Biology subjects

Yao, Y.

Publications and source records attributed to Yao, Y..

At least 127 records · Page 7Linked to original sources

bioRxiv2023

Large-scale population genomics of Malayan pangolins reveals deep diversification and a new species

BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.

genomics↗

bioRxiv2023

Optogenetic strategies for optimizing the performance of biosensors of membrane phospholipids in live cells

High-performance biosensors play a crucial role in elucidating the intricate spatiotemporal regulatory roles and dynamics of membrane lipids. However, enhancing their sensitivity and substrate-detecting capabilities remains a significant challenge. Here, we presented optogenetic-based strategies to optimize phospholipid biosensors. These strategies involved pre-sequestering unbound probes in the cell nucleus to minimize background signals in the cytoplasm. These stored probes could be released from the nucleus in response to blue light according to experimental requirements. Furthermore, we employed optically-controlled phase separation to generate punctate probes that amplified signals and facilitated the visualization of phospholipids in cells. These improved phospholipid biosensors hold great potential for enhancing our understanding of the spatiotemporal dynamics and regulatory roles of membrane lipids in live cells and this methodological insights might be valuable for developing other high-performance biosensors.

cell biology↗

bioRxiv2023

Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasia

About 75% cases of epilepsy begin during childhood, and 10 - 30% of pediatric epilepsy patients are resistant to drug treatment. The predominant seizure type in children is focal cortical dysplasia (FCD) which is highly associated with drug-resistant epilepsy, but its underlying cause is poorly understood. We performed single-cell RNA sequencing and patch-clamp recording on fresh brain tissues obtained from pediatric FCD patients shortly after surgery to reveal critical factors contributing to FCD. We report that known epilepsy genes or significant transcriptomic alterations occur in only a few neuronal subgroups, suggesting that epilepsy-associated neurons cluster into only a few neuronal subtypes. These epilepsy-subtypes displayed significant epilepsy-related transcriptomic alterations, especially in the genes associated with excitation/inhibition balance and neuron functional signal pathways. Among eight epilepsy-subtypes, L2_4_CUX2_YWHAH and PVALB_RGS5 subtypes showed the most prominent alterations in FCD patient tissues. Supporting PV-neurons being important, recording from fast-spiking/parvalbumin-containing neurons in acute FCD patient brain slices revealed reduced excitatory synaptic inputs, implicating lower activity in these neurons and fewer synaptic inputs onto them. A higher percentage of mitochondria genes, and likely higher activity in the pathways associated with oxidative phosphorylation and ATP biosynthetic process, was observed in the epilepsy-subtypes, suggesting a high energy expenditure in them. Interestingly, the activity of the above two pathways in most epilepsy-subtypes was lower in the FCD patients, suggesting these subtypes may be more vulnerable to energy deficit in epilepsy. Altogether, transcriptomics is significantly altered in only a few neuronal subtypes in pediatric FCD patient brains. These selective epilepsy-subtypes may play prominent roles in the genesis of pediatric drug-resistant seizure and targeting them may provide new treatment options.

bioinformatics↗

bioRxiv2023

The MEK-ERK signaling pathway promotes maintenance of cardiac chamber identity

Ventricular and atrial cardiac chambers have unique structural and contractile characteristics that underlie their distinct functions. Intriguingly, the maintenance of chamber-specific features requires active reinforcement, even in differentiated cardiomyocytes. Prior studies in zebrafish have shown that sustained FGF signaling acts upstream of nkx2.5 to maintain ventricular identity, but the rest of this maintenance pathway remains unclear. Here, we show that MEK1/2-ERK1/2 signaling acts downstream of FGF and upstream of nkx2.5 to promote ventricular maintenance. Inhibition of MEK signaling, like inhibition of FGF signaling, results in ectopic atrial gene expression and reduced ventricular gene expression in ventricular cardiomyocytes. FGF and MEK signaling both influence ventricular maintenance over a similar timeframe, when phosphorylated ERK (pERK) is present in the myocardium. However, the role of FGF-MEK activity seems to be context-dependent: some ventricular regions are more sensitive than others to inhibition of FGF-MEK signaling. Additionally, in the atrium, although endogenous pERK does not induce ventricular traits, heightened MEK signaling can provoke ectopic ventricular gene expression. Together, our data reveal chamber-specific roles of MEK-ERK signaling in the maintenance of ventricular and atrial identities. SUMMARY STATEMENTThe MEK-ERK signaling pathway plays distinct roles in the maintenance of ventricular and atrial cardiomyocyte identities.

