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Biology subjects

Bao, C.

Publications and source records attributed to Bao, C..

17 recordsLinked to original sources

A canonical input to the head direction compass carries predominantly eye movement signals

The mammalian head direction (HD) system is thought to update its internal compass using angular head velocity (AHV) signals relayed from the brainstem. We tested this canonical interpretation by recording from the nucleus prepositus hypoglossi (NPH), a proposed AHV relay known to be important for accurate HD tracking, while simultaneously measuring eye and head movements in mice. Neurons classified as AHV-tuned instead predominantly encoded eye movements: most showed saccade-related bursts or pauses, and apparent AHV tuning was largely explained by eye rather than head motion. Optotagging showed that even NPH neurons projecting directly to the HD circuit predominantly encoded eye movements. Empirically constrained population models reconstructed eye position and gaze direction, but head-direction readouts failed when eye and head motion were dissociated. These findings overturn the canonical view of NPH as a dedicated AHV relay, revealing eye movements as a major, previously unmeasured component of the signals entering the mammalian HD circuit and thereby changing the computational problem that the HD system must solve to maintain a stable representation of heading.

neuroscience↗

Extracellular matrix particle treatment induces digit regeneration in soft-tissue preserved amputation (SPA) model of adult mice

BackgroundIn mouse classic amputation model, second phalanx (P2) is incapable of regeneration. Extracellular matrix (ECM) solution has shown limited ability to induce digit regeneration in classical amputation model of the murine digit. However, the effect of solid ECM particles on bone regeneration is not well understood due to difficulties in treating solid particles in classical amputation model. MethodsWe examined the regenerative effects of ECM particles in mice digit by establishing a soft tissue preserved amputation (SPA) model on P2, through removing the amputated bone whilst preserving soft tissue. ECM particles implanted into the amputation site and wrapped in the preserved soft tissues. Bone regeneration was assessed by morphological examination and micro-CT scans. ResultsWe observed bone regeneration in the SPA model; specifically, new bone formed at the P2 distal end. Implantation of ECM particles exerted a pro-regenerative effect, characterized by increased bone volume and decreased bone density. Moreover, the ECM induced the formation of free-floating bone, further supporting its role in bone regeneration. Combined treatment with ECM particles and bone morphogenetic protein 2 (BMP2) resulted in a significant increase in bone volume. ConclusionsWe demonstrate that soft tissue preservation at the amputation site can overcome the intrinsic regenerative limitationsl. Using SPA model, we found that ECM particles have a proven ability to promote bone regeneration, and that the combination of ECM particles with BMP2 further enhances bone regeneration. These findings underscore the therapeutic promise of ECM-based strategies, for clinical translation in non-regenerative finger injuries. Summary statementSolid-state Extracellular matrix can induce mice digit regeneration and has the potential for clinical application. HighlightsThe SPA model we developed enables ECM particles to adhere to wounds, and our research has found that: O_LIDigit bone regeneration was shown in SPA model . C_LIO_LIECM particles treatment promoted bone regeneration and can generate free-floating bone in SPA model. C_LIO_LICombination of ECM + BMP2 treatment induced strong digit regeneration in SPA model. C_LI

cell biology↗

Imaging Intrinsic Stochastic Magnetic Fluctuations in Living Cells

SignificanceThis work establishes a probabilistic magnetometry framework for detecting weak stochastic magnetic fluctuations at the nanoscale, which provides the first quantitative access to intrinsic magnetic activity in living cells. Weak stochastic magnetic fluctuations at nanoscale are difficult to quantify. In living cells, ionic transport and molecular currents generate electromagnetic activity whose magnetic component is likewise nanoscale, weak, stochastic, and rapidly varying and has therefore remained experimentally inaccessible. Here we introduce Bio-Spin Probabilistic Inference (BISPIN), a digital statistical framework that can quantify weak, stochastic magnetic fluctuations at the nanoscale. Using threshold-resolved signals from enhanced nitrogen-vacancy quantum sensors, BISPIN converts unstable analog magnetic readouts into statistically convergent digital observables and infers fluctuation strength through probabilistic modeling, enabling robust quantification under random sensor orientations and biological heterogeneity within the experimental bandwidth. Applied to living cells, this approach distinguishes live from fixed cells, resolves agonist-induced activation, and maps subcellular variations in magnetic fluctuation strength. By providing the first quantitative access to intrinsic stochastic magnetic fluctuations in living cells, this work establishes a probabilistic magnetometry framework for cellular electrodynamics and opens a new magnetic dimension of cellular phenotyping for bio-spin omics.

