Biology subjects

Lou, Y.

Publications and source records attributed to Lou, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

A generalizable codesigned platform for solid-state nanopore sensing beyond the capacitive-noise constraints

Solid-state nanopores offer label-free, real-time single-molecule sensing, yet resolving rapidly translocating biomolecules requires high-bandwidth data acquisition, where increased high-frequency noise fundamentally limits reliable recovery of informative events. Here we establish a hardware-software co-designed nanopore sensing platform that overcomes this bandwidth-noise limitation by integrating scalable low-noise device engineering with deep learning-based signal reconstruction. A wafer-scale dielectric-engineering strategy using low-dielectric SU8 photoresist reduces total device capacitance to the picofarad regime and suppresses high-frequency noise by up to fivefold while maintaining facile, controllable and reproducible fabrication. This extends usable acquisition rate to 40 MHz and enables capture of fast molecular features. Combined with a reconstruction neural network trained on synthetic translocation signals embedded in experimentally measured noise, the platform recovers transient blockade sublevels while preserving temporal fidelity. Using engineered DNA molecules carrying dumbbell-like barcodes, we resolve nanometer-scale structural features on sub-microsecond timescales, and experimentally measure translocation velocity within the sub-5 nm regime. Dual-channel measurement on a single nanopore device further demonstrates transferability of the platform by showing robust cross-channel signal reconstruction across distinct baseline noise levels. This platform provides a general route for reliable recovery of previously inaccessible molecular information from high-bandwidth nanopore measurements.

biophysics↗

bioRxiv2026

Compressive axial-integrated planar scanning (CAPS) microscopy for high-speed volumetric imaging of cardiac dynamics

Investigating cardiac dynamics, including contractile function and intracardiac flow, requires volumetric imaging capable of resolving whole-organ events at micrometer resolution and millisecond timescales. However, the limited readout bandwidth of detectors imposes fundamental trade-offs among spatial sampling, field of view, and achievable volume rates. Here we introduce compressive axial-integrated planar scanning (CAPS) microscopy, a computational imaging framework that combines rapid light-sheet scanning, detection-side axial multiplexing with model-based reconstruction to enhance detector bandwidth utilization for high-speed volumetric imaging. Using widely accessible optical sensors and components, CAPS achieves cellular-scale resolving power across heart chambers at 200 volumes per second with an effective detector pixel rate of 5.82 GHz, representing a [~]15-fold increase in spatiotemporal throughput relative to uncompressed volumetric acquisition. Coordinated high-speed encoding and computational reconstruction further mitigate rolling-shutter distortions in CMOS sensors while preserving frame rate and intrinsic optical sectioning. We demonstrate that CAPS enables beat-resolved imaging of single-cell cardiomyocyte kinematics, chamber-scale contractile dynamics, and intracardiac hemodynamics in zebrafish larvae under both healthy and pharmacologically perturbed conditions. Collectively, these advances establish CAPS as a powerful framework for quantitative, in vivo characterization of coordinated and disrupted cardiac dynamics at cellular resolution, supporting high-speed volumetric interrogation of organ-level function and disease progression.

bioengineering↗

bioRxiv2026

HalluCodon enables species-specific codon optimization using multimodal language models

Codon optimization is widely used in transgenic crop development, plant synthetic biology, and molecular farming to improve heterologous protein expression in plant cells. Increasing availability of plant omics data now enables optimization strategies that account for species-specific sequence features. We developed HalluCodon, a customizable framework that uses multimodal language models to design coding sequences tailored to individual plant species. The framework allows users to fine tune pre-trained protein and RNA language models with their own datasets to build species-specific codon optimization models. The current implementation includes base models trained on coding sequences and proteomes from fifteen plant species. HalluCodon generates coding sequences through a hallucination-based design strategy guided by two predictive modules that evaluate coding sequence naturalness (CodonNAT) and expression potential (CodonEXP). Benchmark tests using representative proteins show that the generated sequences reproduce host-specific codon usage patterns and support high expression levels in plant systems.

bioinformatics↗

bioRxiv2026

Theca cell mechanosensing and regulation of follicular extracellular matrix during ovarian follicle development

