Biology subjects

Versluis, D. M.

Publications and source records attributed to Versluis, D. M..

7 recordsLinked to original sources

bioRxiv2026

DishCam: an open-source 3D-printed darkfield imager for microbial colonies and small organisms on Petri dishes

Petri dishes are routinely photographed using handheld cameras under reflected light. While adequate for large, distinct colonies, this approach fails to capture individual organisms or colonies that are transparent, do not reflect light well, or have fine structures, and is unsuitable for high quality timelapses. Darkfield illumination provides superior contrast for organisms on agar surfaces, but existing solutions rely on improvised setups with inconsistent lighting, or on large and expensive benchtop instruments that cannot be housed inside incubators. We present DishCam, an open-source device consisting entirely of 3D-printed parts and inexpensive off-the-shelf electronics, controlled by a Raspberry Pi running custom open-source software. DishCam produces high-contrast darkfield images using angled LED illumination beneath a Petri dish. All components used are off-the-shelf or easily 3D-printed. The camera and lights can be fully controlled through Raspberry Pi using our software. We demonstrate the device across multiple biological systems: Klebsiella aerogenes colonies of differing densities, Trypanosoma brucei colonies doing social motility, Dictyostelium discoideum streaming aggregation, and Caenorhabditis elegans on feeding substrates. The total cost of the basic device is approximately {pound}166 or $222, with the upgraded configuration costing approximately {pound}413 or $552, which includes a high-quality telephoto lens, SSD storage and incubator-compatible cables.

microbiology↗

bioRxiv2026

Chemotactic responses of Trypanosoma brucei procyclic forms to proline and other metabolites

Many protozoan parasites have complex life cycles entailing migration through different organs in their hosts, but the cues guiding them remain poorly understood. Using a semi-solid plate motility assay, we show that early procyclic forms of Trypanosoma brucei, the first stage to develop in the tsetse fly midgut, perceive several metabolites - including glucose, glycerol and proline - as chemoattractants, while the glycolytic end-product succinate acts as a repellent. During adaptation in the fly, T. brucei switches from glucose/glycerol to proline as its primary energy source. We show that the parasites chemotactic response towards proline requires adenylate cyclase ACP5 and the cyclic AMP response protein CARP3, two components of signalling pathway involved in pH sensing. These results further support a role for T. bruceis expanded repertoire of receptor adenylate cyclases as environmental sensors that guide navigation through the host. HighlightsO_LIThe plate assay reported here can be used to study how trypanosomes sense external signals and migrate in response to them. C_LIO_LIEarly procyclic forms of T. brucei respond to a variety of metabolites and exhibit different patterns of collective migration on plates, depending on the stimulus. C_LIO_LIThe response to proline operates through cAMP signalling and requires ACP5 and CARP3, two components also required for pH sensing. C_LI

microbiology↗

bioRxiv2026

Tell your friends: communication through autoattractants can enhance and limit migration of immune cells

Many eukaryotic cells produce attractant molecules to which they themselves are also attracted. For example, neutrophils produce leukotriene B4 while swarming. These autoattractants create a secondary signalling layer that can coordinate collective cell behaviour during chemotaxis. Here we use a hybrid agent-based computational model to examine how immune cells migrating along a self-generated gradient may communicate with each other using autoattractants. We find that autoattractant signals strongly enhance cells' responses to primary attractant. Efficient removal of autoattractants is also crucial, through depletion by cells, chemical instability, or enzymatic breakdown. Consequently, autoattractants have a lifetime, determined by a balance between production and removal rates. We find that optimal lifetimes exist, and that these are determined by cell speed and attractant diffusion, but are remarkably independent of cell density and primary attractant concentration. We further show that autoattractants whose removal is governed by inherent instability rather than breakdown by cells coordinate migration less efficiently, but work more robustly across different environments. Finally, we find that autoattractant signalling without direct breakdown by the cells involved establishes a characteristic optimal cell-cell distance: too little communication leaves cells uncoordinated, while excessive communication causes cells to aggregate into slow-moving clumps. Strikingly, the conditions that produce optimal chemotaxis lie very close to those that trigger aggregation, suggesting that many autoattractant systems operate near a critical boundary.

cell biology↗

bioRxiv2025

Macrophage chemotaxis steered by complex self-generated gradients of complement C5a

Macrophages rely on efficient chemotaxis to locate sites of infection and tissue damage. One general strategy that enhances chemotactic accuracy is the use of self-generated gradients, where cells locally deplete attractants to create or sharpen guidance cues. Here we show that mouse bone marrow-derived macrophages (BMDMs) migrate toward the complement component C5a using this strategy. Cells actively deplete C5a from their surroundings, establishing local gradients as fresh attractant diffuses inward. We visualized this process in real time with fluorescent C5a and reproduced its dynamics using computational models. C5a depletion is mediated primarily by C5aR1-dependent endocytosis. This mechanism produces complex responses, with different C5a concentrations inducing temporally distinct waves of migration, and maximal chemotaxis occurring below 10 nM C5a. As expected, increasing C5a concentrations recruit more cells. In contrast, human macrophages inactivate C5a mainly through carboxypeptidase-mediated enzymatic degradation, yielding a higher optimal concentration ([~]30 nM) and distinct migratory dynamics. Both species also deplete externally imposed C5a gradients, sharpening them and enhancing guidance. These findings identify C5a degradation as a critical mechanism by which macrophages extract directional information from their environment. Self-generated gradient formation, despite different mechanisms across species, emerges as a conserved and versatile strategy for immune navigation.

