Biology subjects

Zou, L.

Publications and source records attributed to Zou, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Down regulation of Engase in Caenorhabditis elegans may improve its stresses adaptivity

Endo-beta-N-acetylglucosaminidase (ENGASE) is one of the key enzymes involved in the regulation of structure and function of glycoproteins. It is conserved from prokaryotic to eukaryotic cells. Although their activities in vitro and applications have been well studied, the biological function of ENGASE remains to be illustrated. In this study, we analyzed the molecular and physiological function of Engase from Caenorhabditis elegans homolog eng-1(CeEngase). We found that CeEngase knockout or knockdown increased the environmental stresses adaptability, such as heat stress and osmotic stress. Preliminary glycomics analysis showed that the basement membrane proteins of extracellular matrix may be the main targets of CeENGASE. In addition, CeENGASE may selectively prefer to N2H7 glycans on glycoproteins. In conclusion, our data illustrated that the defection and/or down regulation of CeEngase may provide a beneficially adaptation for stresses.

biochemistry↗

bioRxiv2024

Representational drift as the consequence of ongoing memory storage

Memory systems with biologically constrained synapses have been the topic of intense theoretical study for over thirty years. Perhaps the most fundamental and far-reaching finding from this work is that the storage of new memories implies the partial erasure of already-stored ones. This overwriting leads to a decorrelation of sensory-driven activity patterns over time, even if the input patterns remain similar. Representational drift (RD) should therefore be an expected and inevitable consequence of ongoing memory storage. We tested this hypothesis by fitting a network model to data from long-term chronic calcium imaging experiments in mouse hippocampus. Synaptic turnover in the model inputs, consistent with the ongoing encoding of new activity patterns, accounted for the observed statistics of RD. This mechanism also provides a parsimonious explanation for the diverse effects of experience on drift found in experiment. Our results suggest that RD should be observed wherever neuronal circuits are involved in a process of ongoing learning or memory storage.

neuroscience↗

bioRxiv2024

Unraveling the impact of host genetics and factors on the urinary microbiome in a young population

The significance of the urinary microbiome in maintaining health and contributing to disease development is increasingly recognized. However, a comprehensive understanding of this microbiome and its influencing factors remains elusive. Utilizing whole metagenomic and whole-genome sequencing, along with detailed metadata, we characterized the urinary microbiome and its influencing factors in a cohort of 1579 Chinese individuals. Our findings unveil the distinctiveness of the urinary microbiome from other four body sites, delineating five unique urotypes dominated by Gardnerella vaginalis, Sphingobium fluviale, Lactobacillus iners, Variovorax sp PDC80 and Acinetobacter junii, respectively. We identified 108 host factors significantly influencing the urinary microbiome, collectively explaining 12.92% of the variance in microbial composition. Notably, gender-related factors, including sex hormones, emerged as key determinants in defining urotype groups, microbial composition and pathways, with the urinary microbiome exhibiting strong predictive ability for gender (AUC=0.843). Furthermore, we discovered 43 genome-wide significant associations between host genetic loci and specific urinary bacteria, Acinetobacter in particular, linked to 8 host loci (p < 5x10-8). These associations were also modulated by gender and sex hormone levels. In summary, our study provides novel insights into the impact of host genetics and other factors on the urinary microbiome, shedding light on its implications for host health and disease.

microbiology↗

bioRxiv2024

Retrotransposon-mediated variation of a chitin synthase gene confers insect resistance to Bacillus thuringiensis Vip3Aa toxin

