iScience

In the search for universals shaping acoustic communication across species, we increasingly look for patterns known from human languages and music in non-human animals. These parallels are often explored separately and with limited ecological context. Here, we take a deep dive into the temporal structure of a complex call used by the little auk (Alle alle), a pelagic seabird with elaborate vocal behaviour and socially complex colonial life. Based on syllable durations, intervals and silences, we examine its conformance to linguistic laws, rhythmic structure and information content. This reveals intricate problems of temporal organisation: while the calls conform not only to linguistic laws of brevity but also to the initial and final lengthening known from human prosody, these effects interact with the internal structure of the call and information carried within it. To our knowledge, this is the first time that conformance to multiple linguistic laws, exceeding simple vocal efficiency, has been described for a non-human, non-vocal learning animal. The calls rhythmic structure shows a progressive rallentando -- a systematic slowing driven by changes in syllable and silence durations and the intervals between syllable onsets. The exact patterns of this rallentando are indicative of the callers sex and individually specific. These results reveal how seabird communication is shaped not only by efficiency universals, but also the specific pressures of colonial life. Our work highlights the temporal structure as an important axis of communication evolution, but also serves as a reminder to consider the species ecological reality and the function, not only presence, of temporal organisation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/713940v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@13de3a8org.highwire.dtl.DTLVardef@2d64adorg.highwire.dtl.DTLVardef@2ca53aorg.highwire.dtl.DTLVardef@113c38d_HPS_FORMAT_FIGEXP M_FIG C_FIG

The end-Permian mass extinction (EPME) represents the most severe biotic crisis of the Phanerozoic Eon on Earth and has been well documented in marine taxa. However, its impact on terrestrial organisms and ecosystems remains incompletely understood. Here we present a high-resolution reconstruction of terrestrial diversification dynamics and spatial reorganization across the Permo-Triassic boundary (PTB) using comprehensive occurrence data of macroplants, sporomorphs and vertebrates. Terrestrial responses to the EPME show highly temporal, regional and taxonomic heterogeneities. Plants experienced a genus-level diversity loss of [~] 6.7%, across the PTB, whilst vertebrates, a lagged decline from the late Permian, peaking at a diversity loss of [~] 66.7%. Global distributions of plant and vertebrate show converging on similar latitudinal gradients post the PTB. Plant diversity loss is disproportionately high in low-latitude and tropical regions and progressively lower toward mid- and high-latitudes. Our study facilitates a fine-grained understanding to terrestrial macroevolution in geologic history through multi-analysis of a large volume of fossil data. Our findings challenge the long-held notion of global terrestrial collapse and mass extinction in plants during the PTB and offer a deep-time analogue for uneven response of extant terrestrial biodiversity to ongoing climate change.

The bodies of pterosaurs, the first flying vertebrates, are covered with integumentary filaments (pycnofibres) thought to be homologous to feathers in dinosaurs, but their coloration remains unknown. Here, we report a layered internal arrangement of melanosomes containing a photonic nanostructure within the monofilaments in a previously undescribed specimen of tapejarid pterosaur Sinopterus dongi from the Early Cretaceous Jehol Biota. Optical simulations showed that this structure reflects green to magenta iridescent coloration, confirming the presence of melanosome-based iridescent coloration previously thought to be unique to birds. This finding deepens our understanding of structure/color gamut relationships in amniotes, while supporting further shared characteristics associated with derived genetic and regulatory shifts in archosaurs.

Unraveling how adult neurons reshape their architecture is key to understanding post-developmental plasticity. Drosophila clock neurons, which remodel their terminals on a daily basis, offer a unique model to examine the mechanisms underlying structural plasticity. In this study, we examine the impact of the experimental design on the remodeling process. We established a simple fixation protocol that preserves tissue integrity and prevents its deformation while enabling the fixation of a larger number of individuals within the appropriate time window. We show that intrinsic (i.e., targeting fluorescent reporters to the membrane) or extrinsic (i.e., temperature) variables may influence this dynamic process. Examining ex vivo preparations, we found that the s-LNv terminals display numerous thin filopodia extending from their synaptic boutons. However, these fine membrane protrusions are lost upon fixation, as they could only be accurately visualized ex vivo. Finally, we present MorphoScope, a Python-based interface that eliminates observer bias in complexity measurements. Altogether, we present a powerful and robust model to investigate the principles of adult neuronal plasticity, with implications extending beyond circadian biology.

