Biology subjects

Kong, L.

Publications and source records attributed to Kong, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Identifying Key Cells for Fibrosis by Systematically Calling Cell Type-Phenotype Associations across Massive Heterogenous Datasets

Fibrotic diseases pose a significant burden on health care, yet the key pathogenic fibroblasts involved remain unclear. We developed the fibrotic disease fibroblast atlas (FDFA), which comprises 394 single-cell and 38 spatial transcriptomic samples from 11 common fibrotic diseases. To perform a cell-type phenotype association study in large-scale heterogeneous datasets, we developed the single-cell phenotype association research kit for large-scale dataset exploration (SPARKLE). SPARKLE handles heterogeneity by incorporating confounding information into its generalized linear mixed models (GLMMs). The application of SPARKLE to FDFA revealed that matrix fibroblasts (MTFs) constitute a crucial pathogenic cell group in fibrosis. Their increased proportion correlate with the fibrotic process. MTFs also synergize with MYO-Fs, increasing their degree of fibrosis. Based on MTF, we identified 25 potential antifibrotic targets for broad-spectrum antifibrotic therapies. This study enhances our understanding of fibrosis and provides a reliable framework for large-scale cell type-phenotype association research. HighlightsO_LIA cross-tissue, multidisease fibrotic disease fibroblast atlas (FDFA) reveals diverse fibroblast subtypes in fibrosis diseases. C_LIO_LIA new toolkit, SPARKLE, is introduced for detecting robust cell type-phenotype associations in large-scale heterogeneous datasets. C_LIO_LIMultiple pathogenic fibroblasts associated with common fibrosis disease (MTF) onset and progression have been identified, suggesting potential cell-specific therapeutic strategies for fibrosis-related diseases. C_LI

bioinformatics↗

bioRxiv2025

PACAP Signaling Network in the Nucleus Accumbens Core Regulates Reinstatement Behavior in Rat

Cocaine use disorder (CUD) lacks FDA-approved treatments, partly due to the difficulty of creating therapeutics that target behavior-related neural circuits without disrupting signaling throughout the brain. Recent evidence highlights the therapeutic potential of targeting gut-brain axis components, such as GLP-1 receptors, to modulate neural circuits with minimal central nervous system disruption. Like GLP-1, pituitary adenylate cyclase polypeptide (PACAP) is a component of the gut-brain axis that regulates behavior through a network spanning the gut and brain. Here, we investigated the potential existence and function of an endogenous PACAP signaling network within the nucleus accumbens core (NAcc), which is a structure that integrates emotional, cognitive, and reward processes underlying behavior. We found that PACAP and its receptor, PAC1R, are endogenously expressed in the rat NAcc and that PACAP mRNA is present in medial prefrontal cortical projections to the NAcc. Behaviorally, intra-NAcc infusions of PACAP (100 pm) did not induce seeking behavior but blocked cocaine-primed reinstatement (10 mg/kg, IP). Intra-NAcc PACAP also inhibited reinstatement driven by co-infusion of the D1 receptor agonist (SKF 81297, 3 {micro}g) but not the D2 receptor agonist (sumanirole, 10 ng). These findings are significant since D1 and D2 receptor activities in the NAcc govern distinct behavioral mechanisms indicating precise actions of PACAP even within the NAcc. Future research should examine whether NAcc PACAP signaling can be selectively engaged by peripheral gut-brain axis mechanisms, potentially unveiling novel therapeutic approaches for CUD and related disorders.

neuroscience↗

bioRxiv2024

Long-read sequencing reveals extensive size variation and suggests evolutionary patterns of expansion in bivalve mitogenomes

Bilaterian mitochondrial genomes are generally of conserved size and gene content, typically ranging from 14 to 20 kb and coding 37 genes. However, the major exception to this rule has been found in many bivalve species which allow the presence of long unassigned region (regions that are functionally unassigned). It is still unclear whether there are universal patterns to expansions across bivalves. Additionally, the prevalence of highly repetitive sequences within complex mitogenomes has prevented its complete assembly and led to its systematic omission from mitogenomic analyses. Here, leveraging the growing genomic resources in Mollusca, we devised a mitogenome assembly pipeline using long-read sequencing to characterize mitogenome features in 178 mollusk species. Comparing our assemblies with reference mitogenomes based on Sanger/short-read sequencing, we identified missing sequences, repeats and novel gene duplications and found that bivalves exhibit an exceptional diversity in mitogenome size compared to other mollusks. Subsequently, we investigated the factors potentially influencing mitogenome size, the potential functional elements and the patterns of expansion regions. Furthermore, we discussed that the possible selective pressure on mitogenome size and hypothesized that the variability of bivalve mitogenomes may be linked to innate immunity. Our findings underscore the significance of long-read sequencing in elucidating complex mitogenomes and provide new insights into the evolution of bivalve mitogenomes.

