Biology subjects

Zhong, Z.

Publications and source records attributed to Zhong, Z..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

HEAL-KGGen: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Genetic Biomarker-Based Medical Diagnosis

The discovery and validation of genetic biomarkers across diverse diseases demand intelligent systems capable of integrating complex multi-omics data with clinical relevance. We introduce HEAL-KGGen, an end-to-end framework that enhances Large Language Models (LLMs) through a hierarchical multi-agent architecture and an automatically constructed medical knowledge graph. The system includes a General Practitioner (GP) agent for initial biomarker triage and specialist agents for genomics, transcriptomics, proteomics, and clinical interpretation. The core innovation of HEAL-KGGen lies in its dynamic knowledge graph pipeline, which combines entity extraction based on patterns and semantics, ontology-aligned normalization (using UMLS, MeSH, SNOMED CT) and the construction of multi-source relationships from biomedical databases and literature. Retrieved subgraphs are transformed into contextual prompts that guide LLM reasoning via structured, explainable pathways. Our experiments show that HEAL-KGGen significantly improves question-answering accuracy across multiple mainstream large language models, with the highest improvement observed on Claude 3.5 Sonnetachieving a 43.75% increase in accuracy., confirming the value of domain-specific graph knowledge in advancing LLM performance for genetic and molecular diagnostics.

bioinformatics↗

bioRxiv2025

How Good is AlphaFold3 at Ranking Drug Binding Affinities?

Accurate affinity ranking of small molecules is pivotal for drug discovery. We investigate whether structure prediction models like AlphaFold3, pretrained on protein-ligand interactions, can address this task. Zero-shot evaluation of Protenix (an AlphaFold3-like model) demonstrates superior prioritization of active compounds over conventional scoring functions and state-of-the-art deep learning models. By further fine-tuning Protenix on structure-agnostic protein-ligand bioactivity data from ChEMBL and BindingDB, we develop AlphaRank that predicts pairwise affinity relationships. AlphaRank achieves prediction accuracy comparable to computationally intensive free energy perturbation (FEP+) workflows on standard benchmarks, while requiring substantially less computational resources. Our findings highlight the emergent potential of AlphaFold3-derived models in affinity ranking tasks and emphasize the necessity for targeted methodological exploration to fully harness their capabilities in drug discovery applications.

bioinformatics↗

bioRxiv2025

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination Plane

Investigating structural and functional dynamics across large spatial scales in living organisms calls for volumetric microscopy that combines a wide field of view (FOV), high spatial resolution, and sufficient temporal resolution. Swept confocally-aligned planar excitation (SCAPE) microscopy offers a compelling balance of optical sectioning, cellular resolution, and high-speed volumetric imaging. However, extending SCAPE to mesoscopic scales has been hindered by the limited tilting angle of the oblique illumination light sheet achievable with commercial low-magnification objectives. Here, we present a mesoscopic SCAPE microscope that overcomes this constraint by implementing a super-oblique light sheet--tilted up to ~60{degrees} relative to the optical axis of a 0.5-NA primary objective--enabled by an air-to-water bridging reflector. In addition, we introduce a single-galvanometer, self-conjugating rescanning strategy that allows arbitrary customization of the optical-to-mechanical angle ratio. This innovation accommodates the reversed and modulated scan displacement of the reflected light sheet and preserves descanned epi-fluorescence detection. Together, these advancements enable our mesoscopic SCAPE microscope to achieve a lateral FOV of 5.0 mm x 2.9 mm, cellular-level spatial resolution (~9.4 m x ~5.9 m lateral, and ~6.0 m axial), and a volumetric imaging rate of 9 volumes per second.

bioengineering↗

bioRxiv2025

SpatioCell: A Deep Learning Algorithm for High-resolution Single-cell Mapping through Deep Integration of Histology Image and Sequencing Data

