Biology subjects

Liu, W.

Publications and source records attributed to Liu, W..

At least 433 records · Page 24Linked to original sources

bioRxiv2021

Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits

Alfalfa (Medicago sativa L.), the most valuable perennial legume crop, referred to as "Queen of the Forages" for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are of great importance to breed new alfalfa varieties with environmental resilience. Here, we report assembly of the genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China, and identification of SNPs associated with alfalfa agronomic traits by Genome-wide Association Studies (GWAS). Sequence of 32 allelic chromosomes was assembled successfully by single molecule real time sequencing and Hi-C technique with ALLHiC algorithm. About 2.74 Gbp contigs, accounting for 88.39% of the estimated genome, were assembled with 2.56 Gbp contigs anchored to 32 pseudo-chromosomes. In comparison with M. truncatula A17, distinctive inversion and translocation on chromosome 1, and between chromosome 4 and 8, respectively, were detected. Moreover, we conducted resequencing of 220 alfalfa accessions collected globally and performed GWAS analysis based on our assembled genome. Population structure analysis demonstrated that alfalfa has a complex genetic relationship among germplasm with different geographic origins. GWAS identified 101 SNPs associated with 27 out of 93 agronomic traits. The updated chromosome-scale and allele-aware genome sequence, coupled with the resequencing data of most global alfalfa germplasm, provides valuable information for alfalfa genetic research, and further analysis of major SNP loci will accelerate unravelling the molecular basis of important agronomic traits and facilitate genetic improvement of alfalfa.

plant biology↗

bioRxiv2021

Genome-wide prediction and integrative functional characterization of Alzheimer's disease-associated genes

The mechanism of Alzheimers disease (AD) remains elusive, partly due to the incomplete identification of risk genes. We developed an approach to predict AD-associated genes by learning the functional pattern of curated AD-associated genes from brain gene networks. We created a pipeline to evaluate disease-gene association by interrogating heterogeneous biological networks at different molecular levels. Our analysis showed that top-ranked genes were functionally related to AD. We identified gene modules associated with AD pathways, and found that top-ranked genes were correlated with both neuropathological and clinical phenotypes of AD on independent datasets. We also identified potential causal variants for genes such as FYN and PRKAR1A by integrating brain eQTL and ATAC-seq data. Lastly, we created the ALZLINK web interface, enabling users to exploit the functional relevance of predicted genes to AD. The predictions and pipeline could become a valuable resource to advance the identification of therapeutic targets for AD.

bioinformatics↗

bioRxiv2021

Genome-wide Detection of Cytosine Methylations in Plant from Nanopore sequencing data using Deep Learning

Methylation states of DNA bases can be detected from native Nanopore reads directly. At present, there are many computational methods that can detect 5mCs in CpG contexts accurately by Nanopore sequencing. However, there is currently a lack of methods to detect 5mCs in non-CpG contexts. In this study, we propose a computational pipeline which can detect 5mC sites in both CpG and non-CpG contexts of plant genomes by using Nanopore sequencing. And we sequenced two model plants Arabidopsis thaliana (A. thaliana) and Oryza sativa (O. sativa) by using Nanopore sequencing and bisulfite sequencing. The results of our proposed pipeline in the two plants achieved high correlations with bisulfite sequencing: above 0.98, 0.96, 0.85 for CpG, CHG, and CHH (H indicates A, C or T) motif, respectively. Our proposed pipeline also achieved high performance on Brassica nigra (B. nigra). Experiments also showed that our proposed pipeline can achieve high performance even with low coverage of reads. Moreover, by using Nanopore sequencing, our proposed pipeline is capable of profiling methylation of more cytosines than bisulfite sequencing.

