Biology subjects

Weiler, S.

Publications and source records attributed to Weiler, S..

11 recordsLinked to original sources

bioRxiv2026

High-throughput serial two-photon tomography with BakingTray and BrainSaw

Volumetric imaging is increasingly important in fields such as neuroscience, where quantifying structure and mapping features are inherently three-dimensional problems. Block-face serial two-photon tomography (STPT) has emerged as a powerful approach for high-resolution, whole-organ volumetric imaging. STPT avoids complex sample preparation and balances image quality, speed, and scalability. However, STPT remains niche, in part because of the absence of flexible, general-purpose control software. Here we present BakingTray, an open-source software platform for STPT that extends ScanImage. BakingTrays modular framework accommodates diverse hardware configurations and allows users to build systems customised to their needs. Twelve such systems, which we call BrainSaws, have been constructed worldwide since 2016, with more under construction, and have so far contributed to 35 research papers. The three systems at the Sainsbury Wellcome Centre alone have acquired over 7,000 samples in a busy multi-user facility. We demonstrate the platform across its core neuroscience applications: electrode track localisation, brain-wide cell counting, and bulk projection mapping. Beyond these, we map the cell-type-specific synaptic output of inhibitory neurons in the ventral lateral geniculate nucleus and, with whole-mount staining, amyloid plaques brain-wide in a mouse model of Alzheimers disease. BakingTray is a mature platform for groups or facilities needing a customised volumetric imaging solution, whether built new or converted cheaply from an existing two-photon microscope.

neuroscience↗

bioRxiv2025

Resistance Training Reshapes the Gut Microbiome for Better Health

ObjectivesThe gut microbiome plays a critical role in metabolism, immunity, and aging. While endurance training has been shown to beneficially modulate the microbiome, the effects of resistance training remain less clear, with some studies reporting minimal changes. This project aims to investigate whether structured resistance training elicits significant changes in gut microbiome composition and diversity in sedentary, healthy adults. Methods150 participants completed an 8-week supervised resistance training program. Session-level training data, including weights and repetitions, were recorded alongside metrics like load and compliance. Fecal samples were collected throughout the study period at designated timepoints for 16S rRNA gene amplicon sequencing to assess microbiome composition and for metabolomics analyses to evaluate microbial metabolic activity. ResultsNo differences in microbial diversity were observed, and there were no significant changes in microbial community composition or fecal metabolomics across all participants post-training. However, within-individual microbial community changes significantly correlated with strength improvement, and significantly stronger shifts in beta diversity were observed in participants with high average strength gains compared to those with smaller gains. In these high responders, differential abundance analysis revealed time-dependent microbial changes, with more taxa enriched or depleted by week 8 of training. Notably, Faecalibacterium and Roseburia hominis--both associated with a healthier, anti-inflammatory microbiome--were significantly enriched. Many differentially abundant taxa belonged to the Lachnospiraceae family. ConclusionResistance training drives significant, time-dependent gut microbiome changes, particularly in those demonstrating greater improvements in strength. These shifts mirror endurance training effects and may reflect improved overall health. SummaryWhile endurance training has been consistently shown to enhance gut microbiome composition, the effects of resistance training remain less well defined, with findings to date being variable. Our results indicate that resistance training can induce meaningful, time-dependent shifts in the gut microbiome, particularly among sedentary individuals who experience substantial strength gains. Notably, we observed enrichment of key health-associated taxa, including Faecalibacterium and Roseburia hominis, both linked to anti-inflammatory effects and improved gut function. These findings suggest that resistance training may contribute to gut health in conjunction with physical fitness, supporting its broader application in health promotion strategies and future microbiome-focused research.

microbiology↗

bioRxiv2025

Mapping the magnetoreceptive brain: A 3D digital atlas of the migratory bird Eurasian blackcap (Sylvia atricapilla)

