Biology subjects

Zhu, Y.

Publications and source records attributed to Zhu, Y..

At least 649 records · Page 36Linked to original sources

bioRxiv2021

Kinetic structure of recycling vesicle pool at the Calyx of Held synapse under in vivo-like activities

Synaptic transmission at mammalian central synapses has ongoing background activity at physiological temperature. The recycling vesicle pool, with proper kinetics, ensures sustained synaptic transmission. However, the kinetic structure of recycling vesicle pool has never been quantitatively analyzed before, and most studies were performed at room temperature and under resting conditions. With the combination of presynaptic capacitance measurement and postsynaptic EPSC recording on calyx of Held synapses at physiological temperature, we studied vesicle recycling under sustained presynaptic stimulation. The kinetics of vesicle reuse was revealed by impeding transmitter refilling with folimycin. We kinetically dissected the recycling vesicle pool as sequentially connected sub-pools and depicted the complete kinetic structure. The sizes and transition rates among these sub-pools were dynamically regulated by neuronal activity, in order to ensure efficient synaptic transmission. Our work highlights the impact of the vesicle recycling machinery on stable and reliable synaptic transmission under variable levels of neuronal activity. Impact statementThe recycling pool of vesicles are kinetically dissected as four populated pools ensuring stable and reliable synaptic transmission

neuroscience↗

bioRxiv2021

Insights into the susceptibility of rice to a floral disease

Crop floral diseases are economically important as they reduce grain yield and quality and even introduce food toxins. Rice false smut has emerged as a serious floral disease producing mycotoxins. However, very little is known on the interaction mechanisms between rice flower and the causal fungus Ustilaginoidea virens. Here we show that a conserved anti-fungal immunity in rice flower is disarmed by U. virens via a secreted protein UvChi1. UvChi1 functioned as an essential virulence factor and directly interacted with the chitin receptor CEBiP and co-receptor CERK1 in rice to disrupt their oligomerizations and subsequent immune responses. Moreover, intraspecific-conserved UvChi1 could target OsCEBiP/OsCERK1 receptor complex in at least 98.5% of 5232 surveyed rice accessions. These results demonstrate that U. virens utilizes a crucial virulence factor to subvert chitin-triggered flower immunity in most rice varieties, providing new insights into the susceptibility of rice to false smut disease. One Sentence SummaryThe fungal pathogen Ustilaginoidea virens disarms chitin-triggered immunity in rice flower via a secreted chitinase.

plant biology↗

bioRxiv2021

Proteasome maturation factor UMP1 confers broad-spectrum disease resistance by modulating H2O2 accumulation in rice

Crops with broad-spectrum resistance (BSR) to diseases are highly desirable in agricultural production. Identification of BSR loci and dissection of the underlying mechanisms are fundamental for crop resistance breeding. Here, we describe the identification and characterization of a rice UMP1 allele, which confers race-nonspecific BSR against blast pathogen Magnaporthe oryzae. OsUMP1 encodes a proteasome maturation factor that contributes to 26S proteasome abundance and activity in rice. Modulation of OsUMP1 expression leads to proteome changes, particularly affects the amounts and activities of H2O2-degrading enzymes. Consequently, H2O2 accumulation and disease resistance are enhanced in OsUMP1-overexpressing rice but reduced in loss-of-function mutants. Elevation of OsUMP1 expression also promotes rice resistance to foliar pathogens Rhizoctonia solani and Xanthomonas oryzae pv. oryzae and a floral pathogen Ustilaginoidea virens without observable yield penalty. These results indicate a BSR pathway linking the proteasome machinery and H2O2 homeostasis, and provide a candidate gene for balancing BSR and yield traits in rice breeding. One Sentence SummaryA natural allele of rice UMP1 promotes resistance to multiple pathogens by boosting H2O2 accumulation.

