Biology subjects

Saxena, S.

Publications and source records attributed to Saxena, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Relatedness and last male sperm precedence in Cheilomenes sexmaculata: Implications for inbreeding avoidance

Avoidance to mate with relatives is a common evolutionary strategy, as it helps maintain genetic diversity and overall fitness within populations. Females often prefer unrelated males to mitigate the risks associated with inbreeding, such as the expression of deleterious recessive alleles. This preference can involve various post-copulatory mechanisms through which females bias paternity towards males with potentially better genes. The phenomenon of last male sperm precedence, where the last male to mate with a female tends to sire the majority of offspring, is well-documented in ladybird beetles. However, how relatedness affects this phenomenon remains unclear. This study aims to investigate whether paternity share is altered when the last male to mate with a female is related to her. By conducting double mating experiments with two different morphs (typical and intermediate) as phenotypic markers, we seek to determine if relatedness disrupts last male sperm precedence. It was hypothesised that females of Cheilomenes sexmaculata will prefer unrelated males over related ones, irrespective of mating order, potentially breaking down the last male sperm precedence. This preference for unrelated males was reflected in our results with unrelated males exhibiting enhanced reproductive success. Females were more fecund and exhibited higher egg viability with unrelated males. Greater paternity share was observed for unrelated males when the second male was related to the female. This study highlights the dynamic nature of sperm precedence and the role of mate quality in female mate choice, emphasizing the importance of inbreeding avoidance in sexual selection.

zoology↗

bioRxiv2026

Learning Interpretable Switching Dynamics in Shared Neural-Behavioral Latent Space

Modern recording technologies enable simultaneous measurement of high-dimensional neural activity and rich behavioral variables, creating both an opportunity and a modeling challenge: identifying the shared latent structure that mediates the brain-behavior relationship and the underlying dynamics through which it evolves across behavioral states. Existing approaches focus on different parts of this challenge: shared representation learning methods identify neural-behavioral subspaces but typically do not model dynamical structure, while dynamical models capture temporal variation and discrete state transitions in neural activity, but do not explicitly disentangle shared neural-behavioral structure from modality-specific variability. We introduce Switching Shared Latent Dynamics (SSLD), a unified framework that learns a latent representation shared between neural activity and behavior and endows this shared space with nonlinear switching recurrent dynamics to reflect the hypothesis that behaviorally relevant neural representations exhibit structured dynamical changes across behavioral states. Complementary private latent variables capture modality-specific variability, providing a window into neural activity that does not directly interact with behavior. We evaluate SSLD on a simulated dataset and four diverse experimental datasets spanning species, brain regions, and recording modalities: monkey motor and premotor cortex during reaching, somatosensory cortex during a bump task, widefield calcium imaging across mouse dorsal cortex during (a) self-initiated decision-making and (b) spontaneous movements. Across all four datasets, SSLD accurately reconstructs neural and behavioral signals, recovers discrete states in the dynamics that align with experimentally defined behavioral epochs, and isolates behaviorally-relevant neural information in the shared latent while preserving private neural variability. Ablations confirm that shared representation learning, behavioral supervision, and switching dynamics each contribute to performance. SSLD offers an interpretable approach to modeling shared neural-behavioral dynamics that complements ongoing efforts toward foundation models for neuroscience.

neuroscience↗

bioRxiv2026

CopY as a Transcriptional Duet Orchestrating Copper Homeostasis via Asymmetry-Dependent DNA Affinity

Copper is essential yet potentially toxic, requiring tight regulation of intracellular concentration. The copper-responsive transcriptional repressor CopY is unusual among bacterial metalloregulators because it occupies two operator sites within the cop promoter. Although two CopY dimers bind these operators independently, the mechanistic significance of this dual-operator architecture remains unclear. Here, we combine biochemical assays, circular dichroism (CD), and electron paramagnetic resonance (EPR) distance measurements to define the molecular basis of CopY-mediated repression. CopY binds the proximal operator with higher affinity than the distal operator. CD measurements further show that DNA binding increases CopY thermal stability, with greater stabilization by the proximal operator. Conversely, DNA-based EPR measurements reveal comparable CopY-induced compaction of both operators. Thus, protein stabilization and DNA deformation represent distinct components of repression. Moreover, site-directed spin labeling and EPR demonstrate that the metal binding domain is conformationally heterogeneous and highly flexible. DNA binding has only a marginal effect on this flexibility. Thus, the metal site is not a rigid pocket but a dynamic one, even in the DNA-bound repressor, a property that may facilitate Cu(I) capture and hence derepression once copper levels rise. We propose that the proximal operator serves as a high-affinity anchoring site, whereas the distal operator primarily promotes promoter remodeling, and that the plasticity of the metal binding domain is retained in the DNA-bound repressor. Together, these findings support a "transcriptional duet" model in which two CopY dimers bound to non-equivalent operators make distinct and complementary contributions to repression.