Bacillus thuringiensis (Bt) crops expressing Vip3Aa are highly efficacious in controlling major lepidopteran pests and delaying evolution of pest resistance. Although practical resistance to Vip3Aa in the field has not been reported, to proactively manage the pest resistance, there is an urgent need to better understand the genetic basis of resistance to Vip3Aa. This is particularly important for the fall armyworm (Spodoptera frugiperda), one of the most destructive pests around the world, which has evolved practical resistance to Bt crystal (Cry) toxins. Here, a highly Vip3Aa-resistant (resistance ratio: 5,562-fold) strain of S. frugiperda was selected in the laboratory. Results from bulked segregant analysis, fine-scale mapping, and genetic linkage analysis indicate that a mutation in the midgut-specific chitin synthase gene, SfCHS2, is strongly associated with high-level resistance to Vip3Aa. The resistance is ascribed to the transcriptional variation caused by retrotransposon insertion. The same variation of SfCHS2 was also detected in a field population. Importantly, knockout of SfCHS2 via CRISPR/Cas9 in susceptible S. frugiperda confers its complete resistance (>10,000-fold) to Vip3Aa. Also, we demonstrate that knockout of CHS2 can result in complete resistance to Vip3Aa in additional lepidopteran species, suggesting a general role of this gene in Vip3Aa resistance among lepidopteran pests. These results reported here would contribute to monitor and management of pest resistance to Vip3Aa.

genetics↗

bioRxiv2024

Chronic alcohol exposure induces cerebral microbleeds by TGF-β1/Smad signaling pathway mediated remodeling of cerebral small vessels

BackgroundLong-term heavy drinking is a major risk factor for cerebral microbleeds(CMBs), which are increasingly gaining attention as a pathological phenotype of cerebral small vessel diseases(CSVD). Under pathological conditions, remodeling of the extracellular matrix(ECM) on the walls of small vessels causes disarray in the structure and function of these vessels, leading to cerebral small vessel sclerosis and consequent rupture and bleeding. This can result in cognitive and emotional disorders, abnormal gait and increased risk of falling. However, the mechanisms underlying how long-term alcohol consumption leads to CMBs and decline in motor function remain unknown. MethodsWe constructed a chronic alcohol exposure mouse model and measured the deposition of ECMs on the small vessels in motor-related brain regions. The presence of microbleeds was confirmed through Prussian blue staining and Magnetic Resonance Imaging. We also extracted primary cerebral microvascular smooth muscle cells (CMVSMCs) from the newborn mice and explored the effects of alcohol on the phenotypic transformation and substance synthesis function. Additionally, we conducted interventional experiments on the cell and animal models with an anti-fibrotic drugs Pirfenidone(PFD). ResultsWe found that mice with long-term alcohol exposure showed decreased motor function. In their motor-related brain regions, such as the motor cortex(MC), thalamus/basal ganglia(Tha/BG), and cerebellum(CB), we observed microbleeds. On the small vessels in these areas, we detected excessive deposited ECM proteins. In vitro experiments with primary CMVSMCs revealed that after alcohol treatment, the cells underwent a transformation into fibroblast-like phenotypes, and excessive production of the aforementioned ECM proteins, which is regulated by upstream TGF{beta}1/Smad signaling pathway. Additionally, PFD applied on cell and animal models could reverse the above processes to some extent. ConclusionsOur study found that the remodeling of ECM accompanied by activation of TGF-{beta}1/Smad signaling pathway may be involved in alcohol-induced CMBs. It could be a potential therapeutic target for CMBs or CSVD.

molecular biology↗

bioRxiv2024

Unprocessed Genomic Uracil as a Source of DNA Replication Stress in Cancer Cells

Alterations of bases in DNA constitute a major source of genomic instability. It is believed that base alterations trigger base excision repair (BER), generating DNA repair intermediates interfering with DNA replication. Here, we show that genomic uracil, a common base alteration, induces DNA replication stress (RS) without being processed by BER. In the absence of uracil DNA glycosylase (UNG), genomic uracil accumulates to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA. ATR inhibition in UNG-deficient cells blocks repair of uracil-induced gaps, increasing replication fork collapse and cell death. Notably, a subset of cancer cells harboring high levels of genomic uracil upregulate UNG2 to limit RS, and these cancer cells are hypersensitive to co-treatment with ATR inhibitors and drugs increasing genomic uracil. These results reveal unprocessed genomic uracil as an unexpected source of RS and a targetable vulnerability of cancer cells.

