The Journal of Experimental Biology

Oxygen is essential for all terrestrial animals, but there is dramatic variability in how well different animals and even different cell types can adapt to reduced oxygen availability. We used a meta-analysis of the literature, with a focus on mouse studies, to identify pathways that might act to protect animals in low oxygen environments. We identified 108 genes whose mRNA levels change under hypoxia, and 55 genes critical for mounting a response to hypoxia. With this data, we developed a list of conserved genes, and we tested three C.elegans genes previously uncharacterized in hypoxia, mxl-3, yap-1, and ador-1, and found that loss of function altered egg-laying during and after hypoxia. Our method provides a more targeted approach of how to screen for hypoxic phenotypes and study in more genetically tractable organisms to show mechanisms.

Ankle stiffness is decreased during movement compared to posture; however, the etiology of this decrease remains unknown. Determining what gives rise to this decrease is critical for understanding how humans successfully interact with their physical world and how that ability is compromised by functional impairments. While the triceps surae and Achilles tendon primarily dictate ankle stiffness, the relative contributions across posture and movement remain unknown. Therefore, our study sought to quantify the relative contributions of the muscle and tendon to ankle stiffness and how those contributions differ between posture and movement. We used our technique, which combines B-mode ultrasound imaging with joint-level perturbations, to quantify ankle, muscle, and tendon stiffness simultaneously. Since ankle, muscle, and tendon stiffness all scale with torque, participants matched torque between posture and movement tasks. During posture, the Achilles tendon is the dominant contributor to ankle stiffness. However, during movement, the triceps surae and Achilles tendon contribute more equally to ankle stiffness, which can be attributed to a significant decrease in muscle stiffness during movement. Here, we provide the first empirical data on how state-dependent properties of the triceps surae and Achilles tendon contribute to ankle stiffness in conditions relevant to locomotion.

In most muscles, contraction is initiated by neural activation. Some groups of insects break this rule, flapping at frequencies far exceeding the neural drive to their flight muscles. These insects muscles (termed asynchronous) produce force in response to stretch, enabling flight at faster frequencies than would be possible through the slow calcium-dependent processes associated with neural activation. The first flapping insects lacked stretch-activated physiology, which then evolved on top of neural activation dynamics before likely being reduced again in some groups including moths. Stretch and neural activation can co-exist, but it remains unclear if stretch-activation alone is sufficient to generate asynchronous flapping in insect flight muscle. Building on prior closed-loop muscle physiology platforms, we develop a new way to perform a gain-of-function muscle physiology experiment called the physiological dynamic clamp. Inspired by dynamic clamp experiments in neuroscience, we couple isolated intact flight muscle from a hawkmoth, Manduca sexta, to simulated stretch-activation in virtual reality. Tuning virtual reality parameters allows us to manipulate the degree of stretch-activation in silico while retaining all other physiological properties of the muscle. With artificially enhanced stretch activation, we find that hawkmoth muscle can support stretch-activated work at typical wingbeat frequencies. When simultaneously stimulated at wingbeat frequency, interference between stretch and neural activation results in variable work production. However, this interference disappears when the two activation timescales are close to each other resulting in entrainment to the neural drive. Matching time scales suggests an evolutionary path for smoothly transitioning to stretch-activated, asynchronous flight and back again.

Environmental temperature strongly influences muscle contractile mechanics and locomotor performance in ectotherms, yet animals routinely develop across a range of temperatures while maintaining effective movement. We tested the hypothesis that developmental temperature induces compensatory changes in the intrinsic mechanical properties of the muscles that power the fast-start escape response in larval zebrafish (Danio rerio). Larvae were reared at 25{degrees}C, 28{degrees}C, or 32{degrees}C, and contractile properties of intact tail myotomal muscles were measured across experimental temperatures. Acute changes in experimental temperature strongly affected twitch kinetics, particularly relaxation rate (Q10 = 2.1), resulting in substantial changes in twitch duration. In contrast, rearing temperature produced adaptive changes that opposed these acute thermal effects. At a common experimental temperature, muscles from cold-reared larvae exhibited faster intrinsic relaxation and greater force production during shortening at a physiologically relevant velocity, whereas warm-reared larvae showed slower relaxation and reduced shortening force. As a result, twitch kinetics were largely normalized when measurements were made at each group's rearing temperature, reducing the apparent thermal sensitivity of relaxation rate (Q10 = 1.1). To identify molecular correlates of these functional adaptations, we performed label-free quantitative LCMS proteomic analysis. Cold rearing increased the abundance of Sarco/Endoplasmic Reticulum Calcium-ATPase (SERCA) proteins, driven primarily by elevated atp2a1 expression, while warm rearing reduced the abundance of the major parvalbumin isoforms pvalb1 and pvalb2. These changes implicate remodeling of intracellular calcium handling as a mechanism underlying thermal compensation of muscle function. Together, our results demonstrate that developmental temperature modifies the intrinsic mechanical properties of larval zebrafish muscle in ways that counteract the direct effects of environmental temperature, thereby preserving the timing and power-generating capacity required for fast-start escape performance.

