Biology subjects

Cheng, J.-X.

Publications and source records attributed to Cheng, J.-X..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-kingdom microbial diversity and interaction landscapes in mosquitoes revealed by 5,163 individual meta-transcriptomes

Mosquitoes are pathogen vectors embedded within diverse microbial ecosystems. However, the nature and interactions among their multi-kingdom microbiome remain poorly understood. We conducted a nationwide single-mosquito meta-transcriptomic survey of 5,163 mosquitoes representing 100 species across China, integrating viral discovery with marker-gene profiling of bacteria, archaea, fungi, and other eukaryotic microbes. From this, we identified 1,606 microbial species-level taxa, including extensive novel diversity, and revealed pronounced host species-specific organization of mosquito-associated communities. We detected 34 pathogens or potential pathogens of human or animal relevance, whose prevalence, abundance, host range, and geographic distribution defined distinct epidemiological patterns. Network analysis uncovered pervasive cross-kingdom microbial associations, including candidate antiviral relationships involving Wolbachia and other microbial taxa. Our study establishes a detailed view of the full-spectrum microbiome and provides a resource and conceptual framework for studying vector competence, pathogen emergence, and microbiome-informed mosquito-borne disease control.

microbiology↗

bioRxiv2026

Blood-Mediated Opto-Acoustic Stimulation of Brain Cortex at Sub-millimeter Precision

Direct modulation of neural activity with high spatiotemporal precision is a cornerstone in experimental neuroscience. Here, we present a blood-mediated optoacoustic stimulation (BOAS) approach that utilizes blood as an endogenous transducer for brain stimulation. By delivering 532-nm nanosecond pulsed laser to the cortex, we demonstrate that the absorption of hemoglobin generates sufficient acoustic pressure to trigger neuronal activity. By integrating BOAS with calcium imaging in GCaMP6f-expressing mice, localized neuronal responses were observed. Quantitative analysis reveals that BOAS produces responses comparable to natural visual stimulation and is significantly more efficient than the photothermal stimulation. Furthermore, we show that the response is dose-dependent. At high energy doses, BOAS induces cortical spreading depression. Histological evaluation confirmed that the brain maintains tissue integrity even under these stimulation parameters. Together, this work establishes a versatile method for precise brain stimulation as an alternative method for stimulating neuron at cortex.

bioengineering↗

bioRxiv2026

Distinguishing Photoacoustic and Photothermal Neuron Stimulation Through Quantitative Mapping Spatiotemporal Field Evolution

Neuromodulation is a rapidly advancing strategy for modulating brain function and treating neurological disorders, yet the mechanisms of optical neural stimulation remain incompletely understood. A central challenge is that photoacoustic (PA) and photothermal (PT) effects are typically generated simultaneously and evolve on overlapping spatial and temporal scales, making their contributions to neuronal activation difficult to distinguish. Here, we overcome this limitation by integrating two carbon-based emitters with a spatial-offset pump-probe imaging platform to distinguish PA and PT neuromodulation through direct mapping of spatiotemporal field evolution. The two emitters produce nearly identical thermal fields while exhibiting a 26-fold difference in acoustic output, enabling decoupled comparison of thermal and acoustic contributions. To directly characterize the physical fields, we establish a spatial-offset pump-probe imaging system capable of visualizing both temperature and pressure evolution, confirming matched thermal profiles between the two emitters. Neuronal stimulation experiments further show that neurons are markedly more responsive to PA stimulation than to PT stimulation. Beyond resolving a longstanding mechanistic question, this work demonstrates the enhanced efficiency of PA stimulation and provides general guidance for designing high-performance optical neural interfaces.

neuroscience↗

bioRxiv2026

SPEND-hSRS imaging of fumarate uncovers mitochondrial metabolic heterogeneity

Mitochondria, acting as the energy powerhouse, biosynthetic center, and reductive equivalent hub of the cell, participate in cellular metabolic activities. However directly imaging mitochondrial chemical content and quantifying metabolic activity in living cells remain challenging. Here, by Self-PErmutation Noise2noise Denoiser enhanced Hyperspectral Stimulated Raman Scattering (SPEND-hSRS) microscopy, we demonstrate fingerprint-region metabolic imaging of fumarate, a key intermediate in the tricarboxylic acid (TCA) cycle, with sub-millimolar sensitivity. In chemotherapy-stressed bladder cancer cells, fumarate imaging revealed two mitochondrial subpopulations with divergent TCA metabolic preferences quantified by ratio metric analysis. Pixel-wise least absolute shrinkage and selection operator (LASSO) spectral unmixing further reconstructs fumarate and lipid maps, uncovering localized fumarate enrichment in protrusions. Extending to CH-window hyperspectral SRS imaging, we uncover the interplay between mitochondria and lipid droplets (LDs) in protrusions, where fatty acid is found to be released from LDs, to fuel the TCA cycle. Together, our work establishes SPEND-hSRS as high-resolution platform for linking fumarate to mitochondrial heterogeneity. Our results provide new insights into how mitochondrial heterogeneity and interaction with LDs drive cancer cell adaptation to stress.