biophysics↗

bioRxiv2026

Conserved inhibitory mechanisms of root-associated bacteria towardsArabidopsis thaliana and Chlamydomonas reinhardtii

Soil bacteria colonize plants without causing visible disease, yet many suppress host growth. The prevalence and evolutionary reach of this cryptic inhibition are unknown, because phenotyping hundreds of isolates in plants is prohibitively slow. Here we use the unicellular algae Chlamydomonas reinhardtii as a scalable proxy for the green lineage. We screened 148 plant-associated bacteria on Chlamydomonas lawns. Seven of eight Chlamydomonas inhibitors also inhibited the vascular model plant Arabidopsis thaliana. In one of these dual inhibitors, Burkholderia sola MF6, transposon screening and proteomics implicated type VI secretion and tight-adherence pili, and over half the non-inhibitory mutants also failed against Arabidopsis. In the algae, infection triggers rapid deflagellation, then non-lytic regulated cell death. The algal zinc/iron transporter ZIP3 promotes inhibition, whereas the cathepsin X protease CEP12 restrains it, and ZIP3 is epistatic to CEP12. Cryptic inhibition is thus ancient and widespread, and a unicellular algae uncovers it at scale.

plant biology↗

bioRxiv2026

A single cooperative experience increases corticolimbic synaptic density and prosocial behavior

Cooperation is typically studied as an output of the social brain, as opposed to an experience that shapes it. Here, we developed a task in rats that permits interaction while requiring joint action for reward. Cooperation depended on dyad familiarity and visual access. Anterior cingulate cortex (ACC) to basolateral amygdala (BLA) projections were activated during cooperation with a familiar partner, whereas ACC to anterior insula (AI) projections were simultaneously suppressed regardless of familiarity. A single 90 min cooperative experience increased presynaptic marker SV2A, detected by positron emission tomography (PET), in the amygdala and insula one day later. Concurrently, rodents demonstrated heightened attention toward a distressed conspecific. Cooperation is thus an experience that recruits dissociable corticolimbic pathways and changes brain and behavior beyond the encounter itself.

neuroscience↗

bioRxiv2026

Natural prey capture reveals flexible reconfiguration of canonical motor-cortical dynamics for online control

The ability to record neural populations during natural behavior now allows us to ask whether canonical motor-cortical dynamics, defined largely in constrained reaches to static targets, also organize self-paced, feedback-rich actions that require continuous correction. We recorded sensorimotor cortex in marmosets freely capturing live prey, a behavior that separates into ballistic quick captures and dynamic pursuits requiring real-time adjustment. Ballistic captures corresponded to canonical cortical reaching dynamics without an instructed delay, including near-orthogonal premovement and movement subspaces. Pursuits did not recruit additional neural dimensions; despite their elaborate kinematics, dynamics evolved within the same low-dimensional subspace. Corrective movements during pursuit reorganized this geometry into a distinct feedback-dominated regime, in which premovement activity weakly predicted movement, trajectory tangling increased, and a smaller, slower rotation restarted from a shifted initial state. Yet all movement types shared a sequential firing-rate backbone, which during ballistic capture was organized across the cortex as a somatotopically directed propagating wave that weakened when movements required online correction. These results show that sensorimotor cortex preserves canonical dynamical structure while flexibly reconfiguring it for online control in natural behavior.

