Biology subjects

Zhao, B.

Publications and source records attributed to Zhao, B..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

An Integrated Analysis of Network Pharmacology, Molecular Docking, and Experiment Validation to Explore the Mechanism of Danbai Granules in Treating Sequelae of Pelvic Inflammatory Disease

PurposeTo explore the possible pharmacological mechanisms of Danbai Granules (DBG) against sequelae of pelvic inflammatory disease (SPID) by the method of network pharmacology and molecular docking combined with experimental validation. MethodsFirstly, biologically active compounds, targets of DBG, and related targets of SPID were collected from public databases. The protein- protein interaction (PPI) network, Gene GO and KEGG enrichment analysis were carried out via R language to find the potential biological processes and pathways of DBG against SPID. Subsequently, molecular docking was used to calculate the affinity between the top six targets and the top ten compounds, respectively. Finally, the above analysis results were verified by in vivo experiments. ResultsA total of 106 crossover genes were selected from 220 potential medicine genes and 952 SPID-related genes. PPI network analysis indicated that IL-6, IL-1{beta}, VEGFA, CASP3, PTGS2, JUN, etc., were core targets. GO and KEGG enrichment analysis revealed that PI3K-Akt, AGE-RAGE, IL-17, TNF, HIF-1 and Toll-like receptors signaling pathways were the main signaling pathways. Molecular docking showed that 15 pairs of target-ingredient combinations have good binding activity. The animal experiments showed that DBG administration inhibited the expression of TLR4/MyD88/NF-{kappa}B p65 signaling pathway-related proteins expression, altered the high expression of IL-6, IL-1{beta}, and low level of IL-4, IL-10, thereby relieving the pelvic inflammation of SPID. ConclusionThrough the network pharmacology and molecular docking, our findings predicted the active ingredients and potential targets of DBG in treating SPID. The experimental verification preliminarily revealed that DBG may inhibit the inflammatory response of SPID rats by regulating the TLR4/MyD88/NF-{kappa}B p65 signaling pathway. which provides a theoretical basis for the study of the pharmacodynamic material basis and mechanism of DBG against SPID at the comprehensive level.

pharmacology and toxicology↗

bioRxiv2023

Neurovascular Coupling is Required for Amygdala Neuronal Activation and Associated Emotional Behaviors in Mice, Depending on NMDA Receptor Subunit 2D-expressing Cerebral Arteriolar Smooth Muscle Cells

Emotion induces changes in regional cerebral blood flow (CBF), a manifestation of neurovascular coupling (NVC), yet whether NVC might feed back to modulate emotion actively remains unexplored. Here, we demonstrate that NVC actively and bidirectionally modulates stress-induced negative emotions. We established bidirectional manipulations of NVC in freely moving mice by employing integrated pharmacological, genetic, and arteriolar optogenetic approaches. Our results showed that both systemic and basolateral amygdala (BLA) region-specific NVC deficiencies heightened emotional responses when mice transitioned from a safe, familiar environment to anxiogenic environments, and local restoration of NVC in the BLA normalized these responses. Mechanistically, NVC dysfunction impairs the capacity of BLA neuronal scaling during state transitions, manifesting as a characteristic biphasic pattern of c-Fos topology. Namely, the NVC-deficient animal aberrantly adopts high-stress configurations under mild stress but regresses to low-stress templates during high-demand survival threats, thereby compromising defensive sustainability. Notably, the genetic NVC-enhancement model counteracts NVC impairments caused by chronic stress, thereby alleviating stress-driven emotional distress. These findings established NVC in the BLA as an allostatic program that fine-tunes neural circuit activity for emotional responses, with implications for understanding and treating emotional disorders.

neuroscience↗

bioRxiv2023

Endothelial cell derived microvesicles modulate cerebrovascular and brain aging via miR-17-5p and serve as potential biomarkers for vascular aging

