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Mitchell, M.

Publications and source records attributed to Mitchell, M..

At least 19 recordsLinked to original sources

A three-dimensional imaging pipeline for the detection of vasculogenic mimicry in mouse tumor models

Vasculogenic mimicry (VM) describes the ability for tumor cells to mimic endothelial cells and form tumor-lined blood vessels. Although VM is associated with poor prognosis, resistance to therapeutics and metastasis, its presence, relevance and functionality have been debated, largely due to the techniques employed to determine its presence. Dual CD31 and periodic acid-Schiff (PAS) histological staining, the method widely used to detect VM within tumor tissue, is hampered by issues with artifacts of 2D sections and does not assess active blood flow through vessels and hence cannot confirm vessel functionality. Here, we present a 3D imaging pipeline to detect functionally perfused VM and host vessels within mouse tumor models. Mice tumor models are intravenously injected with fluorescently-labelled tomato lectin which binds to the lumen of functional blood vessels. These tumors are thickly sliced, optically-cleared, stained with endothelial markers and imaged using light-sheet microscopy. We apply this imaging modality to image tumors from six breast cancer patient-derived tissue xenograft models, an orthotopic mammary cancer model and two small cell lung cancer circulating-tumor cell explant models, where VM vessels, mosaic vessels and host-VM vessel junctions can be detected. To our knowledge, this is the largest collection of 3D VM vessel images to date, providing convincing evidence of the presence and functionality of VM within tumors and defining the level of evidence necessary to detect VM in vivo.

cancer biology↗

SatCHM (Satellite Canopy Height Model): Leveraging deep learning for site-specific sub-meter canopy height predictions

High-resolution monitoring of forest structure and productivity is essential for effective natural resource management. However, monitoring approaches such as field-based forest inventories or extensive lidar campaigns are costly, time-intensive, and spatially limited. Therefore, inexpensive and accessible methods are needed. SatCHM (Satellite Canopy Height Model) was developed to be an accessible and open-source tool for researchers, allowing for site-specific and temporally flexible predictions of canopy height with limited computational resources. SatCHM requires four inputs: panchromatic satellite imagery, solar and sensor angle metadata of satellite imagery, digital elevation models (DEMs), and lidar-produced CHMs for an area of interest. After SatCHM pre-processes inputs, data is loaded into a collection of convolutional neural networks (CNNs) for image-to-image regression. This ensemble cooperates to yield high-resolution predictions (up to 0.5-meter) of three-dimensional tree structure with discernible tree crowns across a broader defined area of interest. After calculating the mean absolute error for each prediction output, the median of these mean absolute errors was 6.06 meters.

ecology↗

Conformal Uncertainty Quantification for BayesAge Epigenetic Age Predictions

Epigenetic clocks predict chronological age from DNA methylation (DNAm) profiles, yet most provide point estimates without calibrated uncertainty. This limits their use when quantified error bounds are required. We apply conformal prediction to BayesAge, a maximum-likelihood clock that models nonlinear DNAm-age relationships using a small set of CpG loci and a count-based likelihood. Split conformal prediction yields distribution-free prediction intervals with finite-sample marginal coverage guarantees under exchangeability and requires only a single model fit per split. We also evaluate a locally scaled variant that produces age-dependent interval widths using a locally estimated error scale. In our targeted bisulfite sequencing cohort, split conformalized BayesAge attains near-nominal empirical coverage while preserving BayesAge point-prediction accuracy. The locally scaled variant yields wider intervals at older ages, but its coverage is less stable in small-calibration regimes, consistent with additional uncertainty from estimating the local scale. Relative to Monte Carlo intervals that propagate read-sampling variability and to higher-dimensional linear baselines (conformalized linear quantile regression and conformalized Lasso regression), conformalized BayesAge provides calibrated uncertainty using substantially fewer CpG sites and with weaker age-dependent structure in residuals. These results support conformal prediction as a practical approach for uncertainty quantification in DNAm-based age estimation.

bioinformatics↗

PathoBench: an open community-driven benchmark registry for pathogen bioinformatics tools