neuroscience↗

bioRxiv2026

Cells Engage Endogenous Malonate Synthesis to Drive Mitochondrial Metabolism

Malonate is often described as an endogenous inhibitor of complex II of the electron transport chain. However, the cellular source of malonate is unclear, and current knowledge concerning its metabolism is limited to the action of a single enzyme, Acyl-CoA Synthetase Family Member 3 (ACSF3), which converts malonate to malonyl-CoA in the mitochondrial matrix. One potential route of malonate metabolism downstream of ACSF3 is its consumption by the mitochondrial fatty acid synthesis (mtFAS) pathway. However, studies examining the link between ACSF3 and mtFAS have yielded conflicting results. We developed a novel mass spectrometry approach to perform stable isotope tracing into products of mtFAS, and found that while malonate is in fact a carbon source for mtFAS, ACSF3 is not required for malonate incorporation into mtFAS products. Using this method to trace other nutrients into mtFAS, we also found evidence of acetyl-CoA carboxylase 1 (ACC1)-dependent malonate synthesis from glucose. We further show that ACC1 is required for optimal mtFAS activity, with downstream effects on oxidative phosphorylation. Together these findings establish the malonate as a regulated endogenous intermediate that supports mtFAS activity and mitochondrial oxidative function.

biochemistry↗

bioRxiv2026

C-Terminal Domain of Mycobacterium tuberculosis Glutamate Decarboxylase determines the bacterial stress-adaptive metabolic state that steers macrophage polarisation supporting intracellular persistence

Mycobacterium tuberculosis (Mtb) adapts metabolically to survive hostile conditions within alveolar macrophages, but whether specific enzyme-driven metabolic states of Mtb link stress adaptation to host immunomodulation remains unclear. Using LC-MRM/MS metabolite profiling and metabolic modeling, we previously identified elevated {gamma}-aminobutyric acid (GABA) production via the GABA shunt during adaptation to oxidative and acidic stress. Here, we show that stress-responsive enzymatic efficiency of glutamate decarboxylase (GadB) in producing GABA, not only mitigates acidic and oxidative stress but also drives macrophage polarisation towards the M2 phenotype, extending its role beyond bioenergetics into host-pathogen cross-talk. We identify the C-terminal domain (CTD) of mycobacterial GadB as a key regulator. Enzyme kinetics and fluorescence spectroscopy revealed that CTD deletion abolishes pH-dependent regulation of catalytic efficiency (kcat/Km) and substrate affinity (Ka). Under oxidative stress, the CTD enhances catalytic efficiency without altering substrate affinity, suggesting condition-specific roles. Accordingly, in vitro, Mtb::MtbGadB with higher GABA and [~]40% lower ROS outgrew Mtb::MtbGadB{Delta}Ct under acidic and oxidative conditions. These biochemical differences influenced host immunity, wherein infection with high-GABA-producing Mtb::MtbGadB strain induced M2 polarisation, with decreased CD86, reduced RNS, limited endosomal maturation, as indicated by Rab5/Rab7 ratio and Lysotracker-based confocal microscopy, and decreased TNF-, IL-12p70, and IFN-{gamma} release compared to low-GABA-producing Mtb::MtbGadB{Delta}Ct. Consequently, Mtb::MtbGadB{Delta}Ct showed higher clearance. We conclude that by enabling pH-dependent activity of GadB, the CTD orchestrates proton consumption, ROS reduction, and GABA-mediated immunomodulation. Distinct structural features of CTDs in human versus Mtb GADs highlight the CTD as a selective drug target for pathogen-specific, host-compatible therapies. ImportanceThis work establishes a direct mechanistic link between metabolic state of Mycobacterium tuberculosis (Mtb) actively shaping host immune responses, deciding infection outcome. The study identifies the C-terminal domain (CTD) of MtbGadB in steering enzymatic efficiency, regulating intrabacterial GABA production and ROS quenching, determining the stress-responsive metabolic state of the bacteria. Infection with metabolically distinct strains had differential impacts on host immunity, wherein infection with high-GABA-producing Mtb::MtbGadB induced M2-polarisation, reduced RNS, limited endosomal maturation, and reduced proinflammatory cytokine release, compared to low-GABA-producing Mtb::MtbGadB{Delta}Ct. Consequently, Mtb::MtbGadB{Delta}Ct could be cleared, but Mtb::MtbGadB persisted, deciding the fate of the infection. Structural differences between CTDs of human and Mtb GADs, make it a therapeutically-exploitable determinant for developing pathogen-specific drugs that remain compatible with the host.

