Biology subjects

Gao, Z.

Publications and source records attributed to Gao, Z..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Functional, Biotinylproteomic and Bioinformatic Analysis of Both Cytoskeletal and Plastoskeletal Proteins in Plant Mechanoresponse

To investigate the early signaling components of skeletal proteins in mediating Arabidopsis thigmomorphogenesis, both microscopic and proximity labeling (PL)-based quantitative biotinylproteomics were applied to investigate the subcellular location and putative interactors of a touch-responsive WPRa4 protein. These experiments have demonstrated that the cytoskeletal protein WPRa4 is localized nearby the plastid. Several cytosolic Plastid Movement-Impaired (PMI) proteins and a member of the plastidic translocon were identified as putative interactors of WPRa4, suggesting an integrated network of skeletal proteins linking the cytoskeleton with the plastid membrane. Further bioinformatic analysis of both Proximity Labeling- and XL-MS-based proteomic results suggested that Plastid Movement-Impaired 4 (PMI4) protein may serve as a candidate in mediating the plant touch response. The loss-of-function pmi4 mutant showed neither the touch-induced bolting delay nor the rosette size reduction upon repetitive touches, suggesting that pmi4 is a unique type of mutant of Arabidopsis thigmomorphogenesis. Moreover, the null mutant pmi4 displayed a severe defect in the touch-induced Ca2+ oscillation. Further transcriptomic analysis performed on both the wild-type Arabidopsis and pmi4 mutant indicated that the mutated pmi4 gene suppressed the expression of a number of touch rapidly induced transcripts and a JA-responsive gene, LOX2. These findings led us to propose a revised touch force-sensing theory, in which the interconnected cytosolic and plastidic skeletal proteins serve as the early mechano-sensing components mediating Arabidopsis thigmomorphogenesis and the retrograde calcium signaling in response to touch.

plant biology↗

bioRxiv2024

Motor protein-assisted glycan translocation and sequencing using nanopores

The glycan sequencing remains a significant bottleneck in glycoscience. While nanopore platforms have achieved substantial progress in single-molecule nucleic acid sequencing, their application to glycan sequencing has faced considerable challenges, with limited advancements to date. In this study, we propose a novel strategy for controlling glycan translocation through the MspA nanopore as an initial step toward glycan sequencing. By conjugating the target glycan with a helicase-controlled single-stranded DNA, we successfully achieved sequencing reads of up to eleven glycans. For the first time, we isolated glycan-associated electrical signals, enabling the translocation, stretching, and controlled speed of neutral glycans through the nanopore. This method provides a platform for obtaining glycan read lengths and identifying different glycan modifications, demonstrating the capability to resolve monosaccharide composition and glycosidic linkages. To further improve resolution, we propose engineered M2-MspA to reduce the pore constriction size and enhance precision by minimizing the random thermal motion of the translocating glycan. These modifications are expected to increase the sequencing accuracy and reliability. This work represents the first proof-of-concept demonstration of glycan chain nanopore sequencing and lays a promising foundation for the development of single-molecule glycan fingerprinting and sequencing technologies. We anticipate that this approach will significantly advance the development and commercialization of nanopore-based glycan sequencing techniques.

bioengineering↗

bioRxiv2024

Combining Glycosidases and Nanopore Technology for Glycan Sequencing

The efficient characterization of glycan structures remains a critical challenge. Direct glycan sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose a glycan sequencing strategy based on glycosidase -assisted nanopore sensing. We used engineered nanopore -hemolysin (M113R/T115A), which provided high-resolution discrimination of monosaccharide volume differences and sensitivity to variations in glycan chain length. By utilizing the specificity of glycosidases, we sequentially hydrolyzed the terminal residues of the glycan chains and detected the characteristic shifts in electrical signals generated by the translocation of hydrolysis products. The accuracy of recognition of hydrolysis fragments achieved over 90 % using machine learning. This allowed us to efficiently and conveniently determine the sequence of consecutive monosaccharide units in the glycan chains. Based on this principle, we conducted a proof-of-concept demonstration on actual samples and verified the accuracy via HPLC-MS. We achieved the sequencing of consecutive units in glycan chains, confirming the theoretical feasibility of glycosidase -assisted nanopore glycan sequencing. With future optimization, the development of arrayed nanopore glycan sequencing technology based on hydrolysis strategy will provide an innovative approach for rapid decoding of glycans, which could promote the progress of glycomics research and glycobiology.