Birds undisputedly range amongst natures foremost navigators. To successfully navigate between breeding and wintering quarters, they, in addition to other natural orientation cues, rely on their ability to sense the Earths magnetic field. For this reason, migratory birds have become key model species for studying the sensory mechanisms underlying magnetic field-guided navigation, as evidenced by the identification of several brain regions believed to be involved in processing magnetic field information. However, there is as yet no readily accessible, high-resolution three-dimensional (3D) brain atlas to serve as a common reference within and across studies. Here we provide the neuroscience research community with the first freely available, digital, high-resolution (25 {micro}m), 3D bird brain atlas. It is based on light microscopy images from ten Eurasian blackcaps (Sylvia atricapilla), a night-migratory songbird widely used model species in magnetoreception and navigation research. We outline the individual steps for the creation of a brain atlas, from whole-brain imaging using serial-section, two-photon tomography, to the creation of an average template at an isotropic 25-{micro}m voxel size, and finally to brain area segmentation and annotation. In this first version of the atlas, we have mapped a total of 24 brain areas, including 6 principal compartments, 13 conspicuous anatomical subdivisions common to all bird species and 5 functionally defined areas of the visual and trigeminal sensory systems involved in processing magnetic field information. This atlas is accessible via the standardised BrainGlobe Atlas API, making it compatible with a growing suite of computational neuroanatomy tools provided by the BrainGlobe Initiative. This integration enables precise alignment of future experimental data to a common coordinate space, facilitating collaboration, data visualization and sharing. Furthermore, this resource enables the accurate localization and comparison of implanted devices, injection sites, and/or cell populations across individual brains, both within and across studies.

neuroscience↗

bioRxiv2024

Overcoming off-target optical stimulation-evoked cortical activity in the mouse brain in vivo

Genetic engineering of exogenous opsins sensitive to a wide range of lightwavelengths allows the interrogation of brain circuits to an unprecedented temporal and spatial precision. In particular, red-shifted opsins offer access deeper within the brain tissue. It is however crucial to consider the potential unintended back-activation of endogenous opsins due to laser light striking the back of the retina. Here, we found that in complete darkness and with no expression of exogenous opsins, optical fiber laser stimulation at wavelengths of 637 nm (red), 594 nm (orange), or 473 nm (blue) from within the ipsilateral mouse visual cortex resulted in a strong neuronal response in its contralateral counterpart. This neuronal activation occurred even at low laser intensities (1mW at the fiber tip, 31.8mW/mm2) and was most pronounced using red wavelengths. We therefore took advantage of retinal light adaptation using external illumination with a relatively dim ambient light source (20 lux) which was found to completely abolish orange and blue laser-evoked neuronal activation from within the brain, even at high laser intensities (15mW, 477.3mW/mm2). To prevent red laser-evoked retinal activation, however, only much lower intensities (2.5mW, 79.6mW/mm2) combined with external illumination (20 lux) could be used. These findings demonstrate the critical need for careful selection of light wavelengths and intensities for laser stimulation during optogenetic experiments in the mouse brain in vivo. Additionally, light adaptation of the retina through ambient light exposure offers an effective solution to minimize unintended retinal activation.

neuroscience↗

bioRxiv2024

Layer 6 corticocortical cells dominate the anatomical organization of intra and interhemispheric feedback

The mouse neocortex contains at least ninety distinctly defined yet interconnected areas that are symmetrically located across the two hemispheres. Determining the logic of this long range circuitry is necessary for understanding how inter-areal integration enables high level brain function involving multiple sensory, motor and cognitive processes. To address this we have performed a systematic anatomical analysis of the areal and laminar organization of the ipsilateral and contralateral cortical projection onto the primary visual (VISp), primary somatosensory barrel field (SSp-bfd) and primary motor (MOp) cortices. The resultant input maps reveal that although the ipsilateral hemisphere is the primary source of cortical input, there is substantial bilateral symmetry regarding the relative contribution and areal identity of contralateral input. Laminar analysis of these input areas show that excitatory Layer 6 corticocortical cells (L6 CCs) are a major projection pathway from both within and across the two hemispheres. Based on cortical hierarchy analysis that compares the relative contribution of inputs from supra-(feedforward) and infra-granular (feedback) layers, we find that contra-hemispheric projections reflect a dominant feedback organization compared to their ipsi-cortical counterpart. The magnitude of the interhemispheric difference in hierarchy was largest for sensory and motor projection areas compared to frontal, medial or lateral brain areas and can be explained by a proportional increase in input from L6 neurons. L6 CCs therefore not only mediate long-range cortical communication but also reflect its inherent feedback organization.

neuroscience↗

bioRxiv2022

A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration

Tactile sensation and vision are often both utilized for the exploration of objects that are within reach though it is not known whether or how these two distinct sensory systems might combine such information. Here in mice we find that stimulation of the contralateral whisker array suppresses visually evoked activity in a subarea of primary visual cortex (VISp) whose visual space covers the whisker search space. This is mediated by local fast spiking interneurons that receive a direct cortico-cortical input predominantly from layer 6 of the primary somatosensory barrel cortex (SSp-bfd). These data demonstrate functional convergence within and between two primary sensory cortical areas for multisensory object detection and recognition.

