Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 883 records · Page 49Linked to original sources

bioRxiv2023

Polymer Implantable Electrode Foundry: A shared resource for manufacturing polymer-based microelectrodes for neural interfaces

Large scale monitoring of neural activity at the single unit level can be achieved via electrophysiological recording using implanted microelectrodes. While neuroscience researchers have widely employed chronically implanted electrode-based interfaces for this purpose, a commonly encountered limitation is loss of highly resolved signals arising from immunological response over time. Next generation electrode-based interfaces improve longitudinal signal quality using the strategy of stabilizing the device-tissue interface with microelectrode arrays constructed from soft and flexible polymer materials. The limited availability of such polymer microelectrode arrays has restricted access to a small number of researchers able to build their own custom devices or who have developed specific collaborations with engineering researchers who can produce them. Here, a new technology resource model is introduced that seeks to widely increase access to polymer microelectrode arrays by the neuroscience research community. The Polymer Implantable Electrode (PIE) Foundry provides custom and standardized polymer microelectrode arrays as well as training and guidance on best-practices for implantation and chronic experiments.

neuroscience↗

bioRxiv2023

Accurate 3D SMLM localization via Vectorial In-situ PSF Retrieval and Aberration Assessment

In single-molecule localization microscopy (SMLM), achieving precise localization hinges on obtaining an authentic point spread function (PSF) influenced by system and sample-induced aberrations. Here, we introduce VISPR (Vectorial in-situ PSF retrieval) retrieving precise 3D PSF models considering both system and sample-induced aberrations under SMLM conditions. By employing the theory of vectorial PSF model and maximum likelihood estimation (MLE) phase retrieval, VISPR is capable of reconstructing an accurate 3D PSF model achieving the theoretically minimum uncertainty and accurately reflecting three-dimensional information of single molecules. This capability empowers accurate 3D super-resolution reconstruction in 3D SMLM. Additionally, VISPR applies to low signal-to-noise ratio circumstances and is adept at retrieving high-frequency details of the experimental PSF across an extensive depth range--a challenging feat for alternative approaches. As an effective tool, VISPR enables the quantitative assessment of aberrations induced by the system and sample environment. From the simulations and experiments, we verified the superiority and effectiveness of VISPR. It is essential to highlight that VISPR applies to various SMLM microscope modalities.

molecular biology↗

bioRxiv2023

Membrane potential mediates an ancient mechano-transduction mechanism for multi-cellular homeostasis

Mechanical forces have been shown to influence cellular decisions to grow, die, or differentiate, through largely mysterious mechanisms. Separately, changes in resting membrane potential have been observed in development, differentiation, regeneration, and cancer. We now demonstrate that membrane potential is the central mediator of cellular response to mechanical pressure. We show that mechanical forces acting on the cell change cellular biomass density, which in turn alters membrane potential. Membrane potential then regulates cell number density in epithelia by controlling cell growth, proliferation, and cell elimination. Mechanistically, we show that changes in membrane potential control signaling through the Hippo and MAPK pathways, and potentially other signaling pathways that originate at the cell membrane. While many molecular interactions are known to affect Hippo signaling, the upstream signal that activates the canonical Hippo pathway at the membrane has previously been elusive. Our results establish membrane potential as a central regulator of growth and tissue homeostasis.

cell biology↗

bioRxiv2023

IDO-1 inhibition improves outcome after fluid percussion injury in adult male rats

The enzyme indoleamine 2,3 dioxygenase 1 (IDO1) catalyzes the rate-limiting step in the kynurenine pathway (KP) which produces both neuroprotective and neurotoxic metabolites. Neuroinflammatory signals produced as a result of pathological conditions can increase production of IDO1 and boost its enzymatic capacity. IDO1 and the KP have been implicated in behavioral recovery after human traumatic brain injury (TBI), but their roles in experimental models of TBI are for the most part unknown. We hypothesized there is an increase in KP activity in the fluid percussion injury (FPI) model of TBI, and that administration of an IDO1 inhibitor will improve neurological recovery. In this study adult male Sprague-Dawley rats were subjected to FPI or sham injury and received twice-daily oral administration of the IDO1 inhibitor PF-06840003 (100 mg/kg) or vehicle control. FPI resulted in a significant increase in KP activity, as demonstrated by an increased ratio of kynurenine:tryptophan, in the perilesional neocortex and ipsilateral hippocampus three days post-injury (DPI), which normalized by seven DPI. The increase in KP activity was prevented by PF-06840003. IDO1 inhibition also improved memory performance as assessed in the Barnes maze and anxiety behaviors as assessed in open field testing in the first 28 DPI. These results suggest increased KP activity after FPI may mediate neurological dysfunction, and IDO1 inhibition should be further investigated as a potential therapeutic target to improve recovery. Significance StatementThe kynurenine pathway and its rate-limiting enzyme indoleamine 2,3 dioxygenase 1 (IDO1) have been implicated in a variety of neurological disorders, including traumatic brain injury. We have demonstrated increased IDO1 activity in male rats after fluid percussion injury, a widely used model of traumatic brain injury. Pharmacological IDO1 inhibition after fluid percussion injury improved performance on tests of memory and anxiety-like behaviors, demonstrating a role for IDO1 in traumatic brain injury outcomes and supporting further investigation into its potential as a therapeutic target.

