Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 901 records · Page 50Linked to original sources

bioRxiv2021

Ozone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content

The maize pangenome has demonstrate large amounts of presence/absence variation and it has been hypothesized that presence/absence variation contributes to stress response. To uncover whether the observed genetic variation in physiological response to elevated ozone (a secondary air pollutant that causes significant crop yield losses) concentration is due to variation in genic content, and/or variation in gene expression, we examine the impact of sustained elevated ozone concentration on the leaf tissue from 5 diverse maize inbred genotypes (B73, Mo17, Hp301, C123, NC338). Analysis of long reads from the transcriptomes of the 10 conditions found expressed genes in the leaf are part of the shared genome, with 94.5% of expressed genes from syntenic loci. Quantitative analysis of short reads from 120 plants (twelve from each condition) found limited transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes), while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. The genes underpinning the divergence of B73 from the other 4 genotypes implicates ethylene signaling consistent with some findings in Arabidopsis. For the 82 of the 83 genes differentially expressed among all 5 genotypes and the 788 of 789 genes differentially expressed in 4 genotypes (excluding B73) in sensitivity to ozone is associated with oxidative stress tolerance being associated with a weaker response to a reactive oxygen species (ROS) signal and suggests that genetic variation in downstream processes is key to ozone tolerance.

genomics↗

bioRxiv2021

Oligomerization-driven MLKL ubiquitylation antagonises necroptosis

Mixed lineage kinase domain-like (MLKL) is the executioner in the caspase-independent form of programmed cell death called necroptosis. Receptor Interacting serine/threonine Protein Kinase 3 (RIPK3) phosphorylates MLKL, triggering MLKL oligomerization, membrane translocation and membrane disruption. MLKL also undergoes ubiquitylation during necroptosis, yet neither the mechanism nor significance of this event have been demonstrated. Here we show that necroptosis-specific, multi-mono-ubiquitylation of MLKL occurs following its activation and oligomerization. Ubiquitylated MLKL accumulates in a digitonin insoluble cell fraction comprising plasma/organellar membranes and protein aggregates. This ubiquitylated form is diminished by a plasma membrane located deubiquitylating enzyme. MLKL is ubiquitylated on at least 4 separate lysine residues once oligomerized, and this correlates with proteasome- and lysosome-dependent turnover. Using a MLKL-DUB fusion strategy, we show that constitutive removal of ubiquitin from MLKL licences MLKL auto-activity independent of necroptosis signalling in mouse and human cells. Therefore, besides its role in the kinetic regulation of MLKL-induced death following an exogenous necroptotic stimulus, ubiquitylation also contributes to the restraint of basal levels of activated MLKL to avoid errant cell death.

molecular biology↗

bioRxiv2021

Integration of embryo-endosperm interaction into a holistic and dynamic picture of seed development using a rice mutant with notched-belly grains

The interaction between the embryo and endosperm affects seed development, an essential process in yield formation in crops such as rice. Signals that communicate between embryo and endosperm are largely unknown. Here we use the notched-belly (NB) mutant with impaired communication between embryo and endosperm to evaluate 1) the impact of embryo on developmental staging of the endosperm; 2) signaling pathways emanating from the embryo that regulate endosperm development. Hierachical clustering of mRNA datasets from embryo and endosperm samples collected through development in NB and wild type showed a delaying effect of the embryo on the developmental transition of the endosperm by extending the middle stage. K-means clustering further identified coexpression modules of gene sets specific for embryo and endosperm development. Combined gene expression and biochemical analysis showed that T6P-SnRK1, gibberellin and auxin signalling from the embryo regulate endosperm developmental transition. The data enable us to propose a new seed developmental staging system for rice and the most detailed signature of rice grain formation to date, that will direct genetic strategies for rice yield improvement.

plant biology↗

bioRxiv2021

Transcriptomic encoding of sensorimotor transformation in the midbrain

Sensorimotor transformation, a process that converts sensory stimuli into motor actions, is critical for the brain to initiate behaviors. Although the circuitry involved in sensorimotor transformation has been well delineated, the molecular logic behind this process remains poorly understood. Here, we performed high-throughput and circuit-specific single-cell transcriptomic analyses of neurons in the superior colliculus (SC), a midbrain structure implicated in early sensorimotor transformation. We found that SC neurons in distinct laminae express discrete marker genes. Of particular interest, Cbln2 and Pitx2 are key markers that define glutamatergic projection neurons in the optic nerve (Op) and intermediate gray (InG) layers, respectively. The Cbln2+ neurons responded to visual stimuli mimicking cruising predators, while the Pitx2+ neurons encoded prey-derived vibrissal tactile cues. By forming distinct input and output connections with other brain areas, these neuronal subtypes independently mediate behaviors of predator avoidance and prey capture. Our results reveal that, in the midbrain, sensorimotor transformation for different behaviors may be performed by separate circuit modules that are molecularly defined by distinct transcriptomic codes.

neuroscience↗

bioRxiv2021

A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340

BackgroundMaize is not only one of the most important crops grown worldwide for food, forage, and biofuel, but also an important model organism for fundamental research in genetics and genomics. Owing to its importance in crop science, genetics and genomics, several reference genomes of common maize inbred line (genetic material) have been released, but some genomes of important genetic germplasm resources in maize breeding research are still lacking. The maize cultivar Dan340 is an excellent backbone inbred line of the Luda Red Cob Group with several desirable characteristics, such as disease resistance, lodging resistance, high combining ability, and wide adaptability. FindingsIn this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing reads, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of the Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with N50 of 41.49 Mb and 215.35 Mb, respectively. Repeat sequences accounted for 73.40% of the genome size and 39,733 protein-coding genes were annotated. Analysis of genes in the Dan340 genome, together with those from B73, Mo17 and SK, were clustered into 27,654 gene families. There were 1,806 genes from 359 gene families that were specific to Dan340, of which many had functional gene ontology annotations relating to "porphyrin-containing compound metabolic process", "tetrapyrrole biosynthetic process", and "tetrapyrrole metabolic process". ConclusionsThe completeness and continuity of the genome were comparable to those of other important maize inbred lines. The assembly and annotation of this genome not only facilitates our understanding about of intraspecific genome diversity in maize, but also provides a novel resource for maize breeding improvement. Research AreasGenetics and Genomics; Agriculture, Plant Genetics Data Description

genomics↗

bioRxiv2021

Spatial transcriptome sequencing revealed spatial trajectory in the Non-Small Cell Lung Carcinoma

Deepening understanding in the heterogeneity of tumors is critical for clinical treatment. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal lung cancer using the spatial transcriptomics (ST) technology. We identified gene expression gradients in stroma adjacent to tumor regions that allow for re-understanding of the tumor micro-environment. The establishment of these profiles was the first step towards an unbiased view of lung cancer and can serve as a dictionary for future studies. Tumor subclones were detected by ST technology in our research, while we contrast the EMT ability among in subclones which inferred the possible trajectory of tumor metastasis and invasion, which was confirmed by constructing the pseudo-time model of spatial transition within subclones. Together, these results uncovered lung cancer spatial heterogeneity, highlight potential tumor micro-environment differences and spatial evolution trajectory, and served as a resource for further investigation of tumor microenvironment.

cancer biology↗

bioRxiv2021

A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope

With the emergence of SARS-CoV-2 variants with increased transmissibility and potential resistance, antibodies and vaccines with broadly inhibitory activity are needed. Here we developed a panel of neutralizing anti-SARS-CoV-2 mAbs that bind the receptor binding domain of the spike protein at distinct epitopes and block virus attachment to cells and its receptor, human angiotensin converting enzyme-2 (hACE2). While several potently neutralizing mAbs protected K18-hACE2 transgenic mice against infection caused by historical SARS-CoV-2 strains, others induced escape variants in vivo and lost activity against emerging strains. We identified one mAb, SARS2-38, that potently neutralizes all SARS-CoV-2 variants of concern tested and protects mice against challenge by multiple SARS-CoV-2 strains. Structural analysis showed that SARS2-38 engages a conserved epitope proximal to the receptor binding motif. Thus, treatment with or induction of inhibitory antibodies that bind conserved spike epitopes may limit the loss of potency of therapies or vaccines against emerging SARS-CoV-2 variants.

microbiology↗

bioRxiv2021

Megapixel camera arrays for high-resolution animal tracking in multiwell plates

Tracking small laboratory animals such as flies, fish, and worms is used for phenotyping in neuroscience, genetics, disease modelling, and drug discovery. Current imaging systems are limited either in spatial resolution or throughput. A system capable of imaging a large number of animals with sufficient resolution to estimate their pose would enable a new class of experiments where detailed behavioural differences are quantified but at a scale where hundreds of treatments can be tested simultaneously. Here we report a new imaging system consisting of an array of six 12-megapixel cameras that can simultaneously record from all the wells of a 96-well plate with a resolution of 80 pixels/mm at 25 frames per second. We show that this resolution is sufficient to estimate the pose of nematode worms including head identification and to extract high-dimensional phenotypic fingerprints. We use the system to study behavioural variability across wild isolates, the sensitisation of worms to repeated blue light stimulation, the phenotypes of worm disease models, and worms behavioural responses to drug treatment. Because the system is compatible with standard multiwell plates, it makes computational ethological approaches accessible in existing high-throughput pipelines and greatly increases the scale of possible phenotypic screening experiments in C. elegans.

animal behavior and cognition↗

bioRxiv2021

Plasma exosomal miRNA analysis of Alzheimer's disease reveals the dysfunction of a neural network

Exosomal microRNA (miRNA) is an emerging source for biomarkers of Alzheimers disease (AD). Here, we profiled miRNA expression in AD, mild cognitive impairment (MCI), and controls. The assessment and validation of differentially expressed miRNA represented their potential to be novel biomarkers for AD and MCI. We conducted 13 co-expression networks and a miRNA network module linked to neural function emerged as the most significantly associated with AD diagnosis. The conservation analysis revealed the M1 was highly preserved in controls but dysfunction in AD and MCI. The module pattern between MCI and NC was similar, but significantly differed from AD, suggesting that the neural network regulated by miRNA changed during the mild cognitive stage, and the total miRNA expression altered in AD stage. Additionally, 24 out of 26 M1 hub-miRNAs were derived from brain tissue, and 15 had been reported as AD biomarkers. We consequently proposed the other 11 miRNAs could play important roles in AD. Our study highlights that co-expression network analysis can provide a new path for finding novel biomarkers.

bioinformatics↗

bioRxiv2021

Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been endangering worldwide public health and economy. SARS-CoV-2 infects a variety of tissues where the known receptor ACE2 is low or almost absent, suggesting the existence of alternative pathways for virus entry. Here, we performed a genome-wide barcoded-CRISPRa screen to identify novel host factors that enable SARS-CoV-2 infection. In addition to known host proteins, i.e. ACE2, TMPRSS2 and NRP1, we identified multiple host components, among which LDLRAD3, TMEM30A and CLEC4G were confirmed as functional receptors for SARS-CoV-2. All these membrane proteins bind directly to spikes N-terminal domain (NTD). Their essential and physiological roles have all been confirmed in either neuron or liver cells. In particular, LDLRAD3 and CLEC4G mediate SARS-CoV-2 entry and infection in a fashion independent of ACE2. The identification of the novel receptors and entry mechanisms could advance our understanding of the multiorgan tropism of SARS-CoV-2, and may shed light on the development of the therapeutic countermeasures against COVID-19.

microbiology↗

bioRxiv2021

Sustained Oxygenation Accelerates Diabetic Wound Healing by Simultaneously Promoting Epithelialization and Angiogenesis, and Decreasing Tissue Inflammation

Non-healing diabetic wound is one of the most common complications for diabetic patients. Chronic hypoxia is among the prominent factors that delay the wound healing process. Therefore, sustained oxygenation to alleviate hypoxia is hypothesized to promote diabetic wound healing. Yet it cannot be achieved by current clinical approaches including hyperbaric oxygen therapy. Herein, we developed a sustained oxygenation system consisting of oxygen-release microspheres and a reactive oxygen species (ROS)-scavenging hydrogel. The hydrogel was used to capture the ROS that is elevated in the diabetic wounds, and that may be generated due to oxygen release. The sustainedly released oxygen augmented survival and migration of keratinocytes and dermal fibroblasts; promoted angiogenic growth factor expression, and angiogenesis in the diabetic wounds; and decreased M1 macrophage density. These effects led to a significant increase of wound closure rate. These findings reveal that sustained oxygenation alone without using drugs is capable of healing diabetic wounds.

bioengineering↗

bioRxiv2021

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

An ideal anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse SARS-related coronaviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD), including S3094, the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 in vitro neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.

microbiology↗

bioRxiv2021

Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody

The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2x259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2x259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2x259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2x259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.

immunology↗

bioRxiv2021

Fine-tuning of SUMOylation modulates drought tolerance

SUMOylation is involved in various aspects of plant biology, including drought stress. However, the relationship between SUMOylation and drought stress tolerance is complex; whether SUMOylation has a crosstalk with ubiquitination in response to drought stress remains largely unclear. In this study, we found that both increased and decreased SUMOylation led to increased survival of apple (Malus x domestica) under drought stress: both transgenic MdSUMO2A overexpressing (OE) plants and MdSUMO2 RNAi plants exhibited enhanced drought tolerance. We further confirmed that MdDREB2A is one of the MdSUMO2 targets. Both transgenic MdDREB2A OE and MdDREB2AK192R OE plants (which lacked the key site of SUMOylation by MdSUMO2A) were more drought tolerant than wild-type plants. However, MdDREB2AK192R OE plants had a much higher survival rate than MdDREB2A OE plants. We further showed SUMOylated MdDREB2A was conjugated with ubiquitin by MdRNF4 under drought stress, thereby triggering its protein degradation. In addition, MdRNF4 RNAi plants were more tolerant to drought stress. These results revealed the molecular mechanisms that underlie the relationship of SUMOylation with drought tolerance and provided evidence for the tight control of MdDREB2A accumulation under drought stress mediated by SUMOylation and ubiquitination.