biochemistry↗

bioRxiv2024

PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation

Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial chromatin structures comprise conserved compartments, topologically associating domains (TADs), and dynamic, cell-type-specific chromatin loops. Although the role of CTCF in chromatin organization is well-known, the involvement of PRC1 is less understood. In this study, we identified an unexpected, essential role for the canonical Pcgf2-containing PRC1 complex (cPRC1.2), a known transcriptional repressor, in activating bivalent genes during differentiation. Our Hi-C analysis revealed that cPRC1.2 forms chromatin loops at bivalent promoters, rendering them silent yet poised for activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, we found that the loss of Pcgf2, though not affecting the global level of H2AK119ub1, disrupts these cPRC1.2 loops in ESCs and impairs the transcriptional induction of crucial target genes necessary for neuronal differentiation. Furthermore, we identified CTCF enrichment at cPRC1.2 loop anchors and at Polycomb group (PcG) bodies, nuclear foci with concentrated PRC1 and its tethered chromatin domains, suggesting that PRC1 and CTCF cooperatively shape chromatin loop structures. Through virtual 4C and other genomic analyses, we discovered that establishing neuronal progenitor cell (NPC) identity involves a switch from cPRC1.2-mediated chromatin loops to CTCF-mediated active loops, enabling the expression of critical lineage-specific factors. This study uncovers a novel mechanism by which pre-formed PRC1 and CTCF loops at lineage-specific genes maintain a poised state for subsequent gene activation, advancing our understanding of the role of chromatin architecture in controlling cell fate transitions.

genomics↗

bioRxiv2024

Image-based DNA Sequencing Encoding for Detecting Low-Mosaicism Somatic Mobile Element Insertions

Active LINE-1 (L1), Alu, and SVA mobile elements in the human genome are capable of retrotransposition, resulting in novel mobile element insertions (MEIs) in both germline and somatic tissues. Detecting MEIs through DNA sequencing relies on supporting reads overlapping MEI junctions; however, artifacts from DNA amplification, sequencing, and alignment errors produce numerous false positives. Systematic detection of somatic MEIs, particularly those with low mosaicism, remains a significant challenge. Previous methods had required a high number of supporting reads which limits the detection sensitivity, or human inspections that are susceptible to biases. Here, we developed RetroNet, an algorithm that encodes MEI-supporting sequencing reads into images, and employs a deep neural network to identify somatic MEIs with as few as two reads. Trained on extensive and diverse datasets and benchmarked across various conditions, RetroNet surpasses previous methods and eliminates the need for extensive manual examinations. The RetroNet analysis on the Illumina sequencing of 161x or 195x of a cancer cell line achieved an average precision of 0.885 and recall of 0.579 for detecting somatic L1 insertions that are present in as few as 1.79% of the cells. Additionally, we demonstrated that RetroNet is effective for analyzing highly degraded DNA, such as circulating tumor DNA. RetroNet is applicable to the rapidly generated short-read sequencing data and has the potential to provide further insights into the functional and pathological implications of somatic retrotranspositions.

genomics↗

bioRxiv2024

Toxoplasma gondii infection of neurons alters the production and content of extracellular vesicles altering astrocyte phenotype and contributing to the loss of GLT-1 in the infected brain