Neural circuits produce reliable activity even after environmental disturbances. This occurs because neurons respond to perturbations in a compensatory manner, a process termed homeostatic plasticity. Bullfrogs undergo prolonged periods underwater during winter, when lung ventilation and its neural control system ceases activity, but air-breathing resumes unscathed when environmental temperatures increase weeks to months later. Compensatory neural mechanisms that contribute involve upregulation of excitatory synaptic transmission on motoneurons driven by inactivity, but whether inactivity or acclimation to low temperatures drive other forms of compensation is not known. The GABAA receptor contribution to respiratory rhythm generation is downregulated following overwintering, which promotes network excitability. Therefore, we disentangled the contributions of cold temperature acclimation and inactivity experienced during overwintering on reduced GABAergic signaling. Here, we show that cold temperature, and not inactivity, reduces GABAA signaling in the respiratory rhythm generating network, without influencing GABAA transmission onto motoneurons. Therefore, cold temperature acclimation drives reduced GABAergic signaling selectively in inter-neuronal rhythm generating circuits, while excitatory motoneurons synapses are strengthened by inactivity in the overwintering environment. Most work interprets compensatory plasticity as activity-dependent during activity perturbations, but we reveal that different aspects of a disruptive environment elicit distinct forms of plasticity across a motor network.

Tree shrews (Tupaia belangeri) are increasingly used in comparative neuroscience, yet their respiratory physiology remains poorly characterized. We quantified spontaneous breathing and respiratory rhythm variability in awake adult tree shrews (n = 10; 5 males, 5 females) using whole-body plethysmography. Respiratory frequency decreased by approximately 16% with acclimatization to the recording chamber, while respiratory timing, body-mass-normalized respiratory amplitude, inspiratory flow, and minute ventilation remained relatively stable. After acclimatization, mean respiratory parameters were similar between sexes, but short-term breath-to-breath variability (SD1) was greater in males than females, whereas SD2 was comparable. These findings establish baseline respiratory characteristics in awake tree shrews and identify sex-dependent differences in short-term respiratory rhythm stability.

Animals use long-range signals, such as hormones and neural signals, to coordinate the actions of distant organs. There is no precise, quantitative framework that explains the problems these control systems must solve and thus predicts their behavior under varied conditions. We consider this problem in the context of blood glucose regulation by the hormone insulin, the failure of which produces diabetes. We show that existing mathematical models of glucose regulation admit equivalent control strategies with no hormones at all, and thus cannot explain the need for hormonal regulation. We therefore introduce a minimal model of inter-organ variations in local glucose, and show that control strategies based on local glucose measurements face severe trade-offs between different control objectives. In contrast, we show that hormonal control signals from the pancreas can overcome these limitations. By exposing the benefits of hormonal control, our work paves the way to a detailed understanding of physiological design principles, with possible implications for the engineering of an artificial pancreas.

Humans often collaborate under asymmetric information, for example when two people carry a table and only one knows the destination. They coordinate without speech using cues from movement kinematics, interaction forces, and object states. Characterizing this sensorimotor communication is difficult because these signals both execute the task and convey information, whose meaning is context-dependent. Here, we investigated a virtual table-carrying task where one partner knew the target while the other inferred it from visuo-haptic feedback. Participants flexibly adapted kinematic and haptic cues across contexts to convey intention. We introduce an explainable machine-learning framework that decodes intent from ongoing multimodal signals and quantifies where individual features are informative. Incorporating the decoded signals into a drift-diffusion model accurately predicted the uninformed partner's target choices and decision times. Together, our framework explains how humans communicate through action and offers principles for collaborative robots to infer and express intent through physical interaction.