Mammalian folliculogenesis is essential for female hormonal regulation and successful reproduction. While the steroidogenic functions of theca cells (TCs) have been implicated in ovarian diseases and infertility, the physico-structural properties of TCs and their associated extracellular matrix (ECM), or theca matrix, remain poorly understood. Using murine ovaries, we show that a stiff basement membrane (BM) and theca matrix constitute a mechanically instructive niche that modulates TC proliferation and Yes-associated protein (YAP) signalling in secondary follicles. We identify hyaluronic acid (HA) as a key matrix component that is actively secreted by contractile TCs. The HA scaffold, in turn, regulates TC proliferation, YAP signalling and motility, and is required for overall follicle growth. We showed that stiffer substrates enhance YAP nuclear transport in TCs, while mechanical stretch, cell packing, and curvature affect TC proliferation. In addition, TCs exhibit directed migration towards regions of positive curvature. Together, this study reveals a mechanochemical feedback mechanism that establishes TC mechanics and HA as key regulators of theca matrix formation that is essential for mammalian folliculogenesis. SIGNIFICANCEThe structural properties and mechanical functions of the basement membrane and theca cell-matrix encapsulating mammalian ovarian follicles are poorly understood. Our findings reveal that during early stage of follicle development, the basement membrane remains thin and stiff, while the theca cells actively secrete hyaluronic acid in a contractility-dependent manner. The hyaluronic acid scaffold, in turn, regulates theca cell YAP signalling, proliferation and motility that are required for functional growth of follicles. We further showed that the theca cells are mechanosensitive and fine-tune their proliferative capacity and Hippo pathways in response to substrate stiffness, stretch and curvature. Together, our study uncovers mechanoregulatory feedback between theca cells and associated extracellular matrix, offering new insights into environmental control of folliculogenesis in female reproduction.

developmental biology↗

bioRxiv2026

Surf2Spot: A Surface-Informed Geometry-Aware Model for Predicting Binder and Nanobody Design Hotspots

Protein-protein interactions (PPIs) and nanobody-antigen interactions (NAIs) play essential roles in cellular function, yet accurate hotspot prediction remains challenging. We present Surf2Spot, a deep learning framework that integrates sequence embeddings, structural features, and protein surface properties to predict interaction hotspots. By jointly modeling structural and physicochemical determinants, Surf2Spot achieves superior performance on curated PPI and NAI datasets, improving F1-scores by 45.9-46.9% and AUPRC by 43.2% over existing methods. Case studies on NbPDS1 and VdPDA1 demonstrate that Surf2Spot accurately recovers experimentally validated hotspots clustered within functional domains. When incorporated into binder design pipelines (RFdiffusion and BindCraft), Surf2Spot-guided designs yielded a 4-fold increase in successful design throughput and enhanced binding affinities compared to baseline strategies. These results establish Surf2Spot as a powerful tool for hotspot discovery and rational protein engineering.

bioinformatics↗

bioRxiv2026

Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant Acinetobacter baumannii

Antimicrobial-resistant pathogens pose an existential threat to modern medicine, yet the evolutionary forces driving their adaptation in healthcare systems remain largely unexplored. We revealed that hospital network architecture functions as a primary selective pressure, driving pathogen evolution through infrastructure-dependent virulence-transmission trade-offs. Phylogenomic analysis of 5,023 Acinetobacter baumannii isolates across Chinas centralized healthcare system identifies two co-existing evolutionary strategies: a virulence-optimized clade (ESL2.4) that spread slowly (20.4 km per year) in low-connectivity hospitals, and a transmission-optimized clade (ESL2.5) that disseminate rapidly (65.2 km per year) through mega-city healthcare hubs, likely attributed to its capsule conversion and increased upper respiratory colonization. Comparative analysis with European A. baumannii populations demonstrates that healthcare connectivity, not geography, governs pathogen distribution through convergent genomic adaptations. Our simulation suggests competitive asymmetries of the two clades, following the ecotype principle and enabling stable coexistence. The COVID-19 pandemic provided a natural experiment validating these mechanisms: outpatient restrictions reduced transmission-optimized lineage spread by 89%, while virulence-optimized lineage persisted through inpatient networks. These findings establish healthcare infrastructure as a critical evolutionary driver with immediate implications for predicting and controlling antimicrobial resistance emergence across diverse healthcare systems.