genomics↗

bioRxiv2024

Comparative analysis of iPSC-derived human kidney organoid and tubuloid models

BackgroundEpithelial kidney organoids (tubuloids) made from kidney biopsies, urine, or iPSC-derived kidney organoids offer new opportunities in experimental and clinical nephrology. Yet, we have limited knowledge of how tubuloid models differ from each other, from iPSC-derived kidney organoids and from the human kidney. New insight is required to guide model selection for studies in kidney physiology and disease. MethodsTubuloids were generated from adult nephrectomy samples (adult tubuloids n=3), iPSC-derived kidney organoids (iTubuloids n=3), and for the first time, from human fetal kidneys (fetal tubuloids n=3). Kidney organoid and tubuloid models were compared to each other and to adult human kidney using bulk RNA sequencing. Tubuloids were subject to hypoxic insults over three passages and profiled with RNA sequencing to assess cumulative injury and repair. ResultsExpression signatures of proximal and distal tubules were stronger in adult kidneys than any organoid or tubuloid model. Comparative analysis between the models revealed that iPSC-derived kidney organoids had the highest expression of proximal tubule markers, even though adult tubuloids were derived from mature kidneys. Collecting duct signatures were enriched in adult and fetal tubuloids. Adult tubuloids showed stronger signatures of ageing and inflammation, while fetal tubuloids had enhanced ureteric tip progenitor signatures. Over 80 genes linked to inherited disorders were expressed in all tubuloid cultures, while a further 54 were expressed at higher levels in either adult, fetal or iTubuloids. Tubuloids subject to a single hypoxic injury effectively recovered by the end of the passage, while iTubuloids exposed to hypoxia over three passages expressed markers of maladaptive repair. ConclusionsThis study provides new transcriptome-wide reference data to aid in the selection and optimization of disease modelling for the human kidney. It defines common and unique opportunities to model inherited disorders in adult, fetal and iTubuloid models and illustrates new potential to model repetitive injury in long-lived tubuloid cultures.

molecular biology↗

bioRxiv2024

Decrypting the complex phenotyping traits of plants by machine learning

Phenotypes, defining an organisms behaviour and physical attributes, arise from the complex, dynamic interplay of genetics, development, and environment, whose interactions make it enormously challenging to forecast future phenotypic traits of a plant at a given moment. This work reports AMULET, a modular approach that uses imaging-based high-throughput phenotyping and machine learning to predict morphological and physiological plant traits hours to days before they are visible. AMULET streamlines the phenotyping process by integrating plant detection, prediction, segmentation, and data analysis, enhancing workflow efficiency and reducing time. The machine learning models used data from over 30,000 plants, using the Arabidopsis thaliana-Pseudomonas syringae pathosystem. AMULET also demonstrated its adaptability by accurately detecting and predicting phenotypes of in vitro potato plants after minimal fine-tuning with a small dataset. The general approach implemented through AMULET streamlines phenotyping and will improve breeding programs and agricultural management by enabling pre-emptive interventions optimising plant health and productivity.

plant biology↗

bioRxiv2024

Pan-Prediction of MHC-II Restricted Epitopes Across Species via an Alphafold-based Quantification Scheme

Predicting MHC-II restricted epitopes across species used to be challenging, but Alphafold (AF) may provide a structure-based pan-prediction solution. In this study, we established the new tool AF-pred with a clear standard for quantitative prediction results. Compared to the sequence-based tools heavily trained with human ligandome, AF-pred does not show advantage in predicting the binding patterns of human HLA-II but has far better performance in predicting binding patterns of other animals MHC-II. Using recently resolved bat MHC-II structures, we analyzed AF-preds prediction capability, logic and limitation. In addition, we also explored the impact of AF algorithm iterations on the prediction of MHC-II restricted epitopes. The results demonstrated that AF-pred is capable of cross-species prediction of MHC-II restricted epitopes and is conducive to the development of novel veterinary vaccines.

immunology↗

bioRxiv2024

A Novel Partitivirus Confers Dual Contradictory Effect to Its Host Fungus: Growth Attenuation and Virulence Enhancement

