Biology subjects

Ramachandran, R.

Publications and source records attributed to Ramachandran, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Dissociable Stimulus- and Response-Driven Serial Dependence Effects in Auditory, Visual, and Audiovisual Motion Judgments

Efficient motion perception requires integrating immediate sensory evidence with internal representations shaped by experience. This influence of recent history can produce serial dependence effects (SDEs), in which current judgments are biased toward or away from the source of previous information. We examined SDEs in auditory, visual, and cued audiovisual motion-direction discrimination using aggregate psychometric measures and trial-level generalized linear mixed-effects models (GLMMs), which estimated the independent contributions of the previous stimulus direction and the participant's previous response. Participants completed unisensory (n=57) and cued audiovisual (n=48) motion-discrimination tasks. Aggregate analyses indicated attractive SDEs in auditory conditions, repulsive SDEs in visual conditions, and no net SDE in the audiovisual-cued condition. Trial-level modeling revealed a more nuanced structure: previous stimulus direction produced repulsive effects in both unisensory conditions, with previous visual direction influencing judgments across all conditions containing visual motion, whereas previous response produced attractive effects only when visual information was task-relevant. In the audiovisual-cued condition, the absence of a net psychometric shift was consistent with the opposing influences of an attractive response-history effect and a repulsive visual stimulus-history effect rather than an absence of serial dependence. These findings suggest that serial dependence in motion perception reflects dissociable and concurrently operating processes, including a predominantly visual, adaptation-like stimulus-history effect and a task-dependent, decision-related response-history effect.

neuroscience↗

bioRxiv2026

Noise-induced temporary threshold shift in macaques disrupts electrophysiological temporal processing despite recovery of cochlear sensitivity and preserved ribbon synapse counts

Noise exposure can produce lasting auditory dysfunction in the absence of permanent threshold shifts or hair cell loss, yet the functional consequences of temporary threshold shift (TTS) remain poorly defined in translational models. We assessed auditory brainstem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs) in rhesus macaques (n = 13) at 2 and 9-10 months following a single moderate noise exposure that induced TTS. Previous histological analyses of these macaques showed no significant loss of hair cells or ribbon synapses but revealed persistent broadening of inner and outer hair cell ribbon-volume distributions. After exposure, DPOAE amplitudes and thresholds and ABR thresholds returned to pre-exposure values and showed low-frequency enhancement at later time points. Suprathreshold click- and tone-evoked ABR amplitudes were largely preserved or enhanced after exposure, consistent with compensatory gain. In contrast, macaque-specific chirp-evoked ABRs showed modest amplitude reductions and latency prolongation across waves, indicating altered neural synchrony at standard stimulus presentation rates, but with variable time courses. More temporally demanding paradigms revealed persistent impairments. ABRs to faster click rates and shorter paired-click intervals showed reduced adaptability in response amplitude and timing after normalization, with deficits persisting through 9-10 months. Increased inner hair cell ribbon-volume variability was more consistently associated with temporal response measures, including latency, paired-click recovery, and rate adaptation, than with amplitude-based ABR measures. Together, these findings reveal a lasting dissociation between response magnitude and fidelity after TTS: suprathreshold responses may be preserved or enhanced, while neural synchrony and temporal adaptability remain impaired. Increased presynaptic ribbon volume variability may serve as a structural marker of synaptic remodeling accompanying hidden auditory dysfunction, rather than as a direct determinant of suprathreshold response magnitude. Temporally demanding ABR paradigms may supplement threshold-based diagnostics for detecting persistent noise-induced auditory dysfunction.

neuroscience↗

bioRxiv2026

Temporal integration in the subcortical auditory system and behavioral evidence of its dysfunction after "temporary" noise-induced hearing loss