microbiology↗

bioRxiv2025

Critical phenomenon underlies de novo luminogenesis during mammalian follicle development

A key process during mammalian folliculogenesis is the formation of a fluid-filled antrum around the oocyte. While it is known that the antrum is critical for oocyte maturation and the eventual ovulation, the detailed process underlying de novo luminogenesis remains poorly understood. In this study, we investigated the spatiotemporal dynamics of lumen growth and the cellular mechanism driving this process, using advanced microscopy, molecular perturbations and computational modelling. We found that in secondary follicles, the interstitial gaps exist in a near-critical regime, characterised by a highly dynamic and interconnected fluid network with gap size obeying a power-law distribution. Above a critical size of 180 m, we observed an onset of cell death and the emergence of a stably growing dominant fluid cavity resembling phase separation. By modelling the granulosa cells and the interstitial fluid as a binary fluid, we reproduced the near-critical and phase-separated regimes and found that a spatial gradient of cell-fluid interfacial tension, as observed experimentally, is sufficient to robustly maintain the secondary follicles in a near-critical state. Reducing cell-fluid interfacial tension globally by weakening the cell-cell adhesion between granulosa cells leads to fragmentation of fluid and growth arrest of the dominant cavity, as predicted by the model. Importantly, perturbing the critical state in secondary follicles leads to impaired follicle growth. Altogether, our study reveals how collective spatiotemporal regulation of cell junction mechanics and cell death can contribute to the effective transition between distinct regimes of fluids, which are indispensable for functional maturation of follicles.

developmental biology↗

bioRxiv2025

Distinct Bomanins at the Drosophila 55C locus function in resistance and resilience to infections

Host defense against many Gram-positive bacteria and fungal pathogens is mainly provided by the Toll-dependent systemic immune response in Drosophila. While antimicrobial peptides active against these categories of pathogens contribute only modestly to protection, Bomanin peptides are major effectors of the Toll pathway. Remarkably, flies deleted for the 55C locus that contains 10 Bomanin genes are as sensitive as Toll pathway mutant flies to these infections. Yet, the exact functions of single Bomanins in resistance or resilience to infections remain poorly characterized. Here, we have extensively studied the role of these Bomanin genes. BomT1 functions in resistance to Enterococcus faecalis while playing a role in resilience against Metarhizium robertsii infection, like BomS2. BomT1 and BomT2 prevent the dissemination of Candida albicans throughout the host, even though they are not sufficient to confer protection to immunodeficient flies against this pathogen in survival experiments. Furthermore, BomT1 and BomBc1 mutants are sensitive to an Aspergillus fumigatus ribotoxin. We conclude that 55C Bomanins have defined albeit sometimes overlapping roles in the different facets of host defense against infections.

immunology↗

bioRxiv2025

Stress anisotropy in 3D active curved structures

Layers composed of lateral connections prevail in biological systems from subcellular membranes to epithelial sheets. This work presents a continuum framework to describe the effects of mechanical forces within a 3D curved layer with supporting lateral mesh. We provide detailed discussion on the emergence of stress anisotropy as a function of depth in different curvature settings, building on Lou et al. Phys. Rev. Lett. 130, 108401 (2023). We principally consider an epithelial monolayer to explain how the interplay between layer curvature and cell mechanics determines the stress anisotropy. We show that this can lead to irregular cellular shapes in 3D, including scutoid-like geometries. Our framework is general, and can be extended to a diverse set of biologically relevant systems.

biophysics↗

bioRxiv2024

CD24-Fc resolves inflammation and rescues CD8 T cells with polyfunctionality during HIV-1 infection under cART