microbiology↗

bioRxiv2026

The nail mesenchyme creates a regeneration-specific ligand environment that orchestrates mammalian regeneration versus fibrotic wound healing

The adult digit tip is one of a few privileged mammalian tissues that regenerate. Here, we asked why this is so. Using single cell spatial transcriptomics and genetic mouse models we show regeneration requires the nail organ and associated nail mesenchyme, and that in their absence fibrotic wound-healing occurs. We show the nail organ/mesenchyme orchestrates a highly-organized regenerative response that includes reprogramming of tissue-resident mesenchymal cells to a blastema state. It does this by creating a regeneration-specific ligand environment that includes multiple BMPs. Loss of the resultant downstream BMP signaling by genetic deletion of Smad4 in all mesenchymal cells or specifically in the nail mesenchyme inhibits multiple aspects of the regenerative response, including expression of regeneration-specific ligands. Thus, the nail mesenchyme creates a BMP-rich local ligand environment that reprograms mesenchymal cells and orchestrate tissues regeneration versus fibrotic wound-healing, findings with implications for tissue repair and anti-fibrosis strategies.

cell biology↗

bioRxiv2026

Cannabidiol dose modulates behavioral response to acute and repeated administration of Δ9-Tetrahydrocannabinol by strain and sex

Cannabis contains many bioactive compounds, including {Delta}9-Tetrahydrocannabinol (THC) and cannabidiol (CBD), which influence behavior through complex pharmacological interactions with endogenous targets. This study examines whether CBD influences THC-induced changes in motor activity, hypothermia, and antinociception traits across different THC:CBD ratios, sexes, and genetic backgrounds. Traits were measured in C57BL/6J (B6) and DBA/2J (D2) mice of both sexes following baseline intraperitoneal (i.p.) injection of vehicle (VEH) and two consecutive daily doses of VEH or THC (10 mg/kg) alone or in combination with 0.56, 5, or 10 mg/kg CBD (THC:0.56CBD, THC:5CBD, or THC:10CBD, respectively). Motor activity and hypothermia were quantified daily from 0 to 120 min following injection and antinociception was measured daily at 60 min. We found that CBD alters THC-induced changes in motor activity and hypothermia as a function of day, dose, time, sex, and strain. In D2 females, CBD dose-dependently attenuated the hypolocomotor effects of THC immediately following acute injection and enhanced these effects later at 75 min. Following repeated exposure, CBD dose-dependently enhanced THC-induced hypolocomotion in B6 females at 75 min and in D2 males at 30 min while attenuating THC-induced hypolocomotion in D2 females immediately following injection. In D2 females, CBD dose-dependently attenuated THC-induced hypothermia at 15 min and enhanced hypothermia relative to THC at 30 min in D2 males following acute injection. After repeated exposure, CBD dose-dependently enhanced THC-induced hypothermia in B6 females at 15 min and in D2 males from 30 to 120 mins, while attenuating hypothermia in D2 females at 30 min. No significant effects of CBD on antinociception were observed. Our results indicate that CBD can modulate some THC-induced traits acutely and after repeated exposure. Regulation of THC-induced behavioral responses is dependent on CBD dose, genetic background, and sex. A candidate gene search using brain gene expression in recombinant inbred mice revealed greater genetic variation in ion channel genes relative to key metabolic genes, suggesting an underlying pharmacodynamic mechanism. Future research and validation of molecular mechanisms underlying these differences is expected to enhance our understanding of potential health risks and clinical relevance of cannabis and cannabinoid compounds containing THC and CBD.

animal behavior and cognition↗

bioRxiv2025

Optimal feedback solutions recapitulate key features of motorcortical population dynamics