Toxoplasma gondii (T. gondii) cyst formation in the central nervous system only occurs in neurons allowing the parasite to remain latent for the lifetime of the host. Astrocytes are fundamental to neuronal health by providing nutrients and structural support and help regulate neurotransmitters by continuous communication with neurons. It is not yet known how infection and the presence of intracellular cysts, disrupts the crucial relationship between these cells. Extracellular vesicles (EVs) function in intracellular communication and can contain proteins, lipids, DNA, miRNA, and other RNA subtypes. EVs are produced by all cells including neurons and play an important role in neuronal-astrocyte interactions including the regulation of glutamate receptors on astrocytes. Previous work has demonstrated Toxoplasma infection reduces astrocytic expression of the primary glutamate transporter, GLT-1. Here we tested if cyst infection of neurons alters the production and content of EVs. EVs were isolated from uninfected and infected primary murine cortical neurons and their size, concentration, and characterization were confirmed with nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), CD63 ELISA, liquid chromatography (LC)-mass spectrometry (MS)/MS, and microRNA Sequencing. Analysis reveals that infection of neurons reduced neuronal production of EVs and altered their protein and miRNA content. EVs from infected neurons contained secreted Toxoplasma proteins GRA1, GRA2, GRA7, MAG1 and MAG2 associated with cyst formation. Following incubation of neuronal EVs with primary astrocytes, a proportion of EVs colocalize to the nucleus. EVs from infected neurons altered gene expression of astrocytes leading to a downregulation of GLT-1 protein expression and an increase in pro-inflammatory transcriptional signatures. These results demonstrate the ability of a parasitic infection in the brain to alter EV production and the fundamental communication between neurons and astrocytes.

microbiology↗

bioRxiv2024

Deletion of Zyxin Reduces Endothelial Inflammation and Mitigates Atherosclerosis

BACKGROUNDOscillatory shear stress (OSS)-induced endothelial inflammation plays a critical role in the pathogenesis of atherosclerosis. However, the involvement of endothelial zyxin, a mechanosensor, in OSS-associated atherosclerosis and its underlying mechanisms remains unclear. METHODSTo investigate the role of zyxin in vivo, ZyxiniECKOApoE-/- mice were utilized in atherosclerosis model induced by carotid artery ligation; in vitro, endothelial cells were subjected to disturbed flow in Ibidi systerm. RESULTSZyxin was significantly upregulated in the OSS regions of both human and mouse arteries. The specific deletion of zyxin in endothelial cells (ECs) in ApoE-/- (ZyxiniECKOApoE-/-) mice reversed the ECs activation and atherosclerosis induced by OSS. In vitro studies indicated that the absence of zyxin reduced the induction of adhesion molecules and pro-inflammatory cytokines stimulated by OSS. Mechanistic investigations demonstrated that 14-3-3{beta} facilitated yes-associated protein (YAP) phosphorylation at Serine 127, which played a critical role in retaining YAP within the cytoplasm. Under OSS stimulation, zyxin inhibited the phosphorylation of YAP at Serine 127 through its interaction with 14-3-3{beta}, rather than direct regulation of YAP. This inhibition enhanced YAPs nuclear translocation and promoted endothelial inflammation. Furthermore, it was shown that rosuvastatin inhibited zyxin expression in human umbilical vein endothelial cells and the vascular endothelium of ApoE-/- mice. This inhibition led to decreased levels of inflammatory markers and adhesion molecules associated with atherosclerotic lesions observed in the partially ligated left common carotid arteries of ApoE-/- mice. CONCLUSIONSThis study further confirms that zyxin is a mechanoreceptor in endothelial cells and elucidates the indispensable role of the zyxin-14-3-3{beta}-YAP axis in endothelial inflammation and atherogenesis. This indicates that Zyxin plays a crucial role in protecting against atherosclerosis.

cell biology↗

bioRxiv2024

CREATE: cell-type-specific cis-regulatory elements identification via discrete embedding