Sudden and isolated sensory stimuli (SISS) engage the extralemniscal system and elicit widespread electrocortical responses in the brain. These responses, consisting of both time-domain transients and spectral changes, reflect a switch of the global brain state that likely prepares the organism for subsequent urgent behaviours. Crucially, SISS also elicit a short-latency phasic response in a key component of the extralemniscal system in the brainstem, the noradrenergic Locus Coeruleus (LC) nucleus. Such stimulus-evoked LC firing is associated with the electrocortical markers of extralemniscal activation. LC neurons also display burst-like firing spontaneously, i.e., without imposed sensory stimuli, for example, during quiet wakefulness, sleep, or anaesthesia. However, this phenomenon remains underexplored. We therefore measured, in freely behaving rats, the prefrontal electrocorticogram (ECoG) responses following spontaneous LC bursts. In addition, we compared these ECoG responses to those triggered by electrical LC stimulation or auditory SISS. We found that ECoG responses were proportional to the magnitude of the spontaneous LC bursts or microstimulation, and remarkably similar to those elicited by SISS. Finally, suppression of noradrenergic transmission with systemic clonidine administration attenuated the auditory-evoked ECoG response. These results suggest that LC plays a role in generating the transient brain state changes elicited by SISS.

Recent advancements in tomography produce imaging data of geological materials (rocks and fossils) at trillion-voxel scales with multi-channels. Such high-resolution datasets are potentially keys to unveil evolutionary biological information with various shapes and sizes that have not been ever discovered. Volume rendering is an ideal visualization approach for them because it treats all voxels without relying on user-defined surface boundaries. However, these large-scale real-world tomographic data have rarely been volume-rendered at their native resolution, limiting the examination of rich morphological information. Here, we demonstrate a de facto standard volume-rendering pipeline running on a graphical processing unit (GPU)-equipped supercomputing system toward multi-channel, trillion-voxel tomographic data. Our workflow preserves original resolution, capturing detailed morphological information spanning microscopic to macroscopic scales. Systematic comparison of node types shows that GPU memory, rather than host memory, is the primary bottleneck. Our results establish a baseline for large-scale, multi-channel volume rendering of real tomographic data and demonstrate its applicability to geological samples. This work is presented as a practical demonstration of large-scale volume visualization.

Spatiotemporal organisation of biological molecules is a key driver of cellular processes, including many post-transcriptional epigenetic processes. The germline-specific germ granules are biomolecular condensates that act as hubs for mRNA and small RNA processing and are core regulators of germline gene expression programming. Germ granules have been studied extensively in C. elegans, and recent developments have led to many subdivisions of the germ granule into specialised compartments. Rapid advancements in microscopy and protein-protein interaction (PPI) screening techniques have produced a large amount of data towards characterising the localisation of proteins to specific granules. However, common methods used to probe PPIs are limited in their ability to robustly detect valid interactions, especially the multivalent and sometimes transient ones observed in granule environments. Here we perform a meta-analysis of granule protein interaction screens. While these experiments generally enrich for proteins matching the profile of granule-associated proteins, we find that when considering screens individually, reproducibility is surprisingly low, highlighting not only the variability inherent in these methods but also the dynamic nature of the PPI networks present in granules. We developed an algorithm to provide a measure of each proteins association with specific granules across various experiments. By further clustering and investigation of the resulting score matrix, we demonstrate the power of this holistic approach to provide deeper insights into germ granule organisation and highlight novel can provide a resource to better inform future investigations into granules and their constituent proteins.

Feeding is a fundamental animal behavior. Increasing evidence suggests that the timing of food intake--rather than the amount or quality alone--contributes to maintaining health. Although mistimed eating can reset peripheral clocks and desynchronize them from central pacemakers to affect physiology and metabolism, how peripheral clocks can in turn shape rhythmic feeding behavior is less well understood. Here, we investigated the contribution of peripheral clocks to circadian feeding behavior in Drosophila males. Using high-resolution feeding assays combined with complementary analytical approaches that assess both rhythmicity and time-resolved dynamics, we examined the roles of distinct peripheral cell types in feeding regulation. This study reveals the involvement of midgut enteroendocrine cells (EECs) and enterocytes (ECs) in maintaining the stability and strength of feeding rhythms, whereas the fat body clock modulates baseline levels of food intake. Beyond serving as an output behavior of circadian rhythms, feeding also acts as an effective behavioral Zeitgeber that drives molecular clocks. In the absence of the dominant Zeitgeber--light--midgut oscillations decay during prolonged ad libitum feeding in constant darkness, whereas feeding/fasting cycles enable the autonomous persistence of clock oscillations in EECs but not in ECs. These findings are suggestive of regulatory feedback between midgut EECs and feeding, highlighting how timed feeding or dietary interventions could influence metabolic health via specialized gut cells.