biophysics↗

A frontal motor circuit for economic decisions and actions

Flexible behaviour requires transforming abstract cognitive representations, such as value preferences, into concrete motor actions. During economic decision-making, individuals evaluate options to guide choices and then transform these choices into specific actions to obtain rewards. Understanding how neural circuits convert these abstract economic decisions into spatial actions remains challenging because decision formation and motor planning are typically intertwined. Here we introduce a mouse task that temporally dissociates value-guided decisions from spatial action planning, and show that a frontal motor network implements the transformation across decision stages through dynamic circuit reconfiguration. Using cortex-wide imaging and optogenetic perturbations, we identified a frontal motor circuit that was causally required for both abstract and motor stages of choice. During the abstract decision stage, neurons in this circuit encoded option values and economic choices independently of sensorimotor contingencies, and unilateral silencing impaired decisions without spatial bias. In contrast, during spatial planning, value and spatial signals were non-linearly integrated to guide action selection, and unilateral silencing produced an ipsilateral bias. A dynamical model captured this transformation, predicting a mode switch from cooperative interhemispheric maintenance of economic choice to competitive, lateralized control of actions, which we validated with simultaneous bilateral recordings. These findings demonstrate how frontal motor circuits reconfigure their interactions to bridge abstract cognition and concrete actions, providing a circuit-level mechanism for flexible, value-guided behaviour.

neuroscience↗

Flexible selection of working memory representations to reduce cognitive cost

Across psychology 1-4, economics 5,6, machine learning 7, and neuroscience 8,9, it is well established that choosing a good internal representation can make complex problems easier to solve. Thus, intelligent behavior depends not only on what is stored in working memory, but on the format in which it is stored. Selecting a lower-load format can substantially reduce the mental effort required for a task, since working-memory load is a major contributor to cognitive cost 10-12. Whether non-human animals make such representational choices, and how these choices are implemented in neural circuits, has remained unclear. Here we show that rats flexibly adjust the format of working memory to reduce cognitive cost. In an egocentric task that encourages an action-based code, rats maintained the relevant information as a stable motor plan supported by frontal cortex. When the same behavioral problem was reformulated in allocentric coordinates, the action-based code became costly, and rats instead stored a sensory trace in auditory cortex. A cost-sensitive model explains which internal format should be used under each task variant and predicted that simplifying the allocentric task would reduce the advantage of a sensory code and drive reinstatement of frontal motor planning; this prediction was confirmed, as rats rapidly returned to a motorplan representation and the frontal cortex again became necessary for performance. These results demonstrate that flexible representational selection is not unique to humans 13 but is present in rodents and reflected in circuit-level reallocation of working memory. This establishes a neural basis for classic theories linking problem representation to computational efficiency and provides a path toward a circuit-level understanding of how the brain selects internal formats to reduce cognitive cost.

neuroscience↗

CUSP: Complex Spike Sorting from Multi-electrode Array Recordings with U-net Sequence-to-Sequence Prediction