SummaryThe proliferation of pathogen bioinformatics pipelines has outpaced the communitys ability to compare them on common ground. Self-reported performance numbers, ad-hoc evaluation datasets, and inconsistent metrics make pipeline selection difficult for clinical and public-health researchers. We present PathoBench, an open web platform that addresses this gap through three coordinated mechanisms: (i) a curated registry of 26 standard benchmark datasets across 10 human pathogens, each with persistent identifiers and direct download links; (ii) pathogen-specific evaluation metrics that submissions must report, allowing direct head-to-head comparison only on the same dataset; and (iii) a credibility framework combining mandatory dataset attestation, ORCID-linked attribution, public peer comments, and administrator verification. As a case study, four published Mycobacterium tuberculosis drug-resistance pipelines were evaluated against the WHO TB mutation catalogue, demonstrating the frameworks discriminating power. PathoBench is open for community contributions across all ten supported pathogens. Availability and implementationPathoBench is freely available at https://pathobench.vercel.app. Source code is released under the MIT license at https://github.com/BPHL-Molecular/pathobench. The platform requires no installation for end users; programmatic access is available via a Supabase REST API. Contactyibo.dong@flhealth.gov Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

Complete, haplotype-resolved genome assemblies have provided unprecedented insight into the evolution of structurally complex, rapidly evolving regions of human genomes1-6; however, population-scale pangenome resources of our closest relatives, chimpanzees and bonobos (genus, Pan), are necessary to ascertain the origins and evolutionary context of these loci. Here, we sequence and assemble 58 haplotypes from four distinct Pan clades to high contiguity (median contig NG50=54 Mb), including eight near-T2T genomes. These genomes reveal previously intractable genetic variation increasing estimates of genome-wide genetic diversity 6-37% across populations compared to short-read estimates7. We identify recurrent structural polymorphisms across species impacting genes associated with immune response and host-pathogen interaction and find that structural variants (SVs) are 170- to 260-fold more likely than single nucleotide variants (SNVs) to exhibit high-impact effects across species. Contrasting SV patterns across primates we find that transposable element mutation rates differ by as much as threefold between species. We show that human disease-associated short tandem repeat (TR) loci have uniquely expanded in humans sensitizing our species to these TR-expansion disorders. Physically phased haplotypes enable reconstruction of genome-wide genealogical histories, uncovering ancient, functional genetic variation maintained by balancing selection, as well as signatures of recent adaptation in chimpanzee subspecies. Several malaria-associated loci exhibit ancient structural polymorphism, including the African great ape-specific glycophorin (GYP) gene expansion. We characterize the sequence, structure, and composition of diverse glycophorin haplotypes in humans and chimpanzees. We identify independent malaria-protective GYPA-B fusion events in humans and novel chimpanzee glycophorin genes resulting from both ancient and recent fusion events demonstrating parallel adaptations to pathogen resistance across hominins. Together, our resource highlights the critical importance of nonhuman primate population-scale pangenomics for understanding the evolution of complex genome structures and the biodiversity of our endangered closest living relatives.

evolutionary biology↗

Resolving heterogeneity of targeted lipid nanoparticles through solution-based biophysical analyses

Targeted lipid nanoparticles (tLNPs) represent the next frontier in nucleic acid therapeutics, enabling cell-specific delivery through covalent attachment of targeting ligands that drive receptor-mediated uptake. tLNPs are particularly promising for pregnancy-associated applications where precise on-target delivery is required to minimize maternal toxicity and protect fetal health. Yet, their rational design is limited by an incomplete understanding of how tLNP physicochemical properties influence biological performance. Conventional LNPs already exhibit pronounced heterogeneity in size, composition, and RNA loading, which is further amplified in tLNPs by variability in ligand attachment and surface density. Because traditional analytical methods report only ensemble-averaged properties, the nanoscale diversity of tLNPs remains unresolved. Here, we find that tLNP functional behavior is governed by previously inaccessible, structurally distinct tLNP subpopulations that are not captured by bulk measurements. We utilize asymmetric flow field-flow fractionation integrated with in-line UV spectral analysis, light scattering, and synchrotron small-angle X-ray scattering (AF4-UV-DLS-MALS-SAXS) to resolve ligand-dependent tLNP subpopulations that differ in size, shape, composition, and relative abundance. We find that protein conjugation preserves the internal lipid-RNA nanostructure of base LNPs but substantially increases particle heterogeneity, particularly for larger and multivalent targeting ligands. Despite increased heterogeneity, tLNPs functionalized with higher-avidity ligands achieve more effective targeted placental RNA delivery in mice, suggesting that binding avidity can offset the functional consequences of polydispersity. Chemometric SAXS analyses reveal that only SAXS-resolved tLNP subpopulations, not ensemble-averaged parameters, correlate with targeted placental transfection in vivo, whereas bulk-derived physicochemical metrics more strongly associate with nonspecific hepatic delivery. Together, this work harnesses a separation-coupled biophysical platform to resolve previously inaccessible tLNP subpopulations and demonstrates that subpopulation nanoscale structure, rather than bulk-averaged properties, dictates targeted RNA delivery. These insights provide a mechanistic foundation for rational engineering of next-generation precision targeted RNA LNP therapeutics.

