Biology subjects

Liu, Q.

Publications and source records attributed to Liu, Q..

At least 235 records · Page 13Linked to original sources

bioRxiv2024

Magnetically induced magnetosome chain (MAGiC):A biogenic magnetic-particle-imaging tracer with high performance and navigability

Magnetic particle imaging (MPI) enables real-time, sensitive and quantitative visualization of magnetic tracers spatial distribution, augmenting the capability of in vivo imaging technologies. Previous tracer studies in MPI have primarily focused on superparamagnetic nanoparticles; however, their non-ideal sigmoidal magnetization response limits the spatial resolution. Here we demonstrate the utilization of magnetically induced magnetosome chain (MAGiC) as a novel superferromagnetic MPI tracer, exhibiting a 25-fold improvement in resolution and a 91-fold enhancement in signal intensity compared to the commercial tracer VivoTrax+. The spatial resolution of MPI was pushed to an unprecedented 80 m under a 4 T/m gradient field. Additionally, MAGiC can be precisely controlled using magnetic fields, enabling it to function as a MPI trackable microrobot. We provided a theoretical model elucidating MAGiCs unique properties, and validated its imaging and actuation performance through phantom studies and in vivo experiments. As a high-performance MPI tracer and magnetic microrobot with exceptional capabilities, MAGiC holds tremendous potential for diverse applications including cell tracking, targeted drug delivery as well as therapeutic interventions.

bioengineering↗

bioRxiv2024

Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants

Although numerous data have revealed correlations between histone modifications and chromatin activities such as transcription, proofs of their causal importance in gene expression regulation remain limited. Sequence variants within each histone family expand chromatin diversity and may carry specific modifications, further raising the question of how histone modifications coordinate with different variants. Here, we investigate the regulatory role of lysine 4 (K4) of Arabidopsis histone H3 by point mutating K4 in two major H3 variants, H3.1 and H3.3. K4 is essential for the function of H3.3 but not H3.1 in plant development. H3K4 methylation levels decrease drastically upon K4 mutation in H3.3, and the associated transcriptome changes are similar to those observed in a mutant lacking SDG2, a major enzyme responsible for depositing H3K4 trimethylation (H3K4me3). Moreover, H3.3K4 and SDG2 are required for de novo gene activation and RNA Pol II elongation. H3K4 methylation is preferentially accumulated on H3.3 compared to H3.1, likely due to the close association of the H3.3 deposition and H3K4 methylation machineries. Furthermore, we reveal the diverse impacts of K4 nearby residue mutations on H3K4 methylation and H3.3 function. Collectively, these findings suggest that H3.3 serves as a critical substrate for H3K4 methylation, which is important for gene expression regulation. In addition, our work highlights the potential of using plants as a platform to directly investigate the importance of histone amino acids and their modifications.

plant biology↗

bioRxiv2024

Genome-wide mapping of EBV-induced genomic variationsidentifies the role of MUC19 in EBV latency

Epstein-Barr virus (EBV) infects over 95% of the worlds population and is tightly associated with multiple human malignant diseases. As the first discovered human oncovirus, EBV is known to induce genomic instability by promoting various types of genomic modifications in host chromosomes. However, the mechanisms through which EBV interacts with the host genome and regulates cellular gene expression in genomic modifications are not yet fully elucidated. In this study, we conducted primary EBV infection in B cells and performed the analyses of copy number variants using whole genome sequencing. After comparing to other distinct B cells with varying EBV infection backgrounds, we identified susceptible regions and unveiled critical host factors induced by EBV infection on chromosomes. Combined with the genome-wide transcriptomic analyses, we found that the mucin gene MUC19 is distinctively activated by EBV infection and MUC19 promotes oncogenesis through the activation of mTOR signaling in lymphoblastoid cell lines (LCLs). Further results indicate that EBV nuclear antigen 1 (EBNA1) binds to multiple regions within MUC19 and enhances the expression of MUC19. Moreover, sequence alignment has shown intriguing motif homology between the basic repeat unit of MUC19 and EBV genome, suggesting the potential of EBV-specific integration. To conclude, our study maps the genomic perturbations induced by EBV primary infection and offers new insights into the oncogenic roles of MUC19 during EBV latency.