Identifying cis-regulatory elements (CREs) within non-coding genomic regions--such as enhancers, silencers, promoters, and insulators--is pivotal for elucidating the intricate gene regulatory mechanisms underlying complex biological traits. The current prevalent sequence-based methods often focus on singular CRE types, limiting insights into cell-type-specific biological implications. Here, we introduce CREATE, a multimodal deep learning model based on the Vector Quantized Variational AutoEncoder framework, designed to extract discrete CRE embeddings and classify multiple CRE classes using genomic sequences, chromatin accessibility, and chromatin interaction data. CREATE excels in accurate CRE identification and exhibits strong effectiveness and robustness. We showcase CREATEs capability in generating comprehensive CRE-specific feature spectrum, offering quantitative and interpretable insights into CRE specificity. By enabling large-scale prediction of CREs in specific cell types, CREATE facilitates the recognition of disease- or phenotype-related biological variabilities of CREs, thereby expanding our understanding of gene regulation landscapes.

bioinformatics↗

bioRxiv2024

Small mammals in biodiversity hotspot harbor viruses of epidemic potential

Metagenomic sequencing has transformed our understanding of viral diversity in wildlife and its threat to human health. Despite this progress, many studies have lacked systematic and ecologically informed sampling, which has left numerous potentially emergent viruses undiscovered, and the drivers of their ecology and evolution poorly understood. We conducted an extensive analysis of viruses in the lung, spleen, and gut of 1,688 animals from 38 mammalian species across 428 sites in Yunnan, China--a hotspot for zoonotic diseases. We identified 162 mammalian viral species, including 102 novel species and 24 posing potential risks to humans due to their relationships with known pathogens associated with serious diseases and their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-species transmission, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.

microbiology↗

bioRxiv2024

Decreased Astrocytic CCL5 by MiR-324-5p Ameliorates Ischemic Stroke Injury via CCR5/ERK/CREB Pathway

Following ischemic stroke, Ccl5 mRNA expression increased, while miR-324-5p expression decreased in the peri-infarct cortex of middle cerebral artery occlusion (MCAO) mice. However, the roles of CCL5 and miR-324-5p in stroke remained largely unclear. Here, we show that inhibiting CCL5 using antibodies or miR-324-5p not only reduced infarct area and preserved neurological function in MCAO mice but also attenuated astrocyte reactivity and microglial activation, protected dendritic structures, and maintained spine density. In an astrocyte-neuron co-culture system after oxygen-glucose deprivation (OGD), inhibiting astrocytic CCL5 by antibody or miR-324-5p decreased neuronal apoptosis and preserved dendritic structure. Importantly, the suppression of CCL5 enhanced ERK/CREB pathway signaling both in vivo and in vitro. Consistent with these findings, the application of Maraviroc, a CCR5 antagonist, reduced infarct size, decreased neuronal apoptosis, and upregulated the ERK/CREB pathway in neurons treated with OGD. In conclusion, targeting the CCL5 pathway via miR-324-5p represents a promising therapeutic strategy for alleviating ischemic stroke damage through modulation of the neuronal CCR5/ERK/CREB pathway.

neuroscience↗

bioRxiv2024

Multimodal Protein-Ligand Contrastive Pretraining for Effective and Efficient Drug Discovery

Recent advancements in genomics and proteomics have identified numerous clinically significant protein targets, with notably 85% categorized as undruggable. These targets present widespread challenges due to their complex structures and dynamics, rendering conventional drug design strategies not always effective. In this study, we introduce Uni-Clip, a contrastive learning framework that incorporates multi-modal features of proteins (structure and residue) and ligands (conformation and graph). Optimized with a specifically designed CF-InfoNCE loss, Uni-Clip enhances the modeling of protein-ligand interactions for both undruggable and druggable proteins. Uni-Clip demonstrates superior performance in benchmark evaluations on widely acknowledged datasets, LIT-PCBA and DUD-E, achieving a 147% and 218% improvements in enrichment factors at 1% compared to baselines. Furthermore, Uni-Clip proves to be a practical tool for various drug discovery applications. In virtual screening for the challenging protein target GPX4 with flat surface, it identified non-covalent inhibitors with an IC50 of 4.17 M, in contrast to the predominantly covalent inhibitors currently known. Through target fishing for benzbromarone, Uni-Clip identified the intrinsically disordered protein c-Myc as a potential target, highlighting benzbromarones potential for repurposing in cancer therapy. Explainable analyses effectively identified binding sites consistent with molecular dynamics and experimental results, even for challenging undruggable targets.