BackgroundComplex spikes (CSs) in cerebellar Purkinje cells convey unique signals complementary to Simple spike (SS) action potentials, but are infrequent and variable in waveform. Their variability and low spike counts, combined with recording artifacts such as electrode drift, make automated detection challenging. New MethodWe introduce CUSP (CS sorting via U-net Sequence Prediction), a fully automated deep learning framework for CS sorting in high-density multi-electrode array recordings. CUSP uses a U-Net architecture with hybrid self-attention inception blocks to integrate local field potential and action potential signals and outputs CS event probabilities in a sequence-to-sequence manner. Detected events are clustered and paired with concurrently detected SSs to reconstruct the complete Purkinje cell activity. ResultsTrained on cerebellar neuropixels recordings in rhesus macaques, CUSP achieves human-expert performance (F1 = 0.83 {+/-} 0.03) and even captures valid CS events overlooked during manual annotation. Comparison with Existing MethodsCUSP outperforms traditional and state-of-the-art CS and SS sorting algorithms on CS detection. It remains robust to waveform variability, spikelet composition, and electrode drift, enabling accurate CS tracking in long-term recordings. In contrast, existing methods often show false-positive biases or degrade under drift. ConclusionsCUSP provides a scalable, robust framework for analyzing burst-like or dynamically complex spike patterns. Its generalizability makes it valuable for large-scale cerebellar datasets and other neural systems, such as hippocampal pyramidal cells, where complex bursts are critical for computation. By combining expert-level accuracy with automation, CUSP offers a broadly applicable solution for studying information coding across circuits.

neuroscience↗

PFS alleviates bone destruction in collagen-induced arthritis mice associated with macrophage polarization

Periploca forrestii Schltr is a clinical traditional Chinese medicine for the treatment of Rheumatoid arthritis (RA). This study aimed to investigate effects of Periploca forrestii Schltr saponin (PFS) on bone destruction and macrophage polarization in arthritis model mice and to explore its possible mechanism. Arthritis was induced in two species, BALB/c and C57BL/6 mice, by immunization with type II chicken collagen. The arthritic mice were administered PFS for four weeks. The hindfeet, blood and spleen were harvested. Molecular expression was determined by ELISA, RT-PCR and immunoblotting. PFS treatment resulted in a significant reduction in paw swelling in both species of mice. PFS also reduced cartilage destruction and infiltration of osteoclasts in BALB/c mice. Furthermore, it decreased the levels of M1 macrophage cytokines while increasing the levels of M2 macrophage cytokines in the paw and plasma. Micro-CT results in C57BL/6 mice showed that PFS attenuated microstructural damage in bone tissue. PFS inhibited CD68 and affected the expression of M1 macrophage factors such as CCL-2, TLR4, and IL-1{beta} in the mouse paw. In addition, PFS treatment increased the M2 macrophage factor CD206 and CD163. PFS inhibits the activation of ERK, JNK, and p38 and the expression of transcription factors, including STAT3, p65, and c-Fos. PFS may modulate pleiotropic macrophage polarization and thus play an ameliorative role in bone damage, therefore PFS may be an effective alternative drug for the treatment of RA.

immunology↗

Addressing preferred orientation in single-particle cryo-EM through AI-generated auxiliary particles.

The single-particle cryo-EM field faces the persistent challenge of preferred orientation, lacking general computational solutions. We introduce cryoPROS, an AI-based approach designed to address the above issue. By generating the auxiliary particles with a conditional deep generative model, cryoPROS addresses the intrinsic bias in orientation estimation for the observed particles. We effectively employed cryoPROS in the cryo-EM single particle analysis of the hemagglutinin trimer, showing the ability to restore the near-atomic resolution structure on non-tilt data. Moreover, the enhanced version named cryoPROS-MP significantly improves the resolution of the membrane protein NaX using the no-tilted data that contains the effects of micelles. Compared to the classical approaches, cryoPROS does not need special experimental or image acquisition techniques, providing a purely computational yet effective solution for the preferred orientation problem. Finally, we conduct extensive experiments that establish the low risk of model bias and the high robustness of cryoPROS.

biophysics↗

A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma

Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.

