Biology subjects

Arendt, D.

Publications and source records attributed to Arendt, D..

At least 19 recordsLinked to original sources

bioRxiv2026

From promiscuity to specialization: The origin of cholinergic and monoaminergic signaling is pre-bilaterian

The emergence of chemical neurotransmission was key to the evolution of nervous systems, yet when the different transmitter systems arose remains unclear. Biogenic amines (here, acetylcholine and the monoamines) have been reported in non-bilaterian animals and even outside Metazoa, but their physiological role has only recently begun to be resolved, and phylogenetic surveys of the bilaterian machinery have restricted dedicated monoaminergic signaling to Bilateria. Combining targeted metabolomics, molecular phylogenies, structural modeling and binding-affinity prediction, single-cell expression analysis and immunochemistry, we show that cholinergic and monoaminergic signaling predate Bilateria. We detect acetylcholine, dopamine, histamine, adrenaline, tyramine, 2-phenylethylamine and tryptamine in a sponge and two cnidarians, and identify broad-specificity enzymes and transporters able to produce and load them. These genes are co-expressed in both neuronal and non-neuronal cell types, indicating that amine signaling was never confined to the nervous system. Two Hydra vulgaris muscarinic receptor orthologs retain a fully conserved orthosteric site and are predicted to bind acetylcholine as strongly as their bilaterian counterparts, and muscle-type nicotinic receptor subunits are co-expressed with Rapsyn-related genes in cnidarian muscle cells, placing cholinergic neuromuscular signaling in the cnidarian-bilaterian ancestor. Specialization came later in Bilateria, where gene duplications produced substrate-specific enzymes (ChAT, TH, TPH), dedicated vesicular transporters (VAChT, VMAT) and ligand-selective receptors. Biogenic amine signaling is thus not a bilaterian innovation but an ancient mode of cellular communication that evolved from generalist to specialist machinery.

evolutionary biology↗

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

Multi-modal single-cell profiling reveals transcriptional states and commitment dynamics during sexual reproduction in the diatom Pseudo-nitzschia multistriata

Diatoms, single-celled photosynthetic eukaryotes, traditionally considered primarily influenced by resource availability, are now recognized to exhibit complex developmental processes reminiscent of those in multicellular organisms. Sexual reproduction is an obligate choice in many species, albeit with variable frequency and efficiency. In order to explore decision making mechanisms and cellular heterogeneity inherent to this specific phase of the diatom life cycle, we applied a multi-modal strategy to follow sexual reproduction events in the model diatom Pseudo-nitzschia multistriata: i) we employed image-enabled cell sorting to link sexual stages morphology with gene expression ii) we developed a single-nucleus RNA sequencing assay, and iii) conducted proteomic profiling. Combining phenotypes with single-cell profiling allowed us to identify sexual state-specific transcription programs and different states within morphologically identical parental cells, revealing a widespread commitment of the majority of the population to sexual reproduction. This implies that the bottleneck to successful sexual reproduction in this species can be placed downstream of the signalling phase between mating cells, with additional, yet unidentified, factors influencing mating success at sea.

microbiology↗

bioRxiv2025

A flexible Janus head: molecular determinants of a viral protein's RNAi suppressor and capsid forming activities

Viral suppressors of RNA silencing (RNAi) expressed by plant viruses, VSRs, are exceptional proteins. Although not conserved, even within virus families, most VSRs bind small interfering RNAs, siRNAs, thereby blocking antiviral RNAi. Turnip crinkle virus, a member of the Tombusviridae family, encodes a VSR, TCV P38, which also forms the viral capsid. Biochemical studies of the purified protein revealed that the TCV P38 VSR functions as a metastable dimer that binds double-stranded (ds) RNA with high affinity via an induced-fit mechanism of both binding partners. Consistent with its role as a VSR that interferes with antiviral RNAi at various stages, P38 distinguishes between siRNAs of different lengths. Consistent with its capsid-forming function, the protein binds longer dsRNAs cooperatively. Structural data obtained from an RNA-free capsid-like icosahedral crystal and modeling of Tombusviridae capsid proteins suggest that flexible interactions between the P (protruding)-domains of P38 are important determinants for forming both the VSR dimer and the capsid structure. Studies with protein mutants confirmed this and also revealed the central role of the S (shell)- and R (RNA-binding)-domains of TCV P38 in adaptive substrate binding. Our study provides comprehensive insights into the molecular and structural properties of a versatile viral "Janus head" protein. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/690650v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@185f6b1org.highwire.dtl.DTLVardef@6e773org.highwire.dtl.DTLVardef@1456981org.highwire.dtl.DTLVardef@11a63e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

A whole-body cell type atlas mapped into an electron microscopy volume of an annelid worm

