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Gao, W.

Publications and source records attributed to Gao, W..

At least 109 records · Page 6Linked to original sources

Comparative study of curvature sensing mediated by F-BAR domain and an intrinsically disordered region of FBP17

Membrane curvature has emerged as an intriguing physical organization principle underlying biological signaling and membrane trafficking. FBP17 of the CIP4/FBP17/Toca-1 F-BAR family is unique in the BAR family because its structurally folded F-BAR domain does not contain any hydrophobic motifs that insert into lipid bilayer. While it has been widely assumed so, whether the banana-shaped F-BAR domain alone can sense curvature has never been experimentally demonstrated. Using a nanopillar-supported lipid bilayer system, we found that the F-BAR domain of FBP17 displayed minimal curvature sensing in vitro. We further identified an alternatively spliced intrinsically disordered region (IDR) of FBP17 next to its F-BAR domain that is conserved in sequence across species. The IDR senses membrane curvature and its sensing ability greatly exceeds that of F-BAR domain alone. In living cells, presence of the IDR domain changed the dynamics of FBP17 recruitment in a curvature-coupled cortical wave system. Collectively, we propose that FBP17 does sense curvature but contrary to the common belief, its curvature sensing capability largely originates from its disordered region, not F-BAR domain itself.

biophysics↗

Enabling in vivo Analysis Via Nanoparticle-mediated Intracellular Assay Probe Delivery: Using RAS as the Prototype

Many experimental protocols must be executed in vitro due to a lack of cell-permeable analysis probes. For instance, the cellular signaling moderator RAS proteins alternate between the active GTP-binding and the inactive GDP-binding states. Though many GTP analogs can serve as probes for RAS activity analysis, their cell impermeability renders in vivo analysis impossible. On the other hand, the lipid/calcium/phosphate (LCP) nanoparticle has enabled efficient intracellular delivery of a nucleotide analog as a chemotherapy agent. Thus, using RAS analysis and LCP nanoparticle as the prototype, we tackled the cell-impermeability issue via nanoparticle-mediated intracellular delivery of the analysis probe. Briefly, BODIPY-FT-GTP-{gamma}-S, a GTP analog that becomes fluorescent only upon protein binding, was chosen as the analysis probe, so that GTP binding can be quantified by fluorescent activity. BODIPY-FT-GTP-{gamma}-S-loaded LCP-nanoparticle was synthesized for efficient intracellular BODIPY-FT-GTP-{gamma}-S delivery. Binding of the delivered BODIPY-FT-GTP-{gamma}-S to the RAS proteins were consistent with previously reported observations; the RAS GTP binding activity was reduced in serum-starved cells; and a transient activation peak of the binding activity was observed upon subsequent serum reactivation of the cells. In a word, nanoparticle-mediated probe delivery enabled an in vivo RAS analysis method. The approach should be applicable to a wide variety of analysis protocols.

biochemistry↗

A novel biparatopic antibody-ACE2 fusion that blocks SARS-CoV-2 infection: implications for therapy

In the absence of a proven effective vaccine preventing infection by SARS-CoV-2, or a proven drug to treat COVID-19, the positive results of passive immune therapy using convalescent serum provides a strong lead. We have developed a new class of tetravalent, biparatopic therapy, 89C8-ACE2. It combines the specificity of a monoclonal antibody (89C8) that recognizes the relatively conserved N-terminal domain (NTD) of the viral S glycoprotein, and the ectodomain of ACE2, which binds to the receptor-binding domain (RBD) of S. This molecule shows exceptional performance in vitro, inhibiting the interaction of recombinant S1 to ACE2 and transduction of ACE2-overexpressing cells by S-pseudotyped lentivirus with IC50s substantially below 100 pM, and with potency approximately 100-fold greater than ACE2-Fc itself. Moreover, 89C8-ACE2 was able to neutralize authentic virus infection in a standard assay at low nanomolar concentrations, making this class of molecule a promising lead for therapeutic applications.

immunology↗

Cross-neutralization antibodies against SARS-CoV-2 and RBD mutations from convalescent patient antibody libraries