Cruising speed is a key factor affecting prey-search efficiency and migration range in continuously swimming animals. Tunas and lamnid sharks (e.g., white sharks) have convergently evolved traits for high-speed cruising, including the ability to maintain slow-twitch, aerobic red muscle (RM) warmer than ambient water, known as RM endothermy. Despite their well-known high cruising speeds, kinematic features underlying their elevated speeds remain unclear. Swim speed is the product of tailbeat frequency (TBF; Hz) and stride length (SL, the absolute distance traveled per tailbeat; m). RM endothermy is expected to elevate TBF by enhancing muscle contraction performance. Furthermore, within RM-endothermic fishes, tunas and lamnid sharks may exhibit distinct kinematic features because of differences in caudal fin morphology and tailbeat amplitude. Here, we compiled kinematic parameters from 20 fish species, including five RM-endothermic species, measured in the wild using animal-borne sensors. Comparative analyses showed that, for a given body mass and water temperature, RM-endothermic fishes exhibited 1.9 times higher cruising speed and TBF than ectothermic fishes, while SL remained similar. Within RM-endothermic fishes, tunas exhibited 2.3 times higher TBF than similar-sized lamnid sharks, whereas lamnid sharks showed 1.7 times longer SL than similar-sized tunas. These results indicate that RM endothermy is generally associated with higher TBF, while significant kinematic differences remain between tunas and lamnid sharks. This divergence may be partly explained by the greater caudal fin area and tailbeat amplitude in lamnid sharks. It may also reflect contrasting skeletal types of teleosts and elasmobranchs, which potentially influence body stiffness and swimming kinematics.

When sensory modalities yield conflicting information, animals must rapidly reassess stimuli to select their actions. We induced auditory-visual conflict in free-flying echolocating Egyptian fruit bats, by fitting animals with prisms that shifted the perceived visual location of a landing perch while echoes returned from its veridical location. Bats that course-corrected within a single goal-directed flight did so by decoupling sonar gaze from steering, to enable rapid reweighting of visual and auditory cues. We designed artificial agents that used Bayesian inference to construct estimates of goal locations in their environment. When competing estimates directed active-sensing behaviors distinctly from steering, agents course-corrected more rapidly. Consistent with this idea, when bats were fit with prisms and earplugs that attenuated auditory localization cues, they were unable to course-correct. Removing prisms produced no systematic after-effects. Our framework suggests that instead of correcting their behavior after failure, animals could efficiently employ active sensing to resolve sensory conflict before failure occurs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/743555v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@16262edorg.highwire.dtl.DTLVardef@4cd82aorg.highwire.dtl.DTLVardef@103e6fforg.highwire.dtl.DTLVardef@13292bf_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOCover figure.C_FLOATNO Bat wearing helmet with clear-glasses and tracking markers. Photograph (C) 2026 Nikita M. Finger / Moss Laboratory. C_FIG

Motor systems controlling locomotion must generate repetitive rhythmic activity, while also still retaining the ability to generate a diverse range of outputs. How motor systems monitor, regulate, and promote diversity of their own outputs is not well understood. Here, we perform single-step, variable-order and hidden-state Markov modelling (HSMM) on spontaneous fictive locomotor activity in the isolated Drosophila larval nervous system to examine how a motor system balances constraint and promotion of diversity amongst competing motor programs. We show that spontaneous fictive activity is structured by interacting mechanisms operating at multiple levels of sequence organisation. Analysis of one-step transition rules revealed a bias in activity towards activity states underlying exploration that in turn, promote transition to diverse outputs. In contrast, higher-order Markov, N-gram, and HSMM analysis indicated a memory biased towards revisiting recently executed motor programs. These mechanisms together suggest that the Drosophila larval locomotor system maintains a dynamic repertoire of possible motor outputs by monitoring recent activity and biasing future transitions accordingly. In this sense, fictive rhythmogenesis reflects a diversity-generating process: the larval locomotor network does not simply repeat a fixed motor programme or randomly transition from one state to another, but rather continually regulates access to rhythmic states based on recent experience. Together, these findings suggest that fictive locomotor dynamics are consistent with adaptive winner-takes-all competition between central pattern generating (CPG) modules that balance constraint and promotion of motor program diversity.