bioinformatics↗

bioRxiv2024

Enhancing Variant Calling in Whole Exome Sequencing (WES) Data Using Population-Matched Reference Genomes

Whole exon sequencing (WES) data are frequently used for cancer diagnosis and genome-wide association studies (GWAS), hinging upon high-coverage read mapping, informative variant calling, and high-quality reference genomes. The center position of the currently used genome assembly, GRCh38, is now challenged by two newly publicized telomere-to-telomere or T2T genomes, T2T-CHM13 and T2T-YAO, and it becomes urgent to have a comparative study to test population specificity using the three reference genomes based on real case WES data. We here report our analysis along this line for 19 tumor samples collected from Chinese patients. The primary comparison of the exon regions among the three references reveals that the sequences in up to [~]1% target regions in YAO are widely diversified from GRCh38 and may lead to off-target in sequence capture. However, YAO still outperforms GRCh38 genomes by obtaining 7.41% more mapped reads. Due to more reliable read-mapping and closer phylogenetic relationship with the samples than GRCh38, YAO reduces half of variant calls of clinical significance which are mostly benign while keeping sensitivity in identifying pathogenic variants. YAO also outperforms CHM13 in reducing calls of Chinese-specific variants. Our findings highlight the critical need for employing population-specific reference genomes in genomic analysis to ensure accurate variant analysis and the significant benefits of tailoring these approaches to the unique genetic backgrounds of each ethnic group.

genomics↗

bioRxiv2024

FoldToken4: Consistent & Hierarchical Fold Language

Creating protein structure language has attracted increasing attention in unifing the modality of protein sequence and structure. While recent works, such as FoldToken1&2&3 have made great progress in this direction, the relationship between languages created by different models at different scales is still unclear. Moreover, models at multiple scales (different code space size, like 25, 26, [···], 212) need to be trained separately, leading to redundant efforts. We raise the question: Could a single model create multiscale fold languages? In this paper, we propose FoldToken4 to learn the consistent and hierarchical of multiscale fold languages. By introducing multiscale code adapters and token mixing techniques, FoldToken4 can generate multiscale languages from the same model, and discover the hierarchical token-mapping relationships across scales. To the best of our knowledge, FoldToken4 is the first effort to learn multi-scale token consistency and hierarchy in VQ research; Also, it should be more novel in protein structure language learning.

molecular biology↗

bioRxiv2024

Nonergodicity and Simpson's paradox in neurocognitive dynamics of cognitive control

Nonergodicity and Simpsons paradox present significant, yet underappreciated challenges in neuroscience. Leveraging brain imaging and behavioral data from over 4,000 children and a Bayesian computational model of cognitive dynamics, we investigated brain-behavior relationships underlying cognitive control at both between-subjects and within-subjects levels. Strikingly, we observed a reversal of associations of inhibitory control brain activations with dynamic behavioral measures when comparing between-subjects and within-subjects analyses, revealing the nonergodic nature of these processes. This nonergodicity was pervasive throughout the brain but most pronounced in the salience network. Additionally, within-subjects analysis uncovered dissociated brain representations of reactive and proactive control processes, as well as distinct brain-behavior associations for individuals who adaptively versus maladaptively regulated cognitive control. Our findings offer insights into dynamic neural mechanisms of cognitive control during a critical developmental period. This work highlights the importance of embracing nonergodicity in human neuroscience, with implications for both theoretical understanding and applications to AI and psychopathology.

neuroscience↗

bioRxiv2024

FoldToken3: Fold Structures Worth 256 Words or Less

Protein structure tokenization has attracted increasing attention in both protein representation learning and generation. While recent work, like FoldToken2 and ESM3, has achieved good reconstruction performance, the compressoin ratio is still limited. In this work, we propose FoldToken3, a novel protein structure tokenization method that can compress protein structures into 256 tokens or less and ensure the reconstruction quality comparable to FoldToken2. To the best of our knowledge, FoldToken3 is the most efficient, light-weight, and compression-friendly protein structure tokenization method. And it will benifit a wide range of protein structure-related tasks, such as protein structure alignment, generation, and representation learning. The work is still in progress and the code will be available upon acceptance.

