Biology subjects

Smit, J.

Publications and source records attributed to Smit, J..

8 recordsLinked to original sources

bioRxiv2025

Microplastics cross the murine intestine and induce inflammatory cell death after phagocytosis by human monocytes and neutrophils

Microplastics are contaminating the environment but also our food and drinking products. In a crucial study, microplastics have been detected in circulating human blood, urging the investigation of the effects of microplastics on human health. Here we aimed to determine the distribution of microplastics after oral exposure in mice and their interactions with and effects on mouse and human innate immune cells. We established that both 1 and 10m polystyrene (PS) particles penetrated the intestinal epithelium after oral administration and could be detected in blood and liver of mice after ten days of oral administration. Using intravital microscopy we captured the in vivo phagocytosis of 1m PS by mouse neutrophils in the liver. Pristine PS were barely phagocytosed by primary human phagocytes, however, 1 and 10{micro}m PS pre-incubated with plasma were readily phagocytosed by human neutrophils and monocytes. Plasma-coated 1 and 10m PS both increased human neutrophil and monocyte cell death but only after phagocytosis. Importantly, neutrophil cell death occurred a few hours after phagocytosing a single coated 10{micro}m PS while PS of 1{micro}m needed to be administered at a ratio of 27 particles per cell to induce significant neutrophil cell death. Neutrophil cell death upon microplastic exposure was characterized by extracellular DNA, which together with other released DAMPs can potentially trigger inflammation. Our findings suggest that microplastics could negatively impact the immune system and human health.

immunology↗

bioRxiv2021

Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 cells but not in human primary airway epithelium cells

Antiviral therapies are urgently needed to treat and limit the development of severe COVID-19 disease. Ivermectin, a broad-spectrum anti-parasitic agent, has been shown to have anti-SARS-CoV-2 activity in Vero cells at a concentration of 5 {micro}M. These in vitro results triggered the investigation of ivermectin as a treatment option to alleviate COVID-19 disease. In April 2021, the World Health Organization stated, however, the following: "the current evidence on the use of ivermectin to treat COVID-19 patients is inconclusive". It is speculated that the in vivo concentration of ivermectin is too low to exert a strong antiviral effect. Here, we performed a head-to head comparison of the antiviral activity of ivermectin and a structurally related, but metabolically more stable, moxidectin in multiple in vitro models of SARS-CoV-2 infection, including physiologically relevant human respiratory epithelial cells. Both moxidectin and ivermectin exhibited antiviral activity in Vero E6 cells. Subsequent experiments revealed that the compounds predominantly act on a step after virus cell entry. Surprisingly, however, in human airway-derived cell models, moxidectin and ivermectin failed to inhibit SARS-CoV-2 infection, even at a concentration of 10 {micro}M. These disappointing results calls for a word of caution in the interpretation of anti-SARS-CoV-2 activity of drugs solely based on Vero cells. Altogether, these findings suggest that, even by using a high-dose regimen of ivermectin or switching to another drug in the same class are unlikely to be useful for treatment against SARS-CoV-2 in humans.

microbiology↗

bioRxiv2020

Density responses of lesser-studied carnivores to habitat and management strategies in southern Tanzanias Ruaha-Rungwa landscape

Compared to emblematic large carnivores, less charismatic or smaller carnivore species often receive little conservation attention, despite facing increasing anthropogenic pressure, and their status being poorly understood across much of their range. We employed systematic camera trapping and spatially explicit capture-recapture modelling to estimate variation in population density of serval, striped hyaena and aardwolf across the mixed-use Ruaha-Rungwa landscape in southern Tanzania. Three sites were selected as representative of different habitat types, management strategies, and levels of anthropogenic pressure: Ruaha National Parks core tourist area, dominated by Acacia-Commiphora bushlands and thickets; the Parks miombo woodland; and the neighbouring community-run MBOMIPA Wildlife Management Area, also covered in Acacia-Commiphora. Our results show that the Parks miombo woodlands supported a higher serval density than the core tourist area and Wildlife Management Area, with 5.56 [Standard Error = {+/-}2.45], 3.45 [{+/-}1.04] and 2.08 [{+/-}0.74] individuals per 100 km2, respectively. This variation is likely driven by precipitation, the abundance of apex predators, and the level of anthropogenic pressure. Striped hyaena were detected only in the Wildlife Management Area and at low density (1.36 [{+/-}0.5] individuals per 100 km2), potentially due to the location of the surveyed sites at the edge of the species global range, high densities of sympatric competitors and anthropogenic edge effects. Finally, aardwolf were captured in both the Parks core tourist area and the Wildlife Management Area, with a higher density in the Wildlife Management Area (13.25 [{+/-}2.48] versus 9.19 [{+/-}1.66] individuals per 100 km2), possibly as a result of lower intraguild predation and late fire outbreaks in the area surveyed. By shedding light on three understudied African carnivore species, this study highlights the importance of miombo woodland conservation and community-managed conservation, as well as the value of camera trap data to improve ecological knowledge of lesser-studied carnivores.

zoology↗

bioRxiv2020

Cooperative Chikungunya virus membrane fusion and its sub-stoichiometric inhibition by CHK-152 antibody

Chikungunya virus (CHIKV) presents a major burden on healthcare systems worldwide, but specific treatment remains unavailable. Attachment and fusion of CHIKV to the host cell membrane is mediated by the E1/E2 protein spikes. We used an in vitro single-particle fusion assay to study the effect of the potent, neutralizing antibody CHK-152 on CHIKV binding and fusion. We find that CHK-152 shields the virions, inhibiting interaction with the target membrane and inhibiting fusion. Analysis of the ratio of bound antibodies to epitopes implied that CHIKV fusion is a highly cooperative process. Further, dissociation of the antibody at lower pH results in a finely balanced kinetic competition between inhibition and fusion, suggesting a window of opportunity for the spike proteins to act and mediate fusion even in the presence of antibody.