microbiology↗

bioRxiv2024

A non-muscle α-actinin is an intrinsic component of the cardiac Z-disc and regulates sarcomere turnover, contractility, and heart remodeling

Cardiac sarcomeres generate the fundamental forces behind each heartbeat and are thought to contain only muscle-specific cytoskeletal proteins. We show that a widely expressed actin cross-linking protein, -actinin 4 (ACTN4), is a sarcomere component of the human and zebrafish heart in vivo and in human iPSC-derived cardiac myocytes (CMs) in vitro. A confluence of biochemical experiments, immunofluorescence, and AI modeling suggest ACTN4 forms a heterodimeric complex with muscle-specific ACTN2 at the cardiac Z-disc, the cardiac sarcomere border. ACTN4 depletion from human iPSC-CMs stabilizes canonical sarcomere proteins and drives contractility-dependent cellular hypertrophy while ACTN4 overexpression destabilizes sarcomeres. ACTN4 depletion from zebrafish embryos specifically increases ventricular contractility which drives atrial enlargement, suggesting biomechanically driven atrial remodeling. ACTN4-associated phenotypes in both model systems lack hallmarks of cardiac disease models and an ACTN4 variant in humans is associated with reduced risk for disease. Our findings suggest a "non-muscle" actinin regulates heart contractility and influences clinical outcomes related to heart failure.

cell biology↗

bioRxiv2024

Aphid effectors suppress plant immunity via recruiting defence proteins to processing bodies

Aphids are small insects that have developed specialized mouthparts and effector proteins to establish long-term relationships with plants. The peach-potato aphid, Myzus persicae, is a generalist, feeding on many plant species and capable of transmitting numerous pathogens. This study reveals how host-responsive cathepsins B (CathB) in the oral secretions of M. persicae facilitate aphid survival by modulating plant immune responses. Aphid CathB localize to processing bodies (p-bodies) and recruit key immune regulators EDS1, PAD4, and ADR1 to these bodies, suppressing plant defenses. A plant protein, Acd28.9 (Hsp20 family), counteracts this CathB activity and contributes to plant resistance to aphids. These findings highlight a novel role for p-bodies in plant immunity and uncover a plant resistance mechanism to aphid infestation.

plant biology↗

bioRxiv2024

Exploring the Neural Basis and Validity of Ordinal Emotion Representation through EEG

Accurately measuring emotion is a major challenge in advancing the understanding of human emotion and developing emotional artificial intelligence. In many existing studies, participants emotional ratings in interval scales are considered the true reflection of their emotional experiences. However, recent research suggests that ordinal annotations of emotions can more accurately capture the emotional expression process, providing a potential method for more precise emotion measurement. However, our understanding of the characteristics and validity of this new form of emotion representation is still relatively lacking. In particular, there is a lack of research using neural signals to explore the validity and neural basis of ordinal emotion representation. In this study, we used a video-elicited electroencephalogram (EEG) dataset (n = 123) to identify the neural basis of ordinal emotion representation and demonstrate its validity from a neural perspective. Furthermore, we explored various characteristics of ordinal emotion representation, showing how it is superior to the interval form. First, we conducted inter-situation representational similarity analysis (RSA) and inter-subject RSA to test the degree to which ordinal representation captures both group commonalities and individual differences of emotion. Next, we investigated the characteristics of ordinal representation under different combinations of emotion items, including uni-variate and multivariate emotions, positive and negative emotions. Our results show that both group commonalities and inter-subject variations in EEG features are better explained by ordinal emotion representations than by interval ones. Multivariate ordinal representations showed better inter-subject reliability and higher representational similarity with EEG features compared to uni-variate counterparts, highlighting the co-occurrence nature of human emotions. Compared to negative emotions, ordinal representation showed greater improvements for positive emotions, suggesting that the complexity of positive emotions is well captured by ordinal representations. Taken together, these findings demonstrate that multivariate ordinal emotion ratings provide a more accurate measure of real emotional experience, which is crucial for enabling machines to precisely understand and express human emotions.