How sensory information is processed over time is often conceptualized as a process of temporal integration. Recently, auditory temporal integration has received renewed attention as a potential assay of hidden hearing loss caused by cochlear synaptopathy in rodent and avian studies. How these results relate to human hearing is in question due to a lack of studies in primates, and, more generally, the neural basis of auditory temporal integration is unclear, as most subcortical studies of it have been conducted under anesthesia. We have recently introduced a nonhuman primate (NHP) model which can address translational questions about auditory temporal integration and hidden hearing loss. Thus, in this study, we utilized single-unit recordings and compared derived neurometric measures to psychometric measures of temporal integration in normal hearing NHPs performing a tone-in-noise detection task. We then assessed psychometric measures of temporal integration in NHPs before and after noise exposure. In normal hearing NHPs, cochlear nucleus and inferior colliculus (IC) integration rates were significantly greater than psychometric rates. However, in noise only, [~]25% of IC neurons exhibited similar integration rates to behavior. After noise exposure, psychometric integration was disrupted for brief stimuli presented in quiet, but not in noise. The dynamic range of the psychometric function reliably increased, months after recovery from the noise-induced temporary threshold shift (TTS). Together, these data identify a subcortical neural substrate for temporal integration in noisy environments and suggest that behavioral assays of temporal integration may serve as sensitive indicators of subclinical hearing loss.

neuroscience↗

bioRxiv2026

Physiological, Histological, and Cognitive Characterization of a Macaque Model of Presbycusis

Age-related hearing loss (ARHL), or presbycusis, is one of the most prevalent sensory deficits in older adults and has been increasingly implicated in cognitive decline and dementia. This study characterizes ARHL in a rhesus macaque model by combining histological, physiological, and cognitive assessments. Aged macaques exhibited progressive cochlear degeneration, with marked outer hair cell loss at mid-to-high frequencies, elevated auditory thresholds, reduced distortion product otoacoustic emissions, and impaired auditory brainstem responses including amplitude reduction, latency prolongation, and diminished temporal precision. Despite modest reductions in inner hair cell ribbon synapse counts, hypertrophic changes were observed. These auditory deficits correlated with subtle impairments in visual working memory, as measured by a delayed match-to-sample task, underscoring a potential sensory-cognitive link. By capturing cross-domain aging markers in a translationally relevant primate model, this work lays a foundation for mechanistic studies and therapeutic interventions targeting both hearing and cognition in aging populations.

neuroscience↗

bioRxiv2026

Persistent impairment of spatial hearing and neural binaural interaction after temporary noise-induced hearing loss

Many people have trouble understanding speech in noisy environments despite normal audiometric thresholds, a condition referred to as "hidden hearing loss." A leading hypothesis attributes this deficit to inner hair cell synaptic pathology (cochlear synaptopathy), which can persist after recovery from noise-induced temporary elevation of audiometric thresholds. This pathology impairs the temporally precise sound encoding necessary for spatial hearing, but direct evidence in primates, human or nonhuman, is lacking. Here, we show that a single noise exposure, producing only a temporary threshold elevation, induced long-lasting alterations in synaptic morphology, without synapse loss, resulting in persistent spatial hearing deficits for up to 11 months post-exposure in nonhuman primates of both sexes. These perceptual deficits were accompanied by a reduction in a neurophysiological measure of binaural processing - the binaural interaction component (BIC) of the auditory brainstem response (ABR). Both behavioral and neural deficits persisted despite full recovery of audiometric thresholds. Together, these findings provide the first evidence in primates that noise exposure disrupts spatial hearing and binaural neural circuit function without loss of hair cells or synapses. Because spatial hearing tests and the ABR/BIC are clinically accessible, this work also establishes translational biomarkers for early neural dysfunction underlying hidden hearing loss.

neuroscience↗

bioRxiv2026

Energy flow controls the stability of multitrophic ecosystems with stratified nonreciprocity