Vascular aging, characterized by brain endothelial cells (ECs) senescence and dysfunction, has been known to lead to various age-related cerebrovascular and neurodegenerative diseases. However, its underlying mechanisms remain elusive. ECs derived microvesicles (EMVs) and exosomes (EEXs) carry the characteristics of parent cells and transfer their contents to modulate the functions of recipient cells, holding the potential to evaluate or regulate vascular aging. Here, we found that young or aged ECs released EMVs were more effective than their released EEXs on alleviating or aggravating mice cerebrovascular and brain aging as indicated by SA-{beta}-gal staining, cerebral blood flow, blood brain barrier function, aging related markers and cognitive ability test. We further identified that these EMVs regulated cerebrovascular and brain aging by transferring miR-17-5p and could modulate ECs senescence and functions via miR-17-5p/PI3K/Akt pathway. Plasma EMVs and their contained miR-17-5p (EMV-miR-17-5p) were significantly increased or decreased in the elderly, and were closely correlated with vascular aging. Receiver Operating Characteristic (ROC) analysis showed that the area under the curve was 0.724 for EMVs, 0.77 for EMV-miR-17-5p and 0.815 for their combination for distinguishing vascular aging. Our results revealed the novel roles for EMVs that could more effectively modulate vascular and brain aging than EEXs by regulating ECs functions through miR-17-5p/PI3K/Akt pathway, and also suggested that EMVs and EMV-miR-17-5p represent promising biomarkers and therapeutic targets for vascular aging.

neuroscience↗

bioRxiv2023

The mitochondrial multi-omic response to exercise training across tissues

Mitochondria are adaptable organelles with diverse cellular functions critical to whole-body metabolic homeostasis. While chronic endurance exercise training is known to alter mitochondrial activity, these adaptations have not yet been systematically characterized. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) mapped the longitudinal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats endurance trained for 1, 2, 4 or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart and skeletal muscle, while we detected mild responses in the brain, lung, small intestine and testes. The colon response was characterized by non-linear dynamics that resulted in upregulation of mitochondrial function that was more prominent in females. Brown adipose and adrenal tissues were characterized by substantial downregulation of mitochondrial pathways. Training induced a previously unrecognized robust upregulation of mitochondrial protein abundance and acetylation in the liver, and a concomitant shift in lipid metabolism. The striated muscles demonstrated a highly coordinated response to increase oxidative capacity, with the majority of changes occurring in protein abundance and post-translational modifications. We identified exercise upregulated networks that are downregulated in human type 2 diabetes and liver cirrhosis. In both cases HSD17B10, a central dehydrogenase in multiple metabolic pathways and mitochondrial tRNA maturation, was the main hub. In summary, we provide a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.

molecular biology↗

bioRxiv2023

Multiomic identification of key transcriptional regulatory programs during endurance exercise training

Transcription factors (TFs) play a key role in regulating gene expression. We conducted an integrated analysis of chromatin accessibility, DNA methylation, mRNA expression, protein abundance and phosphorylation across eight tissues in fifty rats of equally represented sexes following endurance exercise training (EET) to identify coordinated epigenomic and transcriptional changes and determine key TFs involved. We uncovered tissue-specific EET associated changes and TF motif enrichment across differentially expressed genes (DEGs), accessible regions (DARs), and methylated regions (DMRs). We discovered distinct routes of EET-induced regulation through either epigenomic alterations providing better access for TFs to affect target genes, or via changes in TF expression or activity enabling target gene responses. We identified TF motifs enriched among correlated epigenomic and transcriptomic alterations, DEGs correlated with exercise-related phenotypic and cell type composition changes, and EET-induced activity changes of TFs whose target genes are enriched for DEGs. This analysis elucidates the unique gene regulatory mechanisms mediating diverse transcriptional responses to EET across tissues.

genomics↗

bioRxiv2022

Systematic multi-trait AAV capsid engineering for efficient gene delivery

Broadening gene therapy applications requires manufacturable vectors that efficiently transduce target cells in humans and preclinical models. Conventional selections of adeno-associated virus (AAV) capsid libraries are inefficient at searching the vast sequence space for the small fraction of vectors possessing multiple traits essential for clinical translation. Here, we present Fit4Function, a generalizable machine learning (ML) approach for systematically engineering multi-trait AAV capsids. By leveraging a capsid library that evenly samples the manufacturable sequence space, reproducible screening data are generated to train accurate sequence-to-function models. Combining six models, we designed a multi-trait (liver-targeted, manufacturable) capsid library and validated 89% of library variants on all six predetermined criteria. Furthermore, the models, trained only on mouse in vivo and human in vitro Fit4Function data, accurately predicted AAV capsid variant biodistribution in macaque. Top candidates exhibited high production yields, efficient murine liver transduction, up to 1000-fold greater human hepatocyte transduction, and increased enrichment, relative to AAV9, in a screen for liver transduction in macaques. The Fit4Function strategy ultimately makes it possible to predict cross-species traits of peptide-modified AAV capsids and is a critical step toward assembling an ML atlas that predicts AAV capsid performance across dozens of traits.