developmental biology↗

bioRxiv2023

Accurate quantification of lysyl oxidase concentration in human tissue

The family of Lysyl oxidase enzymes play fundamental roles in the formation of the extracellular matrix, through catalyzing the crosslinking of collagen and elastin fibers. Lysyl oxidase (LOX) -- one of the 5 family members (LOX, LOXL1-4), is a disease biomarker, with blood concentration positively correlating with progression of fibrosis or cancer. An accurate quantification of LOX concentration can support diagnosis, monitoring of disease progression or treatment success. However, reported LOX concentrations in human blood are inconsistent. Therefore, a novel, high-throughput and sensitive digital enzyme-linked immunosorbent assay was developed using two validated and selective human anti-LOX antibodies and single molecule array technology. Both, the 56 kDa pro-form and the 32 kDa active form can be accurately measured from recombinant and native protein. The serum LOX concentration correlated with LOX activity measured in the same platform using a bio-probe. The usefulness of this technology was demonstrated in serum from bladder cancer patients wherein LOX concentration was significantly higher compared to the healthy subjects. This study demonstrates the validation and use of a sensitive and accurate method for measuring LOX concentration in human samples. This novel method may be superior than some commercially available enzyme-linked immunosorbent assay kits for accurate measurement of LOX concentrations in clinical settings.

molecular biology↗

bioRxiv2023

Engineering transposon-associated TnpB-1 ωRNA system for efficient gene editing and disease treatment in mouse

Transposon-associated ribonucleoprotein TnpB is known to be the ancestry endonuclease of diverse Cas12 effector proteins from type-V CRISPR system. Given its small size (409 aa), it is of interest to examine whether engineered TnpB could be used for efficient mammalian genome editing. Here, we showed that the gene editing activity of native TnpB in mouse embryos was already higher than previously identified small-sized Cas12f1. Further stepwise engineering of noncoding RNA ({omega}RNA or reRNA) component of TnpB significantly elevated the nuclease activity of TnpB. Notably, an optimized TnpB-{omega}RNA system could be efficiently delivered in vivo with single adeno-associated virus (AAV) and prevented the disease phenotype in a tyrosinaemia mouse model. Thus, the engineered miniature TnpB system represents a new addition to the current genome editing toolbox, with the unique feature of the smallest effector size that facilitate efficient AAV delivery for editing of cells and tissues.

molecular biology↗

bioRxiv2023

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3 untranslated region alternative polyadenylation). We explored the tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species. One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.

genetics↗

bioRxiv2023

Truly tiny acoustic biomolecules for ultrasound imaging and therapy

Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of conventional bubble-based agents. Here we describe bicones, truly tiny acoustic contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures naturally produced in buoyant microbes. We show that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.

synthetic biology↗

bioRxiv2023

Blood flow directionality establishes the SCN as source and OVLT as target within a new vascular portal pathway

The suprachiasmatic nucleus (SCN) is the locus of a brain clock that sets the phase of oscillation in cells throughout the brain and body. Anatomical evidence reveals a portal system linking the SCN and the OVLT (here termed SCN-OVLTp). This discovery begs the question of the direction of blood flow and the nature of diffusible signals that flow in this specialized vasculature. Here we show unequivocally that the direction of blood flow is from the SCN to the OVLT, that the rate of flow is under circadian regulation, and that vasopressin (AVP) is present in portal vessels following systemic injection. These findings highlight a previously unknown CNS communication pathway. It is well established that the SCN is required for circadian regulation of AVP in the CSF and that the OVLT bears AVP receptors. Specifically, SCN neurons are necessary for time-stamped signals such as the peptide AVP, that can travel via portal veins to a target in the OVLT. The OVLT, a circumventricular organ offering a "window to the brain," can relay neural and diffusible signals to broad brain areas via its efferent connections and via the CSF. We conclude that the SCN-OVLTp, like that of the pituitary portal system, discovered almost a century ago, allows neurosecretions to reach nearby specialized target sites, thereby avoiding dilution in the systemic blood. In both of these brain portal pathways, the target site, namely the pituitary and OVLT respectively, relay signals broadly, to both the brain and the rest of the body.

neuroscience↗

bioRxiv2023

Modeling of lung-liver interaction during infection in a human microfluidic organ-on-a-chip