neuroscience↗

bioRxiv2021

Functional and structural features of L2/3 pyramidal cells continuously covary with pial depth in mouse visual cortex

Pyramidal cells of neocortical layer 2/3 (L2/3 PyrCs) integrate signals from numerous brain areas and project throughout the neocortex. Within L2/3, PyrCs show functional and structural specializations depending on their pial depth, indicating participation in different functional microcircuits. However, it is unknown whether these depth-dependent differences result from separable L2/3 PyrC subtypes or whether functional and structural features represent a continuum while correlating with pial depth. Here, we assessed the stimulus selectivity, electrophysiological properties, dendritic morphology, and excitatory and inhibitory synaptic connectivity across the depth of L2/3 in the binocular visual cortex (bV1) of female mice. We find that the structure of the apical but not the basal dendritic tree varies with pial depth, which is accompanied by differences in passive but not active electrophysiological properties. PyrCs in lower L2/3 receive increased excitatory and inhibitory input from L4, while upper L2/3 PyrCs receive a larger proportion of intralaminar input. Complementary in vivo calcium imaging revealed a systematic change in visual responsiveness, with deeper L2/3 PyrCs showing more robust responses than superficial PyrCs. Furthermore, deeper L2/3 PyrCs are more strongly driven by contralateral than ipsilateral eye stimulation. In contrast, orientation- and direction-selectivity of L2/3 PyrCs are not dependent on pial depth. Importantly, the transitions of the various properties are gradual, and cluster analysis does not support the classification of L2/3 PyrCs into discrete subtypes. These results show that L2/3 PyrCs multiple functional and structural properties systematically correlate with their depth within L2/3, forming a continuum rather than representing discrete subtypes. SIGNIFICANCE STATEMENTNeocortical pyramidal cells in layer 2/3 (L2/3 PyrCs) are crucial for cortical computation and display heterogenous properties. We investigated whether and how these properties vary across the depth of L2/3 and whether L2/3 PyrCs can be subdivided into distinct subtypes. This is important for a better understanding of the coding strategy and information integration processes within L2/3. We find that multiple properties such as morphology, physiology, connectivity, and functional in vivo responses of L2/3 PyrCs correlate with cortical depth in mouse visual cortex. These variations are continuous and do not support classification of L2/3 PyrCs into discrete subtypes. In contrast to L5 and L6, PyrCs in L2/3 therefore process information based on a continuous property space.

neuroscience↗

bioRxiv2021

The crystal structure of the varicella zoster Orf24-Orf27 nuclear egress complex spotlights multiple determinants of herpesvirus subfamily specificity

Varicella zoster virus (VZV) is a human pathogen from the -subfamily of herpesviruses. Here, the crystal structure of the VZV Orf24-Orf27 complex is described, representing the essential viral core nuclear egress complex (NEC) that orchestrates the egress of the preassembled capsids from the nucleus. While previous studies have primarily emphasized the finding that the architecture of core NEC complexes is highly conserved among herpesviruses, the present report focusses on subfamily-specific structural and functional features that help explain the differences in the autologous versus nonautologous interaction patterns observed for NEC formation across herpesviruses. CoIP and confocal imaging data show that Orf24-Orf27 complex formation displays some promiscuity in a herpesvirus subfamily-restricted manner. At the same time, analysis of the NEC formation thermodynamic parameters of three prototypical -, {beta}- and {gamma} herpesviruses, i.e. VZV, human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) reveals highly similar binding affinities for the autologous interaction with some specific differences in the enthalpy and entropy terms. Computational alanine scanning and structural comparisons highlight intermolecular interactions shared among -herpesviruses that are clearly distinct from those seen in {beta}- and {gamma}-herpesviruses. Combined, these data allow to explain the distinct properties of specificity and permissivity so far observed in herpesviral NEC interactions. These findings might prove highly valuable when attempting to target multiple herpesvirus core NECs with selective or broad-acting drug candidates.

biochemistry↗

bioRxiv2020

Selective connectivity limits functional binocularity in the retinogeniculate pathway of the mouse