Mycoviruses represent potential role in the biocontrol approach due to their ability to reduce both virulence and vegetative growth in some phytopathogenic fungi. However, the mycoviruses enhancing the damage caused by these fungi remains poorly identified and characterized. In this study, a novel double-stranded RNA (dsRNA) fungal virus, tentatively named Sinodiscula camellicola partitivirus 1 (ScPV1), was identified in the phytopathogenic fungus Sinodiscula camellicola, isolated from tea leaves. ScPV1 possesses two genomic components of 1835 and 1697 bp, each containing an open reading frame (ORF) that encodes the putative RNA-dependent RNA polymerase (RdRp) and coat protein (CP), respectively, as confirmed by mass spectrometry. Phylogenetic analysis of the amino acid sequences of the RdRps from ScPV1 and related mycoviruses placed ScPV1 within a newly proposed genus, Epsilonpartitivirus, of the family Partitiviridae. Viral purification via ultracentrifugation and transmission electron microscopy observations revealed that ScPV1 dsRNA genomes are encapsidated within virus particles approximately 31 nm in size, ranging from 24.9 to 36.8 nm, along with the RdRp protein in an unexpected size. Transfection experiments with purified virions exhibited transfectants with significant reduced growth rates while increased virulence, indicating that ScPV1 has two-sided effect on its host fungus. This finding represents a significant advancement in understanding the complex interactions between mycoviruses and their host fungi. Author summaryTo characterize new molecular and biological traits of partitiviruses will provide substantial contributions for a better understanding of mycoviruses, as partitiviruses are prevalent across a wide range of hosts, including plants, protists, and fungi. Here, we identified a novel partitivirus, tentatively named Sinodiscula camellicola partitivirus 1 (ScPV1), from a fungus infecting tea plant, marking the first report of a partitivirus from a phytopathogenic fungus infecting tea plant. ScPV1 is characterized by two dsRNA genomic components encapsidated in particles of varying sizes, along with an RNA-dependent RNA polymerase protein of an expected size and containing some unique amino acids, indicating its distinct molecular and morphological traits. Our biological tests on transfectants generated via protoplast transfection with purified virions have rigorously demonstrated that ScPV1 impairs vegetative growth while enhancing virulence in its fungal host. This finding represents the first instance of a mycovirus responsible for hypervirulence and exhibiting dual effects on a phytopathogenic fungus through virion-transfection, as well as the first case of a partitivirus conferring hypervirulence while promoting vegetative growth in a phytopathogenic fungus. We anticipate that these findings will significantly advance our understanding of the complex interactions between mycoviruses and their host fungi.

microbiology↗

bioRxiv2024

A single-molecule nanopore sequencing platform

Nanopore sequencing, a third-generation sequencing technology, has revolutionized the gene sequencing industry with its advantages of long reads, fast speed, real-time sequencing and analysis, and potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments in a single read, providing more comprehensive genomic information compared to previous methods. Nanopore sequencing operates on electrical signals generated by a nanopore embedded in a membrane separating two electrolyte-filled chambers. When single-stranded DNA (ssDNA) passes through the nanopore, it creates variations in the current that correspond to different DNA bases. By analyzing these current fluctuations with machine learning algorithms, the DNA sequence can be determined. In this study, we introduced several improvements to nanopore sequencing, including nanopore local chemistry sequencing, novel motor and pore proteins, chip design, and basecalling algorithms. Our new nanopore sequencing platform, CycloneSEQ, demonstrated long-duration sequencing (107 hours) on a single chip with high yield (>50 Gb). In human genomic DNA sequencing, CycloneSEQ was able to produce long reads with N50 33.6 kb and modal identity 97.0%. Preliminary findings on human whole-genome de novo assembly, variant calling, metagenomics sequencing, and single-cell RNA sequencing have further highlighted CycloneSEQs potential across different areas of genomics.

genomics↗

bioRxiv2024

Study on the phenotypic diversity and comprehensive evaluation analysis of 43 ornamental peonies of Sect. Paeonia.

The peony of Sect. Paeonia was a perennial herbaceous plant with numerous ornamental varieties and riched diversity in flower color and shape. It has ornamental, edible, and medicinal value and a long history of cultivation in China. The study of phenotypic diversity of plants is an important foundation for plants of Sect. Paeonia breeding. This study conducted phenotypic diversity analysis, principal component analysis, and cluster analysis on 43 varieties of Sect. Paeonia germplasm resources. Phenotypic traits included 30 qualitative traits and 7 quantitative traits. Through genetic diversity analysis, principal component analysis, comprehensive evaluation, and cluster analysis, we ultimately concluded that plant samples had relatively rich genetic phenotype traits. In principal component analysis, the first 12 principal components have covered the vast majority of information for phenotypic traits. The comprehensive evaluation results of phenotypic traits indicate that the F values of each variety in the germplasm sample were all positive number. The degree of stamen petals played a key role in determining the phenotypic diversity of plants, and the shape of the cotyledons and leaflets may determine the plants stress resistance performance, which provides a reference for breeding new varieties of peonies of Sect. Paeonia.