molecular biology↗

bioRxiv2023

Distributed evidence accumulation across macaque large-scale neocortical networks during perceptual decision making

Despite the traditional view of parietal cortex as an important region for perceptual decision-making, recent evidence suggests that sensory accumulation occurs simultaneously across many cortical regions. We explored this hypothesis by integrating connectivity, cellular and receptor density datasets and building a large-scale macaque cortical model able to integrate conflicting sensory signals and perform a decision-making task. Our results reveal sensory evidence accumulation supported by a distributed network of temporal, parietal and frontal regions, with flexible sequential bottom-up or top-down modulation pathways depending on task difficulty. The model replicates experimental lesioning effects and reveals that the causal irrelevance of parietal areas like LIP for decision performance is explained by compensatory mechanisms within a distributed integration process. The model also reproduces observed temporal gating effects of distractor timing during and after the integration process. Overall, our work hints at perceptual integration during decision-making as a broad distributed phenomenon, providing multiple testable predictions.

neuroscience↗

bioRxiv2023

Imaging the dynamics of uterine contractions in early pregnancy

The myometrium or smooth muscle of the uterus contracts throughout the life of the organ. Uterine muscle contractility is essential for reproductive processes including sperm and embryo transport, and during the uterine cycle to remove menstrual effluent or estrus debris. Even still, uterine contractions have primarily only been studied in the context of preterm labor. This is partly due to a lack of methods for studying the contractile characteristics of the uterine muscle in the intact organ. Here, we describe an imaging-based method to evaluate the contractility of both the longitudinal and circular muscles of the uterus in the cycling stages and in early pregnancy. By transforming the image-based data into 3D spatiotemporal contractility maps, we calculate waveform characteristics of muscle contractions, including amplitude, frequency, wavelength, and velocity. We report that the native organ is highly contractile during the progesterone-dominant diestrus stage of the cycle when compared to the estrogen-dominant proestrus and estrus stages. We also observed correlations between contractility during pre-implantation stages of pregnancy and observed embryo movement patterns. During the first phase of embryo movement when clustered embryos move towards the middle of the uterine horn, uterine contractions are dynamic and non-uniform between different segments of the uterine horn. In the second phase of embryo movement, contractions are more uniform and rhythmic throughout the uterine horn. Finally, when our method is applied to Lpar3 mutant uteri that display faster embryo movement, we observe global and regional increases in contractility. Our method provides a means to understand the wave characteristics of uterine smooth muscle in response to modulators and in genetic mutants. Better understanding uterine contractility in the early pregnancy stages is critical for the advancement of artificial reproductive technologies and a possibility of modulating embryo movement during clinical embryo transfers.

developmental biology↗

bioRxiv2023

The YTHDF1-3 proteins are bidirectionally influenced by the codon content of their mRNA targets

N6-methyladenosine (m6A) is the most abundant modification in eukaryotic mRNAs and plays critical roles in a broad variety of biological processes. Recognition of m6A by the YTHDF1-3 proteins results in the alteration of the translation efficiency and stability of methylated mRNAs, although their mode of action is still matter of debates. To decode the molecular basis of YTHDF1-3 action in human cells, we performed an unbiased proteomic screen of their full spectrum of interacting proteins using BioID (proximity-dependent biotin identification). Our systematic BioID mapping revealed that each YTHDF protein is a dynamic hub that associates with both mRNA silencing machineries and the translation apparatus. Based on this, we identified a direct interaction between YTHDF2 and the ribosomal protein RACK1, and found that the silencing activity of YTHDF2 is bidirectionally modulated by the codon content of its targeted mRNAs. Using a tethering reporter system that recapitulates this phenomenon, we confirmed that the three YTHDF proteins selectively repress mRNAs enriched in optimal codons, while they activate those enriched in non-optimal codons. Altogether, these results have important implications for understanding the underlying multiplicity of YTHDF1-3 and could reconcile seemingly contradictory data.