The framework of homeostatic plasticity posits that neurons regulate cellular properties through feedback homeostasis to maintain activity during changes in the environment. However, when disturbances occur in wild animals they are often caused by environmental variables that induce their own acclimation effects, making it difficult to discern if activity-sensitive feedback plays a role in ecological settings. We addressed this problem using a natural activity perturbation, where frogs hibernate in cold water, leaving brainstem motor circuits that generate breathing inactive for long periods. We show here that motor inactivity, amid complex environmental variables in the hibernation environment, represents a key signal for increasing AMPA-glutamate receptors (AMPARs) on motoneurons. Homeostatic upregulation of AMPARs do not regulate neural activity per se but instead correspond with enhanced evoked transmission selectively at cool temperatures. The results show how homeostatic synaptic plasticity may allow animals to restart motor behavior after chronic inactivity encountered in the natural environment. More broadly, these results introduce the concept of homeostatic plasticity as a mechanism to shape thermal tolerance ranges of neural performance in ecological settings.

With 302 neurons and a rigorously characterized connectome, the nematode Caenorhabditis elegans represents a powerful model organism to study the fundamental roles of neuronal circuits in behavior. However, despite the breadth of research, many questions remain unanswered regarding how these organisms are able to successfully navigate their environment. Here, we present a biologically grounded dynamical circuit model for the investigation of sensory-guided behavior during C. elegans chemotaxis. Our mathematical model consists of the chemosensory neuron AWA, interneurons RIM and RIA, motor neurons, including SMDs and RMDs, and body wall muscles that provide proprioceptive feedback through stretch receptors. After optimization with an evolutionary algorithm, the model locomotes effectively toward a chemical attractant, realistically capturing nematode chemotactic behavior. Chemotaxis is ensured by sharp turns, which resemble the omega turns of living nematodes, as a key emergent property of the model. The sharp turning behavior is triggered by decreases in the concentration of the attractant. These result in reduced AWA activity, which in turn triggers disinhibition of RIM and subsequent changes in RIA oscillations. The ensuing coordinated changes in downstream motor neurons activity patterns produce sharp turns, which correct the nematodes path, so that the model worm heads toward the attractant, and remains at its proximity, after it reaches the gradient peak. The proposed framework, along with its emergent dynamics, provides new insights into the minimum requirements for C. elegans circuitry to display major features of its chemotactic behavior, including omega turns. In parallel, it generates experimentally testable hypotheses with respect to the participating neuronal elements.

The Marginal Value Theorem (MVT) is an important part of Optimal Foraging Theory, predicting the optimal time to leave a food patch. It has been mostly studied in birds, insects and mammals, even though simpler organisms also need to forage efficiently in patchy environments. Here we test whether the nematode Caenorhabditis elegans implements the MVT. We recorded individual nematodes exploring patchy environments, across four inter-patch distances and three different food qualities, and found that C. elegans behavior matches MVT predictions: When food patches are further away, each food patch is exploited for a longer time. In previous studies animals achieved this by modulating the duration of visits to food patches. Similarly, we found that C. elegans also increases visit duration with inter-patch distance, but this only accounts for half of the increase in total exploitation time. The other half of the increase comes from C. elegans revisiting food patches multiple times, and the number of these revisits increasing with inter-patch distance. This increase in the number of revisits is not due to behavioral changes in response to distance, but rather to a passive interaction between trajectories and environment geometry. These results show that C. elegans can learn the statistics of an environment and use this information in a way consistent with the MVT, but also that part of the fitness-relevant outcomes can emerge passively. SIGNIFICANCEDespite being key in understanding foraging in patchy resources, the Marginal Value Theorem (MVT) has been tested almost exclusively in relatively complex animals. We extensively tested the MVT in a simple, non-visual organism, showing that Caenorhabditis elegans increases patch exploitation time when inter-patch distance increases. This effect is partially driven by the same behavioral adaptation found in complex animals, but also by an increase in the number of patch revisits. This second driver, which had not been reported before and is probably key for non-visual organisms, requires no behavioral adaptation and produces around half of the fitness-relevant outcome. Our results highlight the need for adapting Optimal Foraging Theory to a wide range of taxa spanning from microbes to small invertebrates.