plant biology↗

bioRxiv2024

Fibrillarin modulates fetal hemoglobin silencing

Decoding the molecular mechanisms underlying human fetal ({gamma}) globin gene silencing impacts therapeutic strategies for {beta}-thalassemia and sickle cell disease. Here, we identified a nucleolar protein, fibrillarin (FBL), which mediates the methylation of glutamine104 in histone H2A and functions as a repressor of the {gamma}-globin gene in cultured erythroid cells, including those from {beta}-thalassemia patients. Conditional Fbl depletion in adult {beta}-YAC transgenic mice or in {beta}IVS-2-654-thalassemic mice reactivated the human {gamma}-globin gene or murine embryonic globin expression, respectively, which corrects hematologic and pathologic defects in {beta}-thalassemic mice. We showed that FBL plays a dual role in activating BCL11A expression and repressing {gamma}-globin gene expression, which is dependent on its histone methyltransferase activity. Our study may provide an alternative strategy for therapeutic targeted treatment of {beta}-hemoglobinopathies.

molecular biology↗

bioRxiv2024

Post-flowering photoperiod sensitivity of soybean in pod-setting responses

The development of soybean (Glycine max) is regulated by photoperiod, with genes related to photoperiod sensitivity primarily focused on flowering time. However, their roles in post-flowering reproductive development and the mechanisms by which photoperiod affects them are not yet determined. In this study, we found that pod formation is sensitive to photoperiod. Long-day (LD) conditions tend to extend the time from flowering to pod formation (R1 to R3 stage), and the first wave of flowers tends to fall off. Additionally, photoperiod affects pistil morphology; under short-day (SD) conditions, the stigma has a curved hook-like structure that facilitates better interaction with the filaments when pollen is released, ultimately influencing the timing of pod formation. Photoperiod-insensitive mutants, lacking E1 family and Evening Complex genes, showed no difference in pod formation time under LD or SD conditions. Hormone content analysis and transcriptome data analysis indicated that various hormones, ROS signals, and the application of sucrose solution in vitro might influence floral organ abscission. HighlightPhotoperiod sensitivity after flowering affects the pod-setting time in soybean.

plant biology↗

bioRxiv2024

A connectomics-driven analysis reveals novel characterization of border regions in mouse visual cortex

Leveraging retinotopic maps to parcellate the visual cortex into its respective sub-regions has long been a canonical approach to characterizing the functional organization of visual areas in the mouse brain. However, with the advent of extensive connectomics datasets like MICrONS, we can now perform more granular analyses to better characterize the structure and function of the visual cortex. In this work, we propose a statistical framework for analyzing the MICrONS dataset, particularly the V1, RL, and AL visual areas. In addition to identifying several structural and functional differences between these regions, we focus on the borders between these regions. By comparing the V1-RL and RL-AL border regions, we show that different boundaries between visual regions are distinct in their structure and function. Additionally, we find that the V1-RL border region has greater synaptic connectivity and more synchronous neural activity than the V1 and RL regions individually. We further analyze structure and function in tandem by measuring information flow along synapses, observing that the V1-RL border appears to act as a bridge between the V1 and RL visual areas. Overall, we identify numerous measures that distinguish the V1-RL border from the larger V1-RL network, potentially motivating its characterization as a distinct region in the mouse visual cortex.

neuroscience↗

bioRxiv2024

CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples

Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3{degrees} and sample thickness with an accuracy of 5 nm.

biophysics↗

bioRxiv2024

Modulation of stress granule dynamics by phosphorylation and ubiquitination in plants