bioengineering↗

Community member, community liaison and researcher perspectives on the creation of HapMap and 1000 Genomes Project iPSCs

The National Human Genome Research Institute (NHGRI) Repository for Human Genetic Research (NHGRI Repository) distributes renewable lymphoblastoid cell lines (LCL) and cell line DNAs donated by members of 26 communities who have taken part in the International HapMap and 1000 Genomes Projects. The relatively recent introduction of induced pluripotent stem cell (iPSC) reprogramming technologies offers a new opportunity to create iPSCs from HapMap and 1000 Genomes Project biospecimens. However, since relevant iPSC technology did not exist when the HapMap and 1000 Genomes Projects began, it was not explicitly included in the consent process. To explore donor community and researcher perspectives on potential HapMap and 1000 Genomes Project iPSC creation, we conducted an online, semi-structured survey. The majority of community (86%) and research (86%) respondents agreed that creating iPSCs from HapMap and 1000 Genomes Project biospecimens could benefit the research community; however non-trivial concerns (36% community respondents and 16% researcher respondents) and doubts (21% community respondents and 11% researcher respondents) about HapMap and 1000 Genomes Project iPSC creation were also shared. Given these results, we will continue to explore opportunities to engage with HapMap and 1000 Genomes Project communities that include educational materials and detailed discussions regarding the potential for creating iPSCs from their community biospecimens. In parallel, we will continue to grow the existing NHGRI Repository iPSC collection with new donor submissions through the Human Pangenome Reference Consortium (HPRC) that explicitly consented to the creation of iPSCs.

genomics↗

Rapid turnover and recurrent structural variation at the 17q21.31 locus in modern and ancient human genomes, and primates

The 17q21.31 locus in humans harbors several complex structural haplotypes including a [~]970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is [~]2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the KANSL1 gene which may predispose them to Koolen-de Vries syndrome causing microdeletions. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in [~]5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased [~]6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.

genomics↗

Solution biophysics identifies lipid nanoparticle non-sphericity, polydispersity, and dependence on internal ordering for efficacious mRNA delivery

Designing lipid nanoparticle (LNP) delivery systems with specific targeting, potency and minimal side effects is crucial for their clinical use. However, traditional characterization methods, such as dynamic light scattering, cannot accurately quantify physicochemical properties of LNPs and how they are influenced by the lipid composition and mixing method. Here we structurally characterize polydisperse LNP formulations by applying emerging solution-based biophysical methods that have higher resolution and provide biophysical data beyond size and polydispersity. These techniques include sedimentation velocity analytical ultracentrifugation, field-flow fractionation followed by multi-angle light scattering, and size-exclusion chromatography in-line with synchrotron small-angle X-ray scattering. We show that LNPs have intrinsic polydispersity in size, RNA loading, and shape, which depends on both the formulation technique and lipid composition. Lastly, we predict LNP transfection in vitro and in vivo by examining the relationship between mRNA translation and physicochemical characteristics. Solution-based biophysical methods will be essential for determining LNP structure-function relationships, facilitating the creation of new design rules for LNPs.

bioengineering↗

SC10X/U: A High-density Electrode System for Non-Invasive Recording of Neural Activity of the Cervical Spinal Cord