bioinformatics↗

bioRxiv2021

Evolution of ACE2 and SARS-CoV-2 Interplay Across 247 Vertebrates

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause the most serious pandemics of Coronavirus Disease 2019 (COVID-19), which threatens human health and public safety. SARS-CoV-2 spike (S) protein uses angiotensin-converting enzyme 2 (ACE2) as recognized receptor for its entry into host cell that contributes to the infection of SARS-CoV-2 to hosts. Using computational modeling approach, this study resolved the evolutionary pattern of bonding affinity of ACE2 in 247 jawed vertebrates to the spike (S) protein of SARS-CoV-2. First, high-or-low binding affinity phenotype divergence of ACE2 to the S protein of SARS-CoV-2 has appeared in two ancient species of jawed vertebrates, Scyliorhinus torazame (low-affinity, Chondrichthyes) and Latimeria chalumnae (high-affinity, Coelacanthimorpha). Second, multiple independent affinity divergence events recur in fishes, amphibians-reptiles, birds, and mammals. Third, high affinity phenotypes go up in mammals, possibly implying the rapid expansion of mammals might accelerate the evolution of coronaviruses. Fourth, we found natural mutations at eight amino acid sites of ACE2 can determine most of phenotype divergences of bonding affinity in 247 vertebrates and resolved their related structural basis. Moreover, we also identified high-affinity or low-affinity-associated concomitant mutation group.The group linked to extremely high affinity may provide novel potentials for the development of human recombinant soluble ACE2 (hrsACE2) in treating patients with COVID-19 or for constructing genetically modified SARS-CoV-2 infection models promoting vaccines studies. These findings would offer potential benefits for the treatment and prevention of SARS-CoV-2.

evolutionary biology↗

bioRxiv2021

Targeting cellular metabolism to inhibit synergistic biofilm formation of multi-species isolated from a cooling water system

Biofilm is ubiquitous in natural environments, causing biofouling in industrial water systems and leading to liquidity and heat transfer efficiency decreases. In particular, multi-species coexistence in biofilms can provide the synergy needed to boost biomass production and enhance treatment resistance. In this study, a total of 37 bacterial strains were isolated from a cooling tower where acetic acid and propionic acid were used as the primary carbon sources. These isolates mainly belonged to Proteobacteria and Firmicutes, which occupied more than 80% of the total strains according to the 16S rRNA gene amplicon sequencing. Four species (Acinetobacter sp. CTS3, Corynebacterium sp. CTS5, Providencia sp. CTS12, and Pseudomonas sp. CTS17) were observed to co-exist in the synthetic medium, showing a synergistic effect towards biofilm formation. Three metabolic inhibitors (sulfathiazole, 3-Bromopyruvic acid, and 3-Nitropropionic acid) were employed as possible treatments against biofilm formation due to their inhibition effect on c-di-GMP biosynthesis or assimilation of volatile fatty acids. All of them displayed evident inhibition profiles to biofilm formation. Notably, the combination of these three inhibitors possessed a remarkable ability to block the development of a multi-species biofilm with lower concentrations, suggesting an enhanced effect with their simultaneous use. This study demonstrates that targeting cellular metabolism is an effective way to inhibit biofilm formation derived from multi-species.

microbiology↗

bioRxiv2021

INTEGRATION OF ENGINEERED "SPARK-CELL" SPHEROIDS FOR OPTICAL PACING OF CARDIAC TISSUE

Optogenetic methods for pacing of cardiac tissue can be realized by direct genetic modification of the cardiomyocytes to express light-sensitive actuators, such as channelrhodopsin-2, ChR2, or by introduction of light-sensitized non-myocytes that couple to the cardiac cells and yield responsiveness to optical pacing. In this study, we engineer three-dimensional "spark cells" spheroids, composed of ChR2-expressing human embryonic kidney cells, and characterize their morphology as function of cell density and time. These "spark-cell" spheroids are then deployed to demonstrate site-specific optical pacing of human stem-cell-derived cardiomyocytes (hiPSC-CMs) in 96-well format using non-localized light application and all-optical electrophysiology. We show that the spheroids can be handled using liquid pipetting and can confer optical responsiveness of cardiac tissue earlier than direct viral or liposomal genetic modification of the cardiomyocytes, with 24% providing reliable stimulation of the iPSC-CMs within 6 hours and >80% within 24 hours. Our results demonstrate a scalable, cost-effective method to achieve contactless optical stimulation of cardiac cell constructs that can be integrated in a robotics-amenable workflow for high-throughput drug testing. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/428177v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@156108org.highwire.dtl.DTLVardef@1956092org.highwire.dtl.DTLVardef@1f7237eorg.highwire.dtl.DTLVardef@3b37a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

3D Mapping of Neurofibrillary Tangle Burden in the Human Medial Temporal Lobe

Tau protein neurofibrillary tangles (NFT) are closely linked to neuronal/synaptic loss and cognitive decline in Alzheimers disease (AD) and related dementias. Our knowledge of the pattern of NFT progression in the human brain, critical to the development of imaging biomarkers and interpretation of in vivo imaging studies in AD, is based on conventional 2D histology studies that only sample the brain sparsely. To address this limitation, ex vivo MRI and dense serial histological imaging in 18 human medial temporal lobe (MTL) specimens were used to construct 3D quantitative maps of NFT burden in the MTL at individual and group levels. These maps reveal significant variation in NFT burden along the anterior-posterior axis. While early NFT pathology is thought to be confined to the transentorhinal region, we find similar levels of NFT burden in this region and other MTL subregions, including amygdala, temporopolar cortex, and subiculum/CA1.