The persistence of HIV-1 reservoirs during combination anti-retroviral therapy (cART) leads to chronic immune activation and systemic inflammation in people with HIV (PWH), associating with a suboptimal immune reconstitution as well as an increased risk of non-AIDS events. This highlights the needs to develop novel therapy for HIV-1 related diseases in PWH. In this study, we assessed the therapeutic effect of CD24-Fc, a fusion protein with anti-inflammatory properties that interacts with danger-associated molecular patterns (DAMPs) and siglec-10, in chronic HIV-1 infection model using humanized mice undergoing suppressive cART. Our findings show that CD24-Fc treatment significantly reduced inflammation and immune hyperactivation in vivo when combined with cART. CD24-Fc mediated resolution of inflammation was associated with improved recovery of CD4 T cells, reduced immune activation, restored central memory T cells and reversal of immune cell exhaustion phenotype. Notably, CD24-Fc treatment rescued CXCR5+ CD8 central memory T cell (TCM) which correlated with increased polyfunctionality in HIV-specific T cells in humanized mice and in cultured peripheral blood mononuclear cells (PBMCs) from PWH. This restoration of CXCR5+ memory CD8 T cells was associated with HIV replication inhibition, delayed viral rebound and reduced HIV-1 pathogenesis upon cART cessation. This study suggests that CD24-Fc treatment could represent a promising new therapeutic strategy for managing chronic systemic inflammation and associated diseases in PWH. Author summaryCombination antiretroviral therapy (cART) cannot block viral gene expression from activated HIV proviral DNA in reservoir cells, contributing to chronic immune activation and inflammation associated diseases in people with HIV (PWH). The therapeutic treatment of anti-inflammatory fusion protein CD24-Fc in humanized mice during suppressive cART (i) resolves inflammation and chronic HIV-1 immune pathogenesis during suppressive cART, (ii) rescues CXCR5-expressing CD8 memory T cells and enhances antiviral response in humanized mice and PWH PBMCs, (iii) delays virus rebound and reduces viral pathogenesis after cART cessation. Thus, CD24-Fc could provide a novel therapeutic strategy for treating chronic systemic inflammation and associated diseases in PWH.

immunology↗

bioRxiv2024

Prevalence of Problematic Papers in Non-Coding RNA Research

This study examines the prevalence of problematic papers in the rapidly growing field of non-coding RNA (ncRNA) research. Analysis of 153,826 ncRNA papers during 2000-2023 reveals that around 1.79% have been retracted and an additional 5.68% have raised concerns on PubPeer. The number of problematic papers has steadily increased, peaking in 2019 when the concerning and retraction rates reached nearly 10.8% and 3.7%, respectively. These unreliable papers have been widely disseminated, accumulating hundreds of thousands of citations in academic literature, patents, clinical trials, and policy documents, posing a significant threat to research integrity and public health. The main issues identified include image manipulation, data falsification, fake peer reviews, and ethical lapses. The findings call for urgent, comprehensive scrutiny of ncRNA publications and broader reforms to address systemic problems driving the proliferation of problematic research.

molecular biology↗

bioRxiv2024

Borrelia burgdorferi Secretes c-di-AMP as an Extracellular Pathogen-Associated Molecular Pattern to Elicit Type I Interferon Responses in Mammalian Hosts

Borrelia burgdorferi (B. burgdorferi), an extracellular spirochetal pathogen, elicits a type-I interferon (IFN-I) response that contributes to the pathology of Lyme disease, including the development and severity of Lyme arthritis. However, the specific Pathogen-Associated Molecular Patterns (PAMPs) of B. burgdorferi responsible for triggering the IFN-I response are not well understood. Previous studies have identified an unknown, nuclease-resistant component in B. burgdorferi culture supernatants that significantly stimulates the IFN-I response, but its identity remains unknown. In this study, we reveal that B. burgdorferi secretes cyclic-di-adenosine monophosphate (c-di-AMP) as a key extracellular PAMP, inducing the host IFN-I response in macrophages. Using genetically manipulated B. burgdorferi strains, we demonstrate a requirement of c-di-AMP for stimulating IFN-I response by macrophages ex vivo. Additionally, infecting mice with B. burgdorferi alongside exogenous c-di-AMP resulted in a markedly increased IFN-I response in mouse tissues. Furthermore, inactivation or inhibition of the host STING signaling pathway significantly reduced the IFN-I response, indicating that c-di-AMP-induced IFN-I production is STING-dependent. Our findings identify c-di-AMP as a crucial PAMP secreted by B. burgdorferi to elicit the host IFN-I response via activation of STING signaling pathway, suggesting that targeting c-di-AMP production could represent a novel therapeutic strategy against Lyme arthritis. SUMMARYBorrelia burgdorferi, the bacteria that causes Lyme disease, induces a robust host immune response, including the production of type-I interferon (IFN-I). While this response helps combat the infection, it also contributes to complications such as Lyme arthritis. Our research aimed to identify the specific bacterial component that triggers the IFN-I response. We discovered that Borrelia burgdorferi releases a second messenger molecule, cyclic-di-adenosine monophosphate (c-di-AMP), which is recognized by host immune cells and subsequently triggers IFN-I production. This finding is significant as it advances our understanding of Lyme disease pathogenesis and offers a new strategy to tackle Lyme disease by targeting the production of c-di-AMP, in which we may be able to reduce the severity of the disease and mitigate long-term tissue damage. One sentence summaryBorrelia burgdorferi c-di-AMP induces Type I IFN response