neuroscience↗

bioRxiv2024

Targeting SLC7A11-mediated cysteine metabolism for the treatment of trastuzumab resistant HER2 positive breast cancer

Trastuzumab resistance remains a challenge for HER2 positive breast cancer treatment. Targeting metabolic reprogramming would provide novel insights for therapeutic strategies. Here, we integrated metabolomics, transcriptomics and epigenomics data of trastuzumab sensitive and primary resistant HER2 positive breast cancer to identify metabolic alterations. Aberrant cysteine metabolism was discovered in trastuzumab primary resistant breast cancer at both circulating and intracellular levels. The inhibition of SLC7A11 and cysteine starvation could synergize with trastuzumab to induce ferroptosis. Mechanistically, increased H3K4me3 and decreased DNA methylation enhanced SLC7A11 transcription and cystine uptake in trastuzumab resistant breast cancer. The regulation of epigenetic modifications modulated cysteine metabolism and ferroptosis sensitivity. These results revealed an innovative approach for overcoming trastuzumab resistance by targeting specific amino acid metabolism.

cancer biology↗

bioRxiv2024

Alveolar macrophages initiate the spatially targeted neutrophil recruitment during nanoparticle inhalation

Exposure to air pollution, including nanoparticles (NPs), is a major health concern associated with various diseases, triggered by subtle inflammatory responses in the lung. To investigate the dynamic immune response in vivo, lung intravital microscopy (L-IVM), was used to analyze the behavior of alveolar macrophages (AMs) and neutrophils, combined with ventilator-assisted inhalation of nebulized NPs in mice. Inhalation of fluorescent quantum dot NPs (cQDs) and soot-like carbon black NPs (CNPs, ambient pollutants), led to rapid spatially focused recruitment of neutrophils near alveolar deposited NPs. Neutrophil recruitment was initiated by NPs uptake by AMs, dependent on AM motility and AM NP surface recognition. Prior airway application of neutralizing antibodies against alveolar ICAM-1 and LFA-1, leading to reduced AM motility, inhibition of C5aR1 and Fc{gamma}RI receptor mediated NPs uptake by AMs, as well as neutralizing of TNF and application of a cellular degranulation inhibitor, abolished the early immune response induced by NPs. Overall, our data demonstrates the crucial role of AM activity (migration, phagocytosis, cytokine release) in the rapid and site-specific recruitment of neutrophils during the early phase of particle inhalation, suggesting these processes to be key events in mounting the immune response upon NP inhalation in the lung. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=175 HEIGHT=200 SRC="FIGDIR/small/623349v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@d67e38org.highwire.dtl.DTLVardef@1f8c139org.highwire.dtl.DTLVardef@55be9dorg.highwire.dtl.DTLVardef@1555042_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Generation of a biosafety mouse model infection for SARS-CoV-2 replicon delivery particles

Animal models are essential for understanding the pathogenesis of SARS-CoV-2 and for developing therapeutic strategies. Replicon delivery particles (RDPs) were a component of trans-complementary systems for SARS-CoV-2, which is a safe and convenient tool in researching SARS-CoV-2 in animal biosafety level-II laboratory (ABSL-2). Here, we constructed a mouse model that conditional expressing SARS-CoV-2 N on the background of the K18-hACE2 KI mice. The SARS-CoV-2 N with flanked loxP-stop-loxP sequence was under the CAG promoter, and this cassette was knocked into the Tiger locus of mouse by CRISPR-Cas9 (K18-hACE2-N KI). By mating K18-hACE2-N KI mice with Cre tool mice, the offspring can express SARS-CoV-2 N (Cre-N-hACE2 KI) systemically and in a tissue-specific manner. Cre-N-hACE2 KI exhibited susceptibility to the SARS-CoV-2 {Delta}N-GFP/HBiT infection. The viral loads in lung exhibited a mountain-like trend, peaking at 4 days post-infection, and lung injuries can be observed. Overall, we demonstrated a mouse model infection for SARS-CoV-2 {Delta}N-GFP/HBiT to understand SARS-CoV-2 pathogenesis.