microbiology↗

bioRxiv2019

A Bacterial Surface Layer Protein Exploits Multi-step Crystallization for Rapid Self-assembly

Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the C. crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multi-step assembly pathway. This pathway involves two domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2D crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using time-resolved electron cryo-microscopy (Cryo-EM) reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the two domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.\n\nSignificance StatementMany microbes assemble a crystalline protein layer on their outer surface as an additional barrier and communication platform between the cell and its environment. Surface layer proteins efficiently crystallize to continuously coat the cell and this trait has been utilized to design functional macromolecular nanomaterials. Here, we report that rapid crystallization of a bacterial surface layer protein occurs through a multi-step pathway involving a crystalline intermediate. Upon calcium-binding, sequential changes occur in the structure and arrangement of the protein, which are captured by time-resolved small angle x-ray scattering and transmission electron cryo-microscopy. We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization in vivo.

biophysics↗

bioRxiv2019

Continuous, Topologically Guided Protein Crystallization Controls Bacterial Surface Layer Self-Assembly

Bacteria assemble the cell envelope using localized enzymes to account for growth and division of a topologically complicated surface1-3. However, a regulatory pathway has not been identified for assembly and maintenance of the surface layer (S-layer), a 2D crystalline protein coat surrounding the curved 3D surface of a variety of bacteria4,5. By specifically labeling, imaging, and tracking native and purified RsaA, the S-layer protein (SLP) from C. crescentus, we show that protein self-assembly alone is sufficient to assemble and maintain the S-layer in vivo. By monitoring the location of newly produced S-layer on the surface of living bacteria, we find that S-layer assembly occurs independently of the site of RsaA secretion and that localized production of new cell wall surface area alone is insufficient to explain S-layer assembly patterns. When the cell surface is devoid of a pre-existing S-layer, the location of S-layer assembly depends on the nucleation characteristics of SLP crystals, which grow by capturing RsaA molecules freely diffusing on the outer bacterial surface. Based on these observations, we propose a model of S-layer assembly whereby RsaA monomers are secreted randomly and diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated into growing 2D S-layer crystals. The complicated topology of the cell surface enables formation of defects, gaps, and grain boundaries within the S-layer lattice, thereby guiding the location of S-layer assembly without enzymatic assistance. This unsupervised mechanism poses unique challenges and advantages for designing treatments targeting cell surface structures or utilizing S-layers as self-assembling macromolecular nanomaterials. As an evolutionary driver, 2D protein self-assembly rationalizes the exceptional S-layer subunit sequence and species diversity6.

biophysics↗

bioRxiv2018

Self-healing dyes for super-resolution microscopy

In recent years optical microscopy techniques have emerged that allow optical imaging at unprecented resolution beyond the diffraction limit. Up to date, photostabilizing buffers are the method of choice to realize either photoswitching and/or to enhance the signal brightness and stability of the employed fluorescent probes. This strategy has, however, restricted applicability and is not suitable for live cell imaging. In this paper, we tested the performance of self-healing organic fluorophores with intramolecular photostabilization in super-resolution microscopy with targeted (STED) and stochastic readout (STORM). The overall goal of the study was to improve the spatial and temporal resolution of both techniques without the need for mixtures of photostabilizing agents in the imaging buffer. Due to its past superior performance we identified ATTO647N-photostabilizer conjugates as suitable candidates for STED microscopy. We characterize the photostability and resulting performance of NPA-ATTO647N oligonucleotide conjugates in STED microscopy. We find that the superior photophysical performance results in optimal STED imaging and demonstrate the possibility to obtain single-molecule fluorescent transients of individual fluorophores while illuminating with both the excitation- and STED-laser. Secondly, we show an analysis of photoswitching kinetics of self-healing Cy5 dyes (comprising TX, COT and NPA stabilizers) in the presence of TCEP- and cysteamine, which are typically used in STORM microscopy. In line with previous work, we find that intramolecular photostabilization strongly influences photoswitching kinetics and requires careful attention when designing STORM-experiments. In summary, this contribution explores the possibilities and limitations of self-healing dyes in super-resolution microscopy of differing modalities.

biophysics↗

bioRxiv2018

On the impact of competing intra- and intermolecular triplet-state quenching on photobleaching and photoswitching kinetics of organic fluorophores

While buffer cocktails remain the gold-standard for photostabilization and photoswitching of fluorescent markers, intramolecular triplet-state quenchers emerge as an alternative strategy to impart fluorophores with self-healing or even functional properties such as photoswitching. In this contribution, we evaluated various combinations of both approaches and show that inter- and intramolecular triplet-state quenching processes compete with each other rather than being additive or even synergistic. Often intramolecular processes dominate the photophysical situation for combinations of covalently-linked and solution-based photostabilizers and photoswitching agents. In this context we identified a new function of intramolecular photostabilizers, i.e., protection of fluorophores from reversible off-switching events caused by solution-additives, which were previously misinterpreted as photobleaching. Our studies also provide practical guidance for usage of photostabilizer-dye conjugates for STORM-type super-resolution microscopy permitting the exploitation of their improved photophysics for increased spatio-temporal resolution. Finally, we provide evidence that the biochemical environment, e.g., proximity of aromatic amino-acids such as tryptophan, reduces the photostabilization efficiency of commonly used buffer cocktails. Not only have our results important implications for a deeper mechanistic understanding of self-healing dyes, but they will provide a general framework to select label positions for optimal and reproducible photostability or photoswitching kinetics.

biophysics↗