Biology subjects

Hao, H.

Publications and source records attributed to Hao, H..

At least 19 recordsLinked to original sources

bioRxiv2026

An RBP-J-heparan sulfate-dependent gatekeeper directs macrophage fate between inflammatory regulation and osteoclastogenesis

Macrophages in bone possess a unique bi-potential capacity. Different from their primary roles in inflammation and immunity, these cells can differentiate into bone-resorbing osteoclasts. However, it remains unclear how macrophages determine which function to engage in bone, especially when exposed to the same stimulus, such as TNF, which can drive both pathways. Understanding these mechanisms is particularly important in inflammatory bone diseases, such as rheumatoid arthritis, where inflammation and bone resorption are hallmarks. Here, we identified an RBP-J-Hs2st1-2-O-sulfated heparan sulfate (HS)-IFN{beta} ; dependent molecular network that acts as a gatekeeper balancing macrophage fate inclinations in response to TNF. This network integrates cellular outside-in, inside-out, and relayed outside-in pathways. RBP-J deficiency in macrophages shifts TNF action from inflammatory regulation to osteoclastogenesis. Hs2st1, the exclusive biosynthetic enzyme for 2-O sulfation of HS, is a key target suppressed by RBP-J. Loss of Hs2st1 significantly reduces inflammatory osteoclastogenesis and arthritic bone erosion without affecting physiological bone mass. Elevated Hs2st1 expression and 2-O sulfation shift macrophages toward an osteoclastogenic fate, and vice versa. We further identified residues in IFN{beta} ; that are responsible for binding HS. Mutation of these sites diminished HS binding, augmented type I IFN response, and more strongly suppressed osteoclastogenesis. Our findings reveal a previously unrecognized molecular program fine-tuning macrophage fate and function, and highlight potential therapeutic strategies for inflammatory diseases with bone defects.

immunology↗

bioRxiv2026

Heparan sulfate selectively inhibits the collagenase activity of matrix metalloproteinase 13

Matrix metalloproteinase 13 (MMP13) is a zinc-dependent protease that plays key roles in extracellular matrix remodeling. Like several other MMPs, MMP13 has been shown to interact with heparan sulfate (HS), a highly sulfated glycosaminoglycan found at the cell surface and in the extracellular matrix, but the significance of the interaction remains unknown. Here we report that while zymogen and mature forms of MMP13 both bind HS with high affinity, their interactions with HS display markedly different characteristics in terms of preferred HS structure and binding kinetics. By structure-guided mutagenesis, we identified a large HS-binding site of MMP13 consists of 10 residues in the hemopexin domain, 3 residues in the catalytic domain, and 2 residues in the linker region. While these basic residues participate in binding to both zymogen and mature forms of MMP13, the relative contribution of many residues differs substantially between the two forms, which likely contributes to their distinct HS-binding characteristics. Binding of HS to mature MMP13 resulted in selective inhibition of the collagenase activity of MMP13 in a length- and sulfation-dependent manner, but the binding had no effect on degradation of non-collagen substrates. Mechanistically, the inhibitory effect of HS likely results from reduced interdomain flexibility after binding of HS, and/or HS-induced dimerization of MMP13. In sum, our study establishes HS as a multifaceted regulator of MMP13 activity, and discovers that the HS-binding site of MMP13 is a novel exosite that can be targeted to inhibits its collagenase activity.

biochemistry↗

bioRxiv2026

Mutations in SARS-CoV-2 Nsp1 are critical determinants of viral pathogenicity in mice

Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) nonstructural protein 1 (Nsp1) dampens the host immune response by shutting off host gene expression, a strategy that has remained evolutionary conserved among a diverse range of coronaviruses (CoVs). Residues important for SARS-CoV-2 Nsp1 mediated host shutoff have been incompletely defined. We have generated and characterized the ability of four Nsp1 mutants to inhibit host gene expression in both plasmid-based overexpression assays and utilized reverse genetic approaches to generate recombinant (r)SARS-CoV-2 expressing each Nsp1 mutant to investigate their impact on viral infection. Infection of K18-hACE2 transgenic mice with the rSARS-CoV-2 Nsp1 mutants resulted in reduced pathogenicity as determined by body weight maintenance and survival, attenuated viral replication in lung and nasal turbinate, distinct immune signatures in lung, and less severe lung pathology in comparison to wild-type (WT) virus-infected mice. Our data suggests amino acid residues in the C-terminal domain, in addition to the linker domain, of SARS-CoV-2 Nsp1 are critical determinants of viral pathogenicity as a result of their role in disrupting host gene expression. The reduced pathogenicity of rSARS-CoV-2 Nsp1 mutants highlights the potential for targeting Nsp1 for rational design of viral inhibitors and development of live-attenuated vaccine strategies as effective prophylactic and therapeutic treatments, respectively, to combat SARS-CoV-2 and possibly other CoV infections. IMPORTANCETo mitigate the ongoing public health threat posed by Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) and prepare for future coronavirus (CoV) outbreaks, there is an urgent need for effective prophylactic and therapeutic strategies, including vaccines and antivirals. The nonstructural protein 1 (Nsp1) is a conserved CoV virulence factor that suppresses host gene expression and disrupts immune responses. However, the contribution of specific Nsp1 residues to CoV pathogenesis remains unclear. Here, we identify residues within the C-terminal and linker regions of Nsp1 as critical determinants of SARS-CoV-2 pathogenicity in vivo. These findings advance our understanding of CoV host shutoff mechanisms and support Nsp1 as a promising target for the development of live-attenuated vaccines and antiviral therapeutics.

microbiology↗

bioRxiv2026

ConfDock: Atom-specific Uncertainty Quantification for Molecular Docking via Conformal Prediction

Molecular docking is widely used in structure-based drug discovery, yet most approaches provide point estimates without rigorous uncertainty quantification. This limitation makes it difficult to assess when a predicted pose should be trusted, especially when docking methods are applied to diverse protein-ligand systems. We present ConfDock, a conformal prediction (CP) framework for constructing atom-specific prediction intervals for ligand docking poses. ConfDock combines graph neural network (GNN) based quantile estimation with split conformal calibration, producing intervals that adapt to local protein-ligand environments while retaining distribution-free finite-sample coverage guarantees. We evaluate ConfDock on 238 protein-ligand complexes across four docking methods representing distinct computational paradigms. The proposed approach yields substantially narrower prediction intervals compared to standard split CP (57.2% average reduction in mean interval width, up to 74.5%) while maintaining target coverage across all evaluated settings. Ablation analysis indicates that the GNN captures the dominant structure-dependent variability in uncertainty, whereas the conformal calibration step provides a bounded adjustment to ensure coverage guarantees. These results demonstrate that combining learned, structure-aware quantile estimation with conformal calibration enables rigorous uncertainty quantification for molecular docking at atom-level resolution.

biochemistry↗

bioRxiv2026

Iterative structural homology search identifies new substrates of the protein O-fucosyltransferases POFUT3 and POFUT4

O-fucosylation plays an essential role in controlling protein folding, secretion and protein-protein interactions within the extracellular space. Recently, we identified a new form of protein O-fucosylation occurring on the N-terminal Elastin Microfibril Interaction (EMI) domain of several secreted proteins, mediated by two previously uncharacterized protein O-fucosyltransferases, POFUT3 (FUT10) and POFUT4 (FUT11). As all POFUT enzymes (POFUT1-4) are highly specific for the three-dimensional (3D) structure of their substrate protein domains, we postulated that structural homologues of these domains in other proteins may also be O-fucosylated. Here, we employed iterative protein structural homology searches as a novel strategy for identifying EMI-like domains that may serve as potential substrates for POFUT3/4. We discovered that microfibrillar-associated protein 2 and 5 (MFAP2/MFAP5) contain EMI-like domains and are O-fucosylated at high stoichiometry in human tissues. Unexpectedly, we showed that only POFUT3 is both necessary and sufficient for MFAP2/MFAP5 O-fucosylation, despite POFUT4 also having strong protein-protein interactions with MFAP2/MFAP5. Finally, we determined that O-fucosylation of MFAP2/MFAP5 is required for their efficient secretion, similar to other EMI domain-containing proteins. Together, these data demonstrate the power of sensitive structural homology analysis in identifying new enzyme-substrate relationships and protein-protein interactions.