plant biology↗

bioRxiv2021

A machine learning approach for detecting vicarious trial and error behaviors

Vicarious trial and error behaviors (VTEs) indicate periods of indecision during decision-making, and have been proposed as a behavioral marker of deliberation. In order to understand the neural underpinnings of these putative bridges between behavior and neural dynamics, researchers need the ability to readily distinguish VTEs from non-VTEs. Here we utilize a small set of trajectory-based features and standard machine learning classifiers to identify VTEs from non-VTEs for rats performing a spatial delayed alternation task (SDA) on an elevated plus maze. We also show that previously reported features of the hippocampal field potential oscillation can be used in the same types of classifiers to separate VTEs from non-VTEs with above chance performance. However, we caution that the modest classifier success using hippocampal population dynamics is not sufficient for identifying trials where VTEs occur, and show that combining oscillation-based features with trajectory-based features degrades classifier performance compared to trajectory-based features alone. Overall, we propose a standard set of features useful for trajectory-based VTE classification and support previous suggestions that VTEs are supported by a network including, but likely extending beyond, the hippocampus.

neuroscience↗

bioRxiv2021

Instructor-learner neural synchronization during elaborated feedback predicts learning transfer

The provision of feedback with complex information beyond the correct answer, i.e., elaborated feedback, can powerfully shape learning outcomes such as transfer, i.e., the ability to extend what has been learned in one context to new contexts. However, an understanding of neurocognitive processes of elaborated feedback during instructor-learner interactions remains elusive. Here, a two-person interactive design is used during simultaneous recording of functional near-infrared spectroscopy (fNIRS) signals from adult instructor-learner dyads. Instructors either provided elaborated feedback (i.e., correct answer and an example) or simple feedback (i.e., correct answer only) to learners during a concept learning task. Our results showed that elaborated feedback produced comparable levels of retention to simple feedback, however, transfer was significantly enhanced by elaboration. We also noted significant instructor-learner neural synchronization in frontoparietal regions during the provision of elaborated feedback, especially when examples were provided. Further, interpersonal neural synchronization in the parietal cortex successfully predicted transfer of knowledge to novel contexts. This prediction was retained for both learner-delayed and learner-preceding neural synchronization. These findings point toward transfer effects of elaborated feedback provided in a social context can be predictable through interpersonal neural synchronization, which may hold important implications for real-world learning and pedagogical efficacy. Educational Impact and Implications StatementFeedback provides learners with crucial information regarding the gap between what has currently been achieved and what remains to be achieved, and thus plays a critical role in any learning process. In real-world settings, feedback is typically provided and received through social interaction, and high-quality "elaborated feedback" contains complex information that goes beyond the correct answer. This study aims to elucidate the neurocognitive processes underpinning elaborated feedback during instructor-learner interactions. We detected significant instructor-learner neural synchronization in mutual frontoparietal brain regions during elaborated feedback, particularly during the provision of specific elaborated information (i.e., concrete examples). Moreover, this synchronization (including learner-delayed and learner-preceded synchronization) in the parietal region predicted whether the learners transferred learning to novel examples of learned psychology concepts. This study advances current understanding on the neural mechanisms for elaborated feedback and the role of social interaction in feedback effects. These results may have important implications for successful real-world learning and communication, and related pedagogical applications in educational settings.

scientific communication and education↗

bioRxiv2021

Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry and the S protein glycosylation is strongly implicated in altering viral binding/function and infectivity. However, the structures and relative abundance of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis. Here, we report the complete structural characterization of intact O-glycan proteoforms using native top-down mass spectrometry (MS). By combining trapped ion mobility spectrometry (TIMS), which can separate the protein conformers of S-RBD and analyze their gas phase structural variants, with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analysis, the O-glycoforms of the S-RBD are comprehensively characterized, so that seven O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that native top-down MS can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants, as well as other O-glycoproteins in general.

biochemistry↗

bioRxiv2021

Engineering protease-resistant peptides to inhibit human parainfluenza viral respiratory infection