A delicate balance between the quiescent and proliferative states of neural stem cells (NSCs) is important for neurogenesis and homeostasis. Histone deacetylase 4 (HDAC4) variants are associated with neurodevelopmental disorders, however, its role in early brain development remains elusive. In this study, we demonstrate that Drosophila HDAC4 plays a crucial role in neural stem cells (NSCs) reactivation and brain development. Depletion of HDAC4 results in notable defects in NSC reactivation, while its overexpression leads to premature reactivation. HDAC4 is SUMOylated at Lys902, which enhances its protein stability by preventing HDAC4 from undergoing ubiquitin-proteasome-mediated degradation. Moreover, phosphorylation of HDAC4 by salt-inducible kinase 3 (SIK3), an AMPK-related kinase, allows cytoplasmic localization of HDAC4 and enhances the association between HDAC4 and Warts, a core kinase of the Hippo pathway. This HDAC4-Wts association inhibits Warts activity, and in turn, the inactivation of the Hippo pathway, triggering NSC reactivation. Finally, genetic epistasis experiments support the SIK3-HDAC4-Warts axis during NSC reactivation. In conclusion, our findings identify HDAC4 as a molecular switch that integrates SUMOylation, ubiquitination, and the Hippo pathway to govern NSC reactivation.

Though whole-genome duplication (WGD) contributes to cancer progression, the mechanism of post-WGD cell proliferation remains unclear. Here, using 6-day live-imaging, we analyzed the proliferation dynamics of more than 150 post-WGD HCT116 cell lineages. A quantitative comparison of mitotic patterns and cell fates between proliferative and non-proliferative lineages revealed that multipolar chromosome segregation in early mitosis is a key factor limiting the proliferative capacity of post-WGD progenies. Multipolar chromosome segregation suppressed post-WGD cell viability, particularly when accompanied by drastic chromosome loss or when it repeatedly occurred. Tracing proliferative lineages elucidated that they proliferated mainly by imposing the risk of multipolar chromosome segregation on one of two sub-lineages that formed after the first bipolar division. Meanwhile, a considerable proportion of proliferative lineages consisted entirely of progeny of early multipolar chromosome segregation events. Our results highlight key cellular events that determine the proliferation dynamics and diversity of post-WGD progenies, providing a fundamental reference for understanding WGD-associated bioprocesses. Summary statementLive image tracing of >150 cell lineages reveals the cross-generation dynamics of multipolar chromosome segregation that determine the fates of post-whole-genome duplication progeny cells.

Embryonically, the vertebrate brain begins as an approximately uniform, fluid-filled epithelial tube that undergoes rapid volumetric expansion and regionalization to form the morphologically distinct primary brain vesicles. Hydrostatic pressure from fluid secretion into the inner lumen generates tension in the neural tube that has been implicated as a potential driver of cell proliferation during these early stages of brain development. However, a quantitatively rigorous view of 3D morphology and cellular proliferation has remained elusive. Here, we provide a standardized mapping for the mechanical and biological landscape of the developing neuroepithelium along anatomical axes. Using this 3D morphometric framework in chicken embryos, we show that localized curvature characterizes compartmental boundaries. While rapid inflation would typically be expected to stretch and thin the epithelium, we find the opposite: global expansion is coupled with significant tissue thickening, identifying the early brain as an active shell. Moreover, spatial patterns of thickness remain invariant to local curvature. Our results demonstrate a decoupling of geometry and growth, showing that spatially stable distributions of tissue thickness and mitotic activity are maintained throughout massive volumetric expansion, independent of the dramatic geometric reorganization driven by luminal pressure. We conclude that, while tension in the neuroepithelium may contribute to proliferative growth at some level, biological pre-pattern likely plays a driving role in the regionalized expansion of the early embryonic brain. Why it mattersThe embryonic brain begins as a simple fluid-filled tube that undergoes rapid and heterogeneous expansion to set up the basic organizational plan of the adult brain. Errors in this process are linked to severe neurological and congenital disorders. This work investigates the biophysical basis of expansion and regionalization of the early brain, a complex three-dimensional process driven by inflation from internal fluid pressure together with active cell behaviors that ultimately produce regionally distinct growth and curvature profiles amid a complex mechanical landscape. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/726048v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@17c442forg.highwire.dtl.DTLVardef@1609374org.highwire.dtl.DTLVardef@170c00corg.highwire.dtl.DTLVardef@15080ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