The emergence of coronavirus disease 2019 (COVID-19) pandemic led to an urgent need to develop therapeutic interventions. Among them, neutralizing antibodies play crucial roles for preventing viral infections and contribute to resolution of infection. Here, we describe the generation of antibody libraries from 17 different COVID-19 recovered patients and screening of neutralizing antibodies to SARS-CoV-2. After 3 rounds of panning, 456 positive phage clones were obtained with high affinity to RBD (receptor binding domain). Then the positive clones were sequenced and reconstituted into whole human IgG for epitope binning assays. After that, all 19 IgG were classified into 6 different epitope groups or Bins. Although all these antibodies were shown to have ability to bind RBD, the antibodies in Bin2 have more superiority to inhibit the interaction between spike protein and angiotensin converting enzyme 2 receptor (ACE2). Most importantly, the antibodies from Bin2 can also strongly bind with mutant RBDs (W463R, R408I, N354D, V367F and N354D/D364Y) derived from SARS-CoV-2 strain with increased infectivity, suggesting the great potential of these antibodies in preventing infection of SARS-CoV-2 and its mutations. Furthermore, these neutralizing antibodies strongly restrict the binding of RBD to hACE2 overexpressed 293T cells. Consistently, these antibodies effectively neutralized pseudovirus entry into hACE2 overexpressed 293T cells. In Vero-E6 cells, these antibodies can even block the entry of live SARS-CoV-2 into cells at only 12.5 nM. These results suggest that these neutralizing human antibodies from the patient-derived antibody libraries have the potential to become therapeutic agents against SARS-CoV-2 and its mutants in this global pandemic.

immunology↗

Novel Vβ specific germline contacts shape an elite controller T cell response

Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by V{beta}2, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of V{beta}2-containing TCRs and correlates with an unusual V-V{beta} interface, CDR loop conformations, and V{beta}2-specific germline contacts with peptide. V{beta}2 and Ld may represent "specialist" components for antigen recognition that allow for particularly strong and focused T cell responses.

immunology↗

Light-Sheet Fluorescence Imaging Charts the Gastrula Origin of Vascular Endothelial Cells in Early Zebrafish Embryos

It remains challenging to construct a complete cell lineage map of the origin of vascular endothelial cells in any vertebrate embryo. Here, we report the application of in toto light-sheet fluorescence imaging of embryos to tracing the origin of vascular endothelial cells (ECs) at single-cell resolution in zebrafish. We first adapted a previously-reported method to mount embryos and light-sheet imaging, created an alignment, fusion, and extraction all-in-one software (AFEIO) for processing big data, and performed quantitative analysis of cell lineage relationships using commercially-available Imaris software. Our data revealed that vascular ECs originated from broad regions of the gastrula along the dorsal-ventral and anterior-posterior axes, of which the dorsal-anterior cells contributed to cerebral ECs, the dorsal-lateral cells to anterior trunk ECs, and the ventral-lateral cells to posterior trunk and tail ECs. Therefore, this work, to our knowledge, charts the first comprehensive map of the gastrula origin of vascular ECs in zebrafish, and has potential applications for studying the origin of any embryonic organs in zebrafish and other model organisms.

developmental biology↗

A Chemical-genetics and Nanoparticle Enabled Approach for in vivo Protein Kinase Analysis

The human kinome contains >500 protein kinases, and regulates up to 30% of the proteome. Kinase study is currently hindered by a lack of in vivo analysis approaches due to two factors: our inability to distinguish the kinase reaction of interest from those of other kinases in live cells and the cell impermeability of the ATP analogs. Herein, we tackled this issue by combining the widely used chemical genetic method developed by Dr. Kevan Shokat and colleagues with nanoparticle-mediated intracellular delivery of the ATP analog. The critical AKT1 protein kinase, which has been successfully studied with the method, was used as our initial prototype. Briefly, enlargement of the ATP binding pocket, by mutating the gate-keeper Methionine residue to a Glycine, prompted the mutant AKT1 to preferentially use the bulky ATP analog N6-Benzyl-ATP-{gamma}-S (A*TP{gamma}S) and, thus, differentiating AKT1-catalyzed and other phosphorylation events. The lipid/calcium/phosphate (LCP) nanoparticle was used for efficient intracellular delivery of A*TP{gamma}S, overcoming the cell impermeability issue. The mutant, but not wild-type, AKT1 used the delivered A*TP{gamma}S for autophosphorylation and phosphorylating its substrates in live cells. Thus, an in vivo protein kinase analysis method has been developed. The strategy should be widely applicable to other protein kinases.