Differential gene expression establishes the distinct physiology and morphology of cell types in an animal body. Single-cell sequencing and volume EM represent milestones toward the characterization of cell types, yet are difficult to combine for a comprehensive view on the cellular genotype-phenotype link. Here, we map a whole-body single-cell transcriptome into the PlatyBrowser, a multimodal cellular atlas for the marine annelid Platynereis dumerilii, and establish this combination uniquely for an entire animal. We learn that, in the 6-days-old worm, the majority of genes are tightly co-regulated to jointly implement one of eight major cellular morphotypes representing epidermis, gut, vasculature, myofibres, glia, motile cilia, glands, or neurons. Focusing on neurons, we uncover 14 families that by transcription factor identity, axonal projection, or sensory-secretory apparatus resemble conserved neuron types found in vertebrates, insects, or nematodes. We hypothesize that these existed in urbilaterian ancestors and represent the ancient core of nervous system centralization.

evolutionary biology↗

bioRxiv2025

Developmental landscape of shark telencephalon sheds light on the evolution of telencephalic cell types and the ancient origin of Cajal-Retzius cells

The emergence of predation and associated complex behaviors in jawed vertebrates (gnathostomes) were major driving forces in brain evolution. To gain insight into the neuronal complexity of the last common gnathostome ancestor, we studied the development of the shark telencephalon by combining single-cell and spatial transcriptomics. Our findings suggest an ancient origin of pallial neurogenesis, including basal progenitors, which were previously only identified in tetrapods. We find evidence for migrating gabaergic neurons populating the dorsal pallium, where we observe incipient layering. Finally, we provide evidence for the existence of Cajal-Retzius cells in the developing shark telencephalon, with a conserved molecular profile and tissue localization relative to mammals. Our analyses revealed that major features of the vertebrate pallium arose much earlier than previously thought, in the gnathostome lineage.

developmental biology↗

bioRxiv2025

Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes

Quantifying gene expression across convergent origins of traits clarifies the degree to which those traits arise from shared versus distinct genetic programs, revealing how gene re-use relates to the repeatability of evolution. Eyes are important traits that evolved in many distantly related lineages, including at least nine times within cnidarians. Here, we investigate gene expression in eye-bearing and non-visual tissues from three cnidarian species representing long-diverged lineages where eyes evolved convergently (Cubozoa, Scyphozoa, and Hydrozoa). We find gene expression in eye-bearing tissues to be mostly lineage-specific, with only a small proportion of genes having convergent expression across species. Nevertheless, all species express homologs of deeply conserved vision-related genes known from Bilateria, which likely reflects deep homology (parallel evolution across vast phylogenetic distances) of a metazoan phototransduction toolkit. A gene tree analysis of opsins--the prototypical animal photosensors--shows that convergent eyes recruited different opsin paralogs, with the potential exception of an opsin ortholog shared between scyphozoan and cubozoan eyes. Our results suggest that eyes have mostly lineage-specific patterns of gene expression, yet some key phototransduction components are repeatedly recruited across multiple independent eye origins in Medusozoa.

evolutionary biology↗

bioRxiv2024

A genome resource for the marine annelid Platynereis dumerilii

The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of [~]1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation ([~]3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.

genomics↗

bioRxiv2024

Systemic coordination of whole-body tissue remodeling in sea anemone local regeneration

The complexity of regeneration extends beyond local wound responses (1,2), eliciting systemic processes that engage the entire organism. However, their functional relevance, and the spatial and temporal orchestration of the underlying molecular processes distant from the injury site remain unknown. Here, we demonstrate that local regeneration in the cnidarian Nematostella vectensis involves a systemic homeostatic response, leading to coordinated whole-body remodeling. Leveraging spatial transcriptomics, endogenous protein tagging, and live imaging, we comprehensively dissect this systemic response at the organismal scale. We identify proteolysis as a critical process driven by both local and systemic upregulation of metalloproteases. We show that metalloproteinase expression levels and activity scale with the extent of tissue loss, leading to proportional long-range movement of tissue and its associated extracellular matrix. Our findings illuminate the adaptive nature of the systematic response in regeneration. We propose that this integrated regenerative mechanism, shifting the system from a steady to a dynamic homeostatic state, allows the organism to cope with a wide range of injuries.

developmental biology↗

bioRxiv2024

Somite-independent regeneration of the axolotl primary body axis

Primary body-axis development is a highly conserved process that proceeds through somitogenesis and subsequent subdivision into dermatome, myotome, and sclerotome. Defects in somitic-clock genes such as Hes7 lead to vertebral-segmentation defects in mice and fish. Here we show that in the axolotl, although Hes7 is necessary for proper embryonic vertebral segmentation, it is-- surprisingly--dispensable during tail regeneration. We investigated the mechanism of vertebral segmentation during regeneration which initially occurs through extension of a cartilage rod ventral to the spinal cord. We find that the regenerating cartilage rod undergoes a periodic wrinkling that provides a template for vertebral segmentation. Via direct mechanical measurements and biophysical perturbations, we show that a model of compression-induced buckling instability can predict vertebral segmentation. The cartilage rod and other somitic derivatives (muscle, cartilage, tendon, fibroblasts) arise from tendon-like, Lfng+ multi-potent mesenchymal progenitors, which display a gene regulatory state distinct from somitic progenitors. In summary, we uncover a mechanism of vertebral segmentation during axolotl tail regeneration that is distinct from the somite-based developmental mechanism.