cancer biology↗

bioRxiv2026

IR-AMES uncovers structure and composition of Alzheimer' s tau oligomers

The structure and composition of biomolecular assemblies shape their biological functions and disease processes. Yet existing approaches either require homogeneous samples or lack chemical specificity and sensitivity, limiting the elucidation of transient oligomeric species under native conditions. Here we report infrared absorbance-modulated evanescent scattering (IR-AMES) that enables ultrasensitive structural and compositional profiling of individual biomolecular assemblies in aqueous environments. This capability is achieved by photothermally encoding mid-infrared vibrational absorption into scattering contrast using a total-internal-reflection geometry. Applying IR-AMES to recombinant tau assemblies, we resolve random-coil monomers and the emergence of heterogeneous oligomers beyond ensemble-averaged measurements. In Alzheimer's disease brain-derived tau, IR-AMES reveals enrichment of antiparallel {beta}-sheet structures and RNA components in oligomers. Using lipid nanodiscs as membrane mimics, we find that pathological tau oligomers exhibit enhanced interactions with anionic membranes. IR-AMES enables spectroscopic imaging of diverse biomolecular assemblies, opening opportunities to elucidate structure-function relationships in heterogeneous biomolecular systems.

biophysics↗

bioRxiv2025

Early blood-spinal cord barrier stabilization preserves peri-lesional tissue and improves recovery after SCI

Vascular disruption is an early and critical event in spinal cord injury (SCI), but its contribution remains poorly understood. Using novel in vivo two-photon dual-dye imaging, we found simultaneous blood-spinal cord barrier (BSCB) leakage and venous dilation in both the injury epicenter and adjacent transitional segment after cervical SCI in rats. Notably, vascular permeability in the transitional zone preceded axonal and neuronal loss, revealing a therapeutic window. Systemic delivery of ferulic acid-glycol chitosan (FA-GC) nanoparticles, a membrane-sealant, rapidly stabilized the compromised vasculature, reduced neuronal loss in the transitional region, and improved forelimb muscle strength. These findings identified acute vascular leakage beyond the injury epicenter as a driver of secondary pathology and highlight early vascular stabilization as promising therapeutic strategy.

pathology↗

bioRxiv2025

Mid-Infrared Photothermal Mesoscopy with Millimeter Field of View and Sub-micron Spatial Resolution

By optically sensing mid-infrared absorption through a visible probe beam, mid-infrared photothermal (MIP) microscopy has emerged as a powerful tool for chemical imaging with micromolar sensitivity and submicron spatial resolution. The adoption of spatially multiplexed camera-based widefield detection further enhanced the imaging speed. However, current widefield MIP systems suffer from a small field of view (FOV)--typically tens of square micrometers, which constrains their utility in large-area tissue imaging applications. Here, we report a laser-scan MIP mesoscope that achieves millimeter-scale FOV while preserving submicron resolution. By leveraging an all-reflective laser scanning architecture, low-magnification and medium numerical-aperture objectives, and a defocused signal collection scheme, our MIP mesoscope achieves a 1.2 x 1.2 mm2 FOV, 650 nm lateral resolution, and microsecond-scale pixel dwell time. In vivo chemical imaging of whole Caenorhabditis elegans and high-throughput detection of beta-amyloids in both mouse and human brain tissues associated with Alzheimers disease are demonstrated.

bioengineering↗

bioRxiv2025

Genome-wide CRISPR screen reveals Wnt signaling defects regulate lipid accumulation in APOE4 oligodendrocytes

APOE4 is the largest genetic risk factor for late-onset Alzheimers disease, but the cellular mechanisms by which APOE variants influence risk of disease remain incompletely understood. We have previously found that APOE4 expression led to the intracellular accumulation of lipid droplets in oligodendrocytes, causing decreased myelination. However, the mechanisms by which APOE4 alters lipid metabolism are not fully understood. Here, we leveraged a genome-wide CRISPR screen and ATAC-sequencing in human induced pluripotent stem cell (iPSC)-derived oligodendrocytes to dissect APOE4s lipid-associated mechanisms of action. Using these approaches, we identified decreased Wnt signaling, and overactive GSK3b activity, as regulators of lipid droplet accumulation in oligodendrocytes. Genetic and pharmacological inhibition of GSK3b reduced lipid droplets in APOE4 oligodendrocytes, and increased myelination in three-dimensional iPSC-derived brain organoids. Finally, we show that pharmacological inhibition of GSK3b reduces lipid droplets and improves myelination in APOE4;PS19 Tau transgenic mice. Together, our results provide a framework for understanding the mediation of APOE4-related changes to oligodendrocyte lipid metabolism and myelination.