cell biology↗

Isolating multiple formats of human monoclonal neutralizing antibodies against SARS-CoV-2 by in vitro site-directed antibody screening

Neutralizing antibody is one of the most effective interventions for acute pathogenic infection. Currently, over three million people have been identified for SARS-CoV-2 infection but SARS-CoV-2-specific vaccines and neutralizing antibodies are still lacking. SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Therefore, blocking the interaction of SARS-CoV-2-RBD and ACE2 by antibody would cause a directly neutralizing effect against virus. In the current study, we selected the ACE2 interface of SARS-CoV-2-RBD as the targeting epitope for neutralizing antibody screening. We performed site-directed screening by phage display and finally obtained one IgG antibody (4A3) and several domain antibodies. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. The domain antibody 4A12 was predicted to have the best accessibility to all three ACE2-interfaces on the spike homotrimer. Pseudovirus and authentic SARS-CoV-2 neutralization assays showed that all four antibodies could potently protect host cells from virus infection. Overall, we isolated multiple formats of SARS-CoV-2-neutralizing antibodies via site-directed antibody screening, which could be promising candidate drugs for the prevention and treatment of COVID-19.

immunology↗

Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates

The COVID-19 outbreak has become a global pandemic responsible for over 2,000,000 confirmed cases and over 126,000 deaths worldwide. In this study, we examined the immunogenicity of CHO-expressed recombinant SARS-CoV-2 S1-Fc fusion protein in mice, rabbits, and monkeys as a potential candidate for a COVID-19 vaccine. We demonstrate that the S1-Fc fusion protein is extremely immunogenic, as evidenced by strong antibody titers observed by day 7. Strong virus neutralizing activity was observed on day 14 in rabbits immunized with the S1-Fc fusion protein using a pseudovirus neutralization assay. Most importantly, in less than 20 days and three injections of the S1-Fc fusion protein, two monkeys developed higher virus neutralizing titers than a recovered COVID-19 patient in a live SARS-CoV-2 infection assay. Our data strongly suggests that the CHO-expressed SARS-CoV-2 S1-Fc recombinant protein could be a strong candidate for vaccine development against COVID-19. HighlightsO_LICHO-expressed S1-Fc protein is very immunogenic in various animals and can rapidly induce strong antibody production C_LIO_LIS1-Fc protein solicits strong neutralizing activities against live virus C_LIO_LIStable CHO cell line expressing 50 mg/L of S1-Fc and a 3,000 L Bioreactor can produce 3 million doses of human COVID-19 vaccine every 10 days, making it an accessible and affordable option for worldwide vaccination C_LI

immunology↗

Subcellular structure segmentation from cryo-electron tomograms via machine learning

We describe how to use several machine learning techniques organized in a learning pipeline to segment and identify subcellular structures from cryo electron tomograms. These tomograms are difficult to analyze with traditional segmentation tools. The learning pipeline in our approach starts from supervised learning via a special convolutional neural network trained with simulated data. It continues with semi-supervised reinforcement learning and/or a region merging techniques that try to piece together disconnected components that should belong to the same subcellular structure. A parametric or non-parametric fitting procedure is then used to enhance the segmentation results and quantify uncertainties in the fitting. Domain knowledge is used in generating the training data for the neural network and in guiding the fitting procedure through the use of appropriately chosen priors and constraints. We demonstrate that the approach proposed here work well for extracting membrane surfaces of protein reconstituted liposomes in a cellular environment that contains other artifacts.