developmental biology↗

bioRxiv2023

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals. HighlightsO_LISponge deflation is driven by tension release in actomyosin stress fibers of epithelial pinacocytes C_LIO_LIAkt kinase/Nitric oxide/Protein kinase G/A regulate actomyosin relaxation C_LIO_LIAgitation-induced deflation coincides with an inflammatory state C_LIO_LIThe sponge relaxant-inflammatory response is evolutionary related to similar responses in the vertebrate vascular system C_LI

molecular biology↗

bioRxiv2022

Cross-phyla protein annotation beyond sequence similarity through structural prediction and alignment

BackgroundAnnotating protein function is a major goal in molecular biology, yet experimentally determined knowledge is often limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer function, however this approach loses predictive power with longer evolutionary distances. Here we propose a pipeline for the functional annotation of proteins using structural similarity, exploiting the fact that protein structures are directly linked to function and can be more conserved than protein sequences. ResultsWe propose a pipeline of openly available tools for the functional annotation of proteins via structural similarity (MorF: MorphologFinder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in >90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. Using this, we uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. ConclusionsOur work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.

evolutionary biology↗

bioRxiv2022

MoBIE: A Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data

Facing the challenge of exploring and sharing multi-terabyte, multi-modal and multi-scale image data of heterogeneous dimensionality, we developed MoBIE, a Fiji plugin that provides rich visualization features to enable browsing data from numerous biomedical applications on a standard laptop computer. MoBIE also supports segmentations, associated measurements and annotations. Users can configure complex views of datasets, share them with collaborators, and use them for interactive figure panels. The MoBIE plugin also offers a convenient interface for converting data into compatible data formats; an additional Python library facilitates managing diverse MoBIE projects.

bioinformatics↗

bioRxiv2022

MorphoFeatures: unsupervised exploration of cell types, tissues and organs in volume electron microscopy

Electron microscopy (EM) provides a uniquely detailed view of cellular morphology, including organelles and fine subcellular ultrastructure. While the acquisition and (semi-)automatic segmentation of multicellular EM volumes is now becoming routine, large-scale analysis remains severely limited by the lack of generally applicable pipelines for automatic extraction of comprehensive morphological descriptors. Here, we present a novel unsupervised method for learning cellular morphology features directly from 3D EM data: a convolutional neural network delivers a representation of cells by shape and ultrastructure. Applied to the full volume of an entire three-segmented worm of the annelid Platynereis dumerilii, it yields a visually consistent grouping of cells supported by specific gene expression profiles. Integration of features across spatial neighbours can retrieve tissues and organs, revealing, for example, a detailed organization of the animal foregut. We envision that the unbiased nature of the proposed morphological descriptors will enable rapid exploration of very different biological questions in large EM volumes, greatly increasing the impact of these invaluable, but costly resources.

developmental biology↗

bioRxiv2022

Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas

The vertebrate brain emerged more than [~]500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey - a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits - based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of the core cell type composition, tissue structures, and gene expression programs of the ancestral brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral vertebrate brain was likely devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors on the jawed vertebrate lineage. Our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.

evolutionary biology↗

bioRxiv2021

Single cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non-feeding to feeding larva. We identify 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems. Further subclustering of these reveal a highly detailed portrait of cell diversity across the larva, including the identification of neuronal cell types. We then validate important gene regulatory networks driving sea urchin development and reveal new domains of activity within the larval body. Focusing on neurons that co-express Pdx-1 and Brn1/2/4, we identify an unprecedented number of genes shared by this population of neurons in sea urchin and vertebrate endocrine pancreatic cells. Using differential expression results from Pdx-1 knockdown experiments, we show that Pdx1 is necessary for the acquisition of the neuronal identity of these cells. We hypothesize that a network similar to the one orchestrated by Pdx1 in the sea urchin neurons was active in an ancestral cell type and then inherited by neuronal and pancreatic developmental lineages in sea urchins and vertebrates.

developmental biology↗

bioRxiv2020

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.

bioinformatics↗

bioRxiv2020

Whole-body integration of gene expression and single-cell morphology

Animal bodies are composed of hundreds of cell types that differ in location, morphology, cytoarchitecture, and physiology. This is reflected by cell type-specific transcription factors and downstream effector genes implementing functional specialisation. Here, we establish and explore the link between cell type-specific gene expression and subcellular morphology for the entire body of the marine annelid Platynereis dumerilii. For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, automatically segmented all cell somata and nuclei, and clustered the cells according to gene expression or morphological parameters. We show that collective gene expression most efficiently identifies spatially coherent groups of cells that match anatomical boundaries, which indicates that combinations of regionally expressed transcription factors specify tissue identity. We provide an integrated browser as a Fiji plugin to readily explore, analyse and visualise multimodal datasets with remote on-demand access to all available datasets.

cell biology↗