We present a high-quality chromosome-level reference genome for the Saimaa ringed seal (Pusa saimensis), an endangered freshwater pinniped endemic to Lake Saimaa, Finland. The assembly spans 2.353 Gb and comprises 15 autosomes together with the X and Y sex chromosomes. Using Oxford Nanopore Technologies (ONT) long-read sequencing and Hi-C scaffolding, we achieved a telomere-to-telomere assembly for all chromosomes, except the Y chromosome. Genome annotation identified approximately 21,800 protein-coding genes, consistent with other mammalian genomes. Assembly completeness was high, with BUSCO analysis recovering 99.6% of expected complete single-copy genes (98.2% single-copy and 1.3% duplicated). Comparative analyses revealed a highly conserved chromosomal architecture, with only minor syntenic differences relative to other pinniped chromosome-level assemblies. Previously described cytogenetic fusion events in Phocidae were confirmed (chromosomes 2 and 7). A translocation between chromosomes 6 and 7 distinguishes phocids from the otariids. In general, more distantly related taxa exhibit an increasing degree of intrachromosomal rearrangements. Notably, we identified a large intrachromosomal rearrangement on chromosome 2 that appears specific to the Saimaa ringed seal. Phylogenomic analysis based on 9,226 single-copy orthologues placed the Saimaa ringed seal as a sister lineage to the Baltic ringed seal (Pusa hispida botnica), while confirming also other established evolutionary relationships among pinnipeds. Comparative gene family analysis between the Saimaa ringed seal and the closely related grey seal (Halichoerus grypus) revealed lineage-specific differences driven by a limited number of gene families. In the Saimaa ringed seal, expansions were observed in ion transport, cytoskeleton, and regulatory genes, potentially reflecting adaptation to freshwater conditions. In contrast, the grey seal showed expansions in olfaction, immune-and spermatogenesis-associated gene families, including MAGE/MIA genes, consistent with differences in ecology and mating systems. This reference genome provides an important resource for studies of pinniped genome evolution, as well as conservation and population genomics of the Saimaa ringed seal, facilitating future work on genetic diversity, inbreeding, mutational load and adaptive potential in this highly endangered species.

Background: Chromosome-level genome assemblies are increasingly enabling tests of chromosome evolution, conserved synteny, and sex chromosome conservation across diverse animal lineages, including spiders. Results: Here, we present a chromosome-level genome assembly for the African hermit spider, Nephilingis cruentata, a species with extreme female-biased sexual size dimorphism and a cytogenetically inferred XX2 sex chromosome system. The final Hi-C-assisted assembly spans 1.72 Gbp, with 99.5% of bases assigned to 13 pseudochromosomes, a scaffold N50 of 131.6 Mbp, and a BUSCO completeness score of 98.8%. We annotated 20,021 protein-coding genes, and repetitive elements accounted for 42.7% of the genome. Sex-specific whole-genome resequencing identified Chr02 and Chr07 as candidate X chromosomes based on reduced male coverage, consistent with the expected XX2 system. Using comparative whole-genome alignments across existing chromosome-scale spider assemblies, we also show that sex-linked chromosomes retain broad homologous identity across sampled spider lineages but exhibit lower synteny conservation and greater chromosome-length divergence than autosomes. Conclusions: These results suggest that spider sex chromosomes are conserved in homologous identity but more labile in structure, providing a comparative framework for studying sex chromosome conservation and divergence across Araneae.