Spatial transcriptomics (ST) is a powerful assay to capture gene expression in tissue context. However, due to the limitation of resolution, most existing ST datasets remain at multicellular resolution which hinders comprehensive understanding of the spatial organization. We propose SpatioCell, a computational algorithm to automatically extract both cell type and expression information at single-cell resolution from ST data, through a morpho-transcriptomic spatial reconstruction framework solved via dynamic programming, integrating morphological and transcriptomic information. This framework enables deterministic single-cell spatial reconstruction, assigning cell identities to precise locations rather than inferring spot-level cell-type composition and expression, and further uncovers overlooked microenvironment features while correcting deconvolution errors. Using the ST data from triple negative breast cancer as an example, SpatioCell reveals the significance of the distance between cancer-associated fibroblast (CAF) and tumor or immune cells for disease progression. The establishment of SpatioCell will broaden the biomedical applications of ST and facilitate investigations of single-cell spatial organization.

bioinformatics↗

bioRxiv2025

Bacteriophage protein Dap2 inhibits bacterial type III secretion system and synergizes with Dap1 to evade anti-phage immunity

The evolutionary arms race between bacterial immunity and phages has driven the emergence of sophisticated anti-defense systems (ADSs). However, certain ADSs exhibit incomplete suppression of their cognate defense systems, suggesting functional cooperation between multiple ADSs targeting the same bacterial safeguard. In this study, we characterize Dap2, a protein encoded by a Pseudomonas aeruginosa phage PaoP5, which directly binds to the Lon protease to prevent the degradation of the phage-encoded HNH endonuclease. Deletion of dap2 in PaoP5 exhibits significantly impaired genome packaging due to insufficient levels of HNH. Strikingly, Dap2 synergizes with its genomically adjacent partner Dap1, a previously identified HNH-binding protein providing partial Lon resistance, to achieve complete protection of HNH. Beyond anti-defense activity, Dap2 disrupts host virulence by sequestering the type III secretion system (T3SS) transcriptional activator ExsA, suppressing bacterial pathogenicity while redirecting metabolic resources toward phage progeny production. This study unveils a dual functional ADS that simultaneously modulates bacterial virulence and anti-phage immunity, both aimed at ensuring phage survival and maximizing progeny production. Furthermore, it elucidates a novel mechanism whereby phages employ synergistic ADS pairs (Dap1/Dap2) to achieve complete neutralization of a bacterial defense system, when individual components provide only partial protection. These findings significantly enhance our understanding of the intricate evolutionary arms race between phages and their bacterial hosts.

microbiology↗

bioRxiv2025

The epigenetic reader MORC3 is required for T cell development in the thymus

Cell fate decisions are orchestrated by an interplay of epigenetic factors in collaboration with transcriptional activators and repressors. The epigenetic reader MORC3 is known as a silencer of endogenous retroviruses in mouse embryonic stem cells. Here, we show that mouse MORC3 is expressed in the thymus and reveal that MORC3 loss of function leads to a severe arrest in T cell development at the DN1 stage, accompanied by an expansion of natural killer and myeloid cells. MORC3 function in thymus depends on its ATPase and its ability to bind H3K4me via the CW-type zinc finger domain. We find altered chromatin accessibility at regulatory elements of key T cell transcription factors in DN1 cells and show that re-expressing TCF1 in MORC3-deficient progenitor cells, rescues T cell development. Our work indicates a novel function for MORC3 in modulating regulatory sites essential for T cell lineage commitment at the level of chromatin.

genetics↗

bioRxiv2025

Synergistic neuroprotective and cognitive-enhancing effects of Walnut Peptide and Theanine in human brain organoid and mouse stress models