synthetic biology↗

bioRxiv2022

Comparative transcriptome revealed potential genes related with drug resistance in Melanoma

Chemotherapy remains a relatively ineffective and unsatisfactory treatment because of drug resistance in melanoma (whether due to intrinsic resistance or the use of cytostatic drugs). In order to explore the genes and signaling pathways related to melanoma drug resistance, the study presented here obtained drug-resistant melanoma cell lines of A375 and M14 by gradually increasing the concentration of dacarbazine (DTIC), followed by comparative transcriptomics studies (RNA-seq) and real-time quantitative PCR (RT-qPCR) and Western Blotting validation. The results showed that after 8 months of continuous treatment, the IC50 values of A375 and M14 to DTIC were increased by more than 5 folds. Meanwhile, flow cytometry analysis found that drug-resistant melanoma cells have a significant ability to resist apoptosis induced by DTIC. Subsequently, RNA-seq revealed high expression of SENP1 and abnormal activation of the Hippo signaling pathway in drug-resistant cells. Finally, we found that compared with wild-type cells, the expressions of SENP1 and YAP were both up-regulated in drug-resistant cells via RT-qPCR and Western Blotting. Roles of SENP1 in drug resistance was finally verified via its overexpression in normal A375 cell lines. Therefore, this paper infers that there is a positive correlation between the ubiquitin-specific protease SENP1 and the drug resistance of melanoma. Meanwhile, the up-regulation of its expression may lead to changes in the Hippo signaling pathway and increase the resistance of melanoma to DTIC.

cancer biology↗

bioRxiv2022

Target Recycling Amplification Process for Digital Detection of Exosomal MicroRNAs Through Photonic Resonator Absorption Microscopy

Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of exosomal miRNAs using photonic resonator absorption microscopy (PRAM). Through toehold-mediated DNA strand displacement reactions, we achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. We then applied our TRAP system to quantify miRNA in exosomal total RNAs isolated from human cancer cell lines. Compared with traditional qRT-PCR methods, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulating miRNA biomarker quantification, where the miRNAs are present in low concentrations or sample volume, with potentials for frequent, low-cost, and minimally invasive point-of-care testing.

bioengineering↗

bioRxiv2022

The direct interaction with transcriptional factor TEAD4 implied a straightforward regulation mechanism of tumor suppressor NF2

As an output effecter of Hippo signaling pathway, the transcription factor TEAD and co-activator YAP play crucial functions in promoting cell proliferation and organ size. The tumor suppressor NF2 has been shown to activate LATS1/2 kinases and interplay with Hippo pathway to suppress YAP-TEAD complex. But, whether and how NF2 could directly regulate TEAD remains unknown. We identified a direct link and physical interaction between NF2 and TEAD4. NF2 interacted with TEAD4 through its FERM domain and the C-terminal tail, and decreased protein stability of TEAD4 independently of LATS1/2 and YAP. Furthermore, NF2 inhibited TEAD4 palmitoylation and retained the cytoplasmic translocation of TEAD4, resulting in ubiquitination and dysfunction of TEAD4. Moreover, the interaction with TEAD4 is required for NF2 function to suppress cell proliferation. These findings revealed a new role of NF2 as a binding partner and inhibitor of the transcription factor TEAD, and would shed light on an alternative mechanism of how NF2 functions as a tumor suppressor through the Hippo signaling cascade.

cell biology↗

bioRxiv2022

Monitoring the intestinal magnetic field with optically pumped atomic magnetometers

Research has shown the potential of magnetoenterography (MENG) for detecting intestinal diseases noninvasively by superconducting quantum interference devices (SQUIDs). Nevertheless, these devices need to operate under a cytogenetic environment maintained by liquid helium. In this paper, we record the intestinal magnetic field of a rabbit with optically pumped magnetometers (OPMs) at room temperature. It demonstrates that the OPM-based system has sufficient sensitivity to measure the intestinal magnetic fields of the rabbit, and can be potentially developed into a cost-effective and flexible MENG system.