cell biology↗

Dr AFC: Drug Repositioning Through Anti-Fibrosis Characteristic

Fibrosis is a key component in the pathogenic mechanism of many diseases. These diseases involving fibrosis may share common mechanisms, therapeutic targets and therefore, common intervention strategies and medicines may be applicable for these diseases. For this reason, deliberately introducing anti-fibrosis characteristics into modelling may lead to more success in drug repositioning. In this study, anti-fibrosis knowledge base was first built by collecting data from multiple resources. Both structural and biological profiles were derived from the knowledge base and used for constructing machine learning models including Structural Profile Prediction Model (SPPM) and Biological Profile Prediction Model (BPPM). Three external public data sets were employed for validation purpose and further exploration of potential repositioning drugs in wider chemical space. The resulting SPPM and BPPM models achieve area under the receiver operating characteristic curve (AUC) of 0.879 and 0.972 in the training set, and 0.814 and 0.874 in the testing set. Additionally, our results also demonstrate that substantial amount of multi-targeting natural products possess notable anti-fibrosis characteristics and might serve as encouraging candidates in fibrosis treatment and drug repositioning. To leverage our methodology and findings, we developed repositioning prediction platform, Drug Repositioning based on Anti-Fibrosis Characteristic (Dr AFC) that is freely accessible via https://www.biosino.org/drafc.

bioinformatics↗

Visualizing in vitro-in vivo correlation of miktoarm copolymer nanomicelles in cancer cellular uptake and trafficking

In this study, a clear correlation between the in vitro and in vivo cellular uptake and trafficking was discovered by delivering miktoarm copolymer nanomicelles (MCNs) to cancer cells and tumor tissues. To monitor this process, two different FRET pairs, DiO and DiI, DiD and DiR, were loaded into MCNs to monitor the Forster resonance energy transfer (FRET) efficiency. The change in FRET efficiency in vitro and in vivo demonstrated a similar sequence of events for the transport of MCNs: hyperbranched block PCL inserted into cytomembrane, while the loaded hydrophobic fluorescence probes were released and followed by time-dependent intracellular clustering within endocytic vesicles. Additionally, uptake of loaded fluorescence probes with successively increasing ratios of copolymers suggested that with the increase of mass ratio of copolymer to fluorescence probes, cellular uptake of probes significantly decreased. This result was also consistent with the uptake behavior in cancer tissues. Collectively, the interaction between MCNs and cellular membrane dictated the uptake and trafficking of core-loaded hydrophobic probes. This concept paves a new way to analyze in vitro-in vivo correlation of other nanocarriers for endocytosis mechanism studies as well as further novel copolymers design in biomedical applications.

pharmacology and toxicology↗

Low rate of follow-up colonoscopy after positive results of colorectal cancer screening in a Chinese urban core district

Colorectal cancer (CRC) is one of the most common cancers in China. In 2003, a systematic CRC registry that enables the determination of CRC incidence and mortality and a CRC screening project were introduced in the Jingan district of Shanghai by the municipal government. This study assessed the registry data to determine the status of CRC and CRC screening rates in the core district of an urban area of China. Data were retrieved from the Official registry information systems of Jingan district Shanghai Cance. The incidence and mortality of CRC, as well as population-based CRC screening rates, were analysed. Individuals who screened positive for CRC based upon results of a high-risk factor questionnaire (HRFQ) and a faecal immunochemical test (FIT) were selected for follow-up colonoscopy (CSPY). From the registry data collected between 2003 and 2013, the standardized incidence rate was 26.44/105, with a significant gender difference. The CRC standardized mortality rate was 10.08/105. In 2013, 17,866 individuals (21.6%) enrolled for CRC screening among the 82,602 candidate residents. The positive screening rate was 16.28% (2909/17866). Among the 2909 positives, 508 (17.5%) underwent follow-up CSPY. In 41.3% of these individuals (210/508), abnormal lesions were detected. Of these, 8 (1.57%) lesions were diagnosed as CRC, and 142 (28.0%) were identified as precancerous lesions. During the assessment period, both the incidence and mortality of CRC in the Jingan district were determined in the area of high CRC prevalence in Chin. Nevertheless, the rate of participation in CRC screening was low (21.6%), and the rate of participation in follow-up CSPY for individuals who screened positive was only 17.5%. Improved participation in CRC screening and follow-up CSPY is expected to lower the incidence and mortality of CRC significantly in the rural areas of China. (288)

cancer biology↗

Acetyl-CoA production by specific metabolites promotes cardiac repair after myocardial infarction via mediating histone acetylation