Stress is a prevalent mental health concern emerging predominantly in late adolescence or early adulthood. Since 2007, the Food and Drug Administration (FDA) has not approved any novel anxiolytic pharmaceuticals, fueling interest in nutritional supplements as alternative therapies for stress management. Building on prior zebrafish research, this study investigates the synergistic effects of Theanine (Th) and Walnut Peptide (WP) on stress mitigation and cognitive enhancement. Utilizing the human brain organoid stress (BO-stress) model, WP+ Th were observed to reduce stress and regulate expression of neurotransmitters, including Gamma-Aminobutyric Acid (GABA), serotonin (5-HT), dopamine (DA), and acetylcholine (Ach), as well as brain-derived neurotrophic factor (BDNF) and serotonin transporter (SERT). Subsequent in vivo study using C57BL/6J mouse-stress model demonstrated that the treatment (Th 85 mg/mL + WP 200 mg/mL), or administrated with vehicles, significantly improved their performance in stress and cognitive assessments, partially normalized neurotransmitter imbalances by modulating SERT and BDNF expression. These findings highlighted the potential of using WP + Th, particularly when delivered with vehicles (eg: powder/yogurt/milk), as a novel combined therapeutic approach for stress management and cognitive enhancement. We performed a correlation analysis between BO-stress model and mouse-stress model, revealing a alignement in the SERT levels.In addition, SERT was highly correlated with other markers in the mouse hippocampus and may represent a key target for modulating the balance between stress and cognition. Significance StatementThis study established an innovative human brain organoid-stress model and, in conjunction with mouse-stress model, elucidated the synergistic actions of Theanine and Walnut Peptide in mitigating stress and augmenting cognitive function. Their beneficial effects were mediated through the regulation of SERT and BDNF, presenting a promising non-pharmacological avenue for mental health care. In addition, species differences between humans and mice were also examined through correlation analysis of brain organoids and mouse models. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/640260v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1a81886org.highwire.dtl.DTLVardef@e2281dorg.highwire.dtl.DTLVardef@1b7b167org.highwire.dtl.DTLVardef@dff9aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Activation of KCC2 during development alleviates cognitive, behavioral, and neural excitability in adult CDKL5-deficient mice

Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder (CDD) is a developmental and epileptic encephalopathy (DEE) characterized by severe drug-resistant epileptic disorders beginning in early childhood, along with cognitive and social impairments in later childhood and adulthood. Existing pharmacological therapies for CDD primarily focus on anti-seizure medications, which often have associated sedative side effects. In addition, there are currently no effective treatments for cognitive or behavioral impairments associated with this disorder. Postnatal development expression of CDKL5 has a similar timeline as the developmental activity of the potassium chloride co-transporter (KCC2), the maturation of which is a prerequisite for the developmental switch to fast synaptic hyperpolarizing inhibition mediated by g-aminobutyric acid type A receptors (GABAAR). This developmental GABA switch is determined by changes in the phosphorylation of multiple residues in KCC2. During this initial postnatal period, dramatic changes occur as major neuronal circuits are formed, laying down the initial pathways important for memory consolidation and behavioral processing. Currently, a knowledge gap exists in understanding KCC2 dysfunction in CDD. In adult Cdkl5 KO mice we found aberrant KCC2 phosphorylation and expression, such that KCC2 phosphorylation profile appeared immature. We examined the developmental changes in KCC2 and observed significant alterations in the phosphorylation of key residues and decreased KCC2 expression from p14 to p21. Because KCC2 loss-of-function has been strongly correlated with excessive neuronal excitation, cognitive and behavioral impairments, we examined seizure susceptibility, spatial memory, and social interaction in adult Cdkl5 KO mice following once daily administration of the KCC2 activator (OV350), or vehicle, to infant Cdkl5 KO mice. We found that adult Cdkl5 KO mice are more susceptible to kainate-induced seizures, show poor sociability and deficits in spatial learning and memory compared to WT mice. Twelve days of OV350 treatment as infants (p10 to p21) prevented the development of benzodiazepine-resistant seizures and alleviated cognitive and behavioral deficits in adult Cdkl5 KO mice. In contrast, 12 days of OV350 treatment in adult Cdkl5 KO mice had limited ability to alleviate cognitive and behavioral deficits. In summary, this study demonstrates that enhancing KCC2 function may be a potential therapeutic target for CDD and other DEEs. However, early intervention during critical developmental windows is crucial for optimal outcomes.

neuroscience↗

bioRxiv2025

Exploring Hippocampal Vulnerability: Diminished Angiogenic Capacity in the Hippocampus Compared to the Cortex