cancer biology↗

Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes

Mediated by elongation factor G (EF-G), ribosome translocation along mRNA is accompanied by rotational movement between ribosomal subunits. Here, we reassess whether the intersubunit rotation requires GTP hydrolysis by EF-G or can occur spontaneously. To that end, we employ two independent FRET assays, which are based on labeling either ribosomal proteins (bS6 and bL9) or rRNAs (h44 of 16S and H101 of 23S rRNA). Both FRET pairs reveal three FRET states, corresponding to the non-rotated, rotated and semi-rotated conformations of the ribosome. Both FRET assays show that in the absence of EF-G, pre-translocation ribosomes containing deacylated P-site tRNA undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. While the two FRET pairs exhibit largely similar behavior, they substantially differ in the fraction of ribosomes showing spontaneous fluctuations. Nevertheless, instead of being an invariable intrinsic property of each FRET pair, the fraction of spontaneously fluctuating molecules changes in both FRET assays depending on experimental conditions. Our results underscore importance of using multiple FRET pairs in studies of ribosome dynamics and highlight the role of thermally-driven large-scale ribosome rearrangements in translation.

biochemistry↗

An HBV mRNA vaccine with favorable virological suppression and superior immunity

BRIEF ABSTRACTHere we report on the development and comprehensive evaluations of an mRNA vaccine for chronic hepatitis B (CHB) treatment. In two different HBV carrier mouse models generated by viral vector-mediated HBV transfection (pAAV-HBV1.2 and rAAV8-HBV1.3), this vaccine demonstrates sufficient and persistent virological suppression, and robust immunogenicity in terms of induction of strong innate immune activation, high-level virus-specific antibodies, memory B cells and T cells. mRNA platform therefore holds prospects for therapeutic vaccine development to combat CHB.

immunology↗

Highly synchronized cortical circuit dynamics mediate spontaneous pain

Cortical neural dynamics mediate information processing for the cerebral cortex, implicated in fundamental biological processes, such as vision and olfaction, in addition to neurological and psychiatric diseases. Spontaneous pain is a key feature of human neuropathic pain. Whether spontaneous pain pushes cortical network into an aberrant state, and if so, whether it can be brought back to a normal operating range to ameliorate pain are unknown. Using a clinically relevant mouse model of neuropathic pain with robust spontaneous pain-like behavior, we report that orofacial spontaneous pain activated a specific area within the primary somatosensory cortex (S1), displaying synchronized neural dynamics revealed by intravital two-photon calcium imaging. This synchronization was underpinned by local GABAergic interneuron hypoactivity. Pain-induced cortical synchronization could be attenuated by manipulating local S1 networks or clinically effective pain therapies. Specifically, both chemogenetic inhibition of pain-related c-Fos-expressing neurons, and selective activation of GABAergic interneurons, significantly attenuated S1 synchronization. Clinically effective pain therapies including carbamazepine and nerve root decompression could also dampen S1 synchronization. More importantly, restoring a normal range of neural dynamics, through attenuating pain-induced S1 synchronization, alleviated pain-like behavior. These results suggest spontaneous pain pushes S1 regional network into a synchronized state, whereas reversal of this synchronization alleviates pain.

neuroscience↗

Frontal but not parietal cortex is required for decisions under risk

Neurons in frontal and parietal cortex encode task variables during decision-making, but causal manipulations of the two regions produce strikingly different results. For example, silencing the posterior parietal cortex (PPC) in rats and monkeys produces minimal effects in perceptual decisions requiring integration of sensory evidence, but silencing frontal cortex profoundly impairs the same decisions. Here, we tested the causal roles of the rat frontal orienting field (FOF) and PPC in economic choice under risk. On each trial, rats chose between a lottery and a small but guaranteed surebet. The magnitude of the lottery was independently varied across trials and was indicated to the rat by the pitch of an auditory cue. As in perceptual decisions, both unilateral and bilateral PPC muscimol inactivations produced minimal effects. FOF inactivations produced substantial changes in behavior even though our task had no working memory component. We quantified control and bilateral inactivation behavior with a multi-agent model consisting of a mixture of a rational utility-maximizing agent (U = V{rho}) with two habitual agents that either choose surebet or lottery. Effects of FOF silencing were best accounted for by a decrease in{rho} , the exponent of the utility function. The decrease in{rho} could be parsimoniously explained by a dynamical model where the FOF is part of a network that represents the value of the lottery to compare against a remembered boundary representing the value of the surebet. This dynamical model predicted that neurons in the FOF should increase their activity with increasing lottery values. In line with our predictions, single neurons recorded in the FOF encoded the value of the lottery even when controlling for choice. These results together demonstrate that FOF is a critical node in the neural circuit for decision under risk.

