Biology subjects

Long, Y.

Publications and source records attributed to Long, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2021

CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity

Safe, economical and effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to achieve adequate herd immunity and halt the pandemic. We have constructed a novel SARS-CoV-2 vaccine, CoVac501, which is a self-adjuvanting peptide vaccine conjugated with Toll-like receptor 7 (TLR7) agonists. The vaccine contains two immunodominant peptides screened from receptor-binding domain (RBD) and is fully chemically synthesized. And the vaccine has optimized nanoemulsion formulation, outstanding stability and safety. In non-human primates (NHPs), CoVac501 elicited high and persistent titers of RBD-specific and protective neutralizing antibodies (NAbs), which were also effective to RBD mutations. CoVac501 was found to elicit the increase of memory T cells, antigen-specific CD8+ T cell responses and Th1-biased CD4+ T cell immune responses in NHPs. More importantly, the sera from the immunized NHPs can prevent infection of live SARS-CoV-2 in vitro. One-Sentence SummaryA novel SARS-CoV-2 vaccine we developed, CoVac501, which is a fully chemically synthesized and self-adjuvanting peptides conjugated with TLR7 agonists, can induce high-efficient humoral and cellular immune responses against SARS-CoV-2.

immunology↗

bioRxiv2021

Graph Contextualized Attention Network for Predicting Synthetic Lethality in Human Cancers

MotivationSynthetic Lethality (SL) plays an increasingly critical role in the targeted anticancer therapeutics. In addition, identifying SL interactions can create opportunities to selectively kill cancer cells without harming normal cells. Given the high cost of wet-lab experiments, in silico prediction of SL interactions as an alternative can be a rapid and cost-effective way to guide the experimental screening of candidate SL pairs. Several matrix factorization-based methods have recently been proposed for human SL prediction. However, they are limited in capturing the dependencies of neighbors. In addition, it is also highly challenging to make accurate predictions for new genes without any known SL partners. ResultsIn this work, we propose a novel graph contextualized attention network named GCATSL to learn gene representations for SL prediction. First, we leverage different data sources to construct multiple feature graphs for genes, which serve as the feature inputs for our GCATSL method. Second, for each feature graph, we design node-level attention mechanism to effectively capture the importance of local and global neighbors and learn local and global representations for the nodes, respectively. We further exploit multi-layer perceptron (MLP) to aggregate the original features with the local and global representations and then derive the feature-specific representations. Third, to derive the final representations, we design feature-level attention to integrate feature-specific representations by taking the importance of different feature graphs into account. Extensive experimental results on three datasets under different settings demonstrate that our GCATSL model outperforms 14 state-of-the-art methods consistently. In addition, case studies further validate the effectiveness of our proposed model in identifying novel SL pairs. AvailabilityPython codes and dataset are available at: Contactluojiawei@hnu.edu.cn and xlli@i2r.a-star.edu.sg

bioinformatics↗

bioRxiv2020

Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

The broad application of large-scale single-cell RNA profiling in plants has been restricted by the prerequisite of protoplasting. We recently found that the Arabidopsis nucleus contains abundant polyadenylated mRNAs, many of which are incompletely spliced. To capture the isoform information, we combined 10x Genomics and Nanopore long-read sequencing to develop a protoplasting-free full-length single-nucleus RNA profiling method in plants. Our results demonstrated using Arabidopsis root that nuclear mRNAs faithfully retain cell identity information, and single-molecule full-length RNA sequencing could further improve cell type identification by revealing splicing status and alternative polyadenylation at single-cell level.

genomics↗

bioRxiv2020

A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux

Metabolic heterogeneity, the occurrence of different metabolic phenotypes among cells, represents a key challenge in health and biotechnology. To unravel its molecular basis, tools probing metabolism of single cells are needed. While RNA devices harbor huge potential for the development of such tools, until today, it is challenging to create in vivo-functional sensors for any given metabolite. Here, we developed from scratch an RNA-based sensor for fructose-1,6-bisphosphate (FBP), a doubly phosphorylated intermediate of glycolysis. Starting from in vitro selection of an RNA aptamer and its structural analyses, we developed libraries of RNA-based regulatory devices with this aptamer and the hammerhead ribozyme as an actuator. Through FACS-seq-based high-throughput screening in yeast, we identified in vivo-functional FBP-sensing devices that generate fluorescent readout dependent on intracellular FBP concentration. As FBP reports the flux through glycolysis, the developed RNA device can be used to sense the glycolytic rate in single cells, offering unprecedented possibilities to investigate the causes of metabolic heterogeneity.

synthetic biology↗

bioRxiv2020

A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD

The spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies1-3. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic4,5. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S6. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614G pseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.