Complex systems with nonreciprocal interactions are often stratified into layers. Ecosystems are a prime example, where species at one trophic level grow by consuming those at another. Yet the dynamical consequences of such stratified nonreciprocity--where the correlation between growth and consumption differs across trophic levels--remain unexplored. Here, using an ecological model with three trophic levels, we reveal an emergent asymmetry: nonreciprocal interactions between consumers and predators (top and middle level) destabilize ecosystems far more readily than non-reciprocity between consumers and resources (middle and bottom level). We analytically derive the phase diagram for the model and show that its stability boundary is controlled by energy flow across trophic levels. Because energy flows upward--from resources to predators--diversity is progressively lower at higher trophic levels, which we show explains the asymmetry. Lowering energy flow efficiency flips the asymmetry toward resources and remarkably expands the stable region of the phase diagram, suggesting that the famous "10% energy transfer" seen in natural ecosystems might promote stability. More broadly, our findings show that the location of nonreciprocity within a complex network, not merely its magnitude, determines stability.

ecology↗

bioRxiv2026

Bioglass-embedded alginate scaffold for dental bone tissue engineering applications.

Traumatic dental injury impacts approximately 1 in 10 people globally and it is further challenging to treat with the complications such as inflammation, infection and dynamic oral pH which collectively slow down the dental bone healing. Currently existing approaches address these complications individually which results in suboptimal regenerative outcomes. Our study focuses on developing a multifunctional dental scaffold engineered to tackle inflammation and infection simultaneously and enhance bone regeneration through a dual drug delivery strategy and integration of Bioglass. A novel citric acid mediated process was used to produce bioglass which was further characterized using XRD and SEM analyses. The bioglass was capped with antibiotic and integrated into the alginate scaffold which was further subjected to surface coating of painkiller to enable rapid anti-inflammatory action and sustained antimicrobial release. The composite scaffold was further assessed for its physiochemical properties using swelling and degradation analysis, SEM was carried out to understand the structure and morphology of the scaffold. MTT assays were carried out on osteoblastic and fibroblastic cell lines to understand the cytocompatibility of the scaffold, while the osteogenic property was evaluated through biomineralization assay. The results showed successful synthesis and homogenous integration of bioglass, leading to increased swelling potential, controlled degradation and excellent biocompatibility. Robust osteogenic differentiation validated the scaffolds capacity as an advanced platform for dental bone tissue engineering and effective management of traumatic dental injuries. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/698929v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@6b7ed8org.highwire.dtl.DTLVardef@154b0c4org.highwire.dtl.DTLVardef@1212c22org.highwire.dtl.DTLVardef@d89dff_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

CD2AP's structure and oligomerization are compromised by the K301M mutation: implications for Nephrotic syndrome

IntroductionThe podocyte slit diaphragm (SD) is a complex filtration unit localized to the blood and urine interface and governs the glomerular selectivity. However, the greater details of the SD composition and the mechanism of assembly of the SD protein as a macromolecular complex remain elusive. CD2-associated protein (CD2AP) serves as a central scaffold within the SD, and mutations in CD2AP are strongly associated with nephrotic syndrome (NS) and focal segmental glomerulosclerosis (FSGS). However, the mechanisms by which such mutations alter the architecture and higher-order organization of CD2AP are poorly understood. MethodsWe employed biophysical, structural, and proteomic approaches to investigate the impact of the disease-associated K301M mutation on CD2AP structure and its interaction with Podocin. Oligomerization was analyzed using size-exclusion chromatography, blue native PAGE, Dynamic light scattering, and small-angle X-ray scattering. Secondary and tertiary structural properties were assessed by far- and near-UV circular dichroism, thermal denaturation, and intrinsic fluorescence spectroscopy. CD2AP-podocin interactions were quantified using in vitro pulldown and surface plasmon resonance (SPR), and mutation-dependent changes in interaction networks were examined through interactome profiling. ResultsWild-type (WT) CD2AP assembled into flexible higher-order oligomers ([~]9-12-mers), whereas the K301M variant collapsed into lower-order species ([~]3-6-mers), indicating destabilization of the coiled-coil assembly interface. Spectroscopic analyses revealed subtle secondary-structure rearrangements, but profound tertiary packing defects, as well as reduced and markedly diminished thermal resilience in the mutant. SPR analysis demonstrated loss of binding between Podocin and mutant CD2AP, whereas WT CD2AP showed high-affinity interaction (KD = 211 nM) with Podocin. Complementary interactome profiling revealed widespread rewiring of protein-protein interactions in the case of mutant CD2AP, characterized by the loss of core partners and the emergence of aberrant associations. ConclusionThese findings define a mechanistic model in which the K301M mutation destabilizes CD2AP oligomerization, disrupts podocin recognition, and remodels interaction networks essential for SD stability. This work signifies the importance of CD2AP in SD assembly and the permselective filtration function of the kidney, and the impact of a single mutation in the pathogenesis of NS and FSGS. Translational Statement: Inherited nephrotic syndrome, characterized by heavy proteinuria, frequently arises from mutations in scaffolding proteins of the slit-diaphragm (SD). This study demonstrates that the nephrotic syndrome-associated K301M mutation in CD2-associated protein (CD2AP) compromises higher-order oligomerization, abolishes its binding to the binding partner (Podocin), and reshapes protein-protein interaction networks that are critical for SD assembly and stability. By establishing a direct link between mutation-induced collapse of CD2AP architecture and loss of podocyte scaffolding function, these findings provide mechanistic insight into the pathogenesis of CD2AP-associated proteinuric kidney disease. The results further identify oligomeric assembly interfaces as potential targets for therapeutic strategies aimed at preserving the integrity of the SD and glomerular filtration function. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/698362v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1f49f1dorg.highwire.dtl.DTLVardef@fa2e06org.highwire.dtl.DTLVardef@e399c0org.highwire.dtl.DTLVardef@831c17_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