Neural populations display complex response patterns with marked transitions between distinct underlying computational strategies on very short timescales during motor tasks. Such complex-yet-structured dynamical strategies may reflect computational needs of neural systems, shaped by optimal feedback and autonomous mechanisms, in addition to biological constraints. Are there overarching computational principles that govern complex dynamical strategies exhibited by the neural population response? Here, we explore the hypothesis that computational strategies underlying neural population response represent optimal feedback solutions to the control of musculoskeletal dynamics through space for a goal. To validate this hypothesis, we develop a procedure called neural optimization using dynamical systems (NODS) learning to modify synaptic strengths within a recurrent network for locally-optimal feedback control of anatomically accurate musculoskeletal models during complex sensorimotor tasks. NODS learning works even when the objective function to be minimized is highly non-linear or the muscle model is very complex. The dynamical strategies underlying the neural network response constructed using NODS learning recapitulate key features of recorded population response. Importantly, optimal feedback solutions using NODS learning suggest that feedback mechanisms are essential for neural populations to flexibly transit between complex-yet-structured strategies. We further show that this framework provides theoretical foundations for why the solutions obtained using deep reinforcement learning algorithms extensively used to model sensorimotor tasks may explain the dynamical strategies underlying recorded population response. In summary, we develop novel methods and approaches suggesting that neural dynamics may be more strongly modulated by optimal feedback mechanisms, in addition to autonomous mechanisms, than previously appreciated.

neuroscience↗

bioRxiv2025

Behavioral Thermoceptive Responses and Morphologic Correlates in Mouse Models of CMT1A, HNPP and Aging

BackgroundThermoceptive dysfunction is a frequent but understudied feature of peripheral neuropathies and aging. Patients often report abnormal heat perception, yet the underlying sensory mechanisms remain unclear. This study evaluated thermoceptive behavior and corresponding structural changes in mouse models of inherited dysmyelinating neuropathy and natural aging to identify shared and divergent mechanisms. MethodsThermal preference was assessed using a user-independent gradient apparatus spanning physiological to noxious temperatures, with automated quantification of time in zone, distance traveled, and velocity. Nocifensive responses were evaluated by hot plate latency. Intraepidermal nerve fiber density (IENFD) was measured in paw pads, and TRPV1-positive dorsal root ganglion (DRG) neurons were analyzed by immunofluorescence and confocal imaging. ResultsThermal gradient testing revealed preserved temperature preference in CMT1A and HNPP mice but significantly altered behavior in aged animals, which spent less time in warmer zones. Hot plate testing showed prolonged times to nocifensive behavior in aged and CMT1A mice, whereas HNPP mice exhibited variable responses. IENFD was markedly reduced in aged mice but preserved in CMT1A and HNPP. DRG analysis revealed smaller soma diameters and reduced proportions of TRPV1-positive A{delta} neurons in aged mice, while CMT1A animals maintained normal morphology. InterpretationAging produces thermoceptive deficits through axonal degeneration and selective A{delta}-fiber vulnerability, whereas CMT1A mice display conduction-related impairment due to dysmyelination. Both models reproduce key human sensory phenotypes and provide translational platforms for studying small-fiber dysfunction and therapeutic interventions in peripheral neuropathies. Key PointsO_LIThermoceptive dysfunction is a common but understudied feature of peripheral neuropathy and aging. C_LIO_LIIn aged mice, altered thermal preference, reduced intraepidermal nerve fiber density, and smaller TRPV1-positive A{delta} neurons indicate a degenerative mechanism of sensory loss. C_LIO_LIIn CMT1A mice, delayed noxious heat responses occur despite preserved epidermal and DRG morphology, consistent with dysmyelination rather than axonal degeneration. C_LIO_LIHNPP mice showed inconsistent nocifensive responses without structural fiber loss, suggesting strain- or injury-dependent effects. C_LIO_LIThermal gradient and hot plate assays demonstrate strong reproducibility and provide relevant outcome measures for preclinical modeling of thermoceptive dysfunction. C_LI