Scientific models are widely used across the natural sciences as an interface between scientific theories and empirical data [1]. Such models play a key role, for example, in the study of human and animal learning, where they express algorithmic hypotheses and relate them to psychology and neuroscience data [2, 3]. These models are traditionally handcrafted by expert researchers based on existing theory or new insights. Such handcrafted models, however, are now known to fall short of capturing the full richness of behavior, even in their narrow domains [4-7]. An alternative data-driven approach has emerged, seeking to discover new insights by fitting and interpreting flexible models [8-11]. However, these tools require substantial human effort to derive insight from data, and it has been unclear how to discover new ideas from data efficiently. Here, we present DataDIVER, a general approach for automatically discovering computational models from data, and demonstrate that these models surface novel mechanistic insights into human and animal learning. Our approach delivers models that take the form of short computer programs, which are optimized both to fit data well and to be simple. These programs explicitly connect with existing theoretical frameworks and are readily understandable by human scientists. They can also be used to make novel predictions, some of which we show are borne out in re-analysis of existing data. General-purpose tools for surfacing new ideas from data, especially in combination with the large datasets that are increasingly available in many fields, stand to dramatically accelerate scientific discovery.

The morphology of the palate has long constituted the primary basis for differentiating between the two deepest clades of crown group birds, Neognathae and Palaeognathae. However, published literature on the bird palate is dominated by classical anatomical descriptions pre-dating the advent of contemporary three-dimensional imaging techniques, hindering our understanding of bird palate disparity and development. Pterygoid segmentation, the process by which the rostral portion of the pterygoid separates and fuses with the palatine during ontogeny in neognathous birds, remains a poorly understood aspect of avian cranial development despite giving rise to an important component of the cranial kinetic system. Here, we use micro-computed tomography to explore ontogenetic change of the palate during the process of pterygoid segmentation across an unprecedentedly broad taxonomic sample of immature and mature birds. We found that direct evidence of post-hatching pterygoid segmentation was restricted to the major avian subclade Neoaves. Based on morphological and topological similarities, we hypothesise that the rostral projection of the pterygoid observed in Anatidae/Anseres and potentially Anhimidae and Megapodiidae, which we term the hemipterygoid process, is homologous with the hemipterygoid of neoavians, though it does not undergo segmentation. We posit that the origin of a discrete hemipterygoid (as observable in some crownward stem-birds) originated prior to the origin of the process of pterygoid segmentation; however, it remains ambiguous whether pterygoid segmentation is a synapomorphy of Neornithes, Neognathae, or Neoaves. Overall, our study clarifies the process of avian pterygoid segmentation and raises new questions regarding the major morphological modifications that have characterised the evolutionary history of the avian bony palate.

The blood vasculature has a high capacity for structural regeneration, driven by the blood endothelial cells (BECs) that comprise it. This regenerative process, which involves BEC migration and proliferation to form these complex tissues, is linked to low frequency (< 0.1 Hz) calcium spiking that precedes these activities. However, we need new approaches to stimulating angiogenic responses in tissue engineering applications. By conducting experiments that manipulate local ionic concentrations and developing a simple, yet powerful, computational analysis, we demonstrate that sodium-calcium cross-talk is a crucial component that regulates the calcium signaling and downstream angiogenic responses. Activation and deactivation of the inositol triphosphate 3 receptors (IP3Rs) on the endoplasmic reticulum (ER) and the switch between forward and reverse modes of the sodium-calcium exchanger (NCX) are proposed to be the key mechanisms underlying calcium oscillations when cells are exposed to temporary cationic depletion. The spiking is suggested to be a release of intracellular calcium mediated by IP3R activity, and transport in or out of the cell is driven by NCX for the calcium oscillatory signaling pattern. The NCX and IP3R both contribute to manage intracellular calcium and ionic concentration as initially there is a long ER deactivation period while intracellular sodium slowly increases until a sudden onset of calcium is released by the ER. Other calcium and sodium ion channels can change this resonant coupling of ER and NCX to alter the inter-spike duration. Synchronization of the spiking intervals between cells is triggered by stimulating with vascular endothelial growth factor (VEGF), which induces a propagating wave of intracellular calcium across the 2D tissue culture, prior to coordinated cell migration and proliferation towards the VEGF source. This wave, which can be artificially induced and studied using electrical stimulation, suggests that the underlying sodium-calcium crosstalk mechanism introduces intracellular calcium polarization, whose orientation is transferred across cells through spike synchronization. Thus, control of calcium signaling dynamics through regulation of ionic depletion can serve as useful method for generating angiogenic responses in engineered tissue constructs.