immunology↗

bioRxiv2020

A rapid and efficient screening system for neutralizing antibodies and its application for the discovery of potent neutralizing antibodies to SARS-CoV-2 S-RBD

Neutralizing antibodies (Abs) have been considered as promising therapeutics for the prevention and treatment of pathogens. After the outbreak of COVID-19, potent neutralizing Abs to SARS-CoV-2 were promptly developed, and a few of those neutralizing Abs are being tested in clinical studies. However, there were few methodologies detailly reported on how to rapidly and efficiently generate neutralizing Abs of interest. Here, we present a strategically optimized method for precisive screening of neutralizing monoclonal antibodies (mAbs), which enabled us to identify SARS-CoV-2 receptor-binding domain (RBD) specific Abs within 4 days, followed by another 2 days for neutralization activity evaluation. By applying the screening system, we obtained 198 Abs against the RBD of SARS-CoV-2. Excitingly, we found that approximately 50% (96/198) of them were candidate neutralizing Abs in a preliminary screening of SARS-CoV-2 pseudovirus and 20 of these 96 neutralizing Abs were confirmed with high potency. Furthermore, 2 mAbs with the highest neutralizing potency were identified to block authentic SARS-CoV-2 with the half-maximal inhibitory concentration (IC50) at concentrations of 9.88 ng/ml and 11.13 ng/ml. In this report, we demonstrated that the optimized neutralizing Abs screening system is useful for the rapid and efficient discovery of potent neutralizing Abs against SARS-CoV-2. Our study provides a methodology for the generation of preventive and therapeutic antibody drugs for emerging infectious diseases.

immunology↗

bioRxiv2020

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction1-5. This process is essential for embryonic stem cell (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling progressive spread of H3K27me3 on the linear genome6. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear7-10. Here, we apply H3K27me3 HiChIP11-13, a protein-directed chromosome conformation method, and optical reconstruction of chromatin architecture14 to profile long-range Polycomb-associated DNA loops that span tens to hundreds of megabases across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells7-10. We find that H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors revealed a coupling of Polycomb-associated genome architecture and H3K27me3 deposition evidenced by disruption of spatial contact between distant loci and altered H3K27me3 in cis, both locally and megabases away on the same chromosome. Further, we find that global alterations in PRC2 occupancy resulting from an EZH2 mutant15 selectively deficient in RNA binding is accompanied by loss of Polycomb-associated DNA looping. Together, these results suggest PRC2 acts as a "genomic wormhole", using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Additionally, developmental gene loci have novel roles in Polycomb spreading, emerging as important architectural elements of the epigenome.

genetics↗

bioRxiv2020

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Premise of studyLeaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite "shape of shapes" can better capture variation and predict species identity compared to individual leaves. MethodsUsing homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies. ResultsWe found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping. DiscussionObservations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape--an assemblage of modeled leaf snapshots across the shoot--is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

plant biology↗

bioRxiv2020

Mythical and observable trends in human sex ratio at birth

The human sex ratio at birth (SRB) is defined as the ratio between the number of newborn boys to the total number of newborns per time unit. It is, typically, slightly greater than [Formula] (more boys than girls) and fluctuates over time. In this study, we sought to "myth-check" previously reported associations (and test new hypotheses) using variants of mixed-effect regression analyses and time-series models on two very large electronic health record datasets, representing the populations in the United States and Sweden, respectively. Our results revealed that neither dataset supported models in which the SRB changed seasonally or in response to variations in ambient temperature, and that an increased level of a diverse array of pollutants were associated with lower SRBs. Moreover, we found that increased levels of industrial and agricultural activity, which served as proxies for water pollution, were also associated with lower SRBs.

physiology↗

bioRxiv2020

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning

Alternative polyadenylation (APA) is a crucial step in post-transcriptional regulation. Previous bioinformatic works have mainly focused on the recognition of polyadenylation sites (PAS) in a given genomic sequence, which is a binary classification problem. Recently, computational methods for predicting the usage level of alternative PAS in a same gene have been proposed. However, all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PAS into account. To address this, here we propose a deep learning architecture, DeeReCT-APA, to quantitatively predict the usage of all alternative PAS of a given gene. To accommodate different genes with potentially different numbers of PAS, DeeReCT-APA treats the problem as a regression task with a variable-length target. Based on a CNN-LSTM architecture, DeeReCT-APA extracts sequence features with CNN layers, uses bidirectional LSTM to explicitly model the interactions among competing PAS, and outputs percentage scores representing the usage levels of all PAS of a gene. In addition to the fact that only our method can predict quantitatively the usage of all the PAS within a gene, we show that our method consistently outperforms other existing methods on three different tasks for which they are trained: pairwise comparison task, highest usage prediction task and ranking task. Finally, we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and shed light on future mechanistic understanding in APA regulation. Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.