neuroscience↗

bioRxiv2021

Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs

N6-methyladenosine (m6A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, play important roles in tuning the chromatin state and transcription1. Among diverse RNA-chromatin interacting modes, the nuclear RNA scaffold is considered important for trans-interactions2,3 but has not yet been connected with m6A yet. Here, we found that Ythdc1 played indispensable roles in the embryonic stem cell (ESC) self-renewal and differentiation potency, and these roles highly depended on its m6A-binding ability. Ythdc1 deficiency in ESCs resulted in decreased rRNA synthesis and the activation of 2-cell (2C) embryo-specific transcriptional program, and these observations recapitulated the transcriptome defects induced by dysfunction of the long interspersed nuclear element-1 (LINE1)-scaffold, which were unrelated to the direct targeting of Ythdc1. A detailed analysis revealed that Ythdc1 recognized m6A on LINE1 and was physically involved in the formation of the LINE1-Nucleolin partnership and the chromatin recruitment of Kap1. In summary, our study reveals a new link between m6A and the RNA scaffold and thus provides a new regulatory model for the crosstalk between RNA and the chromatin epigenome.

cell biology↗

bioRxiv2021

Newcastle disease virus induced ferroptosis through p53-SLC7A11-GPX4 axis mediated nutrient deprivation in tumor cells

A number of new cell death processes have been discovered in recent years, including ferroptosis, which is characterized by the accumulation of lipid peroxidation products derived from iron metabolism. The evidence suggests that ferroptosis has a tumor-suppressor function. However, the mechanism by which ferroptosis mediates the response of tumor cells to oncolytic viruses remains poorly understood. Newcastle disease virus can selectively replicate in tumor cells. We show that NDV-induced ferroptosis acts through p53-SLC7A11-GPX4 pathway. The expression of tumor suppressor gene p53 increased after NDV infection, and the expressions of SLC7A11 and SLC3A2 were down-regulated, leading to the inhibition of glutathione synthesis and a decrease in glutathione peroxidase 4 expression. The chemical compound erastin, which induces ferroptosis, also down-regulated glutathione synthase expression and caused lipid peroxide accumulation and cell death. Meanwhile, the levels of intracellular reactive oxygen species and lipid peroxides increased in tumor cells. Ferritinophagy was induced by NDV promotion of ferroptosis through the release of ferrous iron and an enhanced Fenton reaction. Collectively, these observations demonstrated that NDV can kill tumor cells through ferroptosis. Our study provides novel insights into the mechanisms of NDV-induced ferroptosis and highlights the critical role of viruses in treating therapy-resistant cancers.

cancer biology↗

bioRxiv2020

Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patients immunological status, and found dramatic changes in the IGH within the patients immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.

immunology↗

bioRxiv2020

Real-time monitoring epidemic trends and key mutations in SARS-CoV-2 evolution by an automated tool

With the global epidemic of SARS-CoV-2, it is important to monitor the variation, haplotype subgroup epidemic trends and key mutations of SARS-CoV-2 over time effectively, which is of great significance to the development of new vaccines, the update of therapeutic drugs, and the improvement of detection reagents. The AutoVEM tool developed in the present study could complete all mutations detections, haplotypes classification, haplotype subgroup epidemic trends and key mutations analysis for 131,576 SARS-CoV-2 genome sequences in 18 hours on a 1 core CPU and 2G internal storage computer. Through haplotype subgroup epidemic trends analysis of 131,576 genome sequences, the great significance of the previous 4 specific sites (C241T, C3037T, C14408T and A23403G) was further revealed, and 6 new mutation sites of highly linked (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) were discovered for the first time that might be related to the infectivity, pathogenicity or host adaptability of SARS-CoV-2. In brief, we proposed an integrative method and developed an efficient automated tool to monitor haplotype subgroup epidemic trends and screen out the key mutations in the evolution of SARS-CoV-2 over time for the first time, and all data could be updated quickly to track the prevalence of previous key mutations and new key mutations because of high efficiency of the tool. In addition, the idea of combinatorial analysis in the present study can also provide a reference for the mutation monitoring of other viruses.

genomics↗

bioRxiv2020

Unique intramolecular oxidative rearrangement N-nitrosation mechanism of non-heam iron-containing enzyme SznF