cell biology↗

bioRxiv2023

Identification and characterization of a beta-1,4 Galactosidase from Elizabethkingia meningoseptica and its application on living cell surface

The biological function of terminal galactose on glycoprotein is an open field of research. Although progress had being made on enzymes that can remove the terminal galactose on glycoproteins, there is a lack of report on galactosidases that can work directly on living cells. In this study, a unique beta 1,4 galactosidase was isolated from Elizabethkingia meningoseptica (Em). It exhibited favorable stability at various temperatures (4-37) and pH (5-8) levels and can remove {beta}-1, 4 linked galactoses directly from glycoproteins. Using Alanine scanning, we found that two acidic residues (Glu-468, and Glu-531) in the predicted active pocket are critical for galactosidase activity. In addition, we also demonstrated that it could cleave galactose residues present on living cell surface. As the enzyme has a potential application for living cell glycan editing, we named it glycan editing galactosidase I or geGalaseI. In summary, our findings lay the groundwork for prospective investigations by presenting a prompt and gentle approach for the removal of galactose moieties from cell surface.

biochemistry↗

bioRxiv2023

Quantitative Learning of Cellular Features From Single-cell Transcriptomics Data Facilitates Effective Drug Repurposing

In this study, we have devised a computational framework SuperFeat that allows for the training of a machine learning model and evaluate the canonical cellular states/features in pathological tissues that underlie the progression of disease. This framework also enables the identification of potential drugs that target the presumed detrimental cellular features. This framework was constructed on the basis of an artificial neural network with the gene expression profiles serving as input nodes. The training data comprised single-cell RNA-seq datasets that encompassed the specific cell lineage during the developmental progression of cell features. A few models of the canonical cancer-involved cellular states/features were tested by such framework. Finally, we have illustrated the drug repurposing pipeline, utilizing the training parameters derived from the adverse cellular states/features, which has yielded successful validation results both in vitro and in vivo. SuperFeat is accessible at https://github.com/weilin-genomics/rSuperFeat.

cell biology↗

bioRxiv2023

CryoEM architecture of a native stretch-sensitive membrane microdomain

Biological membranes are partitioned into functional zones containing specific lipids and proteins, termed membrane microdomains. Their composition and organization remain controversial owing to a paucity of techniques that can visualize lipids in situ without disrupting their native behavior1,2. The yeast eisosome, a membrane compartment scaffolded by the BAR-domain proteins Pil1 and Lsp1, senses and responds to mechanical stress by flattening and releasing sequestered factors3-7. Here, we isolated native eisosomes as helical filaments of Pil1/Lsp1 lattice bound to plasma membrane lipids and solved their structures by helical reconstruction. We observe remarkable organization within the lipid bilayer density from which we could assign headgroups of PI(4,5)P2 and phosphatidylserine bound to Pil1/Lsp1 and a pattern of membrane voids, signatures of sterols, beneath an amphipathic helix. We verified these assignments using in vitro reconstitutions and molecular dynamics simulations. 3D variability analysis of the native eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects functionally important lipid sequestration, supporting a mechanism in which membrane stretching liberates lipids otherwise anchored by the Pil1/Lsp1 coat. Our results provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain and, more globally, resolve long-standing controversies about the architecture and nature of lipid microdomains.

biophysics↗

bioRxiv2023

ALS-causing SOD1 mutations H46R and G85R form similar novel amyloid fibril structures and promote ferroptosis in cells