ObjectiveThis study investigates knee joint biomechanics during lunges under varying tibial angles and external loads using musculoskeletal modeling and finite element analysis. The goal is to provide a biomechanical basis for understanding knee loading patterns and optimizing sports training and rehabilitation. MethodsTwenty-six healthy young men performed lunges under tibial inclination angles relative to the ground (60{degrees} and 90{degrees}) and two external load conditions (bodyweight and an additional 98 N external load). Kinematic and kinetic data were captured using motion capture and force plates. Musculoskeletal models were used to estimate joint moments, range of motion, and stiffness, with data analyzed using two-way repeated-measures ANOVA. Finite element analysis was performed at 90{degrees} tibial angle to evaluate tissue stress and displacement. ResultsThe joint moment at a 60{degrees} tibial angle was much higher than at a 90{degrees}. External load showed significant effects on knee stiffness, with lower rotational stiffness in the horizontal plane (P < 0.001) and lower coronal plane stiffness at 90{degrees} (P = 0.012) under the 98 N external-load condition, indicating reduced resistance to angular displacement in these planes. Under the 90{degrees} tibial-angle condition with external load, peak stress and displacement were concentrated in the posterior horn of the meniscus, with a maximum displacement of 3.12 mm. ConclusionThe anterior tilt of the tibia increased sagittal-plane knee loading, while external load mainly reduced joint stiffness in the coronal and horizontal planes. Under the 90{degrees} loaded condition, the concentration of stress and displacement in the posterior horn of the meniscus suggests a mechanically unfavorable loading pattern rather than direct evidence of injury risk. These findings may provide useful biomechanical information for load management during lunge-based training and rehabilitation.

The molecular and functional bases of sexual dimorphism in skeletal muscle remain poorly understood. The androgen receptor (AR) is a major regulator of sex-biased gene expression in muscle, but its genomic targets and associated coregulators in vivo are incompletely defined. Using ChIL-seq and an AirID-AR knock-in mouse, we mapped AR-bound genes and AR-associated proteins in skeletal muscle and identified histone deacetylase-linked corepressors. We further identified myosin binding protein H (Mybph) as a female-biased AR-repressed gene conserved in mouse and human muscle. Mybph loss disrupted sarcomeric organization and selectively delayed postinjury force recovery in female mice. These findings define an in vivo AR regulatory network and identify AR-dependent Mybph repression as a potential mechanism contributing to skeletal muscle sexual dimorphism.

The sea star Patiria miniata is a widely used and powerful model organism for cell, developmental, and reproductive biology, but it has lacked genetic tools for expressing transgenes or endogenously tagging proteins. We developed a protocol to endogenously tag a broadly expressed actin gene and to express additional fluorescent markers from the same locus, using CRISPR/Cas9 genome editing. We also identified and isolated a promoter sequence of this actin gene which drives expression of transgenes. This promoter and transgene cassette can be introduced via a plasmid into the genome and persist through metamorphosis into the juvenile stage. Robust methods to induce metamorphosis that result in healthy juveniles are essential for developing stable transgenic lines and have been lacking in the field. Here we report a fast and efficient approach to induce the metamorphosis of larvae into healthy juveniles by introducing surf clam shells. Thus, we present a reliable method to generate both CRISPR/Cas9 knock-in and plasmid-integrated transgenic juvenile P. miniata, enabling future research on their fascinating biology, including regeneration, oogonial stem cells, metamorphosis, and more.

The energetic cost of building human skeletal muscle has never been explicitly calculated or measured. We developed a quantitative bottom-up accounting model that integrates human skeletal-muscle composition with empirically informed estimates of tissue synthesis, physiological deposition, maintenance during accretion, and diet-induced thermogenesis. The calculation was expressed per kg of wet skeletal muscle and organized into five additive components: stored tissue energy, biochemical synthesis cost, physiological deposition cost, resting maintenance during accretion, and diet-induced thermogenesis. Stored tissue energy was approximately 5670 kJ/kg (1355 kcal/kg). Adding biochemical synthesis cost gave 6340 kJ/kg (1515 kcal/kg). Applying empirically derived deposition-efficiency parameters yielded a physiological deposition requirement of 9780 to 11690 kJ/kg (2338 to 2793 kcal/kg), centrally 10830 kJ/kg (2587 kcal/kg). Adding resting maintenance during accretion and diet-induced thermogenesis produced a final additional metabolizable energy intake of 13410 to 15520 kJ/kg (3204 to 3710 kcal/kg), centrally 14570 kJ/kg (3481 kcal/kg). This value provides a first quantitative reference estimate for the energetic cost of human skeletal-muscle accretion.