BackgroundThe hippocampus is one of the first regions affected in various neurodegenerative diseases. In this study, investigated the vascular factors contributing to its susceptibility, aiming to elucidate the underlying vascular mechanisms. MethodUtilizing publicly available single-cell databases, we analyzed the differential expression of genes in blood-brain barrier (BBB)-associated cells within the hippocampus and compared them to those in the cortex. Those genes were further validated in mouse and ischemia rat models. ResultsWe identified differentially expressed genes (DEGs) in endothelial cells, pericytes, and astrocytes in the BBB. Subsequent gene ontology (GO) enrichment analysis and protein-protein interaction (PPI) network analysis identified key hub genes: Kdr, Fn1, Pecam1, Cd34, and Cd93, that related to angiogenesis. They differential expression was then experimentally verified using micro-vessels from mouse and rat brains: In the rat ischemia model, we observed up-regulation of angiogenesis-related genes, including Kdr, Cd34, and Cd93, in the microvasculature of both the hippocampus and cortex, with relatively lower expression in the hippocampus. ConclusionThese findings suggest that the hippocampus has a reduced angiogenic capacity compared to the cortex, which may contribute to its increased vulnerability to neurological disorders.

neuroscience↗

bioRxiv2025

Arabidopsis REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes.

DNA methylation plays crucial roles in gene regulation and transposon silencing. In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific loci is unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes to generate 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific loci. In the absence of GDE1, Pol IV transcription complexes redistribute to sites bound by a different factor called REM8. These results suggest that REM proteins act as sequence specific DNA binding proteins that pattern siRNAs and methylation at specific sites in the genome, highlighting the role of genetic information in determining epigenetic patterns.

plant biology↗

bioRxiv2025

Mobile genetic elements that shape microbial diversity and functions inthawing permafrost soils

The worlds ecosystems are shaped by microbiota. Their niches and their impacts depend on functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, quantitative field data on the rates and impacts of MGE activity remains scarce. Here we leverage large-scale soil meta-omic data to develop and apply analytics for studying MGEs in complex natural systems. In our model permafrost-thaw ecosystem, Stordalen Mire, we identify [~]2.1 million MGE recombinases across 89 microbial phyla to assess ecological distributions, affected functions, past mobility, and current activity. This revealed MGEs shaping natural genetic diversity via differential impacts on major phyla; affecting a wide range of functions, including diverse regulatory and metabolic genes affecting carbon flux and nutrient cycling; and moving at rates that should significantly influence the realized functional profiles of natural microbiomes. These findings and this systematic meta-omic framework open new avenues to better investigate MGE diversity, activity, mobility, and impacts in nature.

microbiology↗

bioRxiv2025

Microbes under climatic refugia: Self-stabilizing subcommunity rank dynamics in large-river deltaic estuaries

Microorganisms, akin to macroorganisms, can be sheltered by climatic refugia, overlooked for optimism about microbial extinction. By categorizing microbial communities into ecologically distinct subcommunities, we conducted a two-year survey of large-river deltaic estuaries (LDEs) which are regarded as refugial hotspots, and established rank hierarchies to monitor temporal changes. We found that, consistent with macroecology, LDEs harbor distinct microbial community structures, with the abundance distribution of subcommunities exhibiting resilience against environmental perturbations, persisting on an annual cycle. In particular, while the evenness of subcommunity rank abundance curves fluctuates frequently, shifts in rank order are less dynamic but, once initiated, have a more pronounced impact on subsequent rank dynamics. Our results suggest that the microbial subcommunity rank structure in LDEs is both persistent and robust, aligning with classic patterns of species abundance distributions. This study emphasizes that, despite differences in their roles, the stable functioning of microbial rank systems is also fundamental to the refugial capacity of ecosystems and should be given equal importance.