physiology↗

bioRxiv2022

A compendium of genetic regulatory effects across pig tissues

The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in animal breeding and human biomedicine. Here we present results from the pilot phase of PigGTEx (http://piggtex.farmgtex.org/), where we processed 9,530 RNA-sequencing and 1,602 whole-genome sequencing samples from pigs. We build a pig genotype imputation panel, characterize the transcriptional landscape across over 100 tissues, and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We study interactions between genotype and breed/cell type, evaluate tissue specificity of regulatory effects, and elucidate the molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying about 80% of the genetic associations for 207 pig complex phenotypes, and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, corroborating the importance of pigs as a human biomedical model.

genomics↗

bioRxiv2022

Targeting AAV vectors to the CNS via de novo engineered capsid-receptor interactions

Viruses have evolved the ability to bind and enter cells through interactions with a wide variety of host cell macromolecules. Here, we screened for AAV capsids that bind two host cell proteins expressed on the mouse blood-brain barrier, LY6A or the related protein LY6C1. Introducing interactions with either protein target generated hundreds of capsids with dramatically enhanced central nervous system (CNS) tropisms. In contrast to the AAV-PHP.B capsid family, which interacts with LY6A and only exhibits its enhanced CNS tropism in a subset of mouse strains, the capsids that engage LY6C1 maintain their CNS tropism in BALB/cJ mice. Compared to conventional in vivo screens for CNS cell transducing capsids, a single round of protein target binding screening recovered significantly more capsids with enhanced performance that were validated in subsequent in vivo screens. Moreover, the initial screening round generated reproducible and quantitative target binding data that enabled the efficient machine learning-guided generation of more diverse targetspecific capsids. This work demonstrates that AAV capsids can be directly targeted to specific proteins to generate potent gene delivery vectors with known mechanisms of action and predictable tropisms.

synthetic biology↗

bioRxiv2022

scCobra: Contrastive cell embedding learning with domain adaptation for single-cell data integration

The rapid development of single-cell technologies has underscored the need for more effective methods in the integration and harmonization of single-cell sequencing data. The prevalent challenge of batch effects, resulting from technical and biological variations across studies, demands accurate and reliable solutions for data integration. Traditional tools often have limitations, both due to reliance on gene expression distribution assumptions and the common issue of over-correction, particularly in methods based on anchor alignments. Here we introduce scCobra, a deep neural network tool designed specifically to address these challenges. By leveraging a deep generative model that combines a contrastive neural network with domain adaptation, scCobra effectively mitigates batch effects and minimizes over-correction without depending on gene expression distribution assumptions. Additionally, scCobra enables online label transfer across datasets with batch effects, facilitating the continuous integration of new data without retraining, and offers features for batch effect simulation and advanced multi-omic batch integration. These capabilities make scCobra a versatile data integration and harmonization tool for achieving accurate and insightful biological interpretations from complex datasets.

bioinformatics↗

bioRxiv2022

Genetic Dissection of Mutual Interference between Two Consecutively Learned Tasks in Drosophila

Animals can continuously learn different tasks to adapt to changing environments and therefore have strategies to effectively cope with inter-task interference, including both proactive interference (Pro-I) and retroactive interference (Retro-I). Many biological mechanisms are known to contribute to learning, memory, and forgetting for a single task, however, mechanisms involved only when learning sequential different tasks are relatively poorly understood. Here, we dissect the respective molecular mechanisms of Pro-I and Retro-I between two consecutive associative learning tasks in Drosophila. Pro-I is more sensitive to inter-task interval (ITI) than Retro-I. They occur together at short ITI (<20 min), while only Retro-I remains significant at ITI beyond 20 min. Acutely overexpressing Corkscrew (CSW), an evolutionarily conserved protein tyrosine phosphatase SHP2, in mushroom body (MB) neurons reduces Pro-I, whereas acute knockdown of CSW exacerbates Pro-I. Such function of CSW is further found to rely on the {gamma} subset of MB neurons and the downstream Raf/MAPK pathway. In contrast, manipulating CSW does not affect Retro-I as well as a single learning task. Interestingly, manipulation of Rac1, a molecule that regulates Retro-I, does not affect Pro-I. Thus, our findings suggest that learning different tasks consecutively triggers distinct molecular mechanisms to tune proactive and retroactive interference.

animal behavior and cognition↗

bioRxiv2022

Genealogical inference and more flexible sequence clustering using iterative PopPUNK