bioinformatics↗

bioRxiv2020

Altered Temporal Variability of Local and Large-scale Resting-state Brain Functional Connectivity Patterns in Schizophrenia and Bipolar Disorder

Schizophrenia and bipolar disorder share some common clinical features and are both characterized by aberrant resting-state functional connectivity (FC). However, little is known about the common and specific aberrant features of the dynamic FC patterns in these two disorders. In this study, we explored the differences in dynamic FC among schizophrenia patients (n = 66), type I bipolar disorder patients (n = 53) and healthy controls (n = 66), by comparing temporal variabilities of FC patterns involved in specific brain regions and large-scale brain networks. Compared with healthy controls, both patient groups showed significantly increased regional FC variabilities in subcortical areas including the thalamus and basal ganglia, as well as increased inter-network FC variability between the thalamus and sensorimotor areas. Specifically, more widespread changes were found in the schizophrenia group, involving increased FC variabilities in sensorimotor, visual, attention, limbic and subcortical areas at both regional and network levels, as well as decreased regional FC variabilities in the default-mode areas. The observed alterations shared by schizophrenia and bipolar disorder may help to explain their overlapped clinical features; meanwhile, the schizophrenia-specific abnormalities in a wider range may support that schizophrenia is associated with more severe functional brain deficits than bipolar disorder.

neuroscience↗

bioRxiv2019

GABA signalling in guard cells acts as a 'stress memory' to optimise plant water loss

The non-protein amino acid {gamma}-aminobutyric acid (GABA) has been proposed to be an ancient messenger for cellular communication conserved across biological kingdoms. GABA has well-defined signalling roles in animals; however, whilst GABA accumulates in plants under stress it has not been determined if, how, where and when GABA acts as an endogenous plant signalling molecule. Here, we establish that endogenous GABA is a bona fide plant signal, acting via a mechanism not found in animals. GABA antagonises stomatal movement in response to opening and closing stimuli in multiple plant families including dicot and monocot crops. Using Arabidopsis thaliana, we show guard cell GABA production is necessary and sufficient to influence stomatal aperture, transpirational water loss and drought tolerance via inhibition of stomatal guard cell plasma membrane and tonoplast-localised anion transporters. This study proposes a novel role for GABA - as a stress memory - opening new avenues for improving plant stress tolerance.

plant biology↗

bioRxiv2019

Asymmetrical cleavages of Sleeping Beauty transposons generate multiple excised transposon fragments during transposition

Although the Sleeping Beauty (SB) transposon is the most validated DNA transposon used as a gene delivery vehicle in vertebrates, many details of the excision and integration steps in the transposition process are unclear. We have probed in detail the products of the excision step and apparent selective integration of a subset of those products during transposition. The standard model of SB transposase-mediated transposition includes symmetrical cleavages at both ends of the transposon for excision and re-integration in another DNA sequence. In our analysis of excised transposon fragments (ETFs), we found evidence for the requirement of certain flanking sequences for efficient cleavage and a significant rate of asymmetrical cleavage during the excision process that generates multiple ETFs. Our results suggest that the cleavage step by SB transposase is not as precise as indicated in most models. Repair of the donor ends can produce eight footprint sequences (TACTGTA, TACAGTA, TACATA, TACGTA, TATGTA, TACTA, TAGTA and TATA). Our data also suggest that mismatch repair (MMR) is not an essential requirement for footprint formation. Among the twenty liberated ETFs, only eight appear to effectively re-integrate into TA sites distributed across the genome, supporting earlier findings of unequal rates of excision and reintegration during SB transposition. These findings may be important in considerations of efficiency of SB transposon remobilization, selection of TA integration sites and detection of SB excision and integration loci, all of which may be important in human gene therapy.

molecular biology↗

bioRxiv2019

Xyloglucan homeostasis and microtubule dynamics synergistically maintain meristem geometry and robustness of phyllotaxis in Arabidopsis

The shoot apical meristem (SAM) gives rise to all aerial organs of the plant. The cell walls are supposed to play a central role in this process, translating molecular regulation into dynamic changes of growth rates and directions, although their precise role in morphogenesis during organ formation remains not well understood. Here we investigate the role of xyloglucans (XyGs), which form a major, yet functionally poorly characterized, wall component in the SAM. Using immunolabeling, biochemical analysis, genetic approaches, micro-indentation, laser ablations and live imaging, we show that XyGs are important for meristem shape and phyllotaxis, although no difference in cell wall stiffness could be observed when XyGs are perturbed. Mutations in enzymes required for XyG synthesis also affect other cell wall components such as cellulose content and the pectin methylation status. Interestingly, we show that the control of cortical microtubules dynamics by the severing enzyme KATANIN becomes vital when XyGs are perturbed or absent. This suggests an active role of the cytoskeleton in compensating for altered wall composition.

