hypotheses regarding features of birds associated with the mortality event: (1) that a significant proportion of affected birds in the total sample are members of the Cornell Feederwatch list (i.e., birds that consume supplemental feed, and their predators), and that (2) ground-feeding species would be significantly represented in the sample. While logistic regression models support the plausibility of the two hypotheses, they are statistically indistinguishable. We discuss the implications of these findings, propose future work, and highlight the importance of ecological and behavioral expertise in understanding epidemiological phenomena.

ecology↗

bioRxiv2024

The value of livestock abortion surveillance in Tanzania: identifying disease priorities and informing interventions

BackgroundLack of reliable data on the aetiology of livestock diseases, especially in Africa, is a major factor constraining the design of effective livestock health interventions to improve livelihoods, food security and public health. RationaleLivestock abortion is an important disease syndrome that affects productivity and livestock economies, and poses risks to public health. Worldwide, several pathogens are associated with livestock abortions but across Africa livestock disease surveillance data rarely include information from abortion events, little is known about the aetiology and impacts of livestock abortions, and data are not available to inform prioritisation of disease interventions. MethodsThis paper describes outcomes from a surveillance platform that was set up in 15 wards in northern Tanzania spanning pastoral, agropastoral and smallholder agro-ecological systems to investigate the causes and impacts of livestock abortion. Abortion cases were reported by farmers to Ministry of Livestock and Fisheries livestock field officers and on to investigation teams. The abortion was eligible for inclusion if the research field team or livestock field officer could attend within 72 hours of the event occurring. If so, a field investigation was carried out to collect diagnostic samples from aborted materials and aborting dams and questionnaire data on herd/flock management. Laboratory diagnostic tests were carried out for a range of abortigenic pathogens, and laboratory and questionnaire data analysed to investigate a) determinants of attribution; b) patterns of investigated events, including species and breed affected, previous abortion history and recent stressful events, and the seasonality of cases; c) determinants of reporting, investigation and attribution; (d) cases in which zoonotic pathogens were detected. ResultsOver a two-year period (2017-2019), 215 abortion events in cattle (n=71), sheep (n=44) and goats (n=100) were investigated from 13 of the 15 wards. The number of investigated cases varied widely across wards, with three of the 15 field officers (20%) reporting 70% of investigated cases. Aetiological attribution, achieved for 19.5% of cases through PCR-based diagnostics, was significantly affected by delays in obtaining samples from field investigation. Histopathology proved less useful than PCR diagnostics due to rapid deterioration of field samples. Vaginal swabs from aborting dams provided a practical and sensitive source of diagnostic material for pathogen detection. Discussion / ConclusionLivestock abortion surveillance, even at a small scale and when capturing only a small proportion of events, can generate valuable information on causes of zoonotic disease outbreaks, livestock reproductive losses and can identify important pathogens that are not easily captured through other forms of livestock disease surveillance. This study demonstrated the feasibility of establishing an effective reporting and investigation system that could be implemented across a range of settings, including remote rural areas. This has been achieved through effective engagement of community-based field officers, establishment of practical sample collection protocols and application of molecular diagnostic platforms.

zoology↗

bioRxiv2023

Multiple, single trait GWAS and supervised machine learning reveal the genetic architecture of Fraxinus excelsior tolerance to ash dieback in Europe

Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among clones in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior remains poorly understood. Here, we integrate quantitative genetics and genome-wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and its relationship to phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). We use whole-genome sequencing of 486 F. excelsior genotypes to confirm the genotypic correlation between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Although, our results suggest that the examined traits are polygenic, a relatively small number of single nucleotide polymorphisms (SNPs) explained a large proportion of the variation in both disease tolerance and autumn leaf yellowing. We could explain up to 63% (based on 9155 unlinked SNPs) of variation in individual response to ash dieback crown damage and up to 72% (based on 3740 unlinked SNPs) of variation in autumn yellowing. We identified eight SNPs encoding non-synonymous substitutions, of which those with the highest predictive power were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). Overall, our results provide insights of a multifaceted defence response, according to which a combination of direct defence mechanisms and phenological avoidance of pathogen spread constitute tolerance to ash dieback.

plant biology↗

bioRxiv2023

Transcript errors generate a continuous stream of amyloid and prion-like proteins in human cells

Aging is characterized by the accumulation of amyloid and prion-like proteins. However, the molecular mechanisms by which these proteins arise remain unclear. Here, we demonstrate that transcript errors generate amyloid and prion-like proteins in a wide variety of human cell types, including stem cells, brain organoids, and fully differentiated neurons. Intriguingly, some of these proteins are identical to proteins previously implicated in familial cases of amyloid diseases, raising the possibility that both familial and non-familial cases are caused by identical mutant proteins. However, transcript errors also generate amyloid proteins that have not been observed before, suggesting that aging cells are exposed to a second class of pathogenic proteins we are currently unaware of. Finally, we show that transcript errors are readily generated by DNA damage, a hallmark of human aging and a staple of multiple proteotoxic diseases, including Alzheimers disease. Together, these observations greatly expand our understanding of mutagenesis in human aging and disease and suggest a new mechanism by which amyloid diseases can develop.

molecular biology↗