Biology subjects

Smeets, K.

Publications and source records attributed to Smeets, K..

9 recordsLinked to original sources

bioRxiv2026

Fast rate coding in heterogeneous spiking networks

A network of spiking neurons is said to operate in the rate coding regime if its dynamics can be accurately described by a continuous rate network. But how can discrete spike-based communication between neurons give rise to continuous rate-based dynamics? Computational studies showing that heterogeneous spiking networks can approximate the dynamics of recurrent neural networks (RNNs), a special case of rate network, assume that spikes are approximately Poisson or that network dynamics are slow. Here, we show that neither assumption is necessary: heterogeneous networks of non-Poisson neurons can produce fast rate-based dynamics. To demonstrate this, we show that signal transmission in feedforward networks of integrate-and-fire-type neurons can be described by a history-dependent rate network that is asymptotically exact as network size grows, even if heterogeneity persists, while linear-nonlinear rate networks fail. By providing a constructive model of fast rate coding in heterogeneous networks, this work lays the foundation for extending rate-based analyses of neural recordings beyond the assumption of slow dynamics or Poisson rate codes.

neuroscience↗

bioRxiv2026

Flavins in Focus: Vitamin B2 as a Metabolic Keystone for Neuronal Repair in Regenerating Planarians

Regeneration imposes substantial metabolic demands to support the reconstruction of functional tissues. Essential vitamins are indispensable metabolic cofactors, yet whether their availability is spatially organized to support local metabolic demands within regenerative tissues remains largely unknown. Here, we identify previously undescribed flavin-rich cells, referred to as 'flavinocytes', that form an extensive network that spatially organizes vitamin B2 metabolism in the planarian Schmidtea mediterranea. Using endogenous flavin autofluorescence as a label-free in vivo metabolic readout, we show that this network consists of elongated cells that form longitudinal varicosity-containing strands closely associated with the central nervous system. RNAi-mediated disruption of riboflavin uptake and metabolism reduced flavin-associated autofluorescence and its spatial distribution within the animal, while affecting blastema formation, eye regeneration, and nervous system reconstruction. These findings demonstrate that riboflavin metabolism is required for successful regeneration. Single-cell transcriptomics, protein localization, and functional perturbations further suggest a reciprocal relationship between flavinocytes and the regenerating nervous system, pointing to coordinated neuro-metabolic interactions during tissue repair. Together, our findings demonstrate the importance of riboflavin metabolism for nervous system regeneration and provide new insight into the spatial organization of metabolism during tissue regeneration.

developmental biology↗

bioRxiv2026

Pigments and microstructure of the colour polymorphic shells of Polymita picta and P. muscarum (Gastropoda: Cepolidae), with observations on a new light-transmitting shell spot system

Colour polymorphism in the Cuban painted snails Polymita picta and P. muscarum is striking, yet the pigmentary and structural bases remain unclear. We combined spectrophotometric screening, Raman micro-spectroscopy, scanning electron microscopy (SEM) and LED transillumination to link pigments, ultrastructure and optics across shell morphs. A Sepia officinalis melanin standard yielded a robust linear calibration used to quantify total melanin pigments at 215 nm in pooled extracts. Melanin was detected in all samples with predominance in darker morphs. Raman spectra (785 nm) confirmed aragonite mineral organization and revealed carotenoid bands, consistent with a mixed-pigment model in which carotenoids contribute to ground and band colours and melanins underlie darker elements. SEM showed a canonical crossed-lamellar layer with alternating transverse and co-marginal layers. At shell spot areas, shell surfaces were cribose; fracturing shells near such spots showed a locally disordered, more porous mineral arrangement enriched in organic matrix, bounded basally by an organic layer. Under transillumination, these spots acted as discrete light-transmitting windows, abundantly in P. muscarum and also sparsely in P. picta; as the spots appear only as pigmented dots but also transmit light, we refer to them as cryptotransmissive domains, which is apparently a novel finding in terrestrial gastropods. We speculate that these may represent a pigment-structure-optics framework in which pigments and microstructural packing jointly play potential roles in photoprotection and behavioural thermoregulation. These results provide a mechanistic context for colour polymorphism in Polymita and suggest testable links to thermal ecology and conservation.

zoology↗

bioRxiv2026

Whole-Brain Co-Mapping of Gene Expression and NeuronalActivity at Cellular Resolution in Behaving Zebrafish

The brains capabilities rely on both the molecular properties of individual cells and their interactions across brain-wide networks. However, relating gene expression to activity in individual neurons across the entire brain remains elusive. Here we developed an experimental-computational platform, WARP, for whole-brain imaging of neuronal activity during behavior, expansion-assisted spatial transcriptomics, and cellular-level registration of these two modalities. Through joint analysis of whole-brain neuronal activity during multiple behaviors, cellular gene expression, and anatomy, we identified functions of molecularly defined populations--including luminance coding in a cckb-pou4f2 midbrain population and task-structured activity in pvalb7-eomesa hippocampal-like neurons--and defined over 2,000 other function-gene-anatomy subpopulations. Analysis of this unprecedented multimodal dataset also revealed that most gene-matched neurons showed stronger activity correlations, highlighting a brain-wide role for gene expression in functional organization. WARP establishes a foundational platform and open-access dataset for cross-experiment discovery, high-throughput function-to-gene mapping, unification of cell biology and systems neuroscience, and scalable circuit modeling at the whole-brain scale.