neuroscience↗

bioRxiv2023

Identification and functional analysis of eRNA markers for hepatocellular carcinoma based on high-throughput data

Hepatocellular carcinoma (HCC) is a common type of liver cancer with a high mortality rate. enhancer RNA (eRNA) has been proved to play an important role in cancer progress and development. However, the eRNA studies in HCC are still limited. In this study, we attempted to identify some eRNA biomarkers for HCC diagnosis and analyzed their biological function. First, we identified three eRNA biomarkers (CAP2e, COLEC10e, and MARCOe), which were significant differentially expressed between tumor and normal tissues in 115 HCC patients across three datasets. CAP2e demonstrated upregulation in tumors while COLEC10e and MARCOe were downregulated. These results could be validated in TCGA-LIHC data. There were significant positive correlations between the expression of these eRNAs and their host genes. Then, functional enrichment analysis of protein-coding genes associated with the eRNA biomarkers revealed their involvement in cancer-related pathways. MARCOe was suggested to be a potential target for therapeutic drugs in HCC by a drug related study. The next, survival analysis demonstrated significant prognostic values of these eRNAs in prediction of overall survival. Immune infiltration analysis revealed a positive correlation between MARCOe expression and immune cell infiltration level. Finally, we found similar expression patterns of these eRNA biomarkers in other cancers, such as cholangiocarcinoma, through a pan-cancer comparison. CAP2e and COLEC10e in HCC were validated by other studies. However, the studies about MARCOe in HCC were limited. In conclusion, as best as our knowledge, it is the first time to identify three eRNA biomarkers for HCC diagnosis. These biomarkers are proved to be involved in HCC progress and development, have prognosis prediction values, and are potential to be therapeutic targets.

cancer biology↗

bioRxiv2023

Virome analysis provides new insights into the pathogenesis mechanism and treatment of SLE disease

Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease. Many viruses have been reported to be associated with SLE, but the diversity of the virome in SLE and the mechanisms underlying the interactions between viral infection and SLE are still unclear. This study identified ten human virus species from 826 RNA-Seq samples of human blood from 688 SLE patients and 138 healthy controls. SLE patients were found to have higher positive rates of viruses than healthy controls, although the virus abundances were low and comparable in both SLE patients and healthy controls. Analysis of the antiviral interferon-stimulated genes (ISGs) in samples showed higher ISG expression levels in virus-positive samples compared to virus-negative samples, which confirmed viral infections in virus-positive samples. Further analysis of differential expression genes between virus-positive and negative SLE patients showed that several genes that were up-regulated in SLE patients were further up-regulated after viral infections, and they were mainly enriched in immune response-related biological processes, suggesting an excess immune response in SLE patients after viral infections. Finally, three marker genes of the SLE severity, namely STAT1, STAT5A, and STAT5B, showed higher expression levels in virus-positive SLE patients compared to those in virus-negative SLE patients, suggesting that viral infections may aggravate the SLE disease. Overall, the study deepens our understanding of the association between viruses and SLE and provides new insights into prevention and control of the disease.

bioinformatics↗

bioRxiv2023

Targeted genome editing restores auditory function in adult mice with progressive hearing loss caused by a human microRNA mutation

Mutations in microRNA-96 (MIR96) cause dominant delayed onset hearing loss DFNA50 without treatment. Genome editing has shown efficacy in hearing recovery by intervention in neonatal mice, yet editing in the adult inner ear is necessary for clinical applications. Here, we developed an editing therapy for a C>A point mutation in the seed region of the Mir96 gene, Mir9614C>A associated with hearing loss by screening gRNAs for genome editors and optimizing Cas9 and sgRNA scaffold for efficient and specific mutation editing in vitro. By AAV delivery in pre-symptomatic (3-week-old) and symptomatic (6-week-old) adult Mir9614C>A mutant mice, hair cell on-target editing significantly improved hearing long-term, with an efficacy inversely correlated with injection age. We achieved transient Cas9 expression without the evidence of AAV genomic integration to significantly reduce the safety concerns associated with editing. We developed an AAV-sgmiR96-master system capable of targeting all known human MIR96 mutations. As mouse and human MIR96 sequences share 100% homology, our approach and sgRNA selection for efficient and specific hair cell editing for long-term hearing recovery lays the foundation for future treatment of DFNA50 caused by MIR96 mutations.

bioengineering↗

bioRxiv2023

Pan-genome analysis of different morphotypes reveals genomic basis of Brassica oleracea domestication and differential organogenesis

