Biology subjects

Arnold, J.

Publications and source records attributed to Arnold, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Mass spectrometric identification of a PSI-LHCI-cytochrome b6f complex in both Arabidopsis stn7 and pph1

Native PAGE separation of digitonin-solubilized thylakoid stroma lamellae resolves PSI and cytochrome b6f into separate bands. Mass spectrometric analysis of the 1D native gel bands showed that the bands are baskets of co-migrating complexes along the molecular size axis. Hierarchical clustering confirmed the separation of dimeric cytochrome b6f from PSI in 1D LN-PAGE. Interval-zone free-flow electrophoresis separated the same extracts by charge in a flowing buffer film, and the continuous fractionation indicated co-migration of complexes without the in-gel structural hindrances. A second-dimension LN-PAGE separated the complexes co-migrating in iZE into complexes with defined molecular size, allowing in-gel mass spectrometry identification in the gel bands. Both genotypes showed a 720 kDa fluorescent band in which cytochrome f (PetA) and cytochrome b6 (PetB) join the PSI-LHCI node (stn7, d = 0.50; pph1, d = 0.34). Lhcb1 and Lhcb2 are absent from the 720 kDa node. The 753 kDa band is specific to pph1 (d = 0.38). Phosphorylated LHCII1,2 joins PSI-LHCI there, and PetB is detected in every slice of that band without becoming a leaf of the tree.

plant biology↗

bioRxiv2026

Temperature-Switchable Genome Editors from Extremophile-Derived Integrases

Integrases are site-specific recombinases encoded by phages and other mobile genetic elements. They mediate DNA integration, excision, and inversion between cognate attachment (att) sites. Although integrases are powerful tools for genetic engineering and synthetic biology, most systems lack intrinsic mechanisms that limit activity after expression, creating potential for unintended recombination. We hypothesized that extremophiles could provide temperature-responsive integrases because their enzymes evolved under selective pressure to operate within the thermal ranges experienced by their hosts. To test this concept, we linked integrase-att pairs from 458,683 prokaryotic genome assemblies to curated host growth-temperature metadata. This analysis revealed temperature-associated structure among integrase clusters and established a candidate pool for testing temperature-responsive recombinases. GC content in tyrosine integrase-associated attB sites showed a modest increase in higher-temperature hosts. We developed an inversion assay using a single-copy reporter plasmid and sacB counterselection to quantify integrase activity across temperatures. Thermophile derived integrases from Thermus thermophilus and Geobacillus stearothermophilus displayed hot-ON/cold-OFF activity profiles, whereas an integrase derived from the psychrotroph Pseudomonas cerasi showed cold-ON/hot-OFF activity. Together, these results establish host thermal niche as a guide for discovering intrinsically temperature switchable integrases and provide a foundation for engineering thermally controlled genome editing systems.

molecular biology↗

bioRxiv2026

Chlorophyll binding to Cytochrome b6f precedes photosystem I and II in barley etioplasts

Chlorophyll (Chl) is essential for oxygenic photosynthesis, binding to membrane proteins for light harvesting and electron transfer. In angiosperms, Chl synthesis is halted in darkness, preventing accumulation of Chl-binding photosynthetic complexes in etioplasts. However, etioplasts assemble a dimeric Cytochrome b6f (Cyt b6f) complex, uniquely binding protochlorophyll (Pchl), the esterified derivative of protochlorophyllide (Pchlide). This indicates an evolutionarily conserved structural or functional role for Pchl distinct from the Chl bound in Cyt b6f in chloroplasts. Here we show that upon light-induced Chl synthesis in-vivo and in-vitro, Chl accumulation in Cyt b6f dimers precedes photosystems I and II. We find that chlorophyllide and Chl bind to the light-harvesting-like protein 3 (LIL3), supporting a role for LIL3 in early Chl allocation that extends its described role in stabilizing geranylgeranyl reductase. We determine a dissociation constant of 246.6 {+/-} 37 nM for Chlide binding to LIL3 in-vitro and show that Cyt b6f monomers and LIL3 co-migrate with Chlide in native PAGE, whereas Cyt b6f dimers and LIL3 co-migrate with Chl. These results indicate that Chlide binding to LIL3 chaperones esterification to Chl and reduction of geranylgeraniol, and that Chl release with Cyt b6f dimerization prioritizes Chl binding to Cyt b6f assembly during de-etiolation.

plant biology↗

bioRxiv2026

A membrane-impermeant nucleic acid dye converts bacteriophage plaque assays into a machine-readable format for automated counting

Plaque assays remain the gold standard for bacteriophage quantification, but routine plaque counting is labor-intensive, time-consuming, and poorly suited to large experiments or automated workflows. Conventional plaque images also often provide insufficient contrast for simple software-based counting, especially when plaques are small, faint, or heterogeneous. Here we show that a membrane-impermeant nucleic acid dye can convert standard bacteriophage plaque assays into a high-contrast, machine-readable format compatible with simple automated counting. In a soft-agar overlay workflow, fluorescent labeling enabled plaque detection and automated enumeration using an open-source ImageJ pipeline based on Find Maxima, without phage engineering, machine learning, or custom software. Because the method improves the image contrast of the assay itself, it may also provide improved input for future machine-learning or other advanced automated counting workflows. The method was evaluated across diverse phage-host systems spanning dsDNA, ssRNA, filamentous, and enveloped phages, including T7, MS2, M13, and phi6. In lytic systems, fluorescent signal emerged prior to or alongside conventional plaque visibility and yielded automated counts that agreed closely with manual counting. M13 exhibited delayed fluorescence consistent with its chronic, nonlytic lifestyle, yet remained machine-countable at the conventional next-day endpoint. A Gram-positive Leo2-Bacillus safensis system revealed an important compatibility limit: dye incorporation at plating inhibited plaque formation, but a post-labeling workflow restored detectability and automated counting. Together, these results show that membrane-impermeant dye labeling can make plaque assays more computationally tractable while preserving the accessibility of standard phage methods. This approach provides a practical path toward higher-throughput, statistically rigorous phage biology in both low-resource and automation-oriented laboratories.

microbiology↗

bioRxiv2026

Benchmarking Short-Read ITS2 and Full-Length ITS Sequencing Reveals Pipeline-Dependent Biases in Indoor Fungal Community Profiling

Short-read amplicon sequencing is widely used for fungal surveys but can limit taxonomic resolution. Long-read sequencing enables recovery of the full internal transcribed spacer (ITS) region and may improve ecological and taxonomic inference. Here, we conducted a paired comparison of Illumina ITS2 and PacBio HiFi full-length ITS sequencing using identical DNA extracts from built-environmental air and surface samples (n = 68) collected across homes, a dormitory, and laboratories. Both datasets were taxonomically assigned using the same algorithm and reference database. We performed paired statistics, in-silico ITS2 trimming of long-read sequences, and cross-platform mapping at multiple identity thresholds. Full-length ITS provided higher taxonomic resolution, assigning a greater fraction of ASVs at the family (98% vs. 88%) and species (42% vs. 32%) ranks than ITS2 (paired Wilcoxon q = 0.002). Alpha-diversity comparisons showed similar Shannon diversity across pipelines, whereas richness metrics were consistently higher for full-length ITS. Beta-diversity analyses indicated broadly comparable community-level patterns, although full-length ITS revealed stronger sample-type- and location-associated structure (PERMANOVA R{superscript 2} [≥] 0.06, p = 0.0001). In-silico ITS2 trimming reduced these differences, indicating that amplicon length is a major contributor to enhanced taxonomic resolution and ecological inference. Cross-platform mapping further showed extensive one-to-many relationships between ITS2 and full-length ITS ASVs, consistent with increased sequence resolution in long-read data. Together, these results show that ITS2 sequencing provides robust community-level profiling, while full-length ITS enables improved richness estimates and finer ecological and taxonomic resolution. This paired, bias-aware framework provides a practical template for selecting fungal amplicon sequencing strategies in built-environment mycobiome studies. ImportanceFungal communities in built environments influence indoor air quality and human exposure, yet their characterization depends strongly on sequencing strategy. This study provides a controlled, paired comparison of short-read ITS2 and long-read full-length ITS sequencing, showing that differences in amplicon length substantially contribute to variation in taxonomic resolution and ecological inference. While both approaches yield comparable community-level patterns, full-length ITS improves richness estimates, species-level assignment, and environmental discrimination by resolving sequence variation collapsed in ITS2 surveys. By integrating paired diversity analyses, in-silico ITS2 trimming, and cross-platform ASV mapping, this work offers a bias-aware framework for evaluating fungal amplicon pipelines. Importantly, improved species-level resolution enables functional interpretation of indoor fungi, for example the identification of taxa associated with pathogenic traits, allergen production, or toxin synthesis, supporting the development of more informative exposure metrics and targeted assays relevant to human health in built environments.

microbiology↗

bioRxiv2026

Whole-brain cellular-resolution functional network properties of seizure susceptibility

Despite its prevalence and clinical impacts, epilepsy remains incompletely understood in terms of the population dynamics that mediate seizure susceptibility, initiation, and propagation across brain-wide networks. In this study, we have performed calcium imaging in zebrafish, brain-wide and at cellular resolution, at baseline and as seizures are induced using the GABAA receptor antagonist pentylenetetrazol (PTZ). We have then modeled the network architecture in wild-type and scn1lab-/- larvae, which are seizure-prone and serve as a model for Dravet syndrome. scn1lab-/- larvae show increased pair-wise correlations between neurons when exposed to PTZ, and graph analyses of these correlations revealed genotype-specific network alterations during seizures, identifying regions and metrics linked to seizure onset. Using generative network modeling, we then explored the wiring rules that govern activity in these networks, identifying specific network properties linked to seizure susceptibility that were only detectable using large-scale, cellular-resolution data. Even at baseline in the absence of seizures, these rules differed by genotype in a way that enabled the identification of scn1lab-/- larvae and predicted individuals seizure risk independently of their observable phenotype. These findings uncover the cellular-resolution network properties of a zebrafish model of Dravet syndrome and establish a predictive framework for seizure susceptibility grounded in multi-scale functional connectivity.

neuroscience↗

bioRxiv2025

How big is enough? Movement-informed zoning for African swine fever mitigation

O_LIAfrican swine fever (ASF) poses a serious threat to domestic pigs and wild boar populations. Wild boar can disperse the virus, making effective containment crucial. One of the main control strategies involves establishing restricted zones around detected cases, i.e., areas with temporary restrictions on access and hunting; however, determining the appropriate size of these zones remains a major challenge. C_LIO_LITo inform the size of restricted zones, we analyzed GPS data from 527 wild boar across 46 European study sites using a two-step approach combining first-passage time analysis and survival modelling to quantify the risk of wild boar leaving areas of different radii (i.e., spatial scales). We investigated how the risk of leaving varied over time and across environmental gradients. To go further, we used our model findings to develop an online application that generates predictive maps of optimal buffer sizes for ASF management at the European scale, based on a given risk threshold (the maximum acceptable probability that a wild boar leaves the area). C_LIO_LIWe found that the relationship between radius and the risk of leaving is negative exponential, and the risk of leaving increased over time, with a more rapid increase for smaller radii. Landscape homogeneity, terrain ruggedness and human impact increased the risk of leaving, with stronger effects at small scales. Contrary to other predictors, agricultural cover exerted a strong effect on risk of leaving over large spatial scales, especially when it was abundant. C_LIO_LIAcross Europe, a buffer radius of [~]8 km is likely sufficient around high-risk infection zones in most areas (considering an infectious period of 14 days and a risk threshold of 5%); however, in certain areas, a radius of up to 20 km may be needed to effectively limit wild boar movement. C_LIO_LISynthesis and applications: Our results highlight the need for adaptive, context-specific restricted zones. Buffers of 8 km around ASF-affected areas can limit the risk of infected wild boar dispersal, but they may be reduced to 5 km in highly heterogeneous landscapes or high-human impacted areas. Larger buffers may be required in agricultural landscapes. We provide spatially explicit outputs (optimal buffer sizes) that can directly inform policy and wildlife disease response strategies. The approach can be adapted to any other infectious disease. C_LI

ecology↗

bioRxiv2025

Engineering butyrate-producing Lachnospiraceae to treat metabolic disease

Engineering native gut bacteria offers a route to persistent, programmable therapeutics, yet many dominant taxa remain genetically intractable. Lachnospiraceae are a prevalent and abundant family in the human gut microbiome, possessing metabolic functions generally associated with health1. Despite their promise as engineered live biotherapeutics, genetic manipulation of Lachnospiraceae remains challenging. Here, we develop a modular toolkit for Lachnospiraceae engineering, including constitutive and inducible expression and chromosomal integration systems. Applying this toolkit to the native commensal Coprococcus comes, we program secretion of the mammalian cytokine interleukin-22 (IL-22) in the mouse intestinal tract where it elicits ileal transcriptional responses consistent with cytokine signaling. In a mouse model of metabolic associated steatotic liver disease, IL-22-secreting C. comes improves glucose homeostasis and attenuates hepatic steatosis. This work demonstrates that a native Lachnospiraceae chassis can be genetically programmed to modulate host metabolic and immune physiology. The toolkit provides a generalizable foundation for Lachnospiraceae-derived microbiome therapeutics and for probing causal links between Lachnospiraceae gene programs and host phenotypes.

synthetic biology↗

bioRxiv2025

The polyamine naphthyl-acetyl spermine trihydrochloride (NASPM) lacks specificity for Ca2+-permeable AMPA receptors and suppresses seizure like activity in human brain tissue by inhibition of NMDA receptors.

For decades, naphthyl-acetyl spermine trihydrochloride (NASPM) has been used as a selective inhibitor of calcium-permeable AMPA receptors (CP-AMPAR). In rodents, NASPM is known to suppress seizures in vivo and seizure-like events (SLE) in vitro, suggesting possible involvement of CP-AMPAR in ictogenesis and epileptogenesis. To address whether these findings can be translated to human brain, we investigated the involvement of glutamatergic receptor subclasses in SLE in human cortex ex vivo, demonstrating that glutamatergic receptor antagonists can block (NASPM and APV) or reduce (UBP302, GYKI52466, GYKI53655) SLE. Using a multimethodological approach we were able to demonstrate that both NASPM and APV inhibit human SLE by inhibition of NMDA receptors. Our results further show that the inhibitory effect of NASPM on NMDA receptors is sufficient to explain its inhibition of seizure like activity, rather than its action on CP-AMPA receptors. Thus, our findings challenge previous knowledge on the use of NASPM as a specific CP-AMPAR inhibitor. Some phenomena previously attributed to CP-AMPAR, may need to be re-examined more closely. Overall, our study raises awareness about potential pitfalls in the use of existing pharmacological agents and sets a new paradigm for the use of NASPM in neuroscience research while questioning its therapeutic potential in a clinical context.

neuroscience↗

bioRxiv2024

Macrophage crosstalk with neural progenitors and fibroblasts controls regenerative neurogenesis via Sema4ab after spinal cord injury in zebrafish

Zebrafish, in contrast to mammals, regenerate neurons after spinal cord injury, but little is known about the control mechanisms of this process. Here we use scRNA-seq and in vivo experiments to show that sema4ab, mainly expressed by lesion-reactive microglia, attenuates regenerative neurogenesis by changing the complex lesion environment. After spinal injury, disruption of sema4ab doubles the number of newly generated progenitor cells and neurons but attenuates axon regrowth and recovery of swimming function. Disruption of the plxnb1a/b receptors, selectively expressed by neural progenitor cells, increases regenerative neurogenesis. In addition, disruption of sema4ab alters activation state and cytokine expression of microglia, such that fibroblasts increase expression of the cytokine tgfb3, which strongly promotes regenerative neurogenesis. Hence, sema4ab in microglia attenuates regenerative neurogenesis in multiple ways, likely directly through plxnb1a/b receptors and indirectly, by controlling the inflammatory milieu and tgfb3 levels. Targeting Sema4A-dependent signalling in non-regenerating vertebrates may be a future strategy to improve regenerative outcomes. HIGHLIGHTS- Microglia suppress pro-regenerative fibroblast signalling in a spinal injury site - Fibroblasts promote regenerative neurogenesis via Tgfb3 signalling - sema4ab promotes microglia activation state after spinal injury - scRNA-seq reveals full complement of sema4ab-dependent changes on different cell types during repair of a spinal lesion site

neuroscience↗

bioRxiv2024

Stable primary brain cell cultures from zebrafish reveal hyperproliferation of non-neuronal cells from scn1lab mutants

Zebrafish are a popular model system for studying the genetic and neural underpinnings of perception and behavior, both in wild-type animals and in the context of disease modelling. Cultured primary neurons provide a key complementary tool for such studies, but existing protocols for culturing embryonic zebrafish primary neurons are limited by short cell survival and low neuronal purity. In this study, we set out to establish a protocol to produce long lived, pure neuronal cultures from zebrafish that could be used to study the mechanistic contributions of genes to neuronal networks. We then used these primary cultures to characterize cell proliferation and differentiation in primary neurons derived from scn1lab mutant embryos, which lack a sodium channel relevant to Dravet syndrome and autism. Using our optimized protocol, we generated cultures that proliferate, diversify, and form stable networks of neurons surviving for months. These stable cultures allowed us to perform genetic experiments, in this case revealing dramatic differences in the cellular composition of cultures derived from scn1lab mutant embryos versus their wild type siblings. Specifically, we find that loss of scn1lab promotes hyperproliferation of non-neuronal cells in mixed cultures of brain cells. In pure neuronal cultures, we find alterations in neurotransmitter subtypes consistent with known effects of scn1lab loss of function. Validating the utility of this approach, we then identify a corresponding hyperproliferation phenotype in live scn1lab mutant embryos, shedding light on potential mechanisms that may be relevant for Dravet syndrome. Significance statementMost existing embryonic zebrafish primary neuron culture protocols describe growing mixed cell types for restricted durations. Here, we report generation of zebrafish mixed type or pure neuronal cultures that are viable for over 100 days. We apply these cultures to gain new insight into scn1lab, a zebrafish orthologue of the Dravet Syndrome-associated sodium channel gene SCN1A. We report that loss of scn1lab results in hyperproliferation of non-neuronal cells, revealing an underappreciated mechanism by which mutations in SCN1A impact the structure and function of neuronal networks. Our in vitro cultures thus faithfully recapitulate in vivo neurobiology and provide a powerful platform to interrogate brain function in health and disease.

neuroscience↗

bioRxiv2024

Brain-wide circuitry underlying altered auditory habituation in zebrafish models of autism.

Auditory processing is widely understood to occur differently in autism, though the patterns of brain activity underlying these differences are not well understood. The diversity of autism also means brain-wide networks may change in various ways to produce similar behavioral outputs. We used larval zebrafish to investigate auditory habituation in four genetic lines relevant to autism: fmr1, mecp2, scn1lab and cntnap2. In free-swimming behavioral tests, we found each line had a unique profile of auditory hypersensitivity and/or delayed habituation. Combining the optical transparency of larval zebrafish with genetically encoded calcium indicators and light-sheet microscopy, we then observed brain-wide activity at cellular resolution during auditory habituation. As with behavior, each line showed unique alterations in brain-wide spontaneous activity, auditory processing, and adaptation in response to repetitive acoustic stimuli. We also observed commonalities in activity across our genetic lines that indicate shared circuit changes underlying certain aspects of their behavioral phenotypes. These were predominantly in regions involved in sensory integration and sensorimotor gating rather than primary auditory areas. Overlapping phenotypes include differences in the activity and functional connectivity of the telencephalon, thalamus, dopaminergic regions, and the locus coeruleus, and excitatory/inhibitory imbalance in the cerebellum. Unique phenotypes include loss of activity in the habenula in scn1lab, increased activity in auditory regions in fmr1, and differences in network activity over time in mecp2 and cntnap2. Comparing these distinct but overlapping brain-wide auditory networks furthers our understanding of how diverse genetic factors can produce similar behavioral effects through a range of circuit- and network-scale mechanisms.

neuroscience↗

bioRxiv2024

Evidence for auditory stimulus-specific adaptation but not deviance detection in larval zebrafish brains

Animals receive a constant stream of sensory input, and detecting changes in this sensory landscape is critical to their survival. One signature of change detection in humans is the auditory mismatch negativity (MMN), a neural response to unexpected stimuli that deviate from a predictable sequence. This process requires the auditory system to adapt to specific repeated stimuli while remaining sensitive to novel input (stimulus-specific adaptation). MMN was originally described in humans, and equivalent responses have been found in other mammals and birds, but it is not known to what extent this deviance detection circuitry is evolutionarily conserved. Here we present the first evidence for stimulus-specific adaptation in the brain of a teleost fish, using whole-brain calcium imaging of larval zebrafish at single-neuron resolution with selective plane illumination microscopy. We found frequency-specific responses across the brain with variable response amplitudes for frequencies of the same volume, and created a loudness curve to model this effect. We presented an auditory oddball stimulus in an otherwise predictable train of pure tone stimuli, and did not find a population of neurons with specific responses to deviant tones that were not otherwise explained by stimulus-specific adaptation. Further, we observed no deviance responses to an unexpected omission of a sound in a repetitive sequence of white noise bursts. These findings extend the known scope of auditory adaptation and deviance responses across the evolutionary tree, and lay groundwork for future studies to describe the circuitry underlying auditory adaptation at the level of individual neurons.

neuroscience↗

bioRxiv2024

Distinct streams for supervised and unsupervised learning in the visual cortex

Representation learning in neural networks may be implemented with supervised or unsupervised algorithms, distinguished by the availability of feedback. In sensory cortex, perceptual learning drives neural plasticity, but it is not known if this is due to supervised or unsupervised learning. Here we recorded populations of up to 90,000 neurons simultaneously from the primary visual cortex (V1) and higher visual areas (HVA), while mice learned multiple tasks as well as during unrewarded exposure to the same stimuli. Similar to previous studies, we found that neural changes in task mice were correlated with their behavioral learning. However, the neural changes were mostly replicated in mice with unrewarded exposure, suggesting that the changes were in fact due to unsupervised learning. The neural plasticity was concentrated in the medial HVAs and obeyed visual, rather than spatial, learning rules. In task mice only, we found a ramping reward prediction signal in anterior HVAs, potentially involved in supervised learning. Our neural results predict that unsupervised learning may accelerate subsequent task learning, a prediction which we validated with behavioral experiments.

neuroscience↗

bioRxiv2024

A double ovulation protocol for Xenopus laevis produces doubled fertilisation yield and moderately transiently elevated corticosterone levels without loss of egg quality

The African claw-toed frog, Xenopus laevis, is a well-established laboratory model for the biology of vertebrate fertilisation and development. For ovulation, X. laevis females are usually injected with chorionic gonadotropin, whereupon they lay typically hundreds to thousands of eggs in a day. Animals are re-used after being rested for a minimum of three months. The literature suggests that adult females can lay much larger numbers of eggs in a short period. Here, we compared the standard "single ovulation" protocol with a "double ovulation" protocol, in which females were ovulated, then re-ovulated after seven days and then rested for three months before re-use. We quantified egg number, fertilisation rate (development to cleavage stage), and corticosterone secretion rate (a measure of stress response) over seven 3-month cycles. We found no differences in egg number-per-ovulation or fertilisation, and no long-term changes in any measures over the trial period. Corticosterone secretion was elevated by ovulation, similarly for the single ovulation as for the first ovulation in the double-ovulation protocol, but more highly for the second ovulation (to a level comparable to that seen following shipment). However, both groups exhibited the same baseline secretion rates by the time of the subsequent cycle. Double ovulation is thus transiently more stressful/demanding than single ovulation but within levels routinely experienced by laboratory X. laevis. Noting that "stress hormone" corticosterone/cortisol secretion is linked to physiological processes, such as ovulation, that are not necessarily harmful to the individual, we suggest that the benefits of a doubling in egg yield-per-cycle per animal without loss of egg quality or signs of acute or long-term harm may outweigh the relatively modest and transient corticosterone elevation we observed. The double ovulation protocol therefore represents a potential new standard practice for promoting the "3Rs" (animal use reduction, refinement and replacement) mission for Xenopus research.

developmental biology↗

bioRxiv2024

Brain-wide impacts of sedation on spontaneous activity and auditory processing in larval zebrafish

Despite their widespread use, we have limited knowledge of the mechanisms by which sedatives mediate their effects on brain-wide networks. This is, in part, due to the technical challenge of observing activity across large populations of neurons in normal and sedated brains. In this study, we examined the effects of the sedative dexmedetomidine, and its antagonist atipamezole, on spontaneous brain dynamics and auditory processing in zebrafish larvae. Our brain-wide, cellular-resolution calcium imaging reveals, for the first time, the brain regions involved in these network-scale dynamics and the individual neurons that are affected within those regions. Further analysis reveals a variety of dynamic changes in the brain at baseline, including marked reductions in spontaneous activity, correlation, and variance. The reductions in activity and variance represent a "quieter" brain state during sedation, an effect that causes highly correlated evoked activity in the auditory system to stand out more than it does in un-sedated brains. We also observe a reduction in auditory response latencies across the brain during sedation, suggesting that the removal of spontaneous activity leaves the core auditory pathway free of impingement from other non-auditory information. Finally, we describe a less dynamic brain-wide network during sedation, with a higher energy barrier and a lower probability of brain state transitions during sedation. In total, our brain-wide, cellular-resolution analysis shows that sedation leads to quieter, more stable, and less dynamic brain, and that against this background, responses across the auditory processing pathway become sharper and more prominent. Significance StatementAnimals brain states constantly fluctuate in response to their environment and context, leading to changes in perception and behavioral choices. Alterations in perception, sensorimotor gating, and behavioral selection are hallmarks of numerous neuropsychiatric disorders, but the circuit- and network-level underpinnings of these alterations are poorly understood. Pharmacological sedation alters perception and responsiveness and provides a controlled and repeatable manipulation for studying brain states and their underlying circuitry. Here, we show that sedation of larval zebrafish with dexmedetomidine reduces brain-wide spontaneous activity and locomotion but leaves portions of brain-wide auditory processing and behavior intact. We describe and computationally model changes at the levels of individual neurons, local circuits, and brain-wide networks that lead to altered brain states and sensory processing during sedation.

neuroscience↗

bioRxiv2024

Giardia Antagonizes Beneficial Functions of Indigenous and Therapeutic Intestinal Bacteria during Malnutrition

Undernutrition in children commonly disrupts the structure and function of the small intestinal microbial community, leading to enteropathies, compromised metabolic health, and impaired growth and development. The mechanisms by which diet and microbes mediate the balance between commensal and pathogenic intestinal flora remain elusive. In a murine model of undernutrition, we investigated the direct interactions Giardia lamblia, a prevalent small intestinal pathogen, on indigenous microbiota and specifically on Lactobacillus strains known for their mucosal and growth homeostatic properties. Our research reveals that Giardia colonization shifts the balance of lactic acid bacteria, causing a relative decrease in Lactobacillus spp. and an increase in Bifidobacterium spp. This alteration corresponds with a decrease in multiple indicators of mucosal and nutritional homeostasis. Additionally, protein-deficient conditions coupled with Giardia infection exacerbate the rise of primary bile acids and susceptibility to bile acid-induced intestinal barrier damage. In epithelial cell monolayers, Lactobacillus spp. mitigated bile acid-induced permeability, showing strain-dependent protective effects. In vivo, L. plantarum, either alone or within a Lactobacillus spp consortium, facilitated growth in protein-deficient mice, an effect attenuated by Giardia, despite not inhibiting Lactobacillus colonization. These results highlight Giardias potential role as a disruptor of probiotic functional activity, underscoring the imperative for further research into the complex interactions between parasites and bacteria under conditions of nutritional deficiency.

microbiology↗

bioRxiv2022

A critical role for touch neurons in a skin-brain pathway for stress resilience

Social touch can act as a stress buffer, reducing behavioral and physiological responses to stressful scenarios. However, skin-brain touch pathways that promote stress resilience remain unknown. Here, we show that mice with an early life genetic ablation of Mrgprb4-lineage touch neurons display stress vulnerability behaviors in adulthood. Chemogenetic activation of these touch neurons reduced corticosterone levels under mild acute stress conditions. In addition, whole-brain c-Fos activity mapping while chemogenetically turning on these neurons uncovered differential neural activity patterns in brain areas relevant to somatosensation, reward, and affect. To gain mechanistic insight into this skin-brain touch pathway for stress susceptibility, we used multi-circuit neurophysiological recordings across seven brain regions at baseline and after stress in mice that had Mrgprb4-lineage touch neurons ablated in early life. Interestingly, the Mrgprb4-lineage neuron-ablated mice have alterations in local field potential phase directionality and power in the theta frequencies in mesolimbic reward regions, which may underlie our observed stress susceptibility phenotype. Together, these studies revealed that sensory neurons in the skin engage networks across the brain to promote stress resilience.

neuroscience↗