Myocardial infarction (MI) is accompanied by severe energy deprivation and extensive epigenetic changes. However, how energy metabolism and chromatin modifications are interlinked during MI and heart repair has been poorly explored. Here, we examined the effect of different carbon sources that involved in the major metabolic pathways of acetyl-CoA synthesis on myocardial infarction and found that elevation of acetyl-CoA significantly improved heart function in I/R rats by administration of sodium octanoate (8C). Mechanistically, 8C prevented I/R injury by promoting histone acetylation which in turn activated the expression of antioxidant genes HO1, NQO1 and SOD2 and inhibited cardiomyocyte apoptosis. Furthermore, we identified that 8C-promoted histone acetylation and heart repair were carried out by metabolic enzyme medium-chain acyl-CoA dehydrogenase (MCAD) and histone acetyltransferase Kat2a. Therefore, our results demonstrate that 8C dramatically improves cardiac function through metabolic acetyl-CoA-mediated histone acetylation. This study uncovers an interlinked metabolic/epigenetic network comprising 8C, acetyl-CoA, MCAD, and Kat2a in stimulating histone acetylation and anti-oxidative stress gene expression to combat heart injury.

cell biology↗

Poor seed quality, reduced germination, and decreased seedling vigor in soybean is linked to exposure of the maternal lines to drought stress

Effects of environmental stressors on the parent may be transmitted to the F1 generation of plants that support global food, oil, and energy production for humans and animals. This study was conducted to determine if the effects of drought stress on parental soybean plants are transmitted to the F1 generation. The germination and seedling vigor of F1 soybean whose maternal parents, Asgrow AG5332 and Progeny P5333RY, were exposed to soil moisture stress, that is, 100, 80, 60, 40, and 20% replacement of evapotranspiration (ET) during reproductive growth, were evaluated under controlled conditions. Pooled over cultivars, effects of soil moisture stress on the parents caused a reduction in the seed germination rate, maximum seed germination, and overall seedling performance in the F1 generation. The effect of soil moisture stress on the parent induced an irreversible change in the seed quality in the F1 generation and the effects on seed quality in the F1 generation were exasperated when exposed to increasing levels of drought stress. Results indicate that seed weight and storage reserve are key factors influencing germination traits and seedling growth. Our data confirm that the effects of drought stress on soybean are transferable, causing reduced germination, seedling vigor, and seed quality in the F1 generation.

plant biology↗

Manure substitution of chemical fertilizer affect soil microbial community diversity, structure and function in greenhouse vegetable production systems

Soil microbial community and enzyme activities together affect various ecosystem functions of soils. Fertilization, as important agricultural management practices, are known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research therefore was to make a comparative study of the effects of different fertilization patterns (No N inputs (No N), 100% chemical fertilizer-N (CN) inputs (4/4CN) and different substitution rates of CN by organic manure-N (MN) (3/4CN+1/4MN, 2/4CN+2/4MN and 1/4CN+3/4MN)) on soil physicochemical properties, enzyme activities and microbial attributes in a GVP of Tianjin, China. Manure substitution of chemical fertilizer, especially at higher substitution rate (2/4CN+2/4MN and 1/4CN+3/4MN), improved soil physicochemical properties (higher soil organic C (SOC) and nutrient contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure addition caused a remarkable increase of the fungi/bacteria ratio and a distinct shift in the fungal (bacterial) community to greater abundance of arbuscular mycorrhizal fungi (G+ bacteria) compared with saprotrophic fungi (G- bacteria). These changes drove shifts toward fungal-dominated soil microbial communities and then optimized microbial community structure. Also, manure application increased soil biodiversity (microbial community and enzyme function), indicated by increased Shannon-Wiener diversity. Redundancy analysis indicated that the most possible mechanism of the impacts of different fertilization patterns on soil microbial characteristics may be the mediation of SOC and nutrient (N) availability (especially SOC) in this GVP of China. In conclusion, manure substitution of chemical fertilizer, especially at higher substitution rate, was more efficient for improving soil quality and biological functions.