neuroscience↗

bioRxiv2025

Cholesterol metabolism modulation facilitates CAR-T induced killing of ovarian cancer

Ovarian cancer is one of the most lethal gynecological cancers worldwide and has one of the highest recurrence rates. Recently developed Chimeric Antigen Receptor T (CAR-T) cell therapy has shown potent clinical efficacy against hematological malignancies. However, solid tumors, including ovarian cancer, possess several mechanisms that hinder T cell activity, and metabolic alteration of cancer cells has been shown to contribute to resistance to immune cell attack against solid tumors. Here, we explored the metabolic response of ovarian cancer cells to CAR-T cell attack using label-free high-content hyperspectral stimulated Raman scattering (h2SRS) imaging. Utilizing visible h2SRS imaging with much improved spatial resolution, we found an altered cholesterol metabolism, featured by increased storage of cholesteryl ester in lipid droplets and free cholesterol, in ovarian cancer cells that survived the CAR-T treatment. Administration of Avasimibe, an inhibitor of cholesteryl esterification, further enhanced CAR-T cytotoxicity. Our study shows the promise of implementing metabolic modulation to facilitate CAR-T cell treatment of solid tumors. Significance StatementOvarian cancer is a major global health challenge, mainly due to relapse driven by chemotherapy resistance development. Meanwhile, immunotherapies such as CAR-T have revolutionized treatment for blood cancers, but their application in solid tumors like ovarian cancer is hindered by limited efficacy. This study uses high-content stimulated Raman scattering (SRS) imaging to reveal metabolic adaptations that help ovarian cancer cells survive CAR-T-mediated cytotoxicity. Guided by these insights, we apply metabolic interventions that enhance CAR-T cytotoxicity efficacy. This approach reveals therapeutic vulnerabilities in ovarian cancer and demonstrates an investigative strategy applicable for overcoming resistance in solid tumors.

cell biology↗

bioRxiv2025

Mid-Infrared Photothermal Imaging of Fatty Acid Desaturation Reaction in Cancer Cells

Direct visualization of metabolic conversions within living systems is essential for understanding metabolic activities yet challenging due to the absence of reaction-specific reporters and the limited sensitivity of current imaging modalities. Herein, we report an approach to monitor fatty acids (FAs) desaturation, primarily catalyzed by stearoyl-CoA desaturase, in cancer cells using deuterium (D)-labeled palmitic acid (PA-d31) as the reaction-specific reporter and mid-infrared photothermal (MIP) microscopy as the bond-selective imaging modality. The desaturation of PA-d31 produced a peak at 2246 cm-1 in the cell-silent region, corresponding to the stretching vibration of unsaturated C-D bonds (D-C=C-D) in unsaturated fatty acids. Penalized least squares fitting was employed to remove water background for enhancing the visibility of this peak. Our study revealed heterogeneous spatial distributions of both saturated FAs and their desaturated metabolites within lipid droplet pools in cancer cells. Furthermore, we observed an increase in fatty acid unsaturation level in OVCAR5 cells under cisplatin-induced stress. By directly visualizing fatty acid desaturation, this study offers new insights into fatty acid metabolism and opens avenues for evaluating new therapeutic strategies targeting fatty acid metabolism.

biochemistry↗

bioRxiv2025

Highly reproduceable tapered fiber optoacoustic emitters by in-situ photothermal curing of PDMS for single neuron stimulation

Precise neural modulation is an important tool in neuroscience research for intervene of specific neural pathways. Photoacoustic is an emerging technology enabling high precision non-genetic neural stimulation in vitro and in vivo. In this paper, we report a new method to prepare a Candle Soot - Tapered Fiber based Optoacoustic Emitter (CSTFOE) through an in-situ photothermal curing process. The emitter created was found with high spatial resolution and efficiency for neuromodulation. In the meanwhile, the in-situ photothermal curing procedure is highly reproducible and allows for fabricating the photoacoustic coating on the tiny tip of the tapered fiber with a diameter less than 20 m. With the high efficiency and reproducibility, we designed an integrated photoacoustic neuromodulation system incorporating the CSTFOE, a nanosecond pulsed laser for photoacoustic generation, and a function generator for synchronization, achieving effective neuromodulation in vitro.

neuroscience↗

bioRxiv2025

Bi-modal microwave neuromodulation via thermal and nonthermal mechanisms

Electrical neuromodulation, the current clinical standard, is invasive, expensive, and prone to malfunction. Electromagnetic waves can perform noninvasive neuromodulation, but existing methods are limited by the tradeoff between penetration depth and spatial precision. Microwaves in the 0.9 - 3 GHz range are widely used for telecommunications and can penetrate to the deep brain. Microwaves have been shown to nonthermally modulate neural activity, but the acute bioeffects remain unclear and under-studied. Here, we employ a microwave rod antenna (MRA) to demonstrate bi-modal neuromodulation via thermal and non-thermal mechanisms. The MRA enabled electrophysiological recordings of neurons exposed to microwaves, which elucidated the differential effects of pulsed and continuous microwaves on neurons. These findings build the foundation for developing microwave-based wireless neuromodulation devices for drug-free treatment of seizures and chronic pain.