neuroscience↗

bioRxiv2025

PLncFire: A Scalable Pipeline for Transcriptome-wide Discovery of Plant lncRNAs

BackgroundLong non-coding RNAs (lncRNAs) play important regulatory roles in plant growth, development, and stress responses. However, their genome-wide identification remains challenging due to low sequence conservation, incomplete reference annotations, and variability across species. Existing workflows often lack standardization and reproducibility, limiting large-scale comparative studies. To address these challenges, we developed PLncFire, a modular computational pipeline designed for automated and reproducible identification and annotation of plant lncRNAs using RNA-seq data. MethodsPLncFire processes standard RNA-seq datasets through a structured workflow comprising quality control, read alignment, transcript assembly, and transcript filtering. A consensus-based coding potential assessment strategy was implemented using CPC2, PlantLncPipe, and FEELnc to improve prediction reliability. Transcripts were filtered based on length, exon structure, and coding probability thresholds to generate high-confidence lncRNA candidates. Identified lncRNAs were further classified as known or novel by comparison with reference annotations. The pipeline also incorporates differential expression analysis to support functional prioritization. Workflow modularity ensures scalability across plant species and enables reproducible execution in diverse computational environments. ResultsApplication of PLncFire to plant RNA-seq datasets enabled systematic identification of high-confidence lncRNA candidates, including both previously annotated and novel transcripts. The consensus coding-potential framework reduced false-positive predictions compared to single-tool approaches. Integration of differential expression analysis facilitated prioritization of lncRNAs associated with specific developmental stages or stress conditions. The modular design demonstrated compatibility across datasets from different plant species, supporting cross-species adaptability and comparative analysis. ConclusionsPLncFire provides a standardized and reproducible framework for genome-wide lncRNA discovery in plants. By integrating multi-tool consensus coding assessment with transcript assembly and expression analysis, the pipeline enhances prediction confidence and scalability. This platform supports large-scale functional genomics studies and facilitates systematic exploration of plant lncRNA landscapes. The source code is available at https://github.com/ahsan-rizvi/PLncFire.git. Trial registrationNot applicable.

bioinformatics↗

bioRxiv2025

Active mitochondria in healthy spiny mouse fibroblasts resemble megamitochondria and remain resilient across lifespan

Although they exhibit limited regenerative ability of some tissues and organs shortly after birth or towards the end of fetal development, humans and laboratory mammals quickly transition to producing scar tissue for tissue repair. In contrast, spiny mice exhibit complex tissue regeneration as adults and provide a blueprint for how regeneration can occur throughout adulthood in mammals. Fibroblasts are key mediators of wound healing outcomes and prior work uncovered that cells from highly regenerative mammals (spiny mice and rabbits) exhibit extreme resistance to oxidative stress compared to those from non-regenerating laboratory mice and rats. Using a battery of cellular tests in primary ear pinna fibroblasts from highly regenerative and non-regenerative mammals, we find that cells from spiny mice and rabbits exhibit a baseline preference for glycolysis supporting a lower ROS-producing basal state. Uniquely, spiny mouse fibroblasts exhibit large, spherical, depolarized mitochondria similar to megamitochondria identified in pathological tissues. The megamitochondria phenotype was present across lifespan in ear pinna fibroblasts from fetal, young and old spiny mice. While rabbit, mouse and rat fibroblasts had polarized tubular mitochondrial networks typical of adult mammalian fibroblasts, isolated rabbit and spiny mice fibroblasts shared lower oxygen consumption efficiency even in the absence of a potential gradient. Taken together, our results support that a shared metabolic signature exists in stromal cells from highly regenerative mammals, although possibly driven by different mechanisms, to converge on a ROS-resistant phenotype which ultimately helps supports tissue regeneration.

cell biology↗

bioRxiv2025

Mobile Eye-Tracking Glasses Capture Ocular and Head Markers of Listening Effort

To extend the assessment of listening effort beyond a sound booth, we validated mobile eye-tracking glasses (Pupil Labs Neon) by comparing them to a stationary system (Eyelink DUO) in a controlled environment. We recorded eye movements, pupil size, and head movements from 26 young adults during a speech-in-noise task. When listening conditions became challenging, we observed reduced gaze dispersion and increased pupil sizes of similar magnitude from both devices, in addition to reduced head movements recorded solely by the mobile device. These findings suggest that mobile eye-trackers reliably capture listening effort, paving the path towards assessments in daily settings.

neuroscience↗

bioRxiv2025

Multitasking Recurrent Networks Utilize CompositionalStrategies for Control of Movement