The Arabidopsis tandem CCCH zinc finger 1 (TZF1) is an RNA-binding protein that plays a crucial role in plant growth and stress response. TZF1 can localize to ribonucleoprotein (RNP) granules in response to various abiotic stresses. However, very little is known about the composition, function, and assembly mechanism of plant RNP granules. In this report, we show that TZF1 contains two intrinsically disordered regions (IDRs) necessary for its localization to stress granules (SGs), a subclass of RNP granules. TZF1 recruits mitogen-activated protein kinase (MAPK) signaling components and an E3 ubiquitin ligase KEEP-ON-GOING (KEG) to SGs. TZF1 is phosphorylated by MPKs and ubiquitinated by KEG. The phosphorylation sites of TZF1 were mapped by mass spectrometry. Mutant studies revealed that phosphorylation and ubiquitination of specific residues played differential roles in enhancing or reducing TZF1 SG assembly and protein-protein interaction with mitogen-activated kinase kinase 5 (MKK5) in SGs. TZF1 is extremely unstable, and its accumulation can be enhanced by proteosome inhibitor MG132. We showed that TZF1 was ubiquitinated in vivo and in vitro by KEG and TZF1 accumulated at a much lower level in gain-of-function mutant keg-4, compared to the WT. Ubiquitination appeared to play a positive role in TZF1 SG assembly, because either single or higher order mutations caused reduced number of SGs per cell, while enhanced the coalescence of small SGs into a large nucleus-like SG encompassing the nucleus. Together, our results demonstrate that the assembly of TZF1 SGs is distinctively regulated by ubiquitination and phosphorylation.

cell biology↗

bioRxiv2024

Direct, bisulfite-free 5mC and 5hmC sequencing at single-cell resolution

We report the first direct sequencing methodologies for quantitative detection of 5mC and 5hmC at single-base resolution and single-cell level, termed scTAPS (for 5mC + 5hmC) and scCAPS+ (for 5hmC specifically). With [~]90% mapping efficiency, our methods accurately benchmark 5mC and 5hmC profiles in CD8+ T and mES cells, respectively. Notably, scCAPS+ revealed a global increase in 5hmC within the hippocampus of aging mice, both in neurons and in non-neurons.

genomics↗

bioRxiv2024

A single-cell 3D spatiotemporal multi-omics atlas from Drosophila embryogenesis to metamorphosis

The development of a multicellular organism is a highly intricate process tightly regulated by numerous genes and pathways in both spatial and temporal manners. Here, we present Flysta3D, a comprehensive multi-omics atlas of the model organism Drosophila, spanning its developmental lifespan from embryo to pupa. Our datasets encompass 3D single-cell spatial transcriptomic, single-cell transcriptomic, and single-cell chromatin accessibility information. By integrating these multi-dimensional data, we constructed cell state trajectories that uncover the detailed profiles of tissue development. With a focus on the central nervous system (CNS) and midgut, we dissected the spatiotemporal dynamics of gene regulatory networks, cell type diversity, and morphological changes from a multi-omics perspective. This extensive atlas provides an unprecedentedly rich resource and serves as a systematic platform for studying Drosophila development with integrated single-cell data at an ultra-high spatiotemporal resolution.

developmental biology↗

bioRxiv2024

3D Bioprinting of Human Neural Tissues with Functional Connectivity

Probing how the human neural networks operate is hindered by the lack of reliable human neural tissues amenable for dynamic functional assessment of neural circuits. We developed a 3D bioprinting platform to assemble tissues with defined human neural cell types in a desired dimension using a commercial bioprinter. The printed neuronal progenitors differentiate to neurons and form functional neural circuits in and between tissue layers with specificity within weeks, evidenced by the cortical-to-striatal projection, spontaneous synaptic currents and synaptic response to neuronal excitation. Printed astrocyte progenitors develop into mature astrocytes with elaborated processes and form functional neuron-astrocyte networks, indicated by calcium flux and glutamate uptake in response to neuronal excitation under physiological and pathological conditions. These designed human neural tissues will likely be useful for understanding the wiring of human neural networks, modeling pathological processes, and serving as platforms for drug testing.

bioengineering↗

bioRxiv2024

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

Pseudouridine ({Psi}) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. To address this challenge, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS) for quantitative profiling of {Psi} at single-base resolution. Based on novel bromoacrylamide cyclization chemistry, BACS enables a {Psi}-to-C transition. Compared to previous methods, BACS allowed the precise identification of {Psi} positions, especially in densely modified {Psi} regions and consecutive uridine sequences. BACS successfully detected all known {Psi} sites in human rRNA and spliceosomal snRNAs and generated the first quantitative {Psi} map of human snoRNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine (A-to-I) editing sites and N1-methyladenosine (m1A). Depletion of three key pseudouridine synthases (PUS) enabled us to elucidate the targets and sequence motifs of TRUB1, PUS7, and PUS1 in HeLa cells. We further applied BACS to Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) and identified a highly abundant {Psi}114 site in EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of {Psi} in their viral transcripts or genomes, shedding light on differences in pseudouridylation between virus families. We anticipate BACS to serve as a powerful tool to uncover the biological importance of {Psi} in future studies.

molecular biology↗