biophysics↗

bioRxiv2025

Alginate Nanohydroxyapatite Composite for Dental Tissue Engineering Application.

Traumatic dental tissue injury is a common health concern globally, with more than a billion people affected worldwide. In this study, we have synthesized green route nanohydroxyapatite utilizing green tea extract, which further enhances the osteogenesis, osteointegration, and biocompatibility of the synthesized hydroxyapatite. This Nanohydroxyapatite was capped with an antibiotic, integrated into an alginate scaffold, and coated with a painkiller to create a dual drug release system, providing rapid release of painkiller and sustained release of antibacterial drug. Biocompatibility and osteoblast proliferation were confirmed through MTT assays, and osteogenesis by ALP activity, validating the suitability of the scaffold for dental bone tissue engineering applications. The developed nanocomposite scaffold shows significant promise in enhancing dental bone repair by simultaneously addressing the inflammation, infection, and regeneration challenges. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/693830v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@124b53forg.highwire.dtl.DTLVardef@f75868org.highwire.dtl.DTLVardef@cd20a6org.highwire.dtl.DTLVardef@11a7dfb_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Cochlear histopathology in macaques after noise-induced temporary threshold shifts

Noise exposures causing transient hearing loss were previously considered benign. However, recent work has revealed that temporary noise-induced threshold shifts may be associated with long-lasting cochlear histopathology. One such effect is cochlear synaptopathy, i.e. changes to the afferent synapse between inner hair cells and auditory nerve fibers. Noise-induced synaptopathy has been extensively characterized in several rodent models, and temporal bone studies suggest similar age-related changes in humans. However, it remains unclear how noise-induced temporary threshold shifts affect cochlear structures in humans and nonhuman primates, which show greater resistance to noise exposure than other animals. Additionally, the long-term sequelae of temporary threshold shifts are largely unknown. Here, we characterized the effects of a noise exposure causing temporary hearing loss on cochlear histopathology in macaque monkeys at long post-exposure survival times. Overall, cochlear histopathology was variable across subjects, similar to the variable susceptibility observed in humans. At 2 and 10 months post-exposure, macaques had no significant loss of hair cells, inner hair cell synapses, or cholinergic efferent innervation. However, enlargement of ribbons in both inner and outer hair cells was observed. Together, these findings provide insight into the cochlear effects of single-exposure temporary threshold shifts in nonhuman primates. HIGHLIGHTS- Macaques exposed to 120 dB SPL noise for 4h showed temporary threshold shifts - Cochlear histopathology was evaluated at 2 and 10 months post-exposure - Macaques had no significant loss of hair cells or inner hair cell synapses - Chronic enlargement of inner and outer hair cell ribbons was observed - Transient loss of outer hair cell ribbons was also observed

neuroscience↗

bioRxiv2025

Comparative ASCL1 interactome analysis reveals CDK2-Cyclin A2 as suppressors of differentiation in MYCN-amplified neuroblastoma