neuroscience↗

bioRxiv2024

Ultrasensitive in vivo infrared spectroscopic imaging via oblique photothermal microscopy

In vivo IR spectroscopy faces challenges due to poor sensitivity in reflection mode and low resolution at micrometer scale. To break this barrier, we report an oblique photothermal microscope (OPTM) to enable ultrasensitive IR spectroscopic imaging of live subjects at sub-micron resolution. Classic photothermal measurement captures only a small fraction of probe photons through a pinhole to extract the photothermal signal. Instead, OPTM uses a differential split detector placed on the sample surface to collect 500-fold more photons and suppress the laser noise by 12 fold via balanced detection. Leveraging its improved sensitivity, OPTM enables low-dose IR imaging of skin without photodamage. Depth-resolved in vivo OPTM imaging of metabolic markers beneath mouse and human skin is shown. Furthermore, we demonstrate in vivo OPTM tracking of topical drug contents within mouse and human skin. Collectively, OPTM presents a highly sensitive imaging platform for in vivo and in situ molecular analysis.

bioengineering↗

bioRxiv2024

A flexible high-precision photoacoustic retinal prosthesis

Retinal degenerative diseases of photoreceptors are a leading cause of blindness with no effective treatment. Retinal prostheses aim to restore sight by stimulating residual retinal cells. Here, we present a photoacoustic retinal stimulation technology. We designed a polydimethylsiloxane and carbon-based flexible film that converts near-infrared laser pulses into a localized acoustic field with 56-{micro}m lateral resolution, allowing precise stimulation of mechanosensitive retinal cells. This photoacoustic stimulation robustly and locally modulated retinal ganglion cell activity in both wild-type and degenerated ex vivo rat retinae. In animals subretinally implanted with a millimeter-sized photoacoustic film, pulsed laser stimulation generated neural modulation along the visual pathway to the superior colliculus, as measured by functional ultrasound imaging. The biosafety of the film was confirmed by the absence of short-term adverse effects , while local thermal increases were measured below 1 {degrees}C. These findings demonstrate the potential of photoacoustic stimulation for high-acuity visual restoration in blind patients.

neuroscience↗

bioRxiv2024

Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe

Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.

cell biology↗

bioRxiv2024

High-precision photoacoustic neural modulation uses a non-thermal mechanism

Neuromodulation is a powerful tool for fundamental studies in neuroscience and potential treatments of neurological disorders. Both photoacoustic (PA) and photothermal (PT) effects have been harnessed for non-genetic high-precision neural stimulation. Using a fiber-based device excitable by a nanosecond pulsed laser and a continuous wave laser for PA and PT stimulation, respectively, we systematically investigated PA and PT neuromodulation at single neuron level. Our results show that the laser energy needed for PA neurostimulaion is 1/40 of that needed for PT stimulation to achieve the same level of cell response recorded by Ca2+ imaging. The threshold energy for PA stimulation is found to be further reduced in neurons overexpressing mechano-sensitive channels, indicating the direct involvement of mechano-sensitive channels in PA stimulation. Electrophysiology study of single neurons upon PA and PT stimulation was performed by patch clamp recordings. Electrophysiological features stimulated by PA are distinct from those induced by PT, confirming that PA and PT stimulations operate through distinct mechanisms. These insights offer a foundation for rational design of more efficient and safer non-genetic neural modulation approaches.

neuroscience↗

bioRxiv2023

The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration

Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.

microbiology↗

bioRxiv2023

High-throughput single-cell sorting by stimulated Raman-activated cell ejection

Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging, in situ image decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 m polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-rich Rhodotorula glutinis cells were successfully sorted from a mixture with Saccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine. Significance statementImage-guided single-cell sorting is a potent tool in diverse biological applications. Current microfluidic cell sorting methods encounter challenges in handling smaller cells and are not applicable to tissue sections. To address these challenges, we have developed a stimulated Raman-activated cell ejection (S-RACE) platform, which is the first demonstration of single-cell ejection coupled with coherent Raman scattering. S-RACE allows label-free chemical imaging guided cell sorting through multispectral stimulated Raman scattering (SRS) imaging, on-the-fly image analysis, and laser-induced cell ejection. Versatile applications of S-RACE to a wide range of samples, such as polymer particles, single-live bacteria, single-live fungus, and tissue sections, are demonstrated.

bioengineering↗