The lower respiratory tract infections affecting children worldwide are in large part caused by the parainfluenza viruses (HPIVs), particularly HPIV3, along with human metapneumovirus and respiratory syncytial virus, enveloped negative-strand RNA viruses. There are no vaccines for these important human pathogens, and existing treatments have limited or no efficacy. Infection by HPIV is initiated by viral glycoprotein-mediated fusion between viral and host cell membranes. A viral fusion protein (F), once activated in proximity to a target cell, undergoes a series of conformational changes that first extend the trimer subunits to allow insertion of the hydrophobic domains into the target cell membrane, and then refold the trimer into a stable postfusion state, driving the merger of the viral and host cell membranes. Lipopeptides derived from the C-terminal heptad repeat (HRC) domain of HPIV3 F inhibit infection by interfering with the structural transitions of the trimeric F assembly. Clinical application of this strategy, however, requires improving the in vivo stability of antiviral peptides. We show that the HRC peptide backbone can be modified via partial replacement of -amino acid residues with {beta}-amino acid residues to generate /{beta}-peptides that retain antiviral activity but are poor protease substrates. Relative to a conventional -lipopeptide, our best /{beta}-lipopeptide exhibits improved persistence in vivo and improved anti-HPIV3 antiviral activity in animals.

microbiology↗

bioRxiv2021

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Global quantification of protein abundances in single cells would provide more direct information on cellular function phenotypes and complement transcriptomics measurements. However, single-cell proteomics (scProteomics) is still immature and confronts technical challenges, including limited proteome coverage, poor reproducibility, as well as low throughput. Here we describe a nested nanoPOTS (N2) chip to dramatically improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip allows reducing cell digestion volume to <30 nL and increasing processing capacity to > 240 single cells in one microchip. In the analysis of [~]100 individual cells from three different cell lines, we demonstrate the N2 chip-based scProteomics platform can robustly quantify [~]1500 proteins and reveal functional differences. Our analysis also reveals low protein abundance variations (median CVs < 16.3%), highlighting the utility of such measurements, and also suggesting the single-cell proteome is highly stable for the cells cultured under identical conditions.

systems biology↗

bioRxiv2021

Single-cell transitional dynamics unravel stimulus- and cell type-dependent signaling outputs of distinct p53 regulatory feedback motifs

Despite myriad of systemic analysis, our quantitative understanding of signaling networks and their differential outputs is still limited, especially at the dynamic level. Here we employed a network motif approach to dissect key regulatory units of p53 pathway and determined how their collective activities generated context-specific dynamic responses. By combining single-cell imaging and mathematical modeling of dose-dependent p53 dynamics induced by three chemotherapeutics of distinct mechanism-of-action, including Etoposide, Nutlin-3a and 5-Fluouracil, and in five cancer cell types, we identified novel p53 dynamic modes and their mechanistic origins with new insight on previously unknown drug mediators and phenotypic heterogeneity of cancer cells. Our results established the functional roles of unique feedback motifs of p53 pathway in generating the stimulus- and cell type-specific signaling responses and demonstrated that transitional dynamics activated at intermediate stimulus levels can be exploited as novel quantitative readouts to uncover and elucidate the key building blocks of bio-networks.

systems biology↗

bioRxiv2021

High-throughput miRNA-sequencing of the human placenta: expression throughout gestation

BackgroundAltered placenta miRNA abundance may impact the maternal-fetal interface and pregnancy outcomes. Understanding miRNA changes across gestation is essential before miRNAs can be used as biomarkers or prognostic indicators during pregnancy. Materials & MethodsUsing next-generation sequencing, we characterize the normative human placenta miRNA transcriptome in first (N=113) and third trimester (N=47). ResultsThere are 801 miRNAs expressed in both first and third trimester, including 182 with similar expression across gestation (P[≥]0.05) and 182 significantly different (FDR<0.05). Of placenta-specific miRNA clusters, C14MC is more upregulated in first trimester and C19MC is more highly expressed overall. ConclusionThis work provides a rich atlas of healthy pregnancies to direct functional studies investigating the epigenetic differences in first and third trimester placentae. Lay AbstractThe human body produces microRNAs which affect the expression of genes and proteins. This study uses next generation sequencing to identify the microRNA profile of first and third trimester human placentae using a large cohort (N=113 first, N=47 third trimester). All pregnancies resulted in healthy babies. We identify microRNAs with significantly different expression between first and third trimester, as well as stably expressed microRNAs. This work provides a baseline for future studies which may use microRNAs to monitor maternal-fetal health throughout pregnancy.