Existing databases of interphase chromosome conformations typically store three-dimensional coordinates of genomic segments. However, since interphase chromatin is highly dynamic, such databases are dominated by transient configurations and unstructured regions, whose positions vary continuously between cells and over time, unlike folded proteins such as globin, which adopt similar structures in every cell. These drawbacks motivated the inception of a database based on strion (a portmanteau of a string capturing structure and function). A strion concisely describes the structure and activity of all transcription units in one cell, by retaining only functionally relevant positional information. Sets of strions describing structures in different cells sampled at different times are compiled into a super-strion. Then, 46 super-strions summarise the range of structure and activity of a human cell type, including information on all transcription units, how often each co-fires and co-clusters with others in transcription factories/hubs, enhancer interactomes and small-world expression networks. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/724942v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@13a1263org.highwire.dtl.DTLVardef@18d2c78org.highwire.dtl.DTLVardef@162865corg.highwire.dtl.DTLVardef@1631d65_HPS_FORMAT_FIGEXP M_FIG C_FIG

Muscular hydrostats, muscular structures with no rigid skeleton, are ubiquitous within the animal kingdom, from vertebrate tongues to cephalopod arms1,2, but how they perform complex actions remains poorly understood. One model hydrostat studied for its neural control3-7 and biomechanics8-17 is the feeding system (buccal mass) of the sea hare Aplysia (Fig. 1). The buccal mass (Fig. 1b) performs multiple feeding behaviors by coordinating intrinsic muscles to move a grasper (odontophore)18,19. In this paper, we investigated how mechanical reconfiguration from interacting shape-changing elements facilitates large odontophore protractions. During rejection behaviors, mechanical reconfiguration of the odontophore (elongating its shape to a higher aspect ratio) stretches a protractor muscle (I2), allowing I2 to generate stronger protractions12. In biting behaviors, the odontophore has a similar range of motion. However, during biting, the odontophore has a lower aspect ratio throughout protraction, meaning the I2 muscle alone is insufficient to reach observed protractions due to its length/tension property and reduced mechanical advantage9,10,12,18. By combining new analysis of MRI movies of Aplysia feeding12,18 (Fig. 1) with a new biomechanical model for biting and rejection (Fig. 2), we demonstrate two context-dependent mechanical reconfiguration mechanisms that explain the different ways large protractions are produced in biting and rejection (Fig. 3). The mechanisms integrate shape changes, bending and conforming of muscle structures, and shifts in contact interactions. We propose two mechanical subclasses of muscular hydrostats, "constrained" or "unconstrained" (Fig. 4), that may be morphologically similar but employ different control strategies depending on whether mechanical constraints are reliably present. O_FIG O_LINKSMALLFIG WIDTH=150 HEIGHT=200 SRC="FIGDIR/small/715937v1_fig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@1c60cbeorg.highwire.dtl.DTLVardef@16ebd04org.highwire.dtl.DTLVardef@13b65d5org.highwire.dtl.DTLVardef@9aafb0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Anatomy and kinematics of the Aplysia feeding system (a1) Adult Aplysia californica searching for food and (a2) feeding on Gracilaria macroalgae ((a1) photo credit: Dr. Jeffrey P. Gill, (a2) modified with permission from Bennington et al. 202514). Gray highlight shows the location of the feeding structure, the buccal mass (b). (b) An anatomical diagram of a midline sagittal view of a buccal mass. During feeding, the odontophore (the internal grasper of the buccal mass) protracts through the tubelike I3 muscle. In the midsagittal plane, the I3 is visible as two longitudinal elements, but is one continuous structure that runs circumferentially around the buccal mass. The inner wall of the distal I3 is shown in dark blue. The dashed white line shows the jaw line, which is used as the reference for both the translation and rotation measurements. (c) Configuration of the buccal mass (left: anatomical diagram; middle: MRI frames) showing (c1) peak