Eye-specific segregation of retinal ganglion cell (RGC) axons in the dorsal lateral geniculate nucleus (dLGN) is considered a hallmark of visual system development. However, a recent anatomical study showed that nearly half of the neurons in dLGN of adult mice still receive input from both retinae, but functional data about binocularity in mature dLGN is conflicting. Here, we found that a variable but small fraction of thalamocortical neurons is binocular in vivo. Using dual-channel optogenetics in vitro we correspondingly found that dLGN neurons are dominated by retinogeniculate input from one eye only, although most neurons also received small but detectable input from the non-dominant eye. Anatomical overlap between RGC axons and dLGN neuron dendrites did not explain this strong bias towards monocularity. Our data rather suggest that functional input selection and refinement, leaving the remaining non-dominant eye inputs in a juvenile-like state, underlies the prevalent monocularity of neurons in dLGN.

neuroscience↗

bioRxiv2020

Relationship between input connectivity, morphology and orientation tuning of layer 2/3 pyramidal cells in mouse visual cortex

Neocortical pyramidal cells (PCs) display functional specializations defined by their excitatory and inhibitory circuit connectivity. For layer 2/3 (L2/3) PCs, little is known about the detailed relationship between their neuronal response properties, dendritic structure and their underlying circuit connectivity at the level of single cells. Here, we ask whether L2/3 PCs in mouse primary visual cortex (V1) differ in their functional intra- and interlaminar connectivity patterns, and how this relates to differences in visual response properties. Using a combined approach, we first characterized the orientation and direction tuning of individual L2/3 PCs with in vivo 2-photon calcium imaging. Subsequently, we performed excitatory and inhibitory synaptic input mapping of the same L2/3 PCs in brain slices using laser scanning photostimulation (LSPS). Our data from this structure-connectivity-function analysis show that the sources of excitatory and inhibitory synaptic input are different in their laminar origin and horizontal location with respect to cell position: On average, L2/3 PCs receive more inhibition than excitation from within L2/3, whereas excitation dominates input from L4 and L5. Horizontally, inhibitory input originates from locations closer to the horizontal position of the soma, while excitatory input arises from more distant locations in L4 and L5. In L2/3, the excitatory and inhibitory inputs spatially overlap on average. Importantly, at the level of individual neurons, PCs receive inputs from presynaptic cells located spatially offset, vertically and horizontally, relative to the soma. These input offsets show a systematic correlation with the preferred orientation of the postsynaptic L2/3 PC in vivo. Unexpectedly, this correlation is higher for inhibitory input offsets within L2/3 than for excitatory input offsets. When relating the dendritic complexity of L2/3 PCs to their orientation tuning, we find that sharply tuned cells have a less complex apical tree compared to broadly tuned cells. These results indicate that the spatial input offsets of the functional input connectivity are linked to orientation preference, while the orientation selectivity of L2/3 PCs is more related to the dendritic complexity.

neuroscience↗

bioRxiv2019

Structural and functional characterisation of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system from Salmonella enterica

Salmonella invasion is mediated by a concerted action of the Salmonella pathogenicity island 4 (SPI4)-encoded type one secretion system (T1SS) and the SPIl-encoded type three secretion system (T3SS-1). The SPI4-encoded T1SS establishes the first contact to the host membrane. It consists of five proteins (SiiABCDF) that secrete the giant adhesin SiiE. The exact mechanism by which the T1SS enables host cell recognition remains unclear. Here, we investigated structure-function relationships in SiiA, a non-canonical T1SS subunit located at the inner membrane (IM). We observe that SiiA consists of a membrane domain, an intrinsically disordered periplasmic linker region and a folded globular periplasmic domain (SiiA-PD). The crystal structure of SiiA-PD shows homology to that of MotB-PD and other peptidoglycan (PG)-binding domains. Indeed, SiiA-PD binds PG in vitro albeit at an acidic pH, only, whereas MotB-PD binds PG from pH 5.8 to 8. Mutation of Arg162 in SiiA impedes PG binding and reduces Salmonella invasion efficacy of polarized epithelial cells. SiiA forms a complex with SiiB at the IM, and the SiiA-MotB homology is likely paralleled by a SiiB-MotA homology. We show that, in addition to PG binding, the SiiAB complex translocates protons across the IM. Substituting Asp13 in SiiA impairs proton translocation. Overall, SiiA displays many properties previously observed in MotB. However, whereas the MotAB complex uses the proton motif force (PMF) to energize the bacterial flagellum, it remains to be shown how the use of the PMF by SiiAB assists T1SS function and ultimately Salmonella invasion.

microbiology↗