immunology↗

bioRxiv2024

Theca cell mechanics and tissue pressure regulate mammalian ovarian folliculogenesis

The maturation of functional eggs within the ovaries is essential for successful reproduction and organismal functions in mammals. Yet, despite its biological and clinical importance, the underlying mechanisms regulating folliculogenesis remain enigmatic. Here, we report a novel role of the surface-anchoring theca cells (TCs) in regulating follicle growth through mechanical signalling. Direct mechanical measurements reveal that these TCs are highly contractile and exert compressive stress to the follicular interior, potentially through active assembly of fibronectin scaffold around the follicles. Abolishing TC contractility disrupts fibronectin assembly, increases follicle size, and decreases intrafollicular pressure and viscosity. We further reveal that the granulosa cells (GCs) within the follicles exhibit spatial patterns of YAP signalling and proliferation, which appear to be decoupled. Transient manipulation of tissue pressure through bulk follicle compression, laser ablation or pharmacological perturbation of TC contractility leads to changes in GC YAP signalling, proliferation, and oocyte-GC communications, while long term abrogation of TC contractility leads to impaired follicle growth. Altogether, our study unveils the unique role of TC-mediated tissue pressure in ensuring robust mammalian ovarian folliculogenesis.

developmental biology↗

bioRxiv2024

Advancing CAR T-Cell Therapy: Simultaneously Attack Tumor and Immunosuppressive Cells in the Tumor Microenvironment

Chimeric antigen receptor (CAR) T-cell therapy has encountered limited success in solid tumors. The lack of dependable antigens and the immunosuppressive tumor microenvironment (TME) are major challenges. Within the TME, tumor cells along with immunosuppressive cells employ an immune-evasion mechanism that upregulates programmed death ligand 1 (PD-L1) to deactivate effector T cells; this makes PD-L1 a reliable, universal target for solid tumors. We developed a novel PD-L1 CAR (MC9999) using our humanized anti-PD-L1 monoclonal antibody, designed to simultaneously target tumor and immunosuppressive cells. The antigen-specific antitumor effects of MC9999 CAR T-cells were observed consistently across four solid tumor models: breast cancer, lung cancer, melanoma, and glioblastoma multiforme (GBM). Notably, intravenous administration of MC9999 CAR T-cells eradicated intracranially established LN229 GBM tumors, suggesting penetration of the blood-brain barrier. The proof-of-concept data demonstrate the cytolytic effect of MC9999 CAR T-cells against immunosuppressive cells, including microglia HMC3 cells and M2 macrophages. Furthermore, MC9999 CAR T-cells elicited cytotoxicity against primary tumor-associated macrophages within GBM tumors. The concept of targeting both tumor and immunosuppressive cells with MC9999 was further validated using CAR T-cells derived from cancer patients. These findings establish MC9999 as a foundation for the development of effective CAR T-cell therapies against solid tumors.

cancer biology↗

bioRxiv2023

In vitro antimicrobial mechanism of diacerein and potential to reverse MRSE resistance to β-lactams