More than two hundred genetic mutations of Cu, Zn-superoxide dismutase (SOD1) have been identified in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by the selective death of motor neurons through ferroptosis. Two ALS-causing SOD1 mutations, H46R and G85R, are metal-binding region mutants with reduced affinity for metal ions. Here, we generated amyloid fibrils from the apo forms of H46R and G85R under reducing conditions and determined their structures using cryo-EM. We built models for the fibril cores, comprising residues 85-153 for H46R and 82-153 for G85R. These mutations disrupt crucial interactions in the wild-type SOD1 fibril, resulting in amyloid fibrils with distinct structures compared to the wild-type fibril. Remarkably, H46R and G85R form similar novel amyloid fibril structures. The fibril cores display a serpentine fold containing seven or eight {beta}-strands, which are stabilized by a hydrophobic cavity. In the G85R fibril core, Arg85 and Asp101 form a salt bridge for stabilization. We demonstrate that fibril seeds from H46R and G85R cause more severe mitochondrial impairment and significantly promote ferroptosis in neuronal cells, compared with those from wild-type SOD1. Our findings reveal how different SOD1 mutations can result in similar amyloid fibril structures and contribute to ALS pathology.

biochemistry↗

bioRxiv2022

Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes

Recurrent proximal 16p11.2 deletion (16p11.2del) is risk factor of diverse neurodevelopmental disorders (NDDs) with variable penetrance. Although previous human induced pluripotent stem cell (hiPSC) models of 16p11.2del confirmed disrupted neuron development, it is not known which gene(s) at this interval are mainly responsible for the abnormal cellular phenotypes and how the NDD penetrance is regulated. After haplotype phasing of 16p11.2 region, we generated hiPSCs for two 16p11.2del families with distinct residual haplotypes and variable NDD phenotypes. We also differentiated the hiPSCs to cortical neural cells and demonstrated MAPK3 as a driver signal of 16p11.2 region contributing to the dysfunctions in multiple pathways related to neuron development, which leads to altered morphological or electrophysiological properties in neuron cells. Furthermore, residual haplotype-specific MAPK3 expression was identified in 16p11.2del neuron cells, associating MAPK3 down-expression with the minor allele of the residual haplotype. Ten SNPs of the residual haplotype are mapped as enhancer SNPs (enSNPs) of MAPK3, eight enSNPs were functionally validated by luciferase assays, implying enSNPs contribute to residual haplotype-specific MAPK3 expression via cis-regulation. Finally, the analyses of three different patient cohorts showed that the residual haplotype of 16p11.2del is associated with variable NDD phenotypes.

genetics↗

bioRxiv2022

Insulated expression of periplasmic uricase in E. coli Nissle 1917 for the treatment of hyperuricemia

Hyperuricemia is a prevalent disease worldwide that is characterized by elevated urate levels in the blood owing to purine metabolic disorders, which can result in gout and comorbidities. As approximately one-third of urate is excreted by the small intestine and cleared by intestinal microorganisms, modulating the gut microbiota could be an attractive approach for hyperuricemia and gout treatment. In this study, we engineered a probiotic E. coli Nissle 1917 (EcN) strain, EcN C6, which expresses periplasmic uricase at an "insulated site", for urate degeneration. Oral administration of EcN C6 successfully alleviated hyperuricemia, related symptom and gut microbiota in a purine-rich food-induced hyperuricemia rat model and a uox-knockout mouse model. Importantly, the expression of periplasmic uricase in the insulated site did not influence the probiotic properties or global gene transcription of EcN, suggesting that EcN C6 is a safe, effective and low cost therapeutic candidate for hyperuricemia treatment.