Bacterial genome data are accumulating at an unprecedented speed due the routine use of sequencing in clinical diagnoses, public health surveillance and population genetics studies. Genealogical reconstruction is fundamental to many of these uses, however, inferring genealogy from large-scale genome datasets quickly, accurately, and flexibly is still a challenge. Here, we extend an alignment- and annotation-free method, PopPUNK, to increase its flexibility and interpretability across datasets. Our method, iterative-PopPUNK, rapidly produces multiple consistent cluster assignments across a range of sequence identities. By constructing a partially resolved genealogical tree with respect to these clusters, users can select a resolution most appropriate for their needs. We demonstrated the accuracy of clusters at all levels of similarity and genealogical inference of iterative-PopPUNK based on simulated data and obtained phylogenetically-concordant results in real datasets from seven bacterial species. Using two example sets of Escherichia/Shigella genomes and Vibrio parahaemolyticus genomes we show that iterative-PopPUNK can achieve cluster resolutions ranging from phylogroup down to sequence typing (ST). The iterative-PopPUNK algorithm is implemented in the PopPUNK_iterate program, available as part of PopPUNK package.

bioinformatics↗

bioRxiv2022

Evolution of spatial and temporal cis-regulatory divergence between marine and freshwater sticklebacks

Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are enriched in genomic regions associated with marine-freshwater divergence, supporting an important role for cis-regulatory differences in adaptive evolution of sticklebacks. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes and supports a fundamental role for cis-regulatory changes in rapid adaptation to new environments.

evolutionary biology↗

bioRxiv2022

Neuronal pentraxin Nptx2 regulates complement activity in the brain

Complement overactivation mediates microglial synapse elimination in neurological diseases like Alzheimers disease and frontotemporal dementia (FTD), but how complement activity is regulated in the brain remains largely unknown. We identified that the secreted neuronal pentraxin Nptx2 binds complement C1q and thereby regulates its activity in the brain. Nptx2-deficient mice show increased complement activity and C1q-dependent microglial synapse engulfment and loss of excitatory synapses. In a neuroinflammation culture model and in aged TauP301S mice, AAV-mediated neuronal overexpression of Nptx2 was sufficient to restrain complement activity and ameliorate microglia-mediated synapse loss. Analysis of human CSF samples from a genetic FTD cohort revealed significantly reduced levels of Nptx2 and Nptx2-C1q protein complexes in symptomatic patients, which correlated with elevated C1q and activated C3. Together, these results show that Nptx2 regulates complement activity and microglial synapse elimination in the healthy and diseased brain and that diminished Nptx2 levels might exacerbate complement-mediated neurodegeneration in FTD patients.

neuroscience↗

bioRxiv2022

Oligomeric polymorphism of HIV-1 Vpu protein in lipid environment and in solution

The HIV-1 encoded protein Vpu forms an oligomeric ion channel/pore in membranes and interacts with multiple host proteins to support virus lifecycle. However, Vpu molecular mechanisms are currently not well understood. The structures of full-length Vpu in its monomeric and oligomeric forms are unknown, although both the monomer and oligomer are deemed important. Here, we report on the diversity of Vpu oligomeric structures and how the environment affects the Vpu oligomer formation. We produced a uniquely designed MBP-Vpu chimera protein in E. coli in soluble form. We subjected this protein to analytical size exclusion chromatography (SEC) and negative staining electron microscopy (nsEM). Strikingly, we found that MBP-Vpu forms stable oligomers in solution, presumably driven by Vpu transmembrane domain self-association. Our coarse modeling suggests that these oligomers are pentamers, in agreement with the pentameric membrane-bound Vpu. To the best of our knowledge, this is the first observation of Vpu self-association out of lipid membrane environment. We further found that MBP-Vpu oligomer stability decreases when the protein was reconstituted in lipid membrane mimetics, such as {beta}-DDM, and mixtures of lyso PC/PG or DHPC/DHPG--In these cases significant oligomer heterogeneity was observed with oligomeric order lesser than that of MBP-Vpu oligomer in solution, but larger oligomers were observed as well. Importantly, we found that in lyso PC/PG, above certain protein concentration, MBP-Vpu forms linear array-like structures, which is also novel. Thus, our studies provide unique information about Vpu protein quaternary organization by capturing multiple Vpu oligomeric structures, which we believe are physiologically relevant.

biochemistry↗