microbiology↗

Enhancing Cardiac Reprogramming by Suppressing Specific C-C Chemokine Signaling Pathways

Reprogramming fibroblasts into induced cardiomyocytes (iCMs) is a potentially promising strategy for heart regeneration. Yet a major challenge is the low conversion rate. To address this challenge, we screened and identified four chemicals, insulin-like growth factor-1, Mll1 inhibitor MM589, transforming growth factor-{beta} inhibitor A83-01, and Bmi1 inhibitor PTC-209, termed as IMAP, that coordinately enhanced reprogramming efficiency.\n\nUsing -muscle heavy chain -green fluorescent protein mouse embryo fibroblasts as the staring cell type, we observed a six-fold increase of iCM formation with IMAP treatment. IMAP stimulated higher cardiac troponin T and -actinin expression and more sarcomere formation with up-regulation of many cardiac genes and down-regulation of fibroblast genes. Furthermore, IMAP promoted higher spontaneous beating and calcium transient activities of iCMs derived from neonatal cardiac fibroblasts. Intriguingly, we identified that many genes involved in immune responses, particularly those in specific C-C chemokine signaling pathways, were repressed with IMAP treatment. We next tested C-C chemokine ligands Ccl3, Ccl6, and Ccl17 in cardiac reprogramming and observed inhibitory effect on iCM formation, while corresponding inhibitors of Ccr1, Ccr4, and Ccr5 had the opposite effect. These results indicated that suppression of specific C-C chemokine signaling pathways was a direct down-stream event of IMAP treatment that enhanced cardiac reprogramming.\n\nIn conclusion, we identified a combination of four chemicals IMAP in suppressing specific C-C chemokine signaling pathways and facilitating MGT-induced cardiac reprogramming. Our studies revealed the role of these specific C-C chemokine signaling pathways in cardiac reprogramming and provide potential targets in iCM formation and its clinical applications.

cell biology↗

Membrane curvature sensing of the lipid-anchored K-Ras small GTPases

Cell morphologies, defined by plasma membrane (PM) local curvature, change during mitogen-dependent function and pathology, such as growth, division and proliferation. The lipid-anchored Ras small GTPases are essential upstream regulators of the mitogen-activated protein kinases (MAPKs) cascades and play key roles in many pathological conditions, especially cancer. Ras signaling is mostly compartmentalized to the cell PM through the formation of nanometer-sized domains, termed as nanoclusters, and undergo selective lipid sorting for efficient effector recruitment and activation. Thus, Ras function might be sensitive to changing PM curvature, potentially regulating mechanosensing of mitogen signaling. We employed nanofabrication and super-resolution imaging and found that Ras functions respond to PM curvature modulations in an isoform specific manner: nanoclustering and signaling of the most oncogenically prevalent isoform K-Ras favor less curved PM, while those of another isoform H-Ras favor more curved PM. We then examined whether Ras membrane curvature sensing is mediated by lipid sorting. We found that anionic phospholipids sense changing PM curvature in distinct manners: phosphatidylserine (PS) localization shows preference for less curved membrane but phosphoinositol 4,5-bisphosphate (PIP2) localization favors more curved PM. Depletion of endogenous PS abolishes K-Ras PM curvature sensing. Exogenous PS addback and synthetic bilayer binding assays further show that only mixed-chain PS species, but not other PS species, mediate K-Ras curvature sensing. Taken together, the Ras proteolipid nano-assemblies on the PM act as relay stations to convert mechanical stimulations to mitogenic signaling circuits, thus a novel mechanism for cancer cell mechanotransduction

biochemistry↗