retraction and (c2) peak protraction. (right) A diagram of the buccal mass was created to highlight key anatomical landmarks for each frame of the MRI video showing a complete biting sequence (d-e). The same diagrammatic representations of the landmarks are shown in (d) and (e) for the protraction and retraction portions of the biting sequence, respectively (See STAR Methods). The frames shown in (c1) and (c2) correspond to the 0 ms and 3410 ms frames, respectively, and are the same between the middle and right portions of the figure. Key frames referred to in the text: t0: start of the behavioral cycle, t1: peak rotation reached, t2: peak translation reached, t3: rotation plateau ended, t4: end of behavioral cycle. (f) Kinematic measurements were taken using the drawn diagrams for each frame in the sequence. See main text for definitions of variables. All scale bars correspond to 10 mm. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/715937v1_fig2.gif" ALT="Figure 2"> View larger version (34K): org.highwire.dtl.DTLVardef@1848bb9org.highwire.dtl.DTLVardef@f126a4org.highwire.dtl.DTLVardef@1ffd5forg.highwire.dtl.DTLVardef@336910_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO Kinetic/Kinematic biomechanical model of the buccal mass (a) Rest geometry of the biomechanical model. The grasper (odontophore) is modeled as a rigid ellipse (magenta with yellow radula). It is connected to the I1/I3 lumen (blue trapezoid) by the hinge muscle (green). The I2 protractor muscle (red) wraps conformally around the odontophore and attaches at the lateral groove. The net force and torque from the I2 on the odontophore are found by performing an instantaneous force balance on a small arc of the ellipse and integrating across the full region of contact between the I2 and the odontophore. The hinge muscle is modeled as a linearly elastic, geometrically exact beam. At each position along the beams midline, a quasistatic force balance is performed (see STAR Methods). (b1) The tension in the I2 is modeled using the length-tension relationship reported in Yu et al. 1999 scaled by a normalized activation level. (b2) The axial and bending stiffness of the beam hinge were calibrated to ex vivo animal data reported in Sutton et al. 2004. Gray region indicates odontophore displacements observed during biting behaviors (Sutton et al. 2004). (c1-c2) To investigate the effects of mechanical reconfiguration on odontophore position at peak protraction, (c1) the aspect ratio of the odontophore ellipse and (c2) the stretch of the lateral groove were added as additional kinematic constraints. (c1) and (c2) show results from the model but do not correspond to any particular behavior or configuration observed in the animal. These constraints impact the biomechanical model via contact forces from the I1/I3 (see STAR Methods). The lateral groove stretch is converted to a depression angle of the dorsal I1/I3 muscle as a proxy for the wrapping of the dorsal I3 around the odontophore observed during in vivo feeding behaviors (Fig 1). (d-e) MRI frames at peak protraction in (d1, with and without overlay) biting (t2) and (e1, with and without overlay) rejection ({tau}2) compared to corresponding frames from the biomechanical model (d2 and e2, respectively). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/715937v1_fig3.gif" ALT="Figure 3"> View larger version (56K): org.highwire.dtl.DTLVardef@1369a90org.highwire.dtl.DTLVardef@1dda429org.highwire.dtl.DTLVardef@4485d5org.highwire.dtl.DTLVardef@ae6523_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3.C_FLOATNO Mechanical reconfiguration of the buccal mass (a) Midsagittal kinematics of the buccal mass during a (left) biting and (right) rejection behavior (see also Figs. S1 and S2). Colored circles (diamonds) show data for an individual frame, and the black line shows the two-point moving average of the signal. Vertical dashed lines show concurrent time points in the different kinematic signals (biting: t0: cycle starts, t1: peak rotation, t2: peak translation, t3: rotation plateau ended, t4: cycle ends. Rejection: {tau}0: cycle starts, {tau}1: rotation plateau ends, {tau}2: peak translation, {tau}3: peak rotation, {tau}4: cycle ends). (b) Model configurations for nine different pairs of aspect ratios ({Phi}) and lateral groove stretches ({lambda}LG ) (numbers correspond to the labeled points in (Fig. S6c)). Note that these simulated results from the model