The brain and body comprise a complex control system that can flexibly perform a diverse range of movements. Despite the high-dimensionality of the musculoskeletal system, both humans and other species are able to quickly adapt their existing repertoire of actions to novel settings. A strategy likely employed by the brain to accomplish such a feat is known as compositionality, or the ability to combine learned computational primitives to perform novel tasks. Previous works have demonstrated that recurrent neural networks (RNNs) are a useful tool to probe compositionality during diverse cognitive tasks. However, the attractor-based computations required for cognition are largely distinct from those required for the generation of movement, and it is unclear whether and how compositional structure extends to RNNs producing complex movements. To address this question, we train a multitasking RNN in feedback with a musculoskeletal arm model to perform ten distinct types of movements at various speeds and directions, using visual and proprioceptive feedback. The trained network expresses two complementary forms of composition: an algebraic organization that groups tasks by kinematic and rotational structure to enable the flexible creation of novel tasks, and a sequential strategy that stitches learned extension and retraction motifs to produce new compound movements. Across tasks, population activity occupied a shared, low-dimensional manifold, whereas activity across task epochs resides in orthogonal subspaces, indicating a principled separation of computations. Models that perform multitasking without the use of feedback or embodiment struggle to form compositional representations, suggesting these mechanisms constrain the network solution space during training. Finally, we demonstrate rapid transfer to held-out movements via simple input weight updates, as well as the generation of target trajectories from composite rule inputs, without altering recurrent dynamics, highlighting a biologically plausible route to within-manifold generalization. Our framework sheds light on how the brain might flexibly perform a diverse range of movements through the use of shared low-dimensional manifolds and compositional representations.

neuroscience↗

bioRxiv2025

Elucidation of Radical Degradation in Native Biofilms by EPR Sheds Light on Bacterial Resistance and Efficient DNP Solid-state NMR

Bacterial biofilms exhibit enhanced antimicrobial resistance, yet the mechanisms determining molecular transport and reactivity within these complex communities remain poorly understood. Here, we combine electron paramagnetic resonance (EPR), solid-state NMR (ssNMR), and dynamic nuclear polarization (DNP) ssNMR to determine how native Pseudomonas fluorescens Pf0-1 colony biofilms regulate nitroxide radicals. EPR measurements reveal that radical reduction depends on biofilm morphology, hydration, and composition of extracellular matrix (ECM). Wild-type biofilms exhibit slower nitroxide reduction than planktonic cells, while isolated ECM and dehydrated biofilms show no radical reduction, indicating that bacterial cells primarily drive radical reduction. Complementary ssNMR measurements identify polysaccharides and lipids within the ECM as primary interaction sites for nitroxide radicals. DNP-enhanced ssNMR further reveals compositional differences across biofilm morphologies, with increasingly polysaccharide-rich ECM environments correlating with slower reduction kinetics. These findings support a mechanism in which the ECM acts as a diffusion barrier and selective interaction region for nitroxide radicals to regulate cellular penetration. This work showcases an integrated magnetic resonance approach that provides molecular insight into how biofilm structure determines the fate of toxic redox-active small molecules. We also set the stage for high-sensitivity measurements of structure-function relationships in these medically relevant assemblies.

biophysics↗

bioRxiv2025

AP-3 complex sorts preferential cargo to govern dense core vesicle function in neuroendocrine cells

This study reveals new insights into the role of the Adaptor protein (AP-3) complex in dense core vesicle function. Despite numerous studies, an existing knowledge lacuna in the role of AP-3 in DCV function prompted us to delve deeper. Advanced microscopy and biochemical analysis revealed compromised DCV exocytosis in AP-3-depleted PC12 cells and C. elegans. AP-3 depletion altered the size and positioning of DCVs. Golgi defects and RUSH (Retention under Selective Hook) substantiated the role of AP-3 in trans-Golgi DCV budding. Proteomics revealed the loss of specific known and putative novel DCV proteins, which were mislocalized and rerouted to lysosomes in AP-3-depleted cells. Bioinformatics, Proximity ligation assays and Co-immunoprecipitation identified interactions of mislocalized proteins with AP-3 subunit. These findings corroborated with functional defects in granule maturation, release modes, Zinc and neurotransmitter mobilisation. Our study highlights the complexity of the AP-3 complex in regulating DCV function and its importance in vesicle transport in neurons and neuroendocrine cells. SummaryThis work reveals the critical role of AP-3 complex in DCV function, highlighting its impact on DCV exocytosis, positioning, and trans-Golgi budding. This study identifies Dlk1 as a novel DCV cargo.

cell biology↗