BackgroundInfections of the respiratory tract such as pneumonia or COVID-19 cause high mortality and morbidity worldwide. Organ-on-a-chip (OC) technologies have been developed in the last years to establish human-based disease models, to study basic disease mechanisms and to provide a tool to speed up drug development. The aim of this study was to establish a lung-liver microfluidic system to study the interaction of both organ modules during infection. MethodsA two organ (lung / liver) microfluidic system was established using primary human bronchial (HBECs) or alveolar type epithelial cells (ATC) for the lung module and Huh-7 cells for the liver module. Inactivated non typeable Haemophilus influenzae (NTHi) and Pseudomonas aeruginosa PAO1 (PAO1) were applied to the lung module. Secreted mediators were screened by dot-blot analysis and quantified. The effect of lung epithelial bacterial stimulation on the liver cell transcriptome was analyzed by mRNA sequencing. ResultsLung and liver cells established stable cultures in a circulatory microfluidic system. Activation of HBECs or ATCs with NTHi or PAO1 resulted in the secretion of multiple inflammatory mediators into the microfluidic medium including TNF-, monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-3 (MIP-3). Addition of lung cells and application of bacterial onto the HBECs module resulted in the gross change of the transcriptome of the liver cell module. Gene ontology enrichment analysis showed the induction of various pathways involved in host defense, metabolisms, repair, and acute phase response. InterpretationIn conclusion, a two-organ lung/liver microfluidic system was established to study the interaction of the organ modules during infection. Mediators released from epithelial culture modules into the microfluidic circulation after exposure to bacterial pathogens significantly modify the gene expression patterns of liver cells. FundingThis research was funded by the German Federal Ministry of Education and Research (BMBF), 031L0153 VISION "Alternativmethoden zum Tierversuch" and the Dr. Rolf M. Schwiete Stiftung.

cell biology↗

bioRxiv2023

A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism

The recent outbreak of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a severe threat to the global public health and economy, however, effective drugs to treat COVID-19 are still lacking. Here, we employ a deep learning-based drug repositioning strategy to systematically screen potential anti-SARS-CoV-2 drug candidates that target the cell entry mechanism of SARS-CoV-2 virus from 2,635 FDA-approved drugs and 1,062 active ingredients from Traditional Chinese Medicine herbs. In silico molecular docking analysis validates the interactions between the top compounds and host receptors or viral spike proteins. Using a SARS-CoV-2 pseudovirus system, we further identify several drug candidates including Fostamatinib, Linagliptin, Lysergol and Sophoridine that can effectively block the cell entry of SARS-CoV-2 variants into human lung cells even at a nanomolar scale. These efforts not only illuminate the feasibility of applying deep learning-based drug repositioning for antiviral agents by targeting a specified mechanism, but also provide a valuable resource of promising drug candidates or lead compounds to treat COVID-19.

microbiology↗

bioRxiv2023

Mechanisms underlying the therapeutic effects of Semen Cuscutae in treating Recurrent Spontaneous Abortion based on Network Pharmacology and Molecular Docking

BackgroundThis paper aims to analyze the active components of SC by network pharmacology and screen the most stable compounds with TNF-a by molecular docking, to explore the mechanism of SC treatment of RSA and provide theoretical basis for drug development. MethodsActive compounds of SC and the potential inflammatory targets of RSA were obtained from the Traditional Chinese Medicine Systematic Pharmacology Database and GeneCard, respectively. The interaction network of RSA-SC-target gene was accomplished and Visualizing by STRING database and Cytoscape software.GO and KEGG pathway enrichment analyses were obtained from DAVID to further explore the RSA mechanism and therapeutic effects of SC. Interactions between TNF- and active compounds were analyzed by molecular docking. Results10 active ingredients and 128 target genes were screened from SC, and 79 of them intersected with RSA target inflammatory genes,which were considered to be potential therapeutic targets. Network pharmacological analysis showed that Sesamin, matrine, matrol and other SC active components had good correlation with the inflammatory target genes of RSA.Related genes include PGR, PTGS1, PTGS2, TGFB1 and CHRNA7. Multiple signaling pathways are involved in RSA pathogenesis,sunh as TNF- signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, proteoglycans in cancer, FoxO signaling pathway, etc. Molecular docking results suggested that sesamin was the most appropriate natural TNFis. ConclusionOur findings provide an important role and basis for further research on the molecular mechanism of SC treatment of RSA and drug development of TNFis.