do not necessarily correspond to configurations observed in the animal but rather show changes in the systems configuration due to changes in the kinematic parameters. All configurations here were achieved with an I2 activation of AI2 = 65%. (c-d) Sensitivity of the model translation and rotation at peak protraction to lateral groove shortening ({lambda}LG, top row) and aspect ratio change ({Phi}, bottom row) for biting (c) and rejection (d). The y-axis for all panels reports the difference between the model prediction and observed animal value at peak protraction (for translation or rotation) normalized by the range of motion (ROM) for each behavior. For each panel, one kinematic parameter is held fixed (top:{Phi} fixed; bottom:{lambda} LG fixed) at the value observed in the animal at peak protraction, and the other is varied to determine the effect of changing this parameter on the translation and rotation of the odontophore. Vertical dashed lines show the observed value of the varied parameter in the animal at peak protraction. The horizontal dashed line shows 0 difference for reference. The steepness of the difference curve in the vicinity of the vertical dashed line indicates how sensitive the system is to changes in each kinematic parameter near peak protraction. Here, a steeper curve (with a positive or negative slope) indicates greater sensitivity. For biting simulations, AI2 = 15%, and for rejection, AI2 = 90% based on the results of the model validation. Each curve in (c) and (d) is a 1D cross-section of the 2D contour plots shown in Figs. S6-S7. For a complete view of the sensitivity of translation and rotation to lateral groove stretch and aspect ratio across the kinematic configuration space at different I2 activations, see Figs. S6-S7. Note that (c) and (d) use different vertical scales. The smaller scale for the rejection plots was chosen to better show the difference curves for rejection, and it reflects the overall decreased sensitivity to both lateral groove stretch and aspect ratio changes for the rejection behaviors. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/715937v1_fig4.gif" ALT="Figure 4"> View larger version (36K): org.highwire.dtl.DTLVardef@171f4c6org.highwire.dtl.DTLVardef@7d11a7org.highwire.dtl.DTLVardef@11206e3org.highwire.dtl.DTLVardef@82489c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4.C_FLOATNO Mechanical reconfiguration facilitates behaviors in a variety of constrained hydrostat systems Combinations of the active shape change of internal structures (cyan), changes to the movement constraints and contact interaction (blue), and bending and conforming of structures (magenta) allow constrained hydrostats to mechanically reconfigure their neuromusculature (purple) to perform various behaviors. This can be seen in various systems across various species. As discussed here, the Aplysia buccal mass uses combinations of these mechanisms in (a) biting and (b) rejection behaviors to protract the buccal mass. (c) The pond snail, Lymnaea, has a morphologically similar buccal mass to Aplysia, but its I1/I3 homolog, the anterior jugalis, sits further posterior to the odontophore35, meaning it may more readily rely on the bending of the anterior jugalis and contact interactions during protraction. (d) The octopus and, more broadly, cephalopod buccal masses contain a beak that lacks a fixed articulation. Instead, by activating the lateral mandibular muscle (LMM), the buccal mass can create a stiff rotation point and may shift the function of the posterior mandibular muscle (PMM) from compressing the buccal mass to opening the beak36,37. (e) The human tongue (and other Type I tongues38) sits within the skull and makes use of contact with the hard palate to push food from the oral cavity into the pharynx27,48. (f) Additionally, by changing how the tongue interacts with the palate and teeth, while maintaining the same internal shape, humans can produce various vowel and consonant sounds39,49,50. This use of contact with the palate and teeth is known in the phonetics community as "bracing." Here, by creating a groove in the middle of the tongue, the phonemes /{varepsilon}/ and /ae/ can be produced. By raising the tongue and creating palatal contact while maintaining that groove, these vowels shift to the fricative consonants /s/ and /{theta}/49. Small insets show which of the mechanical configurations are used in each behavior. C_FIG