ecology↗

bioRxiv2025

Feature-Driven Whole-Tissue Imaging with Subcellular Resolution

Understanding how subcellular structures and events shape tissue-wide phenomena remains a central challenge in biology. We present Multiscale Cleared Tissue Axially Swept Light-Sheet Microscopy (MCT-ASLM), a platform combining cm-scale imaging with targeted high-resolution interrogation of intact tissues in human-guided or autonomous modes. Capable of capturing fields of view up to 21 mm at micron-scale resolution, MCT-ASLM can seamlessly transition to submicron (~300 nm) isotropic resolution for targeted imaging. This versatility enables comprehensive studies of hierarchical organization and spatially complex processes, including mapping neuronal circuits in rat brains, visualizing glomerular innervation in mouse kidneys, and examining metastatic tumor microenvironments. By bridging subcellular to tissue-level scales, MCT-ASLM offers a powerful method for unraveling how local events contribute to global biological phenomena.

biophysics↗

bioRxiv2025

Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana

BackgroundWe investigated the flow of information from genome sequence to protein expression implied by the Central Dogma, to determine the impact of intermediate genomic levels in plants. ResultsWe performed genomic profiling of rosettes in two Arabidopsis accessions, Col-0 and Can-0, and assembled their genomes using long reads and chromatin interaction data. We measured gene and protein expression in biological replicates grown in a controlled environment, also measuring CpG methylation, ribosome-associated transcript levels and tRNA abundance. Each omic level is highly reproducible between biological replicates and between accessions despite their 0.5% sequence divergence; the single best predictor of any level in one accession is the corresponding level in the other. Within each accession, gene codon frequencies accurately model both mRNA and protein expression. The effects of a codon on mRNA and protein expression are highly correlated but are unrelated to genome-wide codon frequencies or to tRNA levels which instead match genome-wide amino acid frequencies. Ribosome-associated transcripts closely track mRNA levels. ConclusionsIn the absence of environmental perturbation, neither methylation, tRNA nor ribosome-associated transcript levels add appreciable information about constitutive protein abundance beyond that in DNA codon frequencies and mRNA expression levels. The impact of constitutive gbM is mostly explained by gene codon composition. tRNA abundance tracks overall amino acid demand. However, genetic differences between accessions associate with differential gbM by inflating differential expression variation. Our data show that the Central Dogma holds only if both sequence and abundance information in mRNA are considered.

plant biology↗

bioRxiv2024

Spatiotemporally restricted Hippo signalings instruct the fate and maturation of hepatobiliary cells

The Hippo pathway is an evolutionary conserved signaling cascade involved in organ size control and tumorigenesis, but its cellular functions and regulatory mechanisms are not fully understood. Recently, we have defined two independent modules (HPO1 and HPO2) in the Hippo signaling network. Here, by using spatially resolved transcriptomic and imaging analysis of mouse livers with defective Hippo signaling, we show that HPO1 and HPO2 operate in distinct cells at different developmental stages to regulate the fate and maturation of liver parenchymal cells. HPO1 controls the maturation of hepatocytes postnatally, and its perturbation leads to the expansion of immature hepatocytes (imHep). HPO2, on the other hand, regulates the maturation of cholangiocytes perinatally, and its ablation results in the accumulation of immature cholangiocytes (imCho2) identical to developing ductal plate cells. Moreover, the inactivation of HPO1 or HPO2 causes the conversion of hepatocytes into immature cholangiocytes (imCho1). These immature cells are also observed in regenerating livers following different damages. In contrast, deletion of Yap/Taz encoding downstream effectors of the Hippo pathway accelerates liver maturation and promotes cell death. These findings suggest that the spatiotemporally restricted Hippo signaling modules act as checkpoints in liver development and may coordinate cell proliferation and maturation to ensure proper liver size and function.