neuroscience↗

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

Translating ribosomes unwind mRNA secondary structures by three basepairs each elongation cycle. Despite the ribosome helicase, certain mRNA stem-loops stimulate programmed ribosomal frameshift by inhibiting translation elongation. Here, using mutagenesis, biochemical and single-molecule experiments, we examine whether high stability of three basepairs, which are unwound by the translating ribosome, is critical for inducing ribosome pauses. We find that encountering frameshift-inducing mRNA stem-loops from the E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) hinders A-site tRNA binding and slows down ribosome translocation by 15-20 folds. By contrast, unwinding of first three basepairs adjacent to the mRNA entry channel slows down the translating ribosome by only 2-3 folds. Rather than high thermodynamic stability, specific length and structure enable regulatory mRNA stem-loops to stall translation by forming inhibitory interactions with the ribosome. Our data provide the basis for rationalizing transcriptome-wide studies of translation and searching for novel regulatory mRNA stem-loops.

biochemistry↗

Origins of cancer genome complexity revealed by haplotype-resolved genomic analysis of evolution of Barretts esophagus to esophageal adenocarcinoma

The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we performed haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barretts esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identified distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.

genomics↗

mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding

Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Forster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.

biochemistry↗

Susceptibility of Spotted Doves (Streptopelia chinensis) to Experimental Infection with the SFTS Phlebovirus

BackgroundSevere fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks, has spread widely during the last few years. Although SFTSV has been detected in wild birds, the natural reservoir and amplifying hosts for the virus have not been well-studied.\n\nMethodology/Principle FindingsHere we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 (hereafter JS2010), a Chinese lineage strain and JS2014-16 (JS2014) from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves were susceptible to SFTSV and the severity of the viremia was dose-dependent. When challenged with 107 and 105 PFU, all doves developed viremia which peaked 3-5 days post-infection (dpi). A subset (25-62.5%) of the birds challenged at 103 PFU, developed viremia. Virulence of SFTSV in spotted doves appeared to be strain-dependent. Infection with the strain of JS2014 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds. The doves inoculated with the JS2010 strain survived infection with relatively lower virus titers in the blood.\n\nConclusions/SignificanceOur results suggest that spotted doves, one of the most abundant bird species in China, could be a competent amplifying host of SFTSV, the strain of the Japanese lineage in particular, with higher viremia titers and play an important role in the transmission of SFTSV. Our observations shed light on the ecology of SFTSV which could benefit the implementation of future surveillance and control programs.\n\nAuthor SummarySevere fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks. Our recent study have showed that some species of migratory birds, such as swan geese and spotted doves, could be parasitized by H. longicornis, and antibodies against the virus could also be determined in these birds, which showed that migratory birds could be infected by SFTSV naturally. Other studies have reported that migratory bird routes and the distribution of H. longicornis in East Asia overlap with the geographic distribution of SFTSV. Migratory birds are known to be carriers and transmitters of infectious agents, like the causative agents of influenza, West Nile encephalitis, and Lyme disease. Wild birds often travel long distances carrying various parasites, including ticks, which may be infected with viruses and bacteria. It is therefore reasonable to hypothesize that migratory birds may have played an important role in dispersing H. longicornis-borne SFTSV in both scenarios, either the birds are infected directly with the virus or the birds are carriers of parasitic ticks that are infected with the virus. Here we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 (hereafter JS2010), a Chinese lineage strain and JS2014-16 (JS2014) from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves were susceptible to SFTSV and the severity of the viremia was dose-dependent.\n\nInterestingly, virulence of SFTSV in spotted doves appeared to be strain-dependent. Infection with the strain of JS2014 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds. The doves inoculated with the JS2010 strain survived infection with relatively lower virus titers in the blood. These findings provide novel insights for understanding the rapid spread of the virus in a short time span, especially the SFTSV strains from the Japanese lineage (genotype E), which presented cross ocean transmission.

microbiology↗