ObjectiveTo design and develop a high-density (HD) electrode system that describes the position of surface electrodes for recording electrophysiological signals from the human cervical spinal cord. The system is intended to standardize experimental recordings and facilitate the subsequent analysis of evoked and spontaneous spinal cord neural activity, using high-density electrospinography (HD-ESG). MethodThe proposed system (SC10-X/U) describes the locations of up to 76 channels with a unique nomenclature, where the division of the spinal cord (SC) electrode space was inspired by the EEG 10-10 system. As proof of concept, spinal evoked potentials in response to median nerve stimulation at the wrist were recorded from 10 participants and characterized based on a 64-channel derivation from the SC10-X/U system. ResultsFollowing the design criteria, the SC10-X/U defines 76 electrode positions and its configuration. HD-ESG system was utilized to successfully record evoked spinal responses and significant N13 and P9 potential were observed in response to the stimulation. The spinal N13 potential had a latency of 13.2 +-1.1ms (mean +-SD) after stimulation. A topographic map of the N13 electro-spinal activity using the 64-channel recording system revealed an epicentre at C5-C7 dorsal-vertebral locations (ML4 - ML6 electrodes). ConclusionThe proposed SC10-X/U system will facilitate standardized recording and analysis of high-density ESG signals from the human cervical spinal cord. The system defines electrode locations to promote standardization across different individuals, studies, and clinical and research centres. The HD-ESG evoked potentials recorded using the proposed system were comparable to those observed in previous non-HD studies. The presented topographic maps conform to known neurophysiological and neuroanatomical findings. This served to validate the design and development of the electrode system and patch for future studies.

neuroscience↗

MicroBayesAge: A Maximum Likelihood Approach to Predict Epigenetic Age Using Microarray Data

Certain epigenetic modifications, such as the methylation of CpG sites, can serve as biomarkers for chronological age. Previously, we introduced our BayesAge frameworks for accurate age prediction through the use of locally weighted scatterplot smoothing (LOWESS) to capture the non-linear relationship between methylation or gene expression and age, and Maximum Likelihood Estimation (MLE) for bulk bisulfite and RNA sequencing data. Here we now introduce MicroBayesAge, a framework that enhances prediction accuracy by subdividing input data into age-specific co-horts and employing a new two-stage process for training and testing. Age prediction for younger patients was significantly improved. MicroBayesAge also exhibited minimal bias in its age predictions. Additionally, we explored the performance of our model for sex-specific age prediction which revealed slight improvements in accuracy for male patients, while no changes were observed for female patients. MicroBayesAge provides more accurate age predictions by accounting for variations in epigenetic markers of aging among different subgroups, which have been over-looked by commonly used models.

bioinformatics↗

Global review of meta-analyses reveals key data gaps in agricultural impact studies on biodiversity in croplands

AimAgriculture depends heavily on biodiversity, yet unsustainable management practices continue to affect a wide range of organisms and ecosystems at unprecedented levels worldwide. Addressing the global challenge of biodiversity loss requires access to consolidated knowledge across management practices, spatial levels, and taxonomic groups. LocationGlobal Time period1994 to 2022 Major taxa studiedAnimals, microorganisms, plants. MethodsWe conducted a comprehensive literature review synthesising data from all meta-analyses about the impacts of agricultural management practices on biodiversity in croplands, covering field, farm, and landscape levels. From 200 retained meta-analyses, we extracted 1,885 mean effect sizes (from 69,850 comparisons between a control and treatment) assessing the impact of management practices on biodiversity, alongside characterising over 9,000 primary papers. ResultsSeven high-income countries, notably the USA, China, and Brazil dominate agricultural impact studies with fertiliser use, phytosanitary interventions and crop diversification receiving widespread attention. The focus on individual practices overshadows research at the farm and landscape level. Taxonomically, Animalia, especially arthropods, are heavily studied while taxa such as annelids and plants receive comparatively less attention. Effect sizes are predominantly calculated from averaged abundance data. Significant gaps persist in terms of studies on the effects of agricultural interventions on specific taxonomic groups (e.g. annelids, mammals) and studies analysing functional traits. Main conclusionsOur study highlights the importance of analysing the effects of combined practices to accurately reflect real-world farming contexts. While abundance metrics are common, reflecting several biodiversity facets and adopting a more balanced research approach across taxa are crucial for understanding biodiversity responses to agricultural changes and informing conservation strategies. Given the unbalanced evidence on impacts of agricultural practices on biodiversity, caution is required when utilising meta-analytical findings for informing public policies or integrating them into global assessment models like life-cycle assessments or global flux models.

ecology↗

Fragile X Mental Retardation Protein (FMRP) expression in human nociceptor axons of the spinal dorsal horn-- Implications for RNA targeting and localized translation