cell biology↗

bioRxiv2024

IGF2 mediates Hippo signaling to control liver size

The Hippo pathway is a central mechanism in organ size control, but the mediator for its function remains elusive. Here, we show that the expression of insulin-like growth factor II (IGF2) is directly induced by YAP/TAZ transcription cofactors of the Hippo pathway in a developmental stage- and cell type-specific manner. In mouse livers, Igf2 expression is sustained by YAP/TAZ in hepatoblasts and immature hepatocytes at fetal and neonatal stages, coupling with rapid cell proliferation and liver size expansion, whereas turned off in matured hepatocytes following YAP/TAZ inactivation to prevent liver overgrowth. In contrast, YAP/TAZ fails to regulate Igf2 expression in cholangiocytes and diverse liver mesenchymal cells where epigenetic barriers, including DNA and histone methylation, are implanted near Igf2 promoters. Furthermore, IGF2 activates IGF1R signaling and promotes normal and neoplastic liver growth, while the inactivation of IGF2 or IGF1R effectively blocks YAP/TAZ-induced hepatomegaly and hepatoblastoma. In conclusion, our findings reveal that IGF2 is a bona fide mediator of the Hippo pathway, indicating a fundamental role of the Hippo-IGF2-IGF1R signaling axis in organ size regulation and malignancies.

cell biology↗

bioRxiv2024

Mapping genomic regions associated with temperature stress in the wheat pathogen Zymoseptoria tritici

Climate change can alter interactions between plants and their pathogens, which could adversely affect crop production. To better understand the molecular mechanisms underlying the responses of pathogenic fungal to temperature stress, we conducted a quantitative trait loci (QTL) mapping study in the wheat pathogen Zymoseptoria tritici to identify genomic regions associated with colony growth and melanisation at three temperatures (10{degrees}C, 18{degrees}C, 27{degrees}C). We then identified likely candidate genes for thermal adaptation within these intervals by combining information regarding gene function, GO annotation enrichment, transcriptional profile, and results from previous genome wide association studies (GWAS) investigating responses to climate, temperature and thermal adaptation. The QTL mapping, conducted for two separate crosses involving four Swiss parents, found significant QTL uniquely associated with traits measured in high and low temperatures. These intervals contained many genes known to regulate responses to temperature stress, including heat shock proteins (HSPs) and proteins involved in the mitogen-activated protein kinase (MAPK) pathways, and were enriched for genes with a zinc ion binding GO annotation. We highlight the most promising candidate genes for thermal adaptation, including an ammonium transporter gene, a stress response factor (Whi1) and two MAPK pathway genes - SSk2 and Opy2. Future validation work on these candidate genes could provide novel insight into the molecular mechanisms underlying temperature adaptation in this important wheat pathogen.

genetics↗

bioRxiv2024

A transgene-free, human peri-gastrulation embryo model with trilaminar embryonic disc-, amnion- and yolk sac-like structures

The ultimate outcome of the gastrulation in mammalian development is a recognizable trilaminar disc structure containing organized cell lineages with spatially defined identities in an emerging coordinate system1-4. Despite its importance in human development, gastrulation remains difficult to study. Stem cell-based embryo models, including those that recapitulate different aspects of pre- and peri-gastrulation human development5-15, are emerging as promising tools for studying human embryogenesis16-18. However, it remains unclear whether existing human embryo models are capable of modeling the development of the trilaminar embryonic disc structure, a hallmark of human gastrulation. Here we report a transgene-free human embryo model derived solely from primed human pluripotent stem cells (hPSCs), which recapitulates various aspects of peri-gastrulation human development, including formation of trilaminar embryonic layers situated between dorsal amnion and ventral definitive yolk sac and primary hematopoiesis. We term this model the peri-gastrulation trilaminar embryonic disc (PTED) embryoid. The development of PTED embryoid does not follow natural developmental sequences of cell lineage diversification or spatial organization. Instead, it exploits both extrinsic control of tissue boundaries and intrinsic self-organizing properties and embryonic plasticity of the diverse peri-gastrulation-stage cell lineages, leading to the emergence of in vivo-like tissue organization and function at a global scale. Our lineage tracing study reveals that in PTED embryoids, embryonic and extraembryonic mesoderm cells, as well as embryonic and extraembryonic endoderm cells, share common progenitors emerging during peri-gastrulation development. Active hematopoiesis and blood cell generation are evident in the yolk sac-like structure of PTED embryoids. Together, PTED embryoids provide a promising and ethically less challenging model for studying self-organizing properties of peri-gastrulation human development.

developmental biology↗