biochemistry↗

bioRxiv2026

The Structural Code of Breast Cancer Proteoform: Alternative Splicing-driven Protein Isoform Variation and Functional Diversification

Alternative splicing generates extensive transcript diversity, but the extent to which this diversity contributes to the translated proteome and reshapes protein function remains unclear. Here, we develop 3DisoGalaxy, an atlas integrating transcript reconstruction, ribosome profiling, structural modelling and regulatory annotation in breast cancer. We find that 58,292 of 90,929 transcripts are linked to translation-supported ORFs, 71.9% of which arise from non-canonical transcript structures. These products are broadly accommodated within established protein fold space, indicating that alternative isoforms frequently preserve recognizable protein architectures despite substantial sequence variation. Functional divergence is instead concentrated in domains, intrinsically disordered regions, localization determinants and regulatory motifs. Motif remodelling is biased towards gains and is more extensive in cancer-driver genes than in other genes, linking isoform-associated regulatory variation to cancer-relevant proteins. As an example of domain remodelling, we identify an AKT1-{Delta}PH isoform that lacks the N-terminal PH domain while retaining the kinase core, with immunoblotting revealing a lower-molecular-weight AKT1 species consistent with this isoform. Together, our results show that alternative transcript diversity extensively enters translation-supported proteoform space and establish a systematic link between transcript variation and protein functional diversification.

cancer biology↗

bioRxiv2026

Thermal Nano-Engineering of Ginger Extracellular Vesicles for Targeted Oral Therapy of Colitis

Plant-derived extracellular vesicles (PEVs) are promising candidates for oral drug delivery, yet their clinical translation is hindered by limited targeting precision and inconsistent systemic absorption. While surface engineering can enhance tissue accumulation, strategies that preserve biocompatibility and enable scalable production remain limited. Here, we introduce a simple thermal processing approach, boiling, to structurally reconfigure ginger EVs into functionally enhanced, thermally reassembled nanoparticles (B-GEVs). The surface architecture of B-GEVs is enriched with key vesicle trafficking regulators, including V-type proton ATPase subunit G, ARF1, and {beta}-adaptin-like protein. This specific composition drives their tissue-specific accumulation in the intestine and liver and potentiates clathrin-dependent cellular uptake in intestinal cells by 8.57-fold. Beyond superior intrinsic anti-inflammatory activity through NLRP3 inflammasome suppression, B-GEVs function as an efficient oral delivery platform. When loaded with TNF- siRNA, they enable a synergistic therapy that simultaneously modulates upstream inflammation and silences key downstream mediators, showing potent efficacy in colitis. Our findings position boiling as a natural strategy for enhancing the bioactivity and targeted oral delivery potential of ginger-derived EVs.

bioengineering↗

bioRxiv2026

Heparan sulfate promotes autoactivation of pro-Cathepsin K by destabilizing the propeptide-catalytic domain interaction

Pro-cathepsin-K (pro-CtsK) is the zymogen of cathepsin-K (CtsK), a collagenase that is essential for bone resorption. pro-CtsK is known to bind heparan sulfate (HS), but the biological significance of the interaction remains unclear. Here we report that HS accelerates the autoprocessing of pro-CtsK in a manner dependent on both sulfation pattern and oligosaccharide length. We discovered a previously unknown electrostatic interaction between the propeptide and the catalytic domain, which stabilizes the conformation of the propeptide and prevents it from intermolecular proteolytic activation. HS accelerates autoprocessing of pro-CtsK by disrupting this critical electrostatic interaction. Mechanistically, HS competes with two glutamic acids in the propeptide for binding to three basic residues on the catalytic domain, thereby substantially alters the conformation of the propeptide and making it more labile for autoprocessing. We further discovered that HS is highly enriched in secretory lysosomes of osteoclasts and might be directly involved in autoactivation of CtsK.

biochemistry↗

bioRxiv2025

Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C.

Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge-domains spanning between organelles at contact sites that allow lipids to transit the cytosol between adjacent membranes. The assembly of BLTPs into complexes with adaptor proteins enables their lipid transfer ability. To address the mechanisms underlying assembly and regulation of BLTP complexes, we used cryo-EM to resolve the structure of one such BLTP, the Parkinsons protein VPS13C, at near-atomic resolution. The structure identifies a lipid-transfer-nonpermissive conformation, where the built-in C-terminal VAB adaptor module blocks the end of the lipid transfer bridge, interfering with lipid delivery. We also identify calmodulin, central to calcium signaling, as a VPS13 partner, suggesting calcium regulation of VPS13 function. Altogether, this structure of intact VPS13C serves as starting point to understand its regulation and, more broadly, that of other BLTPs.

cell biology↗

bioRxiv2025

Symmetric brain-liver circuits mediate lateralized regulation of hepatic glucose output

Neural lateralization is well recognized in the control of contralateral somatic movement, yet its relevance to visceral organ regulation remains poorly understood. This study aimed to determine whether the central nervous system exerts lateralized control over hepatic glucose metabolism and to localize the site of peripheral sympathetic crossover to the liver. Pseudorabies virus (PRV) tracing revealed bilateral projections from the lateral paragigantocellular nucleus (LPGi) with preferential innervation of the contralateral hepatic lobes. Unilateral LPGi activation elevated systemic glucose by enhancing glycogenolysis and gluconeogenesis specifically in contralateral lobes, whereas bilateral activation produced additive effects. Following unilateral hepatic denervation, contralateral LPGi activation induced metabolic compensation in the remaining innervated lobes, characterized by increased norepinephrine release, glucose production, and glycogen depletion. Whole-mount tissue clearing and dual viral tracing localized the sympathetic crossover to the porta hepatis. Developmental analysis showed that lobar-specific innervation along the vasculature emerges by postnatal week 2. These findings demonstrate that the brainstem can exert lobe-specific, lateralized control of hepatic glucose metabolism via bilaterally projecting brain - liver sympathetic pathways. This contralateral regulation arises from a peripheral decussation at the porta hepatis, and the compensatory activation observed after denervation reveals an intrinsic neuroadaptive mechanism that helps safeguard systemic glucose homeostasis. HighlightsO_LIBrain-liver sympathetic projections exhibit predominant contralateral innervation C_LIO_LIUnilateral LPGi activation drives glucose production in contralateral hepatic lobes C_LIO_LIUnilateral denervation augments contralateral LPGi-mediated metabolic compensation C_LIO_LISympathetic crossover to the liver localizes at the porta hepatis C_LI

neuroscience↗

bioRxiv2025

Respiratory syncytial virus infection confers heterologous protection against SARS-CoV-2 via induction of γδ T cell-mediated trained immunity and SARS-CoV-2 reactive mucosal T cells

The respiratory viruses can concurrently or sequentially infect a host and influence the trajectory of each other. The underlying immune mechanisms are not well understood. Here, we investigated whether respiratory syncytial virus (RSV) infection affects host vulnerability to subsequent SARS-CoV-2 infection in two murine models of SARS-CoV-2 infection. We found that prior RSV infection-induced heterologous protection against subsequent SARS-CoV-2 infection was dose and time dependent. RNA-seq and immunological analyses revealed that RSV triggered the activation of lung antigen presenting cells (APC)s and SARS-CoV-2 reactive mucosal T cells at day 9, which declined at 1 month. RSV also induced the expansion of lung {gamma}{delta} T cells and the upregulation of their cellular metabolic pathways. Furthermore, RSV infection in TCR{delta}-/- mice, which are deficient of {gamma}{delta} T cells, resulted in a reduced SARS-CoV-2 reactive mucosal T cell response and subsequent increased viral loads and higher levels of virus-induced inflammatory responses in the lung upon SARS-CoV-2 challenge compared to the wild-type mice. In summary, our findings suggest that RSV infection provides heterologous protection against the subsequent SARS-CoV-2 infection via induction of {gamma}{delta} T cell-mediated trained immunity in the lung and SARS-CoV-2 reactive mucosal T cell responses.