synthetic biology↗

bioRxiv2022

CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer

Prostate cancer (PCa) harboring BRCA1/2 mutations is often exquisitely sensitive to PARP inhibition. However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibitors (PARPis). Here, we perform genome-wide CRISPR-Cas9 knockout screens in BRCA1/2-proficient PCa cell lines and identify novel genes whose loss has a profound impact on PARPi sensitivity and resistance. Specifically, MMS22L deletion, frequently observed (up to 14%) in PCa, renders cells hypersensitive to PARPis by disrupting RAD51 loading required for homologous recombination repair, although this response is TP53-dependent. Unexpectedly, loss of CHEK2 confers resistance rather than sensitivity to PARPis in PCa cells through increased expression of BRCA2, a target of CHEK2-TP53-E2F7-mediated transcriptional repression. Combined PARP and ATR inhibition overcomes PARPi resistance caused by CHEK2 loss. Our findings may inform the use of PARPis beyond BRCA1/2-deficient tumors and support reevaluation of currently used biomarkers for PARPi treatment in PCa.

cancer biology↗

bioRxiv2022

A full spectrum PNGase activity analysis of R328 mutations on NGLY1

In humans, N-glycanase 1 (NGLY1; Peptide: N-glycanase, PNGase) is responsible for the deglycosylation of misfolded glycoproteins. Pathogenic mutations in NGLY1 cause a clinical condition known as congenital disorder of deglycosylation (NGLY1-CDDG), a rare autosomal recessive disease first reported in 2012. Although NGLY1-CDDG was diagnosed through whole-exome or whole-genome sequencing and by evaluating the expression levels of NGLY1, the clinical relevance of a detected mutation in NGLY1 needs to be further confirmed. In this study, an in vitro enzymatic assay system was established to evaluate the thermal stability and substrate specificity of NGLY1, as well as the optimum reaction conditions for its activity. A panel of all mutations at the amino acid site R328 in NGLY1 was subjected to this assay. The results revealed that R328A, R328D, R328E, R328F, R328G, R328I, R328P, R328V, R328W, and R328Y were dysfunctional mutations (10/19); NGLY1 mutations with R328H and R328T exhibited similar activity as wild-type NGLY1 (2/19); and NGLY1 mutations with R328C, R328K, R328L, R328M, R328N, R328Q, and R328S showed decreased activity (7/19) compared to wild-type NGLY1. In addition, the effect of potential regulatory compounds, including N-acetyl-L-cysteine and dithiothreitol, on NGLY1 was examined. This in vitro assay may serve as a standard protocol to facilitate rapid diagnosis of all mutations on NGLY1 and a practical screening method for drugs and compounds with potential therapeutic value for NGLY1-CDDG patients.

biochemistry↗

bioRxiv2022

Single cell Transcriptome and T cell Repertoire Mapping of the Mechanistic Signatures and T cell Trajectories Contributing to Vascular and Dermal Manifestations of Behcet Disease

Behcets disease (BD) is a form of vasculitis characterized by complex multi-organ manifestations that may frequently recur and induce major tissue damage. Although genetic association studies have identified a number of risk factors, the etiology of BD and its tissue manifestations remains unknown, and the landscape of immune responses in BD is opaque, particularly in terms of inflammatory recurrence. In this study, we mapped the transcriptomes of the immune cell compartment in BD at single-cell resolution, sampling both circulation and affected skin in order to chart the immune interplay driving pathogenesis. Through comprehensive expression and communication analysis of the twenty major cell types identified, we observe striking mechanistic differences in immune response between BD skin lesions and peripheral circulation involving TNF signaling and T cell migration. Through integrated TCR sequencing, we further discover a pattern of clonal sharing between circulating and skin CD8+T cell populations along a trajectory defined by the acquisition of tissue-residential properties. In addition, we also identify a population of expanded CD4+ Tregs with the propensity to produce IL-32. Instead of suppressing effector T cell proliferation and function, IL-32 triggers increased expression of CD97, and may thus encourage prolonged local T cell activity in the skin. Collectively, our data serve to advance understandings of contributions of varying immune cell types to BD pathogenesis in the vasculature and skin, as well as the lifecycle patterns of T cells clones in this context. These data may also assist in further investigations of the mechanisms contributing to Treg dysfunction in systemic autoimmunity, while generating a conceptual model of T cell function contributing to BD recurrence.

immunology↗