molecular biology↗

bioRxiv2024

Linalool's Multifaceted Antimicrobial Potential: Unveiling its Antimicrobial Efficacy and Immunomodulatory Role Against Saprolegnia parasitica

Saprolegnia parasitica (S. parasitica) is one of the most virulent oomycete species in freshwater aquatic environments, causing severe saprolegniasis and leading to significant economic losses in the aquaculture industry. Thus far, the prevention and control of saprolegniasis face a shortage of medications. Linalool, a natural antibiotic alternative found in various essential oils, exhibits promising antimicrobial activity against a wide range of pathogens. In this study, the specific role of linalool in protecting S. parasitica infection at both in vitro and in vivo levels was investigated. Linalool showed multifaceted anti-oomycetes potential by both of antimicrobial efficacy and immunomodulatory efficacy. For in vitro test, linalool exhibited strong anti-oomycetes activity and mode of action included: (1) Linalool disrupted the cell membrane of the mycelium, causing the intracellular components leak out; (2) Linalool prohibited ribosome function, thereby inhibiting protein synthesis and ultimately affecting mycelium growth. Surprisingly, meanwhile we found the potential immune protective mechanism of linalool in the in vivo test: (1) Linalool enhanced the complement and coagulation system which in turn activated host immune defense and lysate S. parasitica cells; (2) Linalool promoted wound healing, tissue repair, and phagocytosis to cope with S. parasitica infection; (3) Linalool positively modulated the immune response by increasing the abundance of beneficial Actinobacteriota; (4) Linalool stimulated the production of inflammatory cytokines and chemokines to lyse S. parasitica cells. In all, our findings showed that linalool possessed multifaceted anti-oomycetes potential which would be a promising natural antibiotic alternative to cope with S. parasitica infection in the aquaculture industry.

microbiology↗

bioRxiv2024

FoldToken2: Learning compact, invariant and generative protein structure language

The equivariant nature of 3D coordinates has posed long term challenges in protein structure representation learning, alignment, and generation. Can we create a compact and invariant language that equivalently represents protein structures? Towards this goal, we propose FoldToken2 to transfer equivariant structures into discrete tokens, while maintaining the recoverability of the original structures. From FoldToken1 to FoldToken2, we improve three key components: (1) invariant structure encoder, (2) vector-quantized compressor, and (3) equivariant structure decoder. We evaluate FoldToken2 on the protein structure reconstruction task and show that it outperforms previous FoldToken1 by 20% in TMScore and 81% in RMSD. FoldToken2 is likely the first method that works well for both single-chain and multi-chain protein structure quantization. We believe that FoldToken2 will inspire further improvement in protein structure representation, alignment, and generation tasks. Online example is available at Colab.

molecular biology↗

bioRxiv2024

Cross-modality representation and multi-sample integration of spatially resolved omics data

Spatially resolved sequencing technologies have revolutionized our understanding of biological regulatory processes within the microenvironment by accessing the states of genomic regions, genes and proteins as well as spatial coordinates of cells. However, discrepancies between different modalities and samples hinder the analysis of spatial omics data, necessitating the development of advanced computational methods. In this article, we propose PRESENT, an effective and scalable contrastive learning framework, for the cross-modality representation and multi-sample integration of spatial multi-omics, epigenomics and transcriptomics data. Through comprehensive experiments on spatial datasets, PRESENT demonstrates superior performance across various species, tissues, and technologies. Specifically, PRESENT effectively integrates spatial dependency and omics information simultaneously, facilitating the detection of spatially functional domains and the exploration of biological regulatory mechanisms. Furthermore, PRESENT can be extended for the integrative analysis of tissue samples across different dissected regions or developmental stages, promoting the identification of hierarchical structures from systematic and spatiotemporal perspectives.

bioinformatics↗