Biology subjects

Smit, C.

Publications and source records attributed to Smit, C..

6 recordsLinked to original sources

bioRxiv2025

VP-CLEM-Kit: An accessible pipeline for visual proteomics using super resolution volume correlative light and electron microscopy (SR-vCLEM)

Visual proteomics (VP) aims to allow researchers to visualise, measure and analyse proteins in the context of cell and tissue structure in health and disease. VP is becoming a reality through technological advances across several domains, including in situ structural biology and correlative light and electron microscopy (CLEM). However, widespread adoption remains limited due to the complexity and cost of the various VP approaches reported to date. Here we present the VP-CLEM-Kit, a disruptive cost-effective pipeline for super resolution volume CLEM (SR-vCLEM) that can be implemented with minimal advanced electron microscopy expertise and equipment, making it accessible to light microscopy facilities and research labs. SR-vCLEM is based on in-resin fluorescence (IRF), where fluorophores are preserved through processing into resin. The easyIRF protocol reported here reduces the requirement for complex costly sample preparation equipment and toxic chemicals compared to standard IRF protocols. easyIRF blocks are cut into ultrathin sections that are imaged using tomoSTORM, a new modular and cost-effective openFrame-based light microscope controlled by the open-source software package Micro-Manager that provides serial single molecule localisation microscopy in array tomography format. Sections are then post-stained and imaged using a tabletop scanning electron microscope controlled by open-source SBEMimage software to run in array tomography format. We demonstrate the potential of the VP-CLEM-Kit by imaging organelle reporters in human cell lines and stem cell derived neurons, fluorescently labelled protein in neurons, and immunolabelled cells in human kidney biopsy tissue from transplant patients. The VP-CLEM-Kit delivers a [~]5-fold improvement in resolution at a [~]7-fold lower cost, and thus provides new technical capability as well as a blueprint for more equitable access to advanced imaging workflows.

cell biology↗

bioRxiv2025

Precision in Spinal Cord Injury Research: A Novel Electromagnetic Impactor for a Consistent Porcine Model

PurposeReplicating spinal cord injury (SCI) in large animals is necessary for evaluating therapeutics for potential human translation, yet there is currently no commercial, standardized device for inducing SCI. We present the fabrication and testing of a custom impactor device for producing repeatable contusion SCI in porcine models. MethodsWe first designed and built the device. Mechanical modeling was subsequently utilized to calibrate our benchtop testing setup. Benchtop verification was performed to measure impact force post calibration. We then used the device to generate a contusion SCI model in 2 pigs and the results were compared to an uninjured pig. Intraoperative ultrasound was used to visualize a hematoma in the injured spinal cord. Hematoxylin-eosin (H&E) and Massons trichrome staining were used to confirm injury presence on ex vivo spinal cord samples. ResultsMechanical modeling forces matched benchtop impact forces within 1.4 N, indicating successful calibration of the testing setup. Our device demonstrated repeatability and the potential for modulating injury severity on the benchtop. Impactor forces were demonstrated across a range from 12.8 to 67.6 N, with variability remaining within 0.2 to 0.7 N standard deviation. The device induced two contusion injuries of different severity in vivo, confirmed by intraoperative ultrasound imaging and post-excision histology of the spinal cord. ConclusionOur impactor device is a major advancement towards producing repeatable and titratable contusions in large animal SCI models.

bioengineering↗

bioRxiv2024

Long-term non-trophic effects of large herbivores on plant diversity are underestimated

The positive effects of large herbivores on plant diversity in grasslands have so far been mainly attributed to increased light availability or suppressed dominance, and thus to the consequences of aboveground biomass consumption (trophic effects). However, these insights are mainly derived from short-term experiments. Using a 46-year experiment in a salt marsh, comparing cattle grazing, mowing (as a proxy of aboveground consumption) and the ungrazed control, we found that the non-trophic effects (e.g. trampling, deposition of urine and dung) of large herbivores on plant diversity increased over time, exceeding that of the trophic effects after 23 years. This long-term accumulation of non-trophic effects through slow ecosystem-level feedback highlights the sustainability of using low to moderate densities of large herbivores to conserve plant diversity. Our results emphasize the need for the conservation and re-introduction of large herbivores, domestic or wild, to sustain long-term grassland plant diversity.

ecology↗

bioRxiv2022

Functional traits trade-offs define plant population stability worldwide

O_LIEcological theory posits that temporal stability patterns in plant populations are associated with differences in species ecological strategies. However, empirical evidence is lacking about which traits, or trade-offs, underlie species stability, specially across different ecosystems. C_LIO_LITo address this, we compiled a global collection of long-term permanent vegetation records (>7000 plots from 78 datasets) from a wide range of habitats and combined this with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits and multivariate axes of trait variations (PCoA axes). C_LIO_LIWe found that species with greater leaf dry matter content and seed mass were consistently more stable over time (lower variability in species abundance) although other leaf traits played a significant role as well, albeit weaker. Using multivariate axes did not improve predictions by specific traits. C_LIO_LIOur results confirm existing theory, providing compelling empirical evidence on the importance of specific traits, which point at ecological trade-offs in different resource use and dispersal strategies, on the stability of plant populations worldwide. C_LI

ecology↗

bioRxiv2021

LOTVS: a global collection of permanent vegetation plots

Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of vascular plants in permanent plots. With 79 datasets from five continents and 7789 vegetation time-series monitored for at least six years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally fine-grained vegetation time-series derived from permanent plots and made accessible to the research community. As such, it has an outstanding potential to support innovative research in the fields of vegetation science, plant ecology and temporal ecology.

ecology↗

bioRxiv2021

Long-term cross-scale comparison of grazing and mowing on plant diversity and community composition in a salt-marsh system

O_LILand abandonment is increasing in recent decades in Europe, usually accompanied by a decline in biodiversity. Whether livestock grazing and mowing can safeguard biodiversity across spatial scales in the long term is unclear. C_LIO_LIUsing a 48-year experiment in a salt marsh, we compared land abandonment (without grazing and mowing) and seven management regimes including cattle grazing, early season mowing, late season mowing, both early and late season mowing, and grazing plus each of the mowing regimes on plant diversity at the local (i.e. plot) and landscape scales (i.e. across plots). Also, we compared their effects on community composition (both in identities and abundances) in time and space. C_LIO_LIUnder land abandonment, plant diversity declined in the local communities and this decline became more apparent at the landscape scale, particularly for graminoids and halophytes. All management regimes, except the late season mowing, maintained plant diversity at these scales. C_LIO_LILocal plant communities under all treatments underwent different successional trajectories, in the end, diverged from their initial state except for that under grazing (a cyclic succession). Interannual composition change remained stable over time under land abandonment and grazing plus early season mowing. It increased over time under grazing and late season mowing, it increased in the second half of the experiment under other treatments. Vegetation homogenized in the landscape over time under land abandonment while vegetation was heterogeneous under all management regimes. C_LIO_LISynthesis. Our experiment suggests that late season mowing may not be sustainable to conserve plant diversity in salt marshes. Other management regimes can maintain plant diversity across scales and vegetation heterogeneity in the landscape in the long term, but local community composition may change over time. C_LI

ecology↗