microbiology↗

bioRxiv2024

Land plant-specific H3K27 methyltransferases ATXR5 and ATXR6 control plant development and stress responses

The colonization of land by plants relies on numerous evolutionary innovations crucial for terrestrial adaptation. These include advances in sexual reproduction and the ability to properly respond to various environmental stresses, which involve precise control of their regulatory genes. A notable genetic innovation in land plants is the emergence of histone lysine methyltransferases ATXR5/6, which specifically catalyse the repressive histone H3 lysine 27 monomethylation (H3K27me1). However, the significance of the evolution of these enzymes in land plants remains unclear. In this study, we investigate the importance of ATXR5/6 by generating strong atxr5;atxr6 double mutants in Arabidopsis. Our results show that ATXR5/6 are essential for plant reproductive development and play a critical role in supporting normal plant growth by repressing the transcription of stress responsive genes. In addition, ATXR5/6 are necessary for maintaining H3K27 trimethylation (H3K27me3), likely by providing H3K27me1 as a substrate for further methylation. We also demonstrate that the function of ATXR5/6 in regulating reproductive development and responsive genes is conserved in the monocot rice. We propose that land plants may have evolved ATXR5/6 to assist in the transcriptional regulation necessary for terrestrial adaptation.

plant biology↗

bioRxiv2024

ADAT2/3-mediated tRNA editing promotes cancer cell growth and tumorigenicity

Transfer RNAs (tRNAs) are subject to various chemical modifications that influence their stability or function. Adenosine to Inosine (A-to-I) editing in the tRNA anticodon at position A34 is an important modification that expands anticodon-codon recognition at the wobble position and is required for normal mRNA translation. The relevance of tRNA editing in cancer remains unexplored. Here we show that the genes encoding the ADAT2/3 deaminase complex, responsible for A-to-I tRNA editing in humans, are commonly amplified and/or overexpressed in several tumor types including liposarcoma (LPS). We find that knockdown of the ADAT complex suppresses LPS cell growth and tumorigenicity. Mechanistically, we find that decreased tRNA editing upon ADAT2 depletion leads to defective translation of a subset of mRNAs. Thus, ADAT-mediated tRNA modification promotes oncogenesis by enhancing the translation of growth promoting mRNAs that are enriched in NNC codons that lack cognate tRNAs and therefore depend on A-I tRNA editing for decoding and mRNA translation. Our results uncover an oncogenic role of tRNA editing and identify ADAT2/3 as a potential new cancer therapeutic target.

cancer biology↗

bioRxiv2024

Self-Authenticating Genomic Materials with Advanced Genome Signatures

The authenticity and integrity of synthetic genomic materials containing valuable intellectual property are essential for advancing scientific knowledge and enhancing biosafety. Existing DNA tags and watermarks, however, have limited efficacy due to low mutation tolerance and inadequate digital encoding capacity. Here, we present "Genome Signature", a biochemically stable and tamper-resistant DNA labeling system that enables the creation of self-authenticating genomes. Central to this system is a novel Golomb-ruler-derived Genome-Comb, which efficiently maps extensive nucleotide sequences onto limited codons within endogenous genes, significantly improving error correction and data encoding across millions of nucleotides. Our method successfully recorded a 4.5 million-nucleotide genome in living E. coli. The Genome Signature autonomously identifies and corrects mutations and effectively encodes data within codon orders, ensuring genome integrity and authenticity. Furthermore, it allows precise tracking of sequences across different cells, potentially revolutionizing the development of reliable genomic materials in synthetic biology.

synthetic biology↗

bioRxiv2024

Biocontrol efficiency and mechanism of novel Streptomyces luomodiensis SCA4-21 against banana Fusarium wilt