bioinformatics↗

bioRxiv2023

Effect of Intermittent Pneumatic Compression on Preventing Deep Vein Thrombosis Using Microfluidic Vein Chip

Deep vein thrombosis (DVT) is a common disease often occurring in the lower limb veins of bedridden patients. Intermittent pneumatic compression (IPC) has been considered an effective approach to solve this problem. In our previous research, 264 patients were randomly treated either with IPC for one or eight hours per day. The incidence of severe venous thrombosis was significantly lowered in the IPC group than in the control group. However, it is still a chanllenge to real-time monitoring the blood flow and thrombus formation process during IPC operation periods. Here we made a microfluidic vein chip with valves embedded in a flexible channel that can mimic the compression of vessels by IPC contractrion. Driven by inlet blood velocity obtained clinally, numerical simulation were conducted to identify the shear stress and laminar pressure distribution in the vein. The obtained results showed that the thrombus formation can be reduced with Higher compressive pressure and smaller time interval. 24s interval time and 40mmHg maximum contractive pressure was considered to be the most appropriate parameters for DVT prevention. This vein chip offers a new approach in vitro to observe the working mechanism of IPC device, offering important data for its further clinical standard regulation.

bioengineering↗

bioRxiv2023

GTP signaling links metabolism, DNA repair, and responses to genotoxic stress

How cell metabolism regulates DNA repair is incompletely understood. Here, we define a GTP-mediated signaling cascade that links metabolism to DNA repair and has significant therapeutic implications. GTP, but not other nucleotides, regulates the activity of Rac1, a G protein, that promotes the dephosphorylation of serine 323 on Abl-interactor 1 (Abi-1) by protein phosphatase 5 (PP5). Dephosphorylated Abi-1, a protein previously not known to activate DNA repair, promotes non-homologous end joining. In patients and mouse models of glioblastoma, Rac1 and dephosphorylated Abi-1 mediate DNA repair and resistance to standard of care genotoxic treatments. The GTP-Rac1-PP5-Abi-1 signaling axis is not limited to brain cancer, as GTP supplementation promotes DNA repair and Abi-1-S323 dephosphorylation in non-malignant cells and protects mouse tissues from genotoxic insult. This unexpected ability of GTP to regulate DNA repair independently of deoxynucleotide pools has important implications for normal physiology and cancer treatment.

cancer biology↗

bioRxiv2023

Taste papilla cell differentiation requires tongue mesenchyme via ALK3-BMP signaling to regulate the production of secretory proteins

Taste papillae are specialized organs each of which is comprised of an epithelial wall hosting taste buds and a core of mesenchymal tissue. In the present study, we report that during the early stages of embryonic development, bone morphogenetic protein (BMP) signaling mediated by type 1 receptor ALK3 in the tongue mesenchyme is required for the epithelial Wnt/{beta}-catenin activity and taste papilla cell differentiation. Mesenchyme-specific knockout (cKO) of Alk3 using Wnt1-Cre and Sox10-Cre resulted in an absence of taste papillae at E12.0. Biochemical and cell differentiation analyses demonstrated that mesenchymal ALK3-BMP signaling governs the production of previously unappreciated secretory proteins, i.e., suppresses those that inhibiting and facilitates those promoting taste cell differentiation. Bulk RNA-Sequencing analysis revealed many more differentially expressed genes (DEGs) in the tongue epithelium than in the mesenchyme in Alk3 cKO vs control. Moreover, we detected a down-regulated epithelial Wnt/{beta}-catenin signaling, and taste papilla development in the Alk3 cKO was rescued by GSK3{beta} inhibitor LiCl, but not Wnt3a. Our findings demonstrate for the first time the requirement of tongue mesenchyme in taste papilla cell differentiation. Summary statementThis is the first set of data to implicate the requirement of tongue mesenchyme in taste papilla cell differentiation.

developmental biology↗

bioRxiv2023

Coronary Artery Disease Risk Gene PRDM16 is Preferentially Expressed in Vascular Smooth Muscle Cells and a Potential Novel Regulator of Smooth Muscle Homeostasis