Fragile X Mental Retardation Protein (FMRP) regulates activity-dependent RNA localization and local translation to modulate synaptic plasticity throughout the CNS. Mutations in the FMR1 gene that hinder or ablate FMRP function cause Fragile X Syndrome (FXS), a disorder associated with sensory processing dysfunction. FXS pre-mutations are associated with increased FMRP expression and neurological impairments including sex dimorphic presentations of chronic pain. In mice, FMRP ablation causes dysregulated DRG neuron excitability and synaptic vesicle exocytosis, spinal circuit activity, and decreased translation-dependent nociceptive sensitization. Activity-dependent, local translation is a key mechanism for enhancing primary nociceptor excitability which promotes pain in animals and humans. These works indicate that FMRP likely regulates nociception and pain at the level of the primary nociceptor or spinal cord. Therefore, we sought to better understand FMRP expression in the human dorsal root ganglion (DRG) and spinal cord using immunostaining in organ donor tissues. We find that FMRP is highly expressed in DRG and spinal neuron subsets with substantia gelatinosa exhibiting the most abundant immunoreactivity in spinal synaptic fields. Here, it is expressed in nociceptor axons. FMRP puncta colocalized with Nav1.7 and TRPV1 receptor signals suggesting a pool of axoplasmic FMRP localizes to plasma membrane-associated loci in these branches. Interestingly, FMRP puncta exhibited notable colocalization with calcitonin gene-related peptide (CGRP) immunoreactivity selectively in female spinal cord. Our results support a regulatory role for FMRP in human nociceptor axons of the dorsal horn and implicate it in the sex dimorphic actions of CGRP signaling in nociceptive sensitization and chronic pain.

neuroscience↗

Gut Microbial Trimethylamine is Elevated in Alcohol-Associated Hepatitis and Contributes to Ethanol-Induced Liver Injury in Mice

BACKGROUNDThere is mounting evidence that microbes resident in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcohol-associated hepatitis (AH). However, mechanisms by which gut microbes synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested. METHODSWe used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, finding elevated levels of the microbial metabolite trimethylamine (TMA) in AH. In subsequent studies, we treated mice with non-lethal bacterial choline TMA lyase (CutC/D) inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. RESULTSWe show the gut microbial choline metabolite trimethylamine (TMA) is elevated in AH patients and correlates with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial CutC/D activity protects mice from ethanol-induced liver injury. CutC/D inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome and host liver transcriptome. CONCLUSIONSThe microbial metabolite TMA is elevated in patients with AH, and inhibition of TMA production from gut microbes can protect mice from ethanol-induced liver injury.

biochemistry↗

Phosphorylation dynamics in a flg22 induced, heterotrimeric G protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking

flg22 is a 22-amino peptide released from bacterial flagellin, a Microbe-Associated Molecular Pattern (MAMP) that is recognized by the plant cell as a signal indicating that bacteria are present. On its own, flg22 initiates a rapid increase in cytoplasmic calcium, extracellular reactive oxygen species, and activation of a Mitogen Activated Protein Kinase (MAPK) cascade, all of which are activated within 15 minutes after the cell perceives flg22. Here we show a massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome within this 15-minute duration in wildtype and a mutant deficient in G-protein coupled signaling. Integration of phosphoproteome with protein-protein interactome data followed by network topology analyses discovered that many of the flg22-induced phosphoproteome changes fall on proteins that comprise the G protein interactome and on the most highly populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the G-protein interactome depend on a functional heterotrimeric G protein complex, some occur on proteins that interact directly with components of G-coupled signal transduction. One of these is ATB, a substrate-recognition sub-unit of the PP2A Ser/Thr phosphatase and an interactor to Arabidopsis thaliana REGULATOR OF G SIGNALING 1 protein (AtRGS1), a 7-transmembrane spanning modulator of the nucleotide-binding state of the core G protein complex. AtRGS1 is phosphorylated by BAK1, a component of the flg22 receptor, to initiate AtRGS1 endocytosis. A null mutation of ATB confers high basal endocytosis of AtRGS1, suggesting sustained phosphorylated status. Loss of ATB confers traits associated with loss of AtRGS1. Because the basal level of AtRGS1 is lower in the atb null mutant in a proteasome-dependent manner, we propose that phosphorylation-dependent endocytosis of AtRGS1 is part of a mechanism to degrade AtRGS1 which then sustains activation of the G protein complex. Thus, the role of ATB is now established as a central component of phosphorylation-dependent regulation of system dynamics in innate immunity.