Neuroblastoma is a heterogeneous paediatric cancer arising from developmentally arrested neuronal precursors, where restoring differentiation offers therapeutic promise. ASCL1, a pro-neural transcription factor, is widely expressed in neuroblastoma and can drive either proliferation or differentiation depending on the cellular context. Here, we show that distinct MYCN-amplified neuroblastoma cell lines exhibit differing cell cycle and differentiation responses to ASCL1 overexpression. By comparing genome-wide ASCL1 chromatin binding, transcriptional changes, and protein-protein interactions, we found that ASCL1 binds more extensively to neuronal proteins in a cell line that is more susceptible to ASCL1-driven differentiation, but associates with cell cycle regulators in less responsive cells. We show that CDK2-Cyclin A2 bind ASCL1 in less responsive cells, with CDK-mediated phosphorylation of ASCL1 limiting the ability of ASCL1 to drive differentiation. Our study reveals that context-dependent interactions of ASCL1 with protein partners on the chromatin control its ability to re-engage a differentiation program in neuroblastoma.

cancer biology↗

bioRxiv2025

From spark to wildfire: illuminating single-cell origins of virus infection spread and diversification

When a virus encounters a living cell it triggers infection, cell death, and the release of virus progeny. In lab cultures, such progeny spread to near and distant cells, creating a plaque, a visible record of virus growth and cell death. Plaque-based assays have long enabled amplification and quantification of virus particles, but the earliest infections of a plaque remain poorly characterized. Here, we used a recombinant rhinovirus expressing a fluorescent reporter protein to track the start and spread of infection across HeLa cell monolayers at single-cell resolution. We analyzed reporter expression profiles from eight plaques and over 150 cells, reviewing, testing and applying methods of time-series analysis, clustering, and dimensionality reduction. We identified primary infections based on early reporter expression in isolated cells and secondary infections among their neighbors. Primary infected cells exhibited tightly clustered gene expression profiles, while secondary infected cells showed broader heterogeneity in the timing, intensity, and duration of reporter expression, without correspondence to their associated primary cells. This heterogeneity likely reflects a combination of factors, including noisy gene expression, viral genetic changes, and variation in local cellular environments. The rapid diversification of gene expression highlights the power of single-cell imaging to shed light on infection spread.

bioengineering↗

bioRxiv2025

Behavioral evidence for visually dominant audiovisual motion integration

AO_SCPLOWBSTRACTC_SCPLOWAccurate motion perception is crucial for navigating complex environments, where sensory information is often derived from multiple modalities. While multisensory cues improve performance in tasks involving stationary stimuli, the integration of dynamic motion cues is less understood. Here, we examined the nature of auditory and visual motion integration and determined whether attentional instructions modulate integration. Sixty participants performed direction discrimination tasks under auditory, visual, and audiovisual conditions, with cueing instructions to attend to one or both modalities. Results showed that visual motion direction estimates were more reliable than auditory ones, and audiovisual estimates were superior to either modality alone. Additionally, visual motion estimates were more stable that auditory motion estimates during direction conflict trials. Reliability-weighted models of integration closely predicted audiovisual performance, demonstrating optimal integration. Sensory dominance (visual vs. auditory) influenced sensitivity to audiovisual motion, with visual dominant participants performing better overall. Our results demonstrate that the perception of audiovisual motion is dominated by vision and is shaped by top-down attention.