plant biology↗

bioRxiv2018

Generating a sequence map of the pig pan-genome

Pigs (Sus scrofa) exhibit diverse phenotypes in different breeds shaped by the combined effects of various local adaptation and artificial selection. To comprehensively characterize the genetic diversity of pigs, we construct a pig pan-genome by comparing genome assemblies of 11 representative pig breeds with the reference genome (Sscrofa11.1). Approximately 72.5 Mb non-redundant sequences were identified as pan-sequences which were absent from the Sscrofa11.1. On average, 41.7 kb of spurious heterozygous SNPs per individual are removed and 12.9 kb novel SNPs per individual are recovered using pan-genome as the reference for SNP calling, thereby providing enhanced resolution for genetic diversity in pigs. Homolog annotation and analysis using RNA-seq and Hi-C data indicate that these pan-sequences contain protein-coding regions and regulatory elements. These pan-sequences can further improve the interpretation of local 3D structure. The pan-genome as well as the accompanied web-based database will serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

genomics↗

bioRxiv2018

Regulation of histone methylation by automethylation of PRC2

Polycomb Repressive Complex 2 (PRC2) is a histone methyltransferase whose function is critical for regulating transcriptional repression in many eukaryotes including humans. Its catalytic moiety EZH2 is responsible for the tri-methylation of H3K27 and also undergoes automethylation. Using mass spectroscopic analysis of recombinant human PRC2, we identified three methylated lysine residues (K510, K514, K515) on a disordered but highly conserved loop of EZH2. These lysines were mostly mono- and di-methylated. Either mutation of these lysines or their methylation increases PRC2 histone methyltransferase activity. In addition, mutation of these three lysines in HEK293T cells using CRISPR genome-editing increases global H3K27 methylation levels. EZH2 automethylation occurs intramolecularly (in cis) by methylation of a pseudosubstrate sequence on the flexible loop. This post-translational modification and cis-regulation of PRC2 are analogous to the activation of many protein kinases by autophosphorylation. We therefore propose that EZH2 automethylation provides a way for PRC2 to modulate its histone methyltransferase activity by sensing histone H3 tails, SAM concentration, and perhaps other effectors.

biochemistry↗

bioRxiv2018

Cellular heterogeneity in pressure and growth emerges from tissue topology and geometry

Cell-to-cell heterogeneity prevails in many biological systems, although its origin and function are often unclear. Cell hydrostatic pressure, alias turgor pressure, is essential in physiology and morphogenesis, and its spatial variations are often overlooked. Here, based on a mathematical model describing cell mechanics and water movement in a plant tissue, we predict that cell pressure anticorrelates with cell neighbour number. Using atomic force microscopy, we confirm this prediction in the Arabidopsis shoot apical meristem, a population of stem cells that generate all plant aerial organs. Pressure is predicted to correlate either positively or negatively with cellular growth rate depending on osmotic drive, cell wall extensibility, and hydraulic conductivity. The meristem exhibits one of these two regimes depending on conditions, suggesting that, in this tissue, water conductivity is non-negligible in growth control. Our results illustrate links between local topology, cell mechanical state and cell growth, with potential roles in tissue homeostasis.

biophysics↗

bioRxiv2018

HIR-1 Mediates Response to Hypoxia-Induced Extracellular Matrix Remodeling

Inadequate tissue oxygen, or hypoxia, is a central concept in pathophysiology of ischemic disorders and cancer. Hypoxia promotes extracellular matrix (ECM) remodeling, cellular metabolic adaptation and metastasis. To determine how cells respond to hypoxia-induced ECM remodeling, we performed a large-scale forward genetic screen in C. elegans. We identified a previously uncharacterized receptor tyrosine kinase (RTK) named HIR-1 as a key mediator in a pathway that orchestrates transcriptional responses to hypoxia-induced ECM remodeling. Impaired ECM integrity caused by hypoxia or deficiency of the oxygen-dependent procollagen hydroxylases, heme peroxidases or cuticular collagens activates gene expression through inhibition of HIR-1. Genetic suppressor screens identified NHR-49 and MDT-15 as transcriptional regulators downstream of HIR-1. Cellular responses through HIR-1 maintain ECM homeostasis and promote animal adaptation to severe hypoxia. We propose that C. elegans HIR-1 defines an unprecedented type of RTK that mediates responses to hypoxia-induced ECM remodeling by mechanisms that are likely conserved in other organisms.\n\nONE-SENTENCE SUMMARYA regulatory pathway for ECM homeostasis underlies adaptation to hypoxia and re-oxygenation

cell biology↗