developmental biology↗

bioRxiv2021

Robust, sensitive, and quantitative single-cell proteomics based on ion mobility filtering

Unbiased single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge for current methods is their ability to identify and provide accurate quantitative information for low abundance proteins. Herein, we describe an ion mobility-enhanced mass spectrometry acquisition and peptide identification method, TIFF (Transferring Identification based on FAIMS Filtering), designed to improve the sensitivity and accuracy of label-free scProteomics. TIFF significantly extends the ion accumulation times for peptide ions by filtering out singly charged background ions. The peptide identities are then assigned by a 3-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells with >1,100 proteins consistently quantified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during a lipopolysaccharide stimulation experiment and identified time-dependent proteome profiles.

systems biology↗

bioRxiv2021

SCOPE: Flexible targeting and stringent CARF activation enables type III CRISPR-Cas diagnostics

Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA (rather than DNA) and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of a target RNA and production of cyclic oligoadenylate (cOA) second messenger molecules that may trigger dormancy or cell death. In this study, we discovered that a largely exposed seed region at the 3 end of the crRNA is essential for target RNA binding and cleavage, whereas base pairing at a unique region at the 5 end of the guide is required to trigger cOA production. Moreover, we uncovered that the natural variation in the composition of type III complexes within a single host results in different guide lengths, and hence variable seed regions. This shifting seed may prevent escape by invading genetic elements, while controlling cOA production very tightly to prevent unnecessary damage to the host. Lastly, we used these findings to develop a new diagnostic tool, named SCOPE, which was used for the specific detection of SARS-CoV-2 from human nasal swab samples, showing sensitivities in the atto-molar range.

biochemistry↗

bioRxiv2021

Adiponectin Preserves Metabolic Fitness During Aging

Adiponectin is essential for the regulation of tissue substrate utilization and systemic insulin sensitivity. Clinical studies have suggested a positive association of circulating adiponectin with healthspan and lifespan. However, the direct effects of adiponectin on promoting healthspan and lifespan remain unexplored. Here, we are using an adiponectin null mouse and a transgenic adiponectin overexpression model. We directly assessed the effects of circulating adiponectin on the aging process and found that adiponectin null mice display exacerbated age-related glucose and lipid metabolism disorders. Moreover, adiponectin null mice have a significantly shortened lifespan on both chow and high-fat diet (HFD). In contrast, a transgenic mouse model with elevated circulating adiponectin levels has a dramatically improved systemic insulin sensitivity, reduced age-related tissue inflammation and fibrosis, and a prolonged healthspan and median lifespan. These results support a role of adiponectin as an essential regulator for healthspan and lifespan.

cell biology↗

bioRxiv2021

Deficiency of intellectual disability-related gene Brpf1 reduced inhibitory neurotransmission and Map2k7 expression in GABAergic interneurons

Intellectual disability is closely related to impaired GABA neurotransmission. Brpf1 was specifically expressed in medial ganglionic eminence (MGE), a developmental niche of GABAergic interneurons, and patients with BRPF1 mutations were mentally retarded. To test its role in development and function of MGE-derived GABAergic interneurons, we performed immunofluorescence staining, whole-cell patch-clamp, MGE transplantation and mRNA-Seq to understand its effect on neuronal differentiation, dendritic morphology, electrophysiology, migration and gene regulation, using mouse MGE-derived GABAergic interneurons infected with AAV-shBrpf1. We found a decreasing trend on parvalbumin+ interneuron differentiation. Moreover, increased firing threshold, decreased number of evoked APs, and a reduced amplitude of mIPSCs were observed before any significant change of MAP2+ dendritic morphology and in vivo migration appeared. Finally, mRNA-Seq analysis revealed that genes related to neurodevelopment and synaptic transmission such as Map2k7 were dysregulated. Our results demonstrated a key role of Brpf1 in inhibitory neurotransmission and related gene expression of GABAergic interneurons.

neuroscience↗

bioRxiv2021

Decoupling of global brain activity and cerebrospinal fluid flow in Parkinson's cognitive decline