neuroscience↗

bioRxiv2025

Integration of Audiovisual Motion in Dorsolateral Prefrontal Cortical Neurons

The dorsolateral prefrontal cortex is well recognized for its role in cognitive functions and activating action plans. In contrast, the properties of prefrontal neurons with respect to multisensory processing are less well studied. To address this question, we recorded single units from areas 8a and 46 of two female rhesus macaques while they were presented with visual, auditory, and audiovisual motion stimuli. The majority of dorsolateral prefrontal neurons responded to these sensory stimuli, with similar percentages of auditory-only, visual-only and audiovisual neurons. Approximately one third of responsive neurons exhibited significant super- or sub-additive interactions in response to the pairing of auditory and visual stimuli, revealing significant nonlinearities in their response profiles. Decoding motion signals from the population activity robustly differentiated multisensory from unisensory trials and also unisensory auditory and visual trials from each other. These results demonstrate that dorsolateral prefrontal neurons integrate auditory and visual motion signals, extending multisensory computations beyond sensory cortices into prefrontal circuits that support higher-order cognition. New & NoteworthyWe recorded single neurons in macaque dorsolateral prefrontal cortex during visual, auditory, and audiovisual motion. Nearly half of responsive neurons were multisensory and a third displayed significant super- or sub-additive interactions, while ensemble activity reliably decoded stimulus modality. These findings provide the strongest evidence to date that DLPFC performs rapid, nonlinear audiovisual integration, extending multisensory computations beyond classical posterior regions into the prefrontal circuits that support cognition.

neuroscience↗

bioRxiv2025

Second-Scale Neural Dynamics Shape Hormonal Outputs in Hypothalamic CRH Neurons

The elevation of glucocorticoids is a hallmark of stress, arising from the integration of rapid neuronal signals into sustained hormonal outputs. A key interface for this neuroendocrine signal translation is corticotropin releasing hormone (CRH) neurons in the paraventricular nucleus of the hypothalamus (PVN), which release CRH at the median eminence (ME). We recently discovered that CRHPVN neurons exhibit a characteristic shift in firing patterns from rhythmic short-bursts (low-activity state) to tonic firing (high-activity state) in response to stress. This raised a critical question: how are these distinct firing patterns are integrated into slower, sustained hormonal outputs at neuroendocrine terminals? Here, we implemented optical approaches to detect CRH release ex vivo and in vivo. Using newly developed sniffer cells for CRH, we measured CRH release at ME ex vivo, triggered by the distinct, in vivo-like firing patterns. Our results demonstrated that the primary determinant of neuroendocrine CRH release was the firing rate sustained over the timescale of seconds, with little contribution from specific firing patterns. These results collaborated with second-scale increase in firing rate triggered by stress stimuli. Additionally, we recorded the dynamics of CRH at the ME in the freely moving mice using genetically-encoded GPCR-activation based (GRAB) sensors for CRH. Foot shock stress triggered transient, time-locked increases in CRH release on the timescale of seconds. Importantly, these second-scale CRH pulses, when elicited during repeated foot shocks, were integrated over minutes to scale downstream hormone releases. Together, our data revealed critical roles of second-scale dynamics in CRHPVN neuron activity for the neuroendocrine translation of stress signals.

neuroscience↗

bioRxiv2025

Novel function of Contactin associated protein 1 (Caspr 1)/ Paranodin in embryonic cortical neurons: hypoxia modulated neurite development.