The soil-borne fungi Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes banana Fusarium wilt, which seriously threats global banana production. Biocontrol has been considered viable alternative method to manage banana Fusarium wilt. In previous study, we found that novel S. luomodiensis SCA4-21 exhibited antifungal activity. Here, we revealed that the extracts of strain SCA4-21 significantly inhibited the growth of Foc TR4 hyphae and spore germination, severely disrupting the ultrastructure of Foc TR4 hyphal cells and spore morphology. These extracts also exhibited broad-spectrum antifungal activity against eight other phytopathogenic fungi. Furthermore, we demonstrated that strain SCA4-21 produce 32 volatile organic compounds, including five antifungal compounds. In a pot experiment, we discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, achieving a biocontrol efficiency of 59.3%, and promoted the growth of banana seedlings. Additionally, this inoculation significantly enhanced the abundances of beneficial bacterial genera Streptomyces, Bacillus, Sphingomonas, and Massilia, as well as fungal genera Mortierella, Purpureocillium, Gibellulopsis, and Xenomyrothecium, while significantly reduced the abundances of pathogenic bacteria genus Pantoea and fungal genus Fusarium, in the banana rhizosphere soil. Moreover, the inoculation of strain SCA4-21 significantly increased the enrichment of pathways such as carbohydrate metabolism, amino acid metabolism, and metabolism of terpenoids and polyketides. Therefore, we postulated that strain SCA4-21 may synergistically combat banana Fusarium wilt by producing antifungal compounds and enriching beneficial bacteria and fungi. Our findings present a promising biocontrol agent for the management of banana Fusarium wilt. IMPORTANCEBanana (Musa spp.) is one of the most popular fruit crops and the fourth largest food crop in developing countries within tropical and subtropical regions. However, the emergence and rapid spread of strain Foc TR4 seriously hinder the development of banana industry. Currently, there is no effective control measure available. Biological control holds potential due to its safety and effectiveness. Here, we found that the extracts of S. luomodiensis SCA4-21 exhibited significant inhibitory effects on the hyphal growth and spore germination of Foc TR4, as well as severe destructive effects on its cell morphology and ultrastructure, and broad-spectrum antifungal activity. We also discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, reduced the incidence index of banana Fusarium wilt, promoted the growth of banana seedlings, and enhances beneficial microbes and metabolic pathways, suggesting that strain SCA4-21 is a promising biocontrol agent.

physiology↗

bioRxiv2024

A Comprehensive Engineering Strategy Improves Potency and Manufacturability of a Near Pan-neutralizing Antibody Against HIV

Anti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with "first generation" bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of "enhanced" antibodies will be required for optimal clinical utility, while preserving or enhancing cGMP manufacturing capability. Here we report the engineering of an anti-CD4 binding-site (CD4bs) bnAb, N49P9.3, purified from the plasma of an HIV elite-neutralizer. Through a series of rational modifications we produced a variant that demonstrates: enhanced potency; superior antiviral activity in combination with other bnAbs; low polyreactivity; and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.

bioengineering↗

bioRxiv2024

Multi-omics investigation of spontaneous T2DM macaque reveals gut microbiota promote T2DM by up-regulating the absorption of excess palmitic acid

Although gut microbiota and lipid metabolites have been suggested to be closely associated with type 2 diabetes mellitus (T2DM), the interactions between gut microbiota, lipid metabolites and the host in T2DM development remains unclear. Rhesus macaques may be the best animal model to investigate these relationships given their spontaneous development of T2DM. We identified eight spontaneous T2DM macaques and conducted a comprehensive study investigating the relationships using multi-omics sequencing technology. Our results from 16S rRNA, metagenome, metabolome and transcriptome analyses identified that gut microbiota imbalance, tryptophan metabolism and fatty acid {beta} oxidation disorders, long-chain fatty acid (LCFA) accumulation, and inflammation occurred in T2DM macaques. We verified the accumulation of palmitic acid (PA) and activation of inflammation in T2DM macaques. Importantly, mice transplanted with spontaneous T2DM macaque fecal microbiota and fed a high PA diet developed prediabetes within 120 days. We determined that gut microbiota mediated the absorption of excess PA in the ileum, resulting in the accumulation of PA in the serum consequently leading to T2DM in mice. In particular, we demonstrated that the specific microbiota composition was probably involved in the process. This study provides new insight into interactions between microbiota and metabolites and confirms causative effect of gut microbiota on T2DM development.