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed with high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant (SV) hotspot regions enriched with auxin and flowering-related genes. Population genomic analyses reveal that early domestication of B. oleracea focused on leaf or stem selection. Gene flows resulting from agricultural practices and variety improvement are detected among different morphotypes. Selective sweep analysis identifies an auxin-responsive SAUR gene and a CLE family gene as the crucial players in the leaf-stem differentiation during the early stage of B. oleracea domestication, and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further discover that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

plant biology↗

bioRxiv2023

Geographic Distribution of a Missense Mutation in the KRT38 Gene and Its Association with Heat Tolerance in Chinese Indigenous Cattle Breeds

ContextChina has a vast area across many temperature zones and a variety of cattle breeds. These cattle resources are ideal models to research their adaptability to the environment. The KRT38 gene is an acidic protein, and its coding product can be used as a component of hair production. AimsThe objective of this study was to investigate the diversity of the KRT38 gene in Chinese local cattle and the association of different genotypes with mean temperature (T), relative humidity (RH) and temperature humidity index (THI). MethodsA missense mutation g.41650738 A > G in the KRT38 gene was screened from the database of bovine genomic variation (BGVD), was genotyped in a total of 246 samples from 15 local cattle breeds in China by PCR amplification and sequencing. Finally, the correlation between the locus and the three climatic factors was analysed. Key resultsWe successfully obtained the frequency of this SNP in three groups of cattle in northern, central and southern China. The frequency of allele A gradually declined from north to south, while the frequency of allele G showed the opposite trend with a clear geographic distribution. ConclusionsOur results indicate that KRT38 variation in Chinese indigenous cattle might be linked to heat tolerance. ImplicationsOur analysis may support in finding out its importance as a genetic signal for heat tolerance in cattle reproduction and genetics.

genomics↗

bioRxiv2023

A bioactive peptide from the pearl has dual roles in resisting SARS-CoV-2 infection and its complications

Angiotensin-converting enzyme 2 (ACE2) is a critical receptor for the entry of the SARS-CoV-2 virus into cells. Moreover, a decrease in ACE2 level and its activity due to SARS-CoV-2 infection is considered a crucial reason for the development of Covid-19-associated complications. Here, we report a bioactive peptide derived from the seawater pearl oyster Pinctada fucata, named SCOL polypeptide, which binds strongly to ACE2 and effectively inhibits 65% of the binding of the SARS-CoV-2 S protein to ACE2; thus, this peptide can be used as a blocker to enable cells to resist SARS-CoV-2 infection. The SCOL polypeptide also increases ACE2 enzyme activity by 3.76 times. Previous studies have shown that ACE2 deficiency is associated with inflammation, pain, cardiovascular diseases, insulin resistance, and nervous system injury. Therefore, the SCOL polypeptide can be used to treat or alleviate complications such as lung inflammation, pain, diabetes, cardiovascular diseases, and loss of taste or smell caused by SARS-CoV-2 infection. Thus, the SCOL polypeptide can play a dual role in resisting SARS-CoV-2 infection.

biochemistry↗

bioRxiv2023

Thiolation-Based Protein-Protein Hydrogels for Improved Wound Healing

The limitations of protein-based hydrogels, including their insufficient mechanical properties and restricted biological functions, arise from the highly specific functions of proteins as natural building blocks. A potential solution to overcome these shortcomings is the development of protein-protein hydrogels, which integrate structural and functional proteins. In this study, we introduce a protein-protein hydrogel formed by crosslinking bovine serum albumin (BSA) and a genetically engineered intrinsically disordered collagen-like protein (CLP) through Ag-S bonding. Our approach involves thiolating lysine residues of BSA and crosslinking CLP with Ag+ ions, utilizing thiolation of BSA and the free-cysteines of CLP. The resulting protein-protein hydrogels exhibit exceptional properties, including notable plasticity, inherent self-healing capabilities, and gel-sol transition in response to redox conditions. Furthermore, in comparison to standalone BSA hydrogels, these protein-protein hydrogels demonstrate remarkable antibacterial properties, enhanced cellular viability, and improved cellular migration. In vivo experiments provide conclusive evidence of accelerated wound healing, observed not only in murine models with streptozotocin (Step)-induced diabetes but also in zebrafish models subjected to UV-burn injuries. Detailed mechanistic insights, combined with assessments of pro-inflammatory cytokines and the expression of epidermal differentiation-related proteins, robustly validate the protein-protein hydrogels effectiveness in promoting wound repair. This pioneering approach advances the development of protein-protein hydrogels and serves as a reference for the creation of multifunctional protein-based hydrogels.

bioengineering↗

bioRxiv2023

The function of CozE proteins is linked to lipoteichoic acid biosynthesis in Staphylococcus aureus

To maintain cell integrity and facilitate cell division in Staphylococcus aureus, a well-coordinated interplay between membrane biogenesis, peptidoglycan formation, and teichoic acid synthesis is crucial. However, the molecular mechanisms and regulatory pathways that underpin their coordination are still poorly understood. CozE constitute a conserved family of membrane proteins implicated in cell division via regulation of penicillin binding proteins. It has been shown that the two staphylococcal cozE genes (cozEa and cozEb) constitute a synthetic lethal gene pair. Depletion of CozEa and CