The self-organised morphogenesis of multicellular organisms emerges not only from biochemical but also from mechanical processes operating across spatial scales. Yet, computational tools for simulating tissue-scale mechanics have largely been released as restricted, study-specific codes. Here, we present NewtonBioMorphX, a GPU-accelerated, open-access comprehensive framework for simulating tissue-scale mechanical morphogenesis. Built on a finite-strain finite-element formulation on tetrahedral meshes, the software implements an unusually broad set of mechanical ingredients: isotropic and anisotropic (direction-specific) growth; multi-layer tissue mechanics; neo-Hookean hyperelasticity combined with stretch-based plasticity; Kelvin–Voigt viscoelasticity; passive anisotropic fibres emulating 3D collagen networks; anisotropic active contractile filaments emulating actin; Hertzian contact forces; and multiple orthonormal coordinate bases (Cartesian, normal–tangent, cylindrical, spherical, cone-adapted, and toroidal). Equally central is an extensive, user-friendly graphical interface spanning the entire workflow — mesh generation from geometric primitives or arbitrary mesh input, per-layer material and growth specification (including analytical functions of space and time compiled at runtime), boundary-condition assignment, real-time colour-mapped and glyph-based visualisation of scalar and tensor fields, and structured data export — allowing intricate mechanical modelling of morphogenetic processes without editing or recompiling source code. The NewtonBioMorphX framework is validated using a benchmark implementing the well-known Cook’s membrane problem, and its versatility is illustrated through parameter gradient plots, as well as twelve ready-to-run preset examples spanning diverse morphologies.

In this study, we investigated the feeding behavior of deformed and normal benthic foraminifera (Protista, Rhizaria) of the species Ammonia veneta. The degree of deformation was visualized by scanning electron and light microscopy. Food uptake and assimilation were quantified in undeformed, slight deformed (1–3 abnormal chambers), and heavy deformed (irregular coiling) individuals using isotopic labeling and confocal microscopy. Specimens were collected from the Belle Isle Marsh (Boston, USA) and maintained under controlled laboratory conditions. After a three-day incubation, slight deformed individuals showed food uptake and isotopic enrichment comparable to undeformed specimens. In contrast, heavy deformed foraminifera exhibited significantly reduced carbon and nitrogen assimilation, as well as a lower number of ingested food particles. Confocal observations further indicated reduced food processing in heavy deformed individuals. These results demonstrate that pronounced morphological deformities are associated with impaired feeding and assimilation performance. Our findings highlight that severe test deformation can substantially affect physiological functioning and should be carefully considered when selecting specimens for laboratory experiments or observing them in polluted areas.

Despite the progress in understanding the circadian pacemaker, the specific mechanism by which it regulates sleep remains incompletely understood. We have previously demonstrated that a substantial number of genes are rhythmically expressed in the mushroom body (MB) Kenyon cells (KCs), including Pka-C1, which encodes the catalytic subunit of protein kinase A (PKA). PKA-C1 plays a crucial role in promoting daytime wakefulness; however, the underlying mechanism remains elusive. Here, using a newly developed in vivo luciferase reporter, we show that the γ lobe is the primary site of rhythmic Pka-C1 expression. Through a combination of in silico analysis, CRISPR mutagenesis, and chromatin immunoprecipitation, we identify the transcription factor Onecut as a regulator of Pka-C1 transcriptional rhythms in γ-KCs. Furthermore, genetic trans-synaptic connectivity mapping and neuronal activity imaging reveal that the dorsal lateral clock neurons (LNds) provide inhibitory input to a subset of dopaminergic (DA) neurons in the protocerebral anterior medial (PAM) cluster, PAM-γ5, rhythmically modulating their activity. This, in turn, rhythmically activates MB γ-KCs via excitatory Dop1R signaling. Resulting γ-neuron activity rhythms drive Pka-C1 transcriptional rhythms through Onecut. Furthermore, these PKA-C1 rhythms reinforce neuronal activity rhythms, creating a feedback cycle between transcriptional and neural activity rhythms that promotes daytime wakefulness. Our findings highlight the conserved role of DA in promoting wakefulness and offer mechanistic insights into its complex regulation. More generally, this work provides a mechanistic framework for how circadian rhythms are translated into neural activity to orchestrate complex behaviors such as sleep.

Symbiont-bearing benthic foraminifera, like corals, rely on endosymbionts for growth and nutrition and experience bleaching under heat stress. , found in tropical and subtropical waters, hosts a diverse range of endosymbionts belonging to Symbiodiniaceae. We examined the thermal tolerance of the Red Sea population, which is the source of an established, invasive population of in the Eastern Mediterranean. The Red Sea population is expected to exhibit enhanced thermotolerance, potentially due to its greater variety of endosymbionts. We conducted temperature-manipulation experiments, measuring calcification rates and net photosynthesis, evaluating the thermotolerance of and its endosymbionts. We also analyzed the diversity of Symbiodiniaceae by sequencing the internal transcribed spacer 2 (ITS2). Our results show that exposure to 35°C initially induced stress in the endosymbionts during the first week; however, net photosynthesis gradually recovered in subsequent weeks. In contrast, host calcification rates remained low at 35°C, though not completely inhibited. Amplicon sequencing revealed that by the end of the experiment, a single ITS2 type, belonging to Symbiodiniaceae and initially present in field-collected specimens, became dominant in cultured individuals. Because this type became dominant across all temperature treatments, the observed shift likely reflects a response to laboratory conditions rather than direct thermal selection. Consequently, although the recovery at 35°C is consistent with acclimatory physiological responses, it does not provide direct evidence for symbiont-specific acclimation. Our findings suggest that holobiont physiological recovery and symbiont shuffling under laboratory conditions may contribute to the resilience of in warming oceans.

The mechanisms by which novel differentiation pathways evolve to produce new cell types are still not fully understood. Chromatophores, the pigmented cells in the skin, offer an ideal paradigm because each type independently develops from neural crest cells to produce a distinct colour using well-characterised biosynthetic pathways. Here we show, using single-cell gene expression analyses, that canonical chromatophores develop in the embryonic skin of corn snakes and bearded dragon lizards. Yet, we identify previously undescribed chromatophore subtypes in the bearded dragon. These populations co-express progenitor and mature markers and possibly contribute to embryonic skin patterning, as revealed by whole-mount in situ hybridisation. Comparative analyses uncover that while mature chromatophores show cross-species similarity reflecting shared pigmentary function, progenitor states differ in transcription factor usage, including species-specific deployment of MITF, PAX7, and TFEC. Integration with teleost and amphibian datasets confirms that diversification of pigmentation arises through distinct progenitor trajectories converging on similar mature states.