microbiology↗

bioRxiv2024

Inferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation

Gene regulatory networks (GRNs) are critical blueprints for understanding gene regulation and the intricate interactions that drive biological processes. Recent advances have highlighted the potential of single-cell ATAC-seq (scATAC-seq) data in GRN inference, offering unprecedented insights into how chromatin accessibility plays an important part in gene regulation. However, existing methods often fall short in providing a quantitative and holistic depiction of regulatory relationships, particularly in capturing the strength, direction, and type of gene regulation simultaneously. In this paper, we present a novel approach that addresses these limitations by leveraging genetically perturbed scATAC-seq data to infer more comprehensive and accurate GRNs. Our method advances the field by integrating pre- and post-perturbation chromatin accessibility data, enabling the construction of GRNs that more accurately reflect the dynamic regulatory landscape. Through rigorous evaluation on seven real datasets, we demonstrate the methods superior performance in reconstructing GRNs with enhanced precision and interpretability. This work significantly contributes to the field by providing a robust framework for GRN inference, with broad implications for understanding gene regulation in complex biological systems.

bioinformatics↗

bioRxiv2024

Systematic empirical evaluation of individual base editing targets: validating therapeutic targets in USH2A and comparison of methods

Base editing shows promise for the correction of human mutations at a higher efficiency than other repair methods and is especially attractive for mutations in large genes that are not amenable to gene augmentation therapy. Here, we demonstrate a comprehensive workflow for in vitro screening of potential therapeutic base editing targets for the USH2A gene and empirically validate the efficiency of adenine and cytosine base editor/guide combinations for correcting 35 USH2A mutations. Editing efficiency and bystander edits are compared between different target templates (plasmids versus transgenes) and assays (Next generation sequencing versus Sanger), as well as comparisons between unbiased empirical results and computational predictions. Based on these observations, practical assay recommendations are discussed. Finally, a humanized knock-in mouse model was created with the best-performing target, the nonsense mutation c.11864G>A p.(Trp3955*). Split-intein AAV9 delivery of editing reagents resulted in the restoration of USH2A protein and a correction rate of 65 {+/-} 3% at the mutant base pair and of 52 {+/-} 3% excluding bystander amino acid changes. This efficiency compares favorably to a prior genome editing strategy tested in the retina that completed a clinical trial and demonstrates the effectiveness of this overall strategy to identify and test base editing reagents with the potential for human therapeutic applications.

genetics↗

bioRxiv2024

Immunopeptidomics informs discovery and delivery of Mycobacterium tuberculosis MHC-II antigens for vaccine design

No currently licensed vaccine reliably prevents pulmonary tuberculosis (TB), a leading cause of infectious disease mortality. Developing effective new vaccines will require identifying which of the roughly 4000 proteins in the Mycobacterium tuberculosis (Mtb) proteome are presented on MHC class II (MHC-II) by infected human phagocytes and can be recognized by CD4+ T cells to mediate protective immunity. Vaccines must also elicit T cell responses recognizing the same peptide-MHC complexes presented by infected cells, and successful presentation of target human MHC-II peptides is currently challenging to evaluate and optimize. Here, we define antigenic targets for TB vaccine development by using mass spectrometry (MS) for proteome-wide discovery of Mtb epitopes presented on MHC-II by infected human cells. We next iteratively design and evaluate candidate mRNA vaccine immunogens, revealing design principles that enhance presentation of target MHC-II peptides. Our results will inform the development of new TB vaccine candidates.

microbiology↗