Leukocytosis, or elevated white blood cell count (WBC), is a clinical hallmark of the systemic inflammatory response following acute ischemia or infection. However, WBC population dynamics during the initial inflammatory response are poorly understood. It is unknown whether early WBC dynamics differ by etiology or impact clinical risk. We fit mathematical models to WBC trajectories for patients hospitalized following acute ischemia or infection. We found differences between responses to strong ischemic insult (acute myocardial infarction, AMI) and strong infectious insult (sepsis). Among patients who recovered and survived hospitalization, net WBC growth following ischemia was [~]1.8x faster than following infection. Response kinetics and dynamics were correlated with short-term mortality in AMI. Increased immature neutrophil production over 24h preceding WBC peak was associated with [~]2x increased odds of short-term AMI mortality, suggesting that dysregulated responses to ischemia may involve bone marrow overactivation towards increased proliferation. Our work provides novel insight into fundamental etiology-specific differences in acute inflammatory responses from routine clinical data and is consistent with recent evidence of a maladaptive role for emergency granulopoiesis in AMI. One Sentence SummaryWBC dynamics differ between ischemia and infection in the early response to acute inflammatory insult, and can discriminate clinically maladaptive responses to myocardial infarction.

Common sex chromosome aneuploidies (SCAs) often present with cognitive and cardiovascular dysfunction in humans. To address SCA effects on gene expression and DNA methylation in relevant cell types, we differentiated neural precursor cells (NPCs) and cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) with different numbers of sex chromosomes, including isogenic and independent lines. As expected, the expression of genes that escape X inactivation (escapees) mostly increases with the number of inactive X chromosomes (Xi). However, allelic analysis shows dampening of escapees specifically on the Xi in XXY compared to XX in both NPCs and CMs, revealing a novel type of dosage compensation in SCA. In contrast, Y-linked gene expression is higher in XXY versus XY NPCs, but the opposite is observed in CMs. This may explain the greater number of differentially expressed autosomal genes in NPCs versus CMs with an added Y chromosome, while effects of added X chromosomes are similar between cell types. Concordantly, changes in autosomal DNA methylation are mainly driven by the presence of a Y chromosome. These findings highlight the cell-type specificity of sex-linked and autosomal gene regulation in SCA conditions. HighlightsO_LISex chromosome aneuploidy induces cell-type specific changes in gene expression C_LIO_LIDampening of the inactive X chromosome in XXY alleviate X overexpression C_LIO_LIHigh Y-linked gene expression in XXY neuronal precursor cells but not cardiomyocytes C_LIO_LISex chromosome aneuploidy disrupts sex biases in autosomal gene expression C_LI

The circadian clock genes Bmal1 and Nr1d1/2 (REV-ERB/{beta}) regulate skeletal muscle metabolism and homeostasis, yet the precise genes and mechanisms involved remain incompletely understood. Here, we perform Weighted Gene Co-expression Network Analysis (WGCNA) on skeletal muscle circadian transcriptomes with varying Bmal1 operational status to identify genes central to muscle circadian function. The largest WGCNA module, potentially under Bmal1 regulation, contains clock and muscle-specific output genes governed hierarchically by hub genes including Igf2bp2, an RNA-binding protein involved in muscle progenitor growth and maintenance. Igf2bp2 expression is rhythmic in mouse and human muscle and functional experiments in muscle-specific Bmal1 knockout mice show that Igf2bp2 is upregulated by loss of Bmal1 at ZT8 and negatively correlated with Nr1d2, suggesting de-repression through REV-ERB{beta} as a regulatory mechanism. Luciferase reporter experiments in cultured myotubes show that REV-ERB{beta}, but not REV-ERB, represses Igf2bp2 transcription and that repression is mediated by non-canonical GCC motifs in the Igf2bp2 promoter region. Together, these findings uncover a circadian Nr1d2-Igf2bp2 regulatory axis linking transcriptional and post-transcriptional regulation in skeletal muscle, with implications for muscle homeostasis. HighlightsO_LIIgf2bp2 clusters with Nr1d2 (Rev-erb{beta}) in circadian co-expression network C_LIO_LIBmal1 or Rev-erb[a]/{beta} knockout upregulates Igf2bp2 in muscle C_LIO_LIIgf2bp2 is rhythmic in WT muscle but arrhythmic in clock mutant muscle C_LIO_LIREV-ERB{beta} represses Igf2bp2 transcription in myotubes C_LIO_LIREV-ERB{beta} repression requires GCC motifs in the Igf2bp2 promoter C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/724827v1_ufig1.gif" ALT="Figure 1"> View larger version (89K): org.highwire.dtl.DTLVardef@2f569borg.highwire.dtl.DTLVardef@1df13a7org.highwire.dtl.DTLVardef@83538borg.highwire.dtl.DTLVardef@1e20983_HPS_FORMAT_FIGEXP M_FIG C_FIG

Accurate biological sex determination of ancient remains is critical for archaeological, anthropological, and forensic studies, but remains challenging for morphologically ambiguous and highly degraded endogenous DNA samples. Paleo-proteomics sex identification approaches, targeting sexually dimorphic amelogenin isoforms (AMELX and AMELY), present a promising solution. However, current workflows rely on manual verification of a few specific peptide markers, a process that lacks standardization and is susceptible to false-positive AMELY signals. To overcome these limitations, we developed protSexInferer, a lightweight, open-source bioinformatic pipeline for automated sex estimation from paleo-proteomic data. Our method uses the ratio of AMELY-specific peptides to all detected AMELY- and AMELX-specific peptides (i.e., the RAMELY value) rather than the mere presence or absence of AMELY signals for sex classification. We demonstrated that the RAMELY value clearly distinguishes male and female individuals in both reference and independent validation datasets, enabling reliable sex assignments even in cases where conventional intensity-based comparisons (e.g., AMELY-59M vs. AMELX-60) are ambiguous. This ratio-based approach effectively mitigates the impact of false-positive AMELY signals, therefore eliminating the need for time-consuming manual verification, and remains reliable even for samples with low peptide yields. Equipped with pre-constructed protein reference databases, protSexInferer provides a robust, standardized, and end-to-end solution for paleo-proteomic sex determination.