Hypoxia, a condition of inadequate oxygen supply, is a common phenomenon affecting neurons and brain tissue, leading to significant implications for neuronal health and function. The prevalence of hypoxia in the brain is associated with various neurological conditions, making it a critical area of study. Neuritogenesis, the process of neurite outgrowth, is an essential aspect of neuronal development and connectivity and is particularly sensitive to hypoxic stress. Investigating how hypoxia affects neurite outgrowth is vital for understanding neuronal response and adaptation under low oxygen conditions. This study explores how hypoxic stress affects neurite regulation mediated by Contactin Associated Protein-1 (Caspr1) in primary mouse embryonic cortical neurons. Hypoxia, induced by culturing neurons in a 2% oxygen environment, significantly reduced neurite length and induced notable changes in growth cone morphology. Concurrently, we observed an upregulation in the expression of Caspr1 and its transcriptional regulator C/EBP, suggesting a compensatory role for Caspr1 in neurite extension under low oxygen conditions. Shorter hypoxia exposure periods revealed a dynamic biphasic response in Caspr1 levels, with an initial decrease followed by a substantial increase, correlating with corresponding changes in neurite length. This pattern emphasizes the critical involvement of Caspr1 in adapting neurite growth to fluctuating hypoxia duration. Furthermore, comparative analyses using wild-type and Caspr1 knockout Neuro2a cells demonstrated that the absence of Caspr1 mitigates hypoxia-induced neurite shortening, indicating a potential protective role against hypoxic stress. Additionally, hypoxia profoundly impacted mitochondrial morphology and function. Under hypoxic conditions, mitochondria transitioned to a more spherical shape. Mitochondrial respiration analysis revealed significant reductions in oxygen consumption rates (OCR), highlighting compromised mitochondrial function during hypoxia. These findings underscore the multifaceted role of Caspr1 in neurite regulation and mitochondrial adaptation to hypoxic stress. The study provides insights into the molecular mechanisms underpinning hypoxia-induced changes in neuronal morphology and function. Understanding these processes opens avenues for therapeutic strategies targeting Caspr1 in treating neurological disorders characterized by hypoxic stress. Future research will benefit from extending these investigations to more complex models, such as brain organoids, to further elucidate the metabolic and structural changes under hypoxia and their implications for neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Helix-8 and Carboxyl Terminal Tail Regulation of Proteinase Activated Receptor-4 (PAR4) signalling

The 8th-helix (H8) and carboxyl terminal tail (CT) of GPCRs are crucial for interactions with intracellular signaling molecules and regulatory proteins. We investigated how H8 and CT residues influence signaling in PAR4, a tethered-ligand activated GPCR. Our analysis revealed that PAR4 activation by thrombin or AYPGKF-NH2 stimulates {beta}-arrestin-1/-2 recruitment and activates multiple G proteins (Gq, G11, Gz, G15, G12, G13, Gi1-3, GoA/B). Mutation of the H8 sequence (R352AGLFQRS359) significantly reduced G protein activation and {beta}-arrestin recruitment, with residues Leu355-Glu357 being particularly important. Mutations of specific lysine residues in H8 and CT also impaired signaling. Additionally, we identified a crucial TM7-H8 interaction and found that CT phosphorylation sites regulate {beta}-arrestin recruitment. Finally, using AlphaFold3 we predicted interactions between PAR4, {beta}-arrestins, and G proteins, revealing novel receptor regulatory sites in the intracellular loops, transmembrane domains, H8 and CT.

pharmacology and toxicology↗

bioRxiv2025

YY1 protein is essential for the promotion of Muller glia reprogramming and retina regeneration

Unlike mammals, the Muller glia reprogramming in zebrafish retina restores vision after an acute retinal injury. Here, we explored the Ying yang (Yy1) protein and its multi-faceted roles in different phases of retina regeneration. We show that the acetylation and deacetylation status of Yy1 contribute to its transcriptional activation and repression functions on various target genes, including regeneration-associated genes (RAGs). Yy1 is regulated positively by TGF-{beta} and negatively through Delta-Notch signaling in the injured retina. Yy1-knockdown caused reduced retinal progenitor induction and regeneration, while the opposite was seen in its overexpression. Yy1 collaborates with histone deacetylases, BAF complex, and the effector of TGF-{beta} signaling, pSMAD3, to target the genome differentially. Lastly, the whole transcriptome analysis of the Yy1-debilitated retina revealed differential expression of various RAGs and BMP-signaling. Yy1 facilitates the BMP pathways genes through the downregulation of noggin3. Our study unravels how a single transcription factor, Yy1, could influence many important regulatory steps of retina regeneration.

cell biology↗