ObjectiveVascular smooth muscle cells (VSMCs) are the primary contractile component of blood vessels and can undergo phenotypic switching from a contractile to a synthetic phenotype in vascular diseases such as coronary artery disease (CAD). This process leads to decreased expression of SMC lineage genes and increased proliferative, migratory and secretory abilities that drive disease progression. Super-enhancers (SE) and occupied transcription factors are believed to drive expression of genes that maintain cell identify and homeostasis. The goal of this study is to identify novel regulator of VSMC homeostasis by screening for SE-regulated transcription factors in arterial tissues. Approach and ResultsWe characterized human artery SEs by analyzing the enhancer histone mark H3K27ac ChIP-seq data of multiple arterial tissues. We unexpectedly discovered the transcription factor PRDM16, a GWAS identified CAD risk gene with previously well-documented roles in brown adipocytes but with an unknown function in vascular disease progression, is enriched with artery-specific SEs. Further analysis of public bulk RNA-seq and scRNA-seq datasets, as well as qRT-PCR and Western blotting analysis, demonstrated that PRDM16 is preferentially expressed in arterial tissues and in contractile VSMCs but not in visceral SMCs, and down-regulated in phenotypically modulated VSMCs. To explore the function of Prdm16 in vivo, we generated Prdm16 SMC-specific knockout mice and performed histological and bulk RNA-Seq analysis of aortic tissues. SMC-deficiency of Prdm16 does not affect the aortic morphology but significantly alters expression of many CAD risk genes and genes involved in VSMC phenotypic modulation. Specifically, Prdm16 negatively regulates the expression of Tgfb2 that encodes for an upstream ligand of TGF-{beta} signaling pathway, potentially through binding to the promoter region of Tgfb2. These transcriptomic changes likely disrupt VSMC homeostasis and predispose VSMCs to a disease state. ConclusionsOur results suggest that the CAD risk gene PRDM16 is preferentially expressed in VSMCs and is a novel regulator of VSMC homeostasis. Future studies are warranted to investigate its role in VSMCs under pathological conditions such as atherosclerosis.

cell biology↗

bioRxiv2023

pan-ECM: live brain extracellular matrix imaging with protein-reactive dye

The brain extracellular matrix (ECM), consisting of proteins and glycosaminoglycans, is a critical scaffold in the development, homeostasis, and disorders of the central nervous system (CNS) and undergoes remodeling in response to environmental cues. Live imaging of brain ECM structure represents a native view of the brain ECM but, until now, remains challenging due to the lack of a robust fluorescent labeling approach. Here, we developed a pan-ECM method for labeling the entire (Greek: pan) brain ECM network by screening and delivering a protein-reactive dye into the brain. pan-ECM enables imaging of ECM compartments in live brain tissue, including the interstitial matrix, basement membrane (BM), and perineuronal nets (PNNs), and even the ECM in glioblastoma and stroke mouse brains. This approach provides access to the structure and dynamics of the ECM and enhances our understanding of the complexities of the brain ECM and its contribution to brain health and disease.

neuroscience↗

bioRxiv2023

Dynamics of vegetation cover and its driving factors in the Qinling-Daba Mountains on regional scale for 1986-2019

The Qinling-Daba Mountains is the transitional zone of the north and south of China. The vegetation in this area, characterized by complexity, heterogeneity and transition, is particularly sensitive to global climate change and human activities. Based on the normalized vegetation index (NDVI) data of the growing season from 1986 to 2019, which was synthesized by Landsat series satellite data on Google Earth Engine, this paper uses the methods of spatial analysis and Geo-detectors to clarify dynamics of vegetation cover and its main driving factors in the Qinling-Daba Mountains. The results show that: (1) vegetation coverage in study area shows a U-shaped NDVI distribution pattern in latitude, anti-U-shaped patterns in longitude and with altitude ascending. (2) the dynamics of vegetation coverage can be divided into two periods according to the result of MK mutation test (the breakthrough increasing period around 2005) and the trend of NDVI change: the slow increasing period with an increasing rate of 0.25%/a from 1986 to 2004 (R2 0.74), and the rapid increasing period with an increasing rate of 0.30%/a from 2005 to 2019 (R2 0.92). (3) Soil type, landform, vegetation type, land use type and annual average temperature are the main driving factors of vegetation dynamics in the Qinling-Daba Mountains, while annual precipitation, population density and GDP are the secondary driving factors of vegetation dynamics. The land use type and land management policies in the Qinling-Daba Mountains have a strong impact on vegetation cover change, and the climate warming in recent decades plays more important role than precipitation on the vegetation dynamics. These results are of great significance to comprehensively understand the impact of global climate warming and human activities on the natural environment of the Qinling-Daba Mountains.

ecology↗