neuroscience↗

bioRxiv2026

Genome-wide identification of heat shock proteins (HSP70) in the Cuban painted snail Polymita picta: evolutionary constraints face climate change challenges

Climate change poses a critical threat for biodiversity. Among ectothermal animals, terrestrial molluscs are considered highly vulnerable to temperature increase and drought due to their low vagility and specialized ecological requirements. In response to thermal stress, heat shock proteins (HSP70) play a crucial role in the response syndrome and phenotypic plasticity and mediate the adaptation to fluctuating environments. Here, we performed the first genome-wide identification and characterization of the HSP70 family in a Neotropical terrestrial gastropod of high conservation concern: the Cuban painted snail Polymita picta. Using comprehensive bioinformatic approaches, we identified HSP70 paralogs, analysed their structural features and assessed sequence variation, highlighting their potential relevance for thermoresistance. Our findings reveal an HSP70 repertoire of ten diversified sequences with signatures of functional specialization and possible adaptive variation linked to environmental temperature regimes. Using novel molecular resources, this pioneering analysis establishes a baseline for early warning systems, integrating stress-related biomarkers into conservation management and climate change adaptation strategies for threatened terrestrial molluscs.

genomics↗

bioRxiv2025

SpotDMix: informed mRNA transcript assignment using mixture models

Unveiling the genetic profiles of spatially distinguished cells is an important aspect in many areas of brain research, as the genetic identity contains information about a cells physiological properties and internal state. On top of this, knowledge of the genetic details of each cell can reveal structural organization within tissue. As image-based spatial transcriptomics moves toward applications in tissues with dense cellular packing, accurate assignment of detected mRNA transcripts ("spots") to correct segmented cells becomes increasingly difficult, rendering simple methods insufficient with many incorrect assignments to neighboring cells. Here we introduce SpotDMix, a statistical model for assigning spots to cells by modeling spots as coming from a mixture model of distributions matching segmented cell shapes, with assignment probabilities and shape parameters optimized using the Expectation Maximization algorithm. Performance is assessed and compared against several simple methods in various scenarios on both surrogate data and larval zebrafish data. In all tested scenarios SpotDMix outperforms the simple methods on all evaluated metrics, including individual transcript assignment accuracy, total assigned number of spots per cell error and cell type classification. Further, SpotDMix produces a higher degree of exclusivity between genes which are known to not or rarely co-express.

neuroscience↗

bioRxiv2024

The Recurrent Temporal Restricted Boltzmann Machine Captures Neural Assembly Dynamics in Whole-brain Activity

Animal behaviour alternates between stochastic exploration and goal-directed actions, which are generated by the underlying neural dynamics. Previously, we demonstrated that the compositional Restricted Boltzmann Machine (cRBM) can decompose whole-brain activity of larval zebrafish data at the neural level into a small number ([~]100-200) of assemblies that can account for the stochasticity of the neural activity (van der Plas et al., eLife, 2023). Here we advance this representation by extending to a combined stochastic-dynamical representation to account for both aspects using the Recurrent Temporal RBM (RTRBM) and transfer-learning based on the cRBM estimate. We demonstrate that the functional advantage of the RTRBM is captured in the temporal weights on the hidden units, representing neural assemblies, for both simulated and experimental data. Our results show that the temporal expansion outperforms the stochastic-only cRBM in terms of generalisation error and achieves a more accurate representation of the moments in time. Lastly, we demonstrate that we can identify the original time-scale of assembly dynamics by estimating multiple RTRBMs at different temporal resolutions. Together, we propose that RTRBMs are a valuable tool for capturing the combined stochastic and time-predictive dynamics of large-scale data sets.

neuroscience↗

bioRxiv2021

Somewhere I Belong: Phylogenetic Comparative Methods and Machine Learning to Investigate the Evolution of a Species-Rich Lineage of Parasites

AO_SCPLOWBSTRACTC_SCPLOWA substantial portion of biodiversity evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic, and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological, and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multi-marker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58/137 species and characterise major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a combined molecular-morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data of 136/137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters can mask phylogenetic signals but can be key for characterising species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterisations.

evolutionary biology↗

bioRxiv2019

Hydrogen peroxide as regeneration-initiation signal that activates pERK to trigger planarian regeneration

Despite the extensive research on molecular pathways controlling the process of regeneration in planarians and other regeneration models, little is known about the actual initiation signals necessary to induce regeneration. Previously the involvement of ROS, EGFR and MAPK/ERK has been demonstrated during planarian regeneration, however the exact interplay has not been yet described. By selectively interfering with major mediators in all three key parts (ROS, EGFR & MAPK/ERK), we were able to identify amputation/wound-induced ROS, and H2O2 specifically, as upstream cue in activating regeneration-initiation. In addition, our results demonstrate new relationships between regeneration related ROS production and MAPK/ERK activation at early regeneration stages, as well as the involvement of the EGFR-signaling pathway. In summary, our results suggest a new and more extensive signaling model with ROS, and H2O2, highlighted as upstream initiation-factor and its important functions in the downstream EGFR-MAPK/ERK pathway during planarian regeneration.

developmental biology↗