Non-heam iron-dependent enzyme SznF catalyzes a critical step of the L-arginine derived guanidine group rearrangement to produce the N-nitrosourea pharmacophore in the process of SZN biosynthesis. The intramolecular oxidative rearrangement process is accomplished in the Fe(II)-containing active site located at the cupin domain of SznF, with which the catalytic mechanism remains elusive. In this work, density functional theory methods have been employed to investigate possible catalytic mechanisms of SznF. The N-nitrosation reaction in SznF was found to follow an energetically favorable pathway which includes six consecutive steps: (1) formation of FeII-superoxo species with dioxgen binding on the iron center; (2) superoxo group attacking on the C{varepsilon} of substrate to form the peroxo-bridge complex; (3) C{varepsilon}-N{omega} bond homolysis to release N{omega}O; (4) peroxo bridge heterolytic cleavage; (5) deprotonation of [Formula] by Fe-O group; (6) the [Formula] couples with the N{omega}O group and generates the N-nitroso product. The reaction proceeds in an unexpected way during which the electrons shuttle among two NO groups of the substrate and the peroxo moiety to promote C{varepsilon}-N{omega} bond homolysis and O-O bond heterolysis sequentially without generating high-valent Fe-O species, which is distinct from any known reactions catalyzed by the iron-containing enzyme. The unusual mechanism of SznF shed light on the area of enzymatic N-nitrosation reactions.

biochemistry↗

bioRxiv2020

Phase separation of Mer2 organizes the meiotic loop-axis structure of chromatin during meiosis I

Sexually reproducing organisms acquire genetic diversity through meiotic recombination during meiosis I, which is initiated via programmed DNA double-strand breaks (DSBs) induced by Spo11-containing machinery in each meiotic cell. The combination of programmed DSB sites in each meiotic cell must be diverse, which requires a certain degree of randomness in the distribution of DSBs. The formation of programmed DSBs requires a preestablished loop-axis structure of chromatin. Here, we demonstrate that the axial element protein Mer2 undergoes liquid-liquid phase separation in vitro and in vivo through its intrinsically disordered C-terminal domain. A DNA binding motif within its central domain is responsible for bringing DNA into Mer2 liquid droplets and Mer2-DNA complex could assemble into filamentous structures extending from the droplets. These results suggest that phase separation of Mer2 drives the formation of a droplet-loop structure of meiotic chromatin to facilitate and to diversify programmed DSB formation.

biophysics↗

bioRxiv2020

ORMDL1 is upregulated and associated with favorable outcome in colorectal cancer

BackgroundORMDL1 gene encodes a transmembrane protein for endoplasmic reticulum and is known as crucial negative regulator for sphingolipid biogenesis. However, it has been rarely studied in tumor-related context. Therefore, its prognostic value and functional significance in colorectal cancer (CRC) remain to be explored. MethodsTCGA CRC cohort analysis, qRT-PCR, and immunohistochemistry (IHC) were used to examine the ORMDL1 expression level. The association between ORMDL1 expression and various clinical characteristics were analyzed by Chi-square tests. CRC patients overall survival (OS) was analyzed by Kaplan-Meier analysis. In vitro and in vivo cell-based assays were performed to explore the role of ORMDL1 in cell proliferation, invasion and migration. Transcriptional changes of cells either with ORMDL1 knockdowned or overexpressed were compared and analyzed. ResultsORMDL1 was upregulated in CRC tissues either in TCGA cohort or in our cohort. Interestingly, its expression was significantly lower in patients with metastasis compared to patients without metastasis, and high expression group had longer OS than low expression group. Knockdown of ORMDL1 expression can promote proliferation, colony formation and invasion, while attenuate migration in CRC cell lines. In opposite, forced overexpression of ORMDL1 reduced cell proliferation, colony formation and invasion, while enhanced cell migration. Epithelial-to-mesenchymal transition (EMT) related genes were enriched among differentially expressed genes when ORMDL1 was knockdowned in cells, which was consistent with morphologic change by microscopy observation. Finally, stable knockdown of ORMDL1 can promote cancer cell proliferation in vivo to some extent. ConclusionORMDL1 is upregulated and may serve as biomarker to predict favourable outcome in colorectal cancer.