microbiology↗

bioRxiv2025

Efficacy of vocal cord injection of dedifferentiated fat cells in treating glottis closure insufficiency: Insights from a rat model of recurrent laryngeal nerve resection

Glottic insufficiency results from impaired vocal cord contact, leading to a gap between the cords and manifesting as hoarseness and respiratory difficulties. Vocal cord injection is a commonly utilized therapeutic approach to rectify this gap by augmenting vocal cord volume; however, the optimal injectable material remains undetermined. Dedifferentiated fat cells (DFATs), derived from mature adipocytes, exhibit robust proliferative capacity and multipotency, establishing them as potential candidates for treating glottic insufficiency. This study investigated the therapeutic efficacy of DFATs in a rat model of recurrent laryngeal nerve paralysis. In the experimental design, the recurrent laryngeal nerve of each rat was resected unilaterally, and 5 weeks later, the atrophied vocal cord muscles were injected with either 10 l of saline (control), 1.0 x 106 DFATs in 10 l (DFAT group), or 1.0 x 106 DFATs combined with 500 ng of basic fibroblast growth factor (bFGF) in 10 l (DFAT + bFGF group). At 4 weeks post-injection, laryngeal endoscopy was performed to evaluate the glottic gap, followed by histological analyses to assess vocal muscle atrophy, collagen deposition, and markers of cellular proliferation (Ki-67) and apoptosis (TUNEL). To confirm DFAT engraftment, GFP-labeled DFATs were evaluated at 2, 4, and 6 weeks post-injection. Results indicated that both the DFAT and DFAT + bFGF groups exhibited significantly reduced glottic gaps, increased collagen deposition, and decreased TUNEL-positive apoptotic cells compared to controls. Notably, the DFAT + bFGF group displayed superior outcomes, including a greater vocal muscle area and enhanced Ki-67-positive cell proliferation, indicating mitigation of muscle atrophy. GFP-positive DFATs were detectable in the tissue for up to 6 weeks, confirming engraftment. These findings underscore the potential of DFATs, particularly in combination with bFGF, as an innovative and effective therapeutic approach for glottic insufficiency secondary to recurrent laryngeal nerve paralysis.

cell biology↗

bioRxiv2025

The neuron-intrinsic membrane skeleton is required for motor neuron integrity throughout lifespan

Axons experience physical stress throughout an organisms lifetime, and disruptions in axonal integrity are hallmarks of both neurodegenerative diseases and traumatic injuries. The spectrin-based membrane periodic skeleton (MPS) is proposed to have a crucial role in maintaining axonal strength, flexibility, and resilience. To investigate the importance of the intrinsic MPS for GABAergic motor neuron integrity in C. elegans, we employed the auxin-inducible degron system to degrade {beta}-spectrin/UNC-70 in a cell-type specific and time-dependent manner. Degradation of {beta}-spectrin from all neurons beginning at larval development resulted in widespread axon breakage and regeneration in VD/DD GABAergic motor neurons in both larval and adult animals. Similarly, targeted degradation of {beta}-spectrin in GABA neurons alone resulted in extensive breakage. Moreover, we found that depleting {beta}-spectrin from the mature nervous system also induced axon breaks. By contrast, epidermal {beta}-spectrin was not required for axon integrity of VD/DD neurons. These findings demonstrate the cell-intrinsic importance of neuronal {beta}-spectrin/UNC-70 for axon integrity both during development and in adulthood.

neuroscience↗

bioRxiv2025

Circulating extracellular vesicles from HIV-1 gp120-treated mice act as endogenous algogens, mediating and maintaining HIV-associated chronic pain