immunology↗

bioRxiv2024

Simulations of the infant gut microbiota suggest that complex ecological interactions regulate effects of human milk oligosaccharides on microbial mucin consumption

Intestinal mucin acts as a barrier protecting the infant gut wall against diseases such as colitis and rotavirus. In vitro experiments have shown that the gut microbiota of breastfed infants consumes less mucin than the microbiota of non-breastfed infants, but the mechanisms are incompletely understood. The main difference between human milk and most infant formulas is the presence of human milk oligosaccharides (HMOs) in human milk. We hypothesize that HMOs protect mucin by stimulating non-mucin consuming bacteria. To understand the un-derlying mechanisms we developed a computational model that describes the metabolism and ecology of the infant gut microbiota. Model simulations suggest that extracellular digestion of the HMO 2-fucosyllactose by the mucin-consumer Bifidobacterium bifidum may make this species vulnerable to competitors. The digestion products of HMOs become public goods that can be consumed by competing species such as Bacteroides vulgatus instead.Bifidobacterium longum, which does not consume mucin or produce public goods, can then become dominant, despite growing less efficiently on HMOs in monocultures than B. bifidum. In conclusion, our model simulations suggest that, through complex ecological interactions, HMOs may help lower mucin consumption by stimulating the non-mucin consumer B. longum at the expense of the mucin consumer B. bifidum.

systems biology↗

bioRxiv2023

2'-Fucosyllactose helps butyrate producers outgrow competitors in the infant gut

A reduced capacity for butyrate production by the early infant gut microbiota is associated with negative health effects, such as inflammation and the development of allergies. Here we develop new hypotheses on the effect of the prebiotic galacto-oligosaccharides (GOS) or 2-fucosyllactose (2-FL) on butyrate production by the infant gut microbiota using a multiscale, spatiotemporal mathematical model of the infant gut. The model simulates a community of cross-feeding gut bacteria at metabolic detail. It represents the gut microbiome as a grid of bacterial populations that exchange intermediary metabolites, using 20 different subspecies-specific metabolic networks taken from the AGORA database. The simulations predict that both GOS and 2-FL promote the growth of Bifidobacterium, whereas butyrate producing bacteria are only consistently abundant in the presence of propane-1,2-diol, a product of 2-FL metabolism. The results suggest that in absence of prebiotics or in presence of only GOS, bacterial species, including Cutibacterium acnes and Bacteroides vulgatus, outcompete butyrate producers by feeding on intermediary metabolites. In presence of 2-FL, however, production of propane-1,2-diol specifically supports butyrate producers.

systems biology↗

bioRxiv2021

A multiscale spatiotemporal model explains succession in the early infant gut microbiota as a switch from aerobic to anaerobic metabolism

The human intestinal microbiota starts to form immediately after birth, and is important for the health of the host. During the first days facultatively anaerobic bacterial species generally dominate, such as Enterobacteriaceae. These are succeeded by strictly anaerobic species, particularly Bifidobacterium species. An early transition to Bifidobacterium species is associated with health benefits: for example, Bifidobacterium species repress growth of pathogenic competitors and modulate the immune response. Succession to Bifidobacterium is thought to be due to consumption of intracolonic oxygen present in newborns by facultative anaerobes, including Enterobacteriaceae. To study if oxygen depletion suffices for the transition to Bifidobacterium species, here we introduce a multiscale mathematical model that considers metabolism, spatial bacterial population dynamics and cross-feeding. Using publicly available metabolic network data from the AGORA collection, the model simulates ab initio the competition of strictly and facultatively anaerobic species in a gut-like environment under the influence of lactose and oxygen. The model predicts that individual differences in intracolonic oxygen in newborn infants can explain the observed individual variation in succession to anaerobic species, in particular Bifidobacterium species. Bifidobacterium species become dominant in the model by using the bifid shunt, which allows Bifidobacterium to switch to sub-optimal yield metabolism with fast growth at high lactose concentrations as predicted here using flux-balance analysis. The computational model thus allows us to test the internal plausibility of hypotheses for bacterial colonization and succession in the infant colon. IMPORTANCEThe composition of the infant microbiota has a great impact on infant health, but its controlling factors are still incompletely understood. The frequently dominant anaerobic Bifidobacterium species benefit health, e.g., because they can keep harmful competitors under control and modulate the intestinal immune response. Controlling factors could include nutritional composition and intestinal mucus composition, as well as environmental factors, such as antibiotics. We introduce a modeling framework of a metabolically realistic intestinal microbial ecology in which hypothetical scenarios can be tested and compared. We present simulations that suggest that greater levels of intra-intestinal oxygenation more strongly delay the dominance of Bifidobacterium species, explaining the observed variety of microbial composition and demonstrating the use of the model for hypothesis generation. The framework allows us to test a variety of controlling factors, including intestinal mixing and transit time. Future versions will also include detailed modeling of oligosaccharide and mucin metabolism.

systems biology↗