systems biology↗

Self-regulation of the brain's Beta rhythm using a brain-computer interface improves inhibitory control

Neural oscillations, or brain rhythms, fluctuate in a manner reflecting ongoing behavior. Whether these fluctuations are instrumental or epiphenomenal to the behavior remains elusive. Attempts to experimentally manipulate neural oscillations exogenously using non-invasive brain stimulation have shown some promise, but difficulty with tailoring stimulation parameters to individuals has hindered progress in this field. We demonstrate here using electroencephalography (EEG) neurofeedback in a brain-computer interface that human participants (n=44) learned over multiple sessions across a 6-day period to self-regulate their Beta rhythm (13-20 Hz) over the right inferior frontal cortex (rIFC). The modulation was evident only during neurofeedback task performance but did not lead to offline alteration of Beta rhythm characteristics at rest, nor to changes in subsequent cognitive behavior. Likewise, a control group (n=38) who underwent training of the Alpha rhythm (8-12 Hz) did not exhibit behavioral changes. Although the right frontal Beta rhythm has been repeatedly implicated as a key component of the brains inhibitory control system, the present data suggest that its manipulation offline prior to cognitive task performance does not result in behavioral change. Thus, this form of neurofeedback training of the tonic Beta rhythm would not serve as a useful therapeutic target for disorders with dysfunctional inhibitory control as their basis.

neuroscience↗

The right time and place: time- and age-dependent vaccine-enhanced mucosal immunity to parasite infection

Individuals vary broadly in their response to vaccination and subsequent exposure to infection, causing persistence of both infection and transmission. The prevalence of poor vaccine responders hampers the development of vaccines, especially against parasitic helminths. Yet despite having substantial economic and societal impact, the immune mechanisms that underlie such variability, especially at the site of parasite infection, remain poorly understood. Previous trials using a prototype vaccine for the control of the gastric parasitic Teladorsagia circumcincta, one of the highest impact parasites affecting sheep, revealed substantial variation in protection between individuals, which we hypothesised may in part be driven by age at vaccination. Here, to characterise how immunity at the mucosal site of infection developed in vaccinated lambs, we inserted gastric cannulae into the abomasa (true stomachs) of three-month- and six-month-old lambs before vaccination, and performed a longitudinal analysis of their local immune response during subsequent challenge infection. We found that the vaccine caused systemic changes in the baseline immune profile within the abomasum before any parasite exposure had occurred and reduced parasite burden and egg output once lambs were infected, regardless of age. However, age affected how vaccinated lambs responded to subsequent infection across multiple immune pathways, with only a minority of protective immune pathways being independent of age. This resulted in younger lambs being more susceptible to infection regardless of vaccine status. The identification of age-dependent (mostly adaptive) and age-independent (mostly innate) protective immune pathways should help refine the formulation of vaccines against these and potentially other helminth parasites of ruminants, and could indicate specificities of anti-helminth immunity more generally.

immunology↗

An open source platform for presenting dynamic visual stimuli

Operant behavior procedures often rely on visual stimuli to cue the initiation or secession of a response, and to provide a means for discriminating between two or more simultaneously available responses. While primate and human studies typically use LCD or OLED monitors and touch screens, rodent studies use a variety of methods to present visual cues ranging from traditional incandescent light bulbs, single LEDs, and, more recently, touch screen monitors. Commercially available systems for visual stimulus presentation are costly, challenging to customize, and are typically closed source. We developed an open-source, highly-modifiable visual stimulus presentation platform that can be combined with a 3D-printed operant response device. The device uses an eight by eight matrix of LEDs, and can be expanded to control much larger LED matrices. Implementing the platform is low-cost (<$70 USD per device in the year 2020). Using the platform, we trained rats to make nosepoke responses and discriminate between two distinct visual cues in a location-independent manner. This visual stimulus presentation platform is a cost-effective way to implement complex visually-guided operant behavior, including the use of moving or dynamically changing visual stimuli. Significance StatementThe design of an open source and low cost device for presenting visual stimuli is described. It is capable of presenting complex visual patterns and dynamically changing stimuli. A practical demonstration of the device is also reported, from an experiment in which rats performed a luminance based visual discrimination. The device has utility for studying visual processing, psychophysics, and decision making in a variety of species.

neuroscience↗