HIV-associated chronic pain (HIV-PAIN) remains prevalent in the post combined antiretroviral therapy era, affecting 30-60% of HIV patients worldwide. The underlying mechanism responsible for the development and maintenance of chronic pain remains unclear. gp120 is a causal factor of the HIV-PAIN and functions as an exogenous algogen. The pain experienced by human HIV-PAIN has been modeled in mice (referred to as mHIV-PAIN) using intrathecal (i.t.) injections of gp120. gp120 is a relatively short-term, static, exogenous algogen that is exhaustible in vivo. In authentic infection, HIV virions serve as the primary source of exogenous gp120, which initiates the early phase of clinical HIV-PAIN. Interestingly, while the source of replenishing gp120 decreases after antiretroviral therapy by suppressing viremia, the prevalence of chronic HIV-PAIN remains stable. To induce chronic pain in mice, gp120 needs to be repeatedly applied by the i.t. route. This raises a key question: Is an endogenous inexhaustible algogen responsible for maintaining the chronicity of HIV-PAIN? In the present study, we isolated circulating small extracellular vesicles (sEV) from mice using our mHIV-PAIN model that is i.t. injected with gp120. We refer to such sEV as gp120-sEV herein. We observed that gp120 is absent in gp120-sEV. Following transfusion of gp120-sEV intrathecally, naive recipient mice exhibit an extensive pain phenotype, including cold pain tested with we newly invented dry ice vapor cold test. RNA-sequence analysis suggests that gp120-sEVs induced expression of genes related to nociception and neuroinflammation pathways. These findings provide direct evidence that circulating sEV function as endogenous long-term "dynamic" algogens that enhance initial pain and extend the chronification of HIV-PAIN in mice, suggesting that chronic HIV-PAIN requires an exogenous algogen (gp120) paired with endogenous algogen (gp120-sEV), and that these components work synchronically to initiate and extend pain chronification. This double algogen concept provides a new insight into the pathogenesis of HIV-PAIN chronification. Our new mechanistic understanding will also assist in identifying new therapeutics to alleviate HIV-PAIN by targeting pathological gp120-sEV.

neuroscience↗

bioRxiv2025

Giant KASH proteins and ribosomes synergistically establish cytoplasmic biophysical properties in vivo

Understanding how cells control their biophysical properties during development remains a fundamental challenge. While cytoplasmic macromolecular crowding affects multiple cellular processes in single cells, its regulation in living animals remains poorly understood. Using genetically encoded multimeric nanoparticles for in vivo rheology, we discovered that C. elegans tissues maintain distinct cytoplasmic biophysical properties that differ from those observed across diverse systems, including bacteria, yeast species, and cultured mammalian cells. We identified two conserved mechanisms controlling cytoplasmic macromolecular diffusion: ribosome concentration, a known regulator of cytoplasmic crowding, works in concert with a previously unknown function for the giant KASH protein ANC-1 scaffolding the endoplasmic reticulum. These findings reveal mechanisms by which tissues establish and maintain distinct cytoplasmic biophysical properties, with implications for understanding cellular organization across species. One-Sentence SummaryLiving tissues maintain unique intracellular biophysical properties under the control of cytoplasmic constraints and crowding.

biophysics↗

bioRxiv2025

Single-nucleus RNA sequencing revealed the impact of post-mortem interval on the cellular component and gene expression analysis of mouse brains

Accurate analysis of cell atlas and gene expression in biological tissues using single-nucleus RNA sequencing (snRNA-seq) is dependent on the quality of source material, and post-mortem interval (PMI) is one of the major sources of variation in RNA quality. Although the use of RNA-degraded tissues in transcriptome analysis remains controversial, such samples are sometimes the sole means to address specific questions. Current studies on the impact of PMI on transcriptome data are limited to large-scale RNA-seq, which ignores cellular heterogeneity. Thus, deciphering the non-cell- autonomous effects caused by PMI is imperative for understanding the cellular and molecular disruption it elicits. Here, we investigated the impact of PMI on cellular components and gene expression using snRNA-seq data from mouse brain tissues of post-mortem. We collected samples that were allowed to decay for varying amounts of time at 25{degrees}C prior to snRNA-seq, covering the entire range of RIN values. The different effects on the PMI to the degradation rate of mRNA and rRNA within nuclei, and the mRNA presented a more stable state. Multi-channel analysis revealed the preferential transient depletion oligodendrocytes and OPCs with increasing PMI. In addition, a rapid widespread overregulation of ribosomal transient recruitment to protein (RP) genes in various cells, and reached a plateau at PMI of 36h. Although state depletion of neuronal cells was not detected, we reported significant upregulation of PMI-dependent RP genes in its subpopulations and their cell loss. Moreover, RP genes showed the greatest differential expression in the subpopulations with greater cell perturbation, and we speculated that aberrant expression of these genes might be associated with cell death. In this study, we systematically investigated the changes in the transcriptome profile of brain tissue induced by PMI at single-cell resolution, and revealed one of the important factors that might be responsible for the changes. In addition, our data complemented a possible explanation for the changes in the cellular state of brain tissue induced by postmortem hypoxia-ischemia, and provided a reference for transcriptome studies of RNA degradation samples.