cancer biology↗

bioRxiv2020

Data-informed discovery of hydrolytic nanozymes

Nanozyme is a collection of nanomaterials with enzyme-like activity but exhibits higher environmental tolerance and long-term stability than their natural counterparts. Improving the catalytic activity and expanding the category of nanozymes are prerequisites to complement or even supersede natural enzymes. Specifically, a powerful hydrolytic nanozyme is demanded to degrade the unsustainable substance which natural enzymes hardly achieve. However, the development of hydrolytic nanozymes is still hindered by diverse hydrolytic substrates and following complicated mechanisms. Here, we apply two strategies which are informed by data to screen and predict catalytic active sites of MOF (metal-organic framework) based hydrolytic nanozymes. One is to increase the intrinsic activity by finely tuned Lewis acidity of the metal clusters. The other is to adjust the volume density of the active sites by shortening the length of ligands. Finally, we construct a Ce-FMA-MOF-based hydrolytic nanozyme with robust cleavage ability towards phosphate bonds, amide bonds, glycosidic bonds whose energy ascend in order; and even their mixture, biofilms. This work provides a rational methodology to design hydrolytic nanozyme, enriches the diversity of nanozymes, and potentially sheds a light on the evolution of enzyme engineering in the future.

biophysics↗

bioRxiv2020

Loss of phosphatidylserine flippase β-subunit Tmem30a in podocytes leads to albuminuria and glomerulosclerosis

Phosphatidylserine (PS) is asymmetrically concentrated in the cytoplasmic leaflet of eukaryotic cell plasma membranes. This asymmetry is regulated by a group of P4 ATPases (named PS flippases) and its {beta}-subunit TMEM30A. The disruption of PS flippase leads to severe human diseases. Tmem30a is essential in the mouse retina, cerebellum and liver. However, the role of Tmem30a in the kidney, where it is highly expressed, remains unclear. Podocytes in the glomerulus form a branched interdigitating filtration barrier that can prevent the traversing of large cellular elements and macromolecules from the blood into the urinary space. Damage to podocytes can disrupt the filtration barrier and lead to proteinuria and podocytopathy, including focal segmental glomerulosclerosis, minimal change disease, membranous nephropathy, and diabetic nephropathy. To investigate the role of Tmem30a in the kidney, we generated a podocyte-specific Tmem30a knockout (cKO) mouse model using the NPHS2-Cre line. Tmem30a KO mice displayed albuminuria, podocyte degeneration, mesangial cell proliferation with prominent extracellular matrix accumulation and eventual progression to focal segmental glomerulosclerosis (FSGS). Reduced TMEM30A expression was observed in patients with minimal change disease and membranous nephropathy, highlighting the clinical importance of TMEM30A in podocytopathy. Our data demonstrate a critical role of Tmem30a in maintaining podocyte survival and glomerular filtration barrier integrity. Understanding the dynamic regulation of the PS distribution in the glomerulus provides a unique perspective to pinpoint the mechanism of podocyte damage and potential therapeutic targets.

pathology↗

bioRxiv2020

A body map of somatic mutagenesis in morphologically normal human tissues

Somatic mutations accumulated in normal tissues are associated with aging and disease. Here, we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies (~ 600 cells each), mostly from the epithelia, of nine organs from five donors. We found that somatic mutation accumulations and clonal expansions are widespread, although with variable extent, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for tissues from esophagus and cardia. Endogenous mutational processes like SBS1 and SBS5 are ubiquitous among normal tissues though exhibiting different relative activities. Exogenous mutational processes like SBS22 were found in different tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimeter resolution. In epithelial tissues from esophagus and cardia, macroscopic somatic clones expanded to several millimeters were frequently seen, whereas in tissues from colon, rectum, and duodenum somatic clones were microscopic in size and evolved independently. Our study depicted a body map of somatic mutations and clonal expansions from the same individuals, and it revealed that the degree of somatic clonal expansion and enrichment of driver mutations are highly organ specific.

genomics↗

bioRxiv2020

Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage

Efficient peptide and protein identification from data-independent acquisition mass spectrometric (DIA-MS) data typically rely on an experiment-specific spectral library with a suitable size. Here, we report a computational strategy for optimizing the spectral library for a specific DIA dataset based on a comprehensive spectral library, which is accomplished by a priori analysis of the DIA dataset. This strategy achieved up to 44.7% increase in peptide identification and 38.1% increase in protein identification in the test dataset of six colorectal tumor samples compared with the comprehensive pan-human library strategy. We further applied this strategy to 389 carcinoma samples from 15 tumor datasets and observed up to 39.2% increase in peptide identification and 19.0% increase in protein identification. In summary, we present a computational strategy for spectral library size optimization to achieve deeper proteome coverage of DIA-MS data.

bioinformatics↗