plant biology↗

bioRxiv2021

The Cdc42 GTPase activating protein Rga6 promotes the cortical localization of Septin

Septins are a family of filament-forming GTP-binding proteins that regulate fundamental cellular activities such as cytokinesis, cell polarity, and membrane remodelling. In general, Septin filaments function as barriers and scaffolds on the cell cortex. However, little is known about the mechanism that governs the recruitment and localization of the Septin complex to the cell cortex. Here, we identified the Cdc42 GTPase activating protein Rga6 as a key protein involved in promoting the localization of the Septin complex to the cell cortex in the fission yeast Schizosaccharomyces pombe. Rga6 interacts with the Septin complex and colocalizes with the Septin complex on the cell cortex. Live-cell microscopic analysis further showed Septin enrichment at the cortical regions adjacent to the growing cell tip. The Septin enrichment likely plays a crucial role in confining active Cdc42 to the growing cell tip. Hence, our findings support a model that Rga6 regulates polarized cell growth partly through promoting targeted localization of the Septin complex on the cell cortex.

cell biology↗

bioRxiv2021

Phase separation of RNA-binding protein promotes polymerase engagement and transcription

An RNA-involved phase-separation model has been proposed for transcription control. Yet, the molecular links that connect RNA binding to the transcription machinery remain missing. Here we find RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), and some are colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs--such as PSPC1 and PTBP1--show that the paraspeckle protein PSPC1 not only prevents the RNA-induced premature release of Pol II, and also makes use of RNA as multivalent molecules to promote Pol II engagement and activity, by enhancing the phase separation and subsequent phosphorylation and release of polymerase condensates. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II phosphorylation and chromatin-binding and nascent transcription. We propose that the synergistic interplay of RBPs and RNA aids in the rate-limiting step of polymerase condensate formation to promote active transcription.

biochemistry↗

bioRxiv2021

A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants

The emergence of antigenically distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility is a public health threat. Some of these variants show substantial resistance to neutralization by SARS-CoV-2 infection- or vaccination-induced antibodies, which principally target the receptor binding domain (RBD) on the virus spike glycoprotein. Here, we describe 2C08, a SARS-CoV-2 mRNA vaccine-induced germinal center B cell-derived human monoclonal antibody that binds to the receptor binding motif within the RBD. 2C08 broadly neutralizes SARS-CoV-2 variants with remarkable potency and reduces lung inflammation, viral load, and morbidity in hamsters challenged with either an ancestral SARS-CoV-2 strain or a recent variant of concern. Clonal analysis identified 2C08-like public clonotypes among B cell clones responding to SARS-CoV-2 infection or vaccination in at least 20 out of 78 individuals. Thus, 2C08-like antibodies can be readily induced by SARS-CoV-2 vaccines and mitigate resistance by circulating variants of concern. One Sentence SummaryProtection against SARS-CoV-2 variants by a potently neutralizing vaccine-induced human monoclonal antibody.

immunology↗

bioRxiv2021

Bayestrat: Population Stratification Correction Using Bayesian Shrinkage Prior for Genetic Association Studies

In genetic association studies with common diseases, population stratification is a major source of confounding. Principle component regression (PCR) and linear mixed model (LMM) are two commonly used approaches to account for population stratification. Previous studies have shown that LMM can be interpreted as including all principle components (PCs) as random-effect covariates. However, including all PCs in LMM may inflate type I error in some scenarios due to redundancy, while including only a few pre-selected PCs in PCR may fail to fully capture the genetic diversity. Here, we propose a statistical method under the Bayesian framework, Bayestrat, that utilizes appropriate shrinkage priors to shrink the effects of non- or minimally confounded PCs and improve the identification of highly confounded ones. Simulation results show that Bayestrat consistently achieves lower type I error rates yet higher power, especially when the number of PCs included in the model is large. We also apply our method to two real datasets, the Dallas Heart Studies (DHS) and the Multi-Ethnic Study of Atherosclerosis (MESA), and demonstrate the superiority of Bayestrat over commonly used methods.

genetics↗