molecular biology↗

bioRxiv2024

An ancient competition for the conserved branchpoint sequence influences physiological and evolutionary outcomes in splicing

Recognition of the intron branch point during spliceosome assembly is a multistep process that can influence mRNA structure and levels. A branch point sequence motif UACUAAC is variably conserved in eukaryotic genomes, but in some organisms, more than one protein can recognize it. Here, we show that SF1 and Quaking (QKI) compete for a subset of intron branch sites with the sequence ACUAA. SF1 activates exon inclusion through this sequence, but QKI represses the inclusion of alternatively spliced exons with this intron branch point sequence. Using mutant reporters derived from a natural intron with two branch site-like sequences, we find that when either branch point sequence is mutated, the other is utilized; however, when both are present, neither is used due to high-affinity binding and strong splicing repression by QKI. QKI occupancy at the dual branch site directly prevents SF1 binding and subsequent recruitment of spliceosome-associated factors. Finally, the ectopic expression of QKI in budding yeast (which lacks QKI) is lethal, at least in part due to the widespread repression of splicing. In conclusion, QKI can function as a splicing repressor by directly competing with SF1/BBP for a subset of branch point sequences that closely mirror its high-affinity binding site.

molecular biology↗

bioRxiv2024

Dynamic Models of Neural Population Dynamics

The recent developments in artificial intelligence (AI) increase the hope that AI can provide a powerful tool to facilitate scientific discovery and to generate and validate new ideas for scientific research autonomously. Large Language Models (LLMs), such as ChatGPT4 have demonstrated remarkable capabilities in understanding and generating human-like text. Their potential extends beyond simple language tasks, offering transformative possibilities in scientific research of all fields. By leveraging vast amounts of data and advanced computational power, LLMs can assist researchers in generating novel ideas, automating routine tasks, and fostering interdisciplinary collaborations. On September 12, 2024, OpenAI released their updated generative artificial intelligence system called ChatGPTo1. This new AI system, built upon chain-of-thought and reinforcement learning, has greatly enhanced logical reasoning abilities and can effectively solve various complex problems from elementary-level mathematical problems to modern scientific research issues in physics, chemistry, and biology. Unlike previous LLMs in which logical reasoning and data analysis abilities are developed through training on actual data, ChatGPTo1 logical reasoning ability and capacity to generate new scientific ideas are primarily acquired through chain-of-thought processes and reinforcement learning rather than pre-training. To examine this, we specifically tested ChatGPTo1 current reasoning and scientific discovery capabilities by developing theoretically complex and quantitatively challenging scientific equations in various fields of neuroscience, such as dynamical systems, nonlinear dynamical systems, dynamical systems on differential manifolds, neural field theory, nonlinear divergence theorems, nonlinear heat conduction equations and Laplace equations and their extensions on differential manifolds, nonlinear statistical analysis methods, deep learning, and other topics involving multiple fields. The current large language models may illustrate a certain degree of general intelligence, even if fundamentally it may be different from human intelligence. However, it does not mean the current LLMs can fully apply such ability in practical applications or that their reasoning potential can be fully tapped. It is essential to explore specific pathways and methods to cultivate their potential for scientific discovery. To accomplish this, we consider how to integrate them with common search engines (such as Google) capabilities and ChatGPT4o cross-modal abilities to better understand new disciplines and scientific discoveries. To this point, the major shortcoming of ChatGPTo1 is that it is not an end-to-end scientific discovery method and lacks the ability to achieve full automation. It also lacks methods for image analysis and full-scale data analysis, making it difficult to use simulation and data analysis to evaluate and test proposed new theories and methods.

neuroscience↗