BackgroundDeposition and spreading of misfolded proteins (-synuclein and tau) have been linked to Parkinsons cognitive dysfunction. The glymphatic system may play an important role in the clearance of these toxic proteins via cerebrospinal fluid (CSF) flow through perivascular and interstitial spaces. Recent studies discovered that sleep-dependent global brain activity is coupled to CSF flow that may reflect glymphatic function. ObjectiveTo determine if the decoupling of brain activity-CSF flow is linked to Parkinsons cognitive dysfunction. MethodsFunctional and structural MRI data, clinical motor (Unified Parkinson's Disease Rating Scale), and cognitive (Montreal Cognitive Assessment, MoCA) scores were collected from 60 Parkinsons and 58 control subjects. Parkinsons patients were subgrouped into those with (MoCA < 26; N = 29) and without (MoCA [≥] 26; N = 31) mild cognitive impairment (MCI). The coupling strength between the resting-state global blood-oxygen-level-dependent signal (gBOLD) and associated CSF flow was quantified, compared among groups, and associated with clinical and structural measurements. ResultsgBOLD-CSF coupling decreased significantly (p < 0.006) in Parkinsons patients showing MCI, compared to those without MCI and controls. Reduced gBOLD-CSF coupling was associated with decreased MoCA scores that was present in Parkinsons patients (p = 0.005) but not in controls (p = 0.65). Weaker gBOLD-CSF coupling in Parkinsons patients also was associated with a thinner right entorhinal cortex (Spearmans correlation = - 0.36; p = 0.012), an early structural change often seen in Alzheimers. ConclusionsThe decoupling between global brain activity and associated CSF flow is related to Parkinsons cognitive impairment.

neuroscience↗

bioRxiv2021

Rapid fabrication of hydrogel micropatterns by projection stereolithography for studying self-organized developmental patterning

Self-organized patterning of mammalian embryonic stem cells on micropatterned surfaces has previously been established as an in vitro platform for early mammalian developmental studies, complimentary to in vivo studies. Traditional micropatterning methods, such as micro-contact printing (CP), involve relatively complicated fabrication procedures, which restricts widespread adoption by biologists. Here, we demonstrate a rapid method of micropatterning by printing hydrogel micro-features onto a glass-bottomed culture vessel. The micro-features are printed using a projection stereolithography bioprinter yielding hydrogel structures that geometrically restrict the attachment of cells or protein. Compared to traditional, physical photomasks, a digitally tunable virtual photomask is used in the projector to generate blue light patterns that enable rapid iteration with minimal cost and effort. We show that a protocol that makes use of this method together with LN521 coating creates a surface suitable for human embryonic stem cell (hESC) attachment and growth with minimal non-specific adhesion. We further demonstrate that self-patterning of hESCs following previously published gastrulation and ectodermal induction protocols achieves results comparable with those obtained with commercially available plates (CYTOO).

developmental biology↗

bioRxiv2020

Ferritin nanoparticle based SARS-CoV-2 RBD vaccine induces persistent antibody response and long-term memory in mice

Since the outbreak of COVID-19, over 200 vaccine candidates have been documented and some of them have advanced to clinical trials with encouraging results. However, the antibody persistence over 3 months post immunization and the long-term memory have been rarely reported. Here, we report that a ferritin nanoparticle based SARS-CoV-2 RBD vaccine induced in mice an efficient antibody response which lasts for at least 7 months post immunization. Significantly higher number of memory B cells were maintained and a significantly higher level of recall response was induced upon antigen challenge. Thus, we believe our current study provide the first information about the long-term antibody persistence and memory response of a COVID-19 vaccine. This information would be also timely useful for the development and evaluation of other vaccines.

immunology↗

bioRxiv2020

XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications

Software tools that allow visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a large selection of plugins for interpretation of protein interaction data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for such interaction data, but there are currently no Cytoscape tools to analyze XL-MS results. In light of the suitability of Cytoscape platform but also to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plugin for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers rapid and easy visualization of intra and intermolecular cross-links and the locations of protein domains in a rectangular bar style, allowing subdomain-level interrogation of the interaction network. XlinkCyNET is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/xlinkcynet and at https://www.theliulab.com/software/xlinkcynet.

bioinformatics↗