Staphylococcus epidermidis is the most common pathogens causing ocular infection. With the increase of drug resistance rate, it poses a new challenge to anti-infection treatment. In this study, we analyzed the drug resistance of S. epidermidis isolated from the eye in the past 5 years to guide empirical antibiotics treatment. Then, the MIC and MBC of diacerein against MRSE were detected, and continuous induced resistance experiments confirmed that MRSE not easily induce resistance to diacerein. In addition, it was observed that diacerein induced MRSE cell lysis, increased membrane permeability and resulted in intracellular ROS accumulation. Diacerein does not have toxic effects to HCEC at effective bacteriostatic concentrations. The results of checkerboard assay indicated that the combination of diacerein and {beta}-lactams had additive effect on MRSE. We also observed that diacerein may reverse MRSE resistance to {beta}-lactam drugs by affecting the active efflux system. In conclusion, our results provide strong evidence for the high therapeutic potential of diacerein against MRSE.

microbiology↗

bioRxiv2023

TIPE drives a cancer stem-like phenotype by promoting glycolysis via PKM2/HIF-1alpha axis in melanoma

TIPE (TNFAIP8) has been identified as an oncogene and participates in tumor biology. However, how its role in the metabolism of tumor cells during melanoma development remains unclear. Here, we demonstrated that TIPE promoted glycolysis by interacting with pyruvate kinase M2 (PKM2) in melanoma. We found that TIPE induced PKM2 dimerization, thereby facilitating its translocation from the cytoplasm to the nucleus. TIPE-mediated PKM2 dimerization consequently promoted HIF-1 activation and glycolysis, which contributed to melanoma progression and increased its stemness features. Notably, TIPE specifically phosphorylated PKM2 at Ser 37 in an ERK-dependent manner. Consistently, the expression of TIPE was positively correlated with the levels of PKM2 Ser37 phosphorylation and cancer stem cell markers in melanoma tissues from clinical samples and tumor bearing mice. In summary, our findings indicate that the TIPE/PKM2/HIF-1 signaling pathway plays a pivotal role in promoting cancer stem cell properties by facilitating the glycolysis, which would provide a promising therapeutic target for melanoma intervention.

cancer biology↗

bioRxiv2023

Co-evolution of spheroid fluidization and mechanical fracture in a morphogenic cascade

Cells migrate and invade tissues during development, immune responses, and cancer. Collective invasion is generally understood to be driven by invading cells unjamming and pushing through barriers such as the extracellular matrix and surrounding tissues. Whether these barriers actively contribute to invasion remains unclear. Using ovarian adenocarcinoma spheroids invading mesothelium derived from benign pleural effusions as an experimental model, combined with modelling, we examine invasion across molecular to multicellular scales. We identify intercellular integrin adhesions linking invasive leader cells to the tissue barrier, triggering apical constrictions within the barrier. This constriction shrinks cell-cell contacts, leading to barrier rupture. Thus, the tissue barrier plays a mechanically active role in invasion. Rather than cells pushing through, we find that coordinated subcellular contractility between the invading leader cell and the barrier drives barrier tensile rupture and invasion, independent of a jamming transition. Together, our findings challenge prevailing paradigms of collective cell invasion.

cell biology↗

bioRxiv2022

Mechanism of repression of the glycerol utilization operon in Borrelia burgdorferi

Lyme disease pathogen Borrelia burgdorferi, switches carbohydrate utilization while transmitting between two disparate hosts, an Ixodes tick vector and a mammalian host. The ability to use glycerol is important for B. burgdorferi to colonize and persist in the tick vector, and expression of the glpFKD (glp) operon for glycerol uptake/utilization is tightly regulated during the enzootic cycle of B. burgdorferi between ticks and mammals. In present study, we identified a cis element within the 5 untranslated region of glp that negatively regulates the glp expression. This repression of glp is independent of RpoS. We further show that BadR directly binds to this cis element and represses glp. The efficiency of BadR binding in the presence of c-di-GMP and various carbohydrates were also assessed. This finding, along with previous findings of positive regulation of glp expression by the c-di-GMP signaling pathway and negative regulation by the alternative sigma factor RpoS, demonstrates that B. burgdorferi employs multi-layer regulatory mechanisms to coordinate glp expression during its enzootic cycle.

microbiology↗