Biology subjects

Feng, J.

Publications and source records attributed to Feng, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Genomic Surveillance Reveals Global Spread of Macrolide-Resistant Bordetella pertussis Linked to Vaccine Changes

The resurgence of whooping cough in regions utilizing acellular pertussis vaccines underscopes emerging public health challenges. Here, we characterized 178 Bordetella pertussis isolates collected from patients across all age groups in Shanghai (2018-2024) to assess genomic evolution and antibiotic susceptibility. Macrolide resistance to erythromycin, azithromycin, clarithromycin and clindamycin escalated from [≤]50% (pre-2020) to nearly 100% (post-2020), mechanistically linked to the 23S rRNA A2047G mutation. Genome-based analysis identified a genotype MT28-ptxP3-MRBP rapidlly dominated post-2020, exhibiting significantly higher prevalence in adults versus than age groups. Phylogenetic analysis of 178 Shanghai and 1596 global genomes revealed two major lineages corresponding to ptxP1 and ptxP3 alleles. MT28-ptxP3-MRBP cluster was identified in France, Japan and the United States in 2024, indicating potential cross-border dissemination. These findings advocate for intergrated surveillance spanning all ages and international borders to contain the global spread of macrolide-resistant Bordetella pertussis. HighlightsO_LIAfter 2020, MT28-ptxP3-MRBP lineage rapidly dominated, comprising 61.7% of isolates. C_LIO_LIMT28-ptxP3-MRBP exhibits a significant transmission advantage among older individuals. C_LIO_LIThe primary affected group shifted from [≤]36 months (pre-2020) to 37 months-18 years (post-2020). C_LIO_LIMacrolide resistance rose from [≤]50% pre-2020 to nearly 100% post-2020, with all resistant isolates carrying the A2047G mutation. C_LI

microbiology↗

bioRxiv2025

Curcumin activates distinct programming of redox metabolism towards differential regulation of gene expression mediated by Nrf1 and Nrf2

AbstractionCurcumin (CUR), a naturally occurring phenolic small molecule, has been extensively applied in the treatment of diverse diseases for over half a century. Currently, this chemical has also been verified to exhibit a wide array of its biopharmacological activities, such as enhancing immunity, possessing antiviral, anti-cardiovascular, and anti-cancer properties. Besides, also as a nutritional supplement, CUR enables inflammatory prevention and enhance the combined efficacy of it with chemotherapy. Such characteristic of safeguarding normal organisms while treating or alleviating diseases is manifested as a common bidirectional regulation and its hormetin effect of phenolic compounds, particularly in response to stress. In this redox process, two antioxidant transcription factors Nrf1 and Nrf2 (encoded by Nfe2l1 and Nfe2l2, respectively) play distinct and crucial roles. Thereby, we investigated their expression profiles of genes regulated by Nrf1 and Nrf2 in different signaling responses modulated by CUR. The resulting evidence has been provided, demonstrating that distinctive cellular metabolisms, molecular pathways, and signaling mechanisms account for Nrf1 and Nrf2, as drug targets. Both factors also play diverse roles in the anticancer effects of CUR on HepG2 cells and xenograft mice. However, the effect of CUR on xenograft tumors in vivo is not entirely satisfactory, although such anti-cancer effect was achieved by promoting Nrf1 expression, it appeared more reliant on Nrf2 (particularly in the absence of Nrf1). As such, we unexpectedly discovered there is not a simple regulatory relationship between CUR and Nrf2. This is supported by substantial inhibition of Nrf2 by CUR in the aberrantly proliferating Nrf1-/- cells, even albeit this chemical stimulates the expression of Nrf1 and Nrf2 in wild-type cells.

cancer biology↗

bioRxiv2025

Myocyte Damage and Mass Loss Drives Increasing Water Content, Compliance, and Survival in Septic Cardiomyopathy

Introduction/PurposeDuring the septic cardiomyopathy, the mechanism and relationship to outcome of changes in left ventricular (LV) end diastolic volume (EDV) and ejection fraction (EF) remains obscure. We compared serial changes in LVEF and LVEDV to successive alterations in LV wall ultrastructure, water content, and total mass to investigate whether these measures can explain their basis. MethodsWe performed cardiac magnetic resonance imaging at 0,6,18,30,42,54, and 92h post-bacterial challenge in a large-animal model (n=57) that mimics human septic cardiomyopathy. LV tissue was obtained for electron microscopy (EM) upon death and 66h in sacrificed survivors. ResultsBetween 0-6h post-challenge, LV compliance and EDV reached its greatest decline. Non-survivors (n=18) exhibited significantly greater reductions in LVEDV, along with more myocyte edema, mitochondrial swelling and myofilament fragmentation on EM. This increased tissue damage may explain why non-survivors developed worse LV compliance and a greater decline in LVEDV, which persisted until death. From 6-30h, LVEDV significantly improved to baseline in non-survivors, while survivors experienced [~]20% increases (n=39). Concurrently, there was significant LV mass loss and increases in percent water content that were significantly associated with increases in LVEDV. This is consistent with a passive mechanism for rapidly improving LV compliance and EDV. Full recovery of EF required additional days. We hypothesize the prolonged significant mass loss over 5d reflects an active process for remodeling fragmented myofilaments, eliminating myocyte edema, and mitochondrial swelling, ultimately restoring contractile function. ConclusionThe septic cardiomyopathy constitutes a diffuse ultrastructural injury to myocytes with three phases. Initially, there is a decrease in LVEDV, and EF due to myocyte damage within 6h of bacterial challenge; next, the patient sees a passive LVEDV recovery from 6-30h, where LV mass loss increases relative wall percent water content, which facilitates wall compliance and LVEDV; and lastly, the patient sees mass loss beyond 30h consistent with an active repair mechanism of myocytes, returning systolic function to normal. Therefore, EDV changes are a pathophysiological biomarker for sepsis outcomes. A lower LVEDV indicates persistent unrepairable ultrastructure damage with worsening wall compliance and poorer outcomes. LVEDV dilation is a sign of near-full recovery of ultrastructure injury, augmenting wall compliance and improving outcomes. Clinical ImplicationsWe explain herein why septic cardiomyopathy findings dont have clinical implications like heart failure. Septic patients who exhibit signs of heart failure, low LVEF with high EDVs, are doing well - reflecting mild myocyte injury, effective damaged tissues clearance, increased relative LV wall water content, and compliance. This augments the LVEDV, lowering the LVEF. Septic patients who deteriorate rapidly, contrary to heart failure patients, show high/normal LVEF and low/normal LVEDV. Here, the myocyte damage is severe, leading to insufficient wall repair, and this decreased wall compliance persists, preventing the LV from dilating and making LVEDV low which ultimately raises the LVEF.

physiology↗

bioRxiv2025

Benchmarking fungal species classification using Oxford Nanopore Technologies long-read ITS metabarcodes

The gold standard for fungal classification has long been specimen or culture-based, however, many Fungi display simple morphological characteristics, or are unculturable by current methods. Using DNA metabarcodes, many taxa can be identified from a single sample simultaneously, but annotating these sequences with species-level taxonomy often requires more information than short-read sequences afford. Oxford Nanopore Technologies (ONT) long-read sequencing has achieved species-level resolution in metabarcoding of bacteria and invertebrates, but complex fungal taxonomy and biology has been a hurdle to the application of this technology for Fungi. In this work, we use a mock community of real ONT long-read metabarcodes from 54 fungi from the Dikarya subkingdom to extensively benchmark classification approaches to assign species-level taxonomy. We compare eight classification approaches spanning alignment and k-mer based algorithms, to emerging machine learning methods, and assess the sensitivity, precision, and diversity estimation of each classifier at the species level. Our results indicate that classifiers which determine informed thresholds of sequence similarity based on a provided reference database are not only more accurate at the species level, but more consistent to correct species abundance distributions, and better able to place sequences from unknown species taxonomically closer to their true origin. We demonstrate the power of machine learning classifiers to leverage long-read metabarcodes, and their promise as emerging methods in DNA sequence classification. We present our results in the context of real-world use cases, to demonstrate that species-level taxonomic inference is achievable, precise, and reliable with ONT long-read fungal metabarcodes.

molecular biology↗

bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

bioRxiv2025

Diffusion Neuroimaging of Speech Acquisition in Infants

How multisystem white-matter maturation supports early speech acquisition in infancy remains unclear. Using longitudinal diffusion MRI from the Baby Con-nectome Project, we quantified neurite density maturation from birth to 24 months across 33 white-matter tracts spanning motor, auditory, visual, ventral-language, and dorsal-language systems. Maturation was coordinated across systems rather than confined to canonical language pathways: dorsal-language association tracts began relatively immature near birth but showed steep postnatal growth, pro-gressively rebalancing with motor and sensory systems. Tract-behavior coupling was likewise distributed across developmental domains, with broadly positive age-adjusted associations for motor outcomes, a sparser, partly motor-like profile for gesture-related phrase comprehension, and predominantly negative associa-tions for lexical speech-related outcomes. Exploratory follow-up analyses further suggested motor and social precursor capacities that may help mediate these in-direct developmental routes from structural maturation to later speech-related outcomes. These findings support a multisystem developmental account in which early speech acquisition emerges not from an isolated language pathway, but from coordinated maturation across multiple systems and the precursor skills that link them.

neuroscience↗

bioRxiv2025

Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States

Pan-GSK3/{beta} inhibition promotes stem cell self-renewal through activation of WNT/{beta}-catenin signaling, but its broad effects complicate the precise control of stem cell states. Here, we show that selective inhibition of GSK3 with BRD0705 supports the long-term self-renewal of mouse embryonic stem cells (ESCs), epiblast stem cells (EpiSCs), and neural stem cells (NSCs), independent of {beta}-catenin signaling. When combined with the tankyrase inhibitor IWR1, BRD0705 broadly supports the maintenance of diverse pluripotent stem cell states, including ESCs, EpiSCs, and formative pluripotent stem cells. This BRD0705/IWR1 cocktail enables stable co-culture of naive ESCs and primed EpiSCs while preserving their distinct molecular and functional identities. Single-cell transcriptomics, epigenomic profiling, and functional assays confirm sustained lineage-specific features across stem cell types. These findings demonstrate that selective GSK3 inhibition enhances stemness by buffering against differentiation cues and promoting intrinsic self-renewal capacity. This work identifies GSK3 as a key regulator of self-renewal across distinct stem cell states and establishes a versatile culture system with broad applications. In BriefWang et al. demonstrate that selective GSK3 inhibition with BRD0705 supports self-renewal of pluripotent and neural stem cells. Combined with IWR1, it enables long-term co-culture of naive and primed stem cells while preserving their distinct molecular and functional identities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=181 HEIGHT=200 SRC="FIGDIR/small/653860v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@4e371eorg.highwire.dtl.DTLVardef@104b287org.highwire.dtl.DTLVardef@164bd96org.highwire.dtl.DTLVardef@daf1ba_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGSK3 inhibition by BRD0705 promotes self-renewal of ESCs, EpiSCs, and NSCs C_LIO_LIBRD0705/IWR1 enables long-term co-culture of ESCs and EpiSCs C_LIO_LICo-cultured ESCs and EpiSCs retain distinct naive or primed identities C_LIO_LIBRD0705 preserves stem cell states independently of {beta}-catenin signaling C_LI

cell biology↗

bioRxiv2025

Brain Diffusion Transformer for Personalized Neuroscience and Psychiatry

Task-fMRI analyses typically focus on localized activation contrasts between stimuli, neglecting the brains dynamic hierarchy. We introduce Brain Diffusion Transformer (Brain-DiT), a deep generative model capturing recurrent processing underlying individualized neurocognitive state transitions via functional networks. Without prior assumptions, Brain-DiT identifies canonical cognitive regions in the brain and reveals replicable subgroups with distinct neural circuits in large cohorts, offering critical clinical insights overlooked by traditional methods: individuals exhibiting negative emotion bias, linked to language-related regions, had a 12-fold higher likelihood of major depression, and those with maladaptive inhibition strategies, associated with overactive medial frontal regions, showed a 9-fold increased risk of alcohol abuse. By bridging cognitive theory and psychiatric applications, Brain-DiT provides a unified analytical paradigm, paving the way for operational personalized medicine in psychiatry.

neuroscience↗

bioRxiv2025

Silicon regulation of pectin methyl-esterification and cellulose microfibril organization modulates FERONIA-mediated cell wall integrity signaling for rice adaption to salt stress

The beneficial element silicon (Si) plays a crucial role in mitigating salt stress in plants and can activate intracellular signal transduction pathways that reprogram the transcriptome of salt-stressed plants. However, the mechanisms by which plants perceive Si nutrition, induce the expression of Si-responsive genes, and regulate the activity of Si-responsive proteins remain inadequately understood. In this study, we found that Si enhances cell wall integrity by increasing the degree of pectin methyl-esterification and changing the cellulose microfibril arrangement and functions as a regulatory switch for the activities of cell wall integrity sensors (FER homologs OsFLR1 and OsFLR2) during rice plant adaptation to high salinity. Furthermore, the inhibition of OsFLR1 and OsFLR2 through FER-specific inhibitors could negate the beneficial effects of Si and affect the uptake and accumulation of Si in rice seedlings. In conclusion, these findings suggest that Si signaling initiation involves FER-mediated cell wall integrity signaling pathways during salt stress adaptation in rice.

plant biology↗

bioRxiv2025

Sex-specific and age-related progression of auditory neurophysiological deficits in the Cln3 mouse model of Batten disease

CLN3 disease is a prevalent form of Neuronal Ceroid Lipofuscinosis (NCL) caused by inherited mutations in the CLN3 gene, with symptoms such as vision loss, language impairment, and cognitive decline. The early onset of visual deficits complicates neurological assessment of brain pathophysiology underlying cognitive decline, while the small number of CLN3 mutation cases in humans hinders the study of sex differences. Building on our recent progress in assessing auditory neurophysiological changes in CLN3 patients, we developed a parallel approach using electroencephalography arrays in Cln3 knockout (Cln3-/-) mice to investigate the longitudinal progression of auditory processing deficits in both sexes. We employed a duration mismatch negativity (MMN) paradigm, similar to that used in our CLN3 patient studies, to assess the automatic detection of pattern changes in a sequence of stimuli. Wild-type mice of both sexes showed robust duration MMN responses when assessed longitudinally in the same subjects from 3 to 9 months of age. In contrast, female Cln3-/- mice developed consistent MMN deficits throughout this age range, while male Cln3-/- mice exhibited MMN deficits at younger ages that were mitigated at older ages. Analyses of auditory brainstem responses indicate that MMN abnormalities in Cln3-/- mice are not due to peripheral hearing loss. Instead, these deficits originate centrally from sex-specific and age-related changes in auditory evoked potentials elicited by standard and deviant stimuli. Our findings reveal a sex-specific progression of central auditory processing deficits in Cln3-/- mice, supporting auditory duration MMN as a translational neurophysiological biomarker for mechanistic studies and therapeutic development. Significance StatementCLN3 disease is an inherited neurodegenerative disorder with progressive decline in cognitive functioning and verbal abilities. The neuropathophysiological mechanisms underlying this decline remain poorly understood, highlighting the urgent need for objective neurological biomarkers to advance mechanistic insights and therapeutic development. Our identification of central auditory processing and change detection deficits in Cln3-/- mice, mirroring findings from our recent studies in CLN3 patients, validates auditory MMN as a translational neurophysiological biomarker bridging pre-clinical and clinical research. Moreover, our discovery of sex-specific, non-linear progression of MMN deficits emphasizes the necessity of developing disease management strategies tailored to each sex. This finding also provides a foundation for investigating both pathogenic and compensatory neural mechanisms to inform the development of individualized treatments.

neuroscience↗

bioRxiv2025

Chimeric Collagen-like Proteins with Tunable Structural Heterogeneity for Precise Control and Targeted Doxorubicin Delivery

Protein-based drug delivery systems offer advantages such as genetic tunability, structural homogeneity, and high biocompatibility. However, precisely controlling the assembly of protein nanoparticles and establishing correlations between their macroscopic properties and molecular architecture remain significant challenges. Here, inspired by chimeric collagen-like proteins, we rationally designed a series of de novo chimeric proteins comprising an N-terminal globular domain fused to a linear collagen-like domain. These structurally heterogeneous proteins were conjugated with doxorubicin (DOX) and homogenized to form chimeric collagen-like protein-DOX nanocomplexes (CDCNs). By fine-tuning the protein structure and domain organization, we achieved precise control over CDCN architecture and drug release kinetics. Furthermore, to enhance tumor specificity, triple-negative breast cancer (TNBC)- and glioblastoma (GBM)-targeting peptides were genetically fused to the chimeric proteins, respectively. In both in vitro and in vivo models of TNBC and GBM, CDCNs facilitated selective tumor accumulation, enhanced cellular uptake, and promoted apoptosis while minimizing off-target toxicity. This work establishes a strategy for designing protein-based nanoplatforms with programmable structures and tunable functionalities, offering promising potential for precisely controlling of protein-based delivery system.

bioengineering↗

bioRxiv2025

Formaldehyde Exposure Induces Systemic Epigenetic Alterations in Histone Methylation and Acetylation

Formaldehyde (FA) is a pervasive environmental organic pollutant and a Group 1 human carcinogen. While FA has been implicated in various cancers, its genotoxic effects, including DNA damage and DNA-protein crosslinking, have proven insufficient to fully explain its role in carcinogenesis, suggesting the involvement of epigenetic mechanisms. Histone post-translational modifications (PTMs) on H3 and H4, critical for regulating gene expression, may contribute to FA-induced pathogenesis as lysine and arginine residues serve as targets for FA-protein adduct formation. This study aimed to elucidate the effects of FA on histone methylation and acetylation patterns. Human bronchial epithelial cells (BEAS-2B) were exposed to low-dose (100 M) and high-dose (500 M) FA for 1 hour, and their histone extracts were analyzed using high-resolution liquid chromatography-tandem mass spectrometry-based proteomics, followed by PTM-combined peptide analysis and single PTM site/type comparisons. We identified 40 peptides on histone H3 and 16 on histone H4 bearing epigenetic marks. Our findings revealed that FA exposure induced systemic alterations in H3 and H4 methylation and acetylation, including hypomethylation of H3K4 and H3K79 and changes in H3K9, H3K14, H3K18, H3K23, H3K27, H3K36, H3K37, and H3R40, as well as modifications in H4K5, H4K8, H4K12, and H4K16. These FA-induced histone modifications exhibited strong parallels with epigenetic alterations observed in cancers, leukemia, and Alzheimers disease. This study provides novel evidence of FA epigenetic toxicity, offering new insights into the potential mechanisms underlying FA-driven pathogenesis.

pharmacology and toxicology↗

bioRxiv2025

Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning

Cell Painting (CP), as a high-throughput imaging technology, generates extensive cell-stained imaging data, providing unique morphological insights for biological research. However, CP data contains three types of technical effects, referred to as triple effects, including batch effects, gradient-influenced row and column effects (well position effects). The interaction of various technical effects can obscure true biological signals and complicate the characterization of CP data, making correction essential for reliable analysis. Here, we propose cpDistiller, a triple-effect correction method specially designed for CP data, which leverages a pre-trained segmentation model coupled with a semi-supervised Gaussian mixture variational autoencoder utilizing contrastive and domain-adversarial learning. Through extensive qualitative and quantitative experiments across various CP profiles, we demonstrate that cpDistiller effectively corrects triple effects, especially well position effects, a challenge that no current methods address, while preserving cellular heterogeneity. Moreover, cpDistiller effectively captures system-level phenotypic responses to genetic perturbations and reliably infers gene functions and interactions both when combined with scRNA-seq data and independently. cpDistiller also excels at identifying gene and compound targets, which is a critical step in drug discovery and broader biological research.

bioinformatics↗

bioRxiv2025

Auditory tract maturation in early infancy: Links to speech production

Infants exhibit remarkable language acquisition abilities, supported by highly plastic neural substrates that dynamically interact with early speech experiences. However, the developmental mechanisms of these neural substrates and their specific role in speech acquisition remain incompletely understood. Here, we present NeoAudi Tract (NAT), a robust automated toolbox for extracting the full set of auditory tracts in infants from birth to 24 months using 3T diffusion MRI data. By characterizing the microstructural changes in these tracts, we demonstrate a gradual and continuous maturation process of the auditory system. Additionally, we identify significant correlations between auditory tract maturation and both fine-motor skills and expressive language t-scores from the Mullen Scales of Early Learning tests. Our findings highlight the role of the auditory system in speech production and indicate the intertwined development of auditory and motor systems that underlies speech acquisition, particularly during perceptual reorganization.

neuroscience↗

bioRxiv2024

Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo

The neurotransmitter acetylcholine (ACh) is essential in both the central and peripheral nervous systems. Recent studies highlight the significance of interactions between ACh and various neuromodulators in regulating complex behaviors. The ability to simultaneously image ACh and other neuromodulators can provide valuable information regarding the mechanisms underlying these behaviors. Here, we developed a series of red fluorescent G protein-coupled receptor activation-based (GRAB) ACh sensors, with a wide detection range and expanded spectral profile. The high-affinity sensor, rACh1h, reliably detects ACh release in various brain regions, including the nucleus accumbens, amygdala, hippocampus, and cortex. Moreover, rACh1h can be co-expressed with green fluorescent sensors in order to record ACh release together with other neurochemicals in various behavioral contexts using fiber photometry and two-photon imaging, with high spatiotemporal resolution. These new ACh sensors can therefore provide valuable new insights regarding the functional role of the cholinergic system under both physiological and pathological conditions.

neuroscience↗

bioRxiv2024

Do-it-yourself de novo antibody sequencing workflow that achieves complete accuracy of the variable regions

Antibodies are widely used as research tools or therapeutic agents. Knowing the sequences of the variable regions of an antibody--both the heavy chain and the light chain--is a prerequisite for the production of recombinant antibodies. Mass spectrometry-based de novo sequencing is a frequently used, and sometimes the only approach to gaining this information. Here, we describe a workflow that enables accurate sequence determination of monoclonal antibodies based on mass spectrometry data and freely available software tools. This workflow, which we developed using a homemade anti-FLAG monoclonal antibody as a reference sample, achieved 100% accuracy of the variable regions with clear distinction between leucine (L) and isoleucine (I). Using this workflow, we successfully decoded a monoclonal anti-HA antibody, for which we had no prior knowledge of its sequence. Based on the de novo sequencing result, we generated a recombinant anti-HA antibody, and demonstrated that it has the same specificity, sensitivity, and affinity as the commercial antibody. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/630060v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@180c502org.highwire.dtl.DTLVardef@1064399org.highwire.dtl.DTLVardef@4005d3org.highwire.dtl.DTLVardef@13e65ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Time-resolved fluorescent proteins towards fluorescence microscopy in the temporal and spectral domains

Fluorescence microscopy has been widely applied in life sciences. While steady-state fluorescence intensity is mostly used, the time-resolved detection mode relying on fluorescence lifetime remains underexplored. Herein, we present a family of time-resolved fluorescent proteins (TRFP). Using a strategy that regulates lifetime without affecting spectra of FPs, we have developed different TRFPs that cover the visible spectrum and a wide range of lifetime. TRFPs are employed in the temporal-spectral resolved microscopy, allowing the simultaneous imaging of 9 different proteins in live cells and correlation of multiple activities to cell cycles. Finally, TRFPs are integrated into multiplexing super-resolution microscopy to concurrently visualize 4 proteins in live cells, acquiring a remarkable 50 nm spatial resolution using lifetime as signal. TRFPs represent a transformative toolset towards fluorescence microscopy in both the temporal and spectral domains. Beyond the multiplexing imaging, TRFPs could introduce unprecedented opportunities of system complexity and quantitative accuracy into biological research.

biochemistry↗

bioRxiv2024

Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases

Spatial transcriptomics (ST) has revolutionized our understanding of tissue architecture, yet constructing comprehensive three-dimensional (3D) cell atlases remains challenging due to technical limitations and high cost. Current approaches typically capture only sparsely sampled two-dimensional sections, leaving substantial gaps that limit our understanding of continuous organ organization. Here, we present SpatialZ, a computational framework that bridges these gaps by generating virtual slices between experimentally measured sections, enabling the construction of dense 3D cell atlases from planar ST data. SpatialZ is designed to operate at single-cell resolution and function independently of gene coverage limitations inherent to specific spatial technologies. Comprehensive validation using real 3D ST and independent serial sectioning datasets demonstrates that SpatialZ accurately reconstructs virtual slices while preserving cell identities, gene expression patterns, and spatial relationships. Leveraging the BRAIN Initiative Cell Census Network data, we constructed a 3D hemisphere atlas comprising over 38 million cells, a scale not feasible experimentally. This dense atlas enables unprecedented capabilities, including in silico sectioning at arbitrary angles, explorations of gene expression across both 3D volumes and surfaces, and 3D mapping of query tissue sections. While currently validated for spatial transcriptomics, the underlying principles of SpatialZ could potentially be adapted for spatial proteomics, spatial metabolomics, and even spatial multi-omics. Validated through internal and external testing, our computationally generated atlas maintains biological accuracy, providing unprecedented resolution of spatial molecular landscapes and demonstrating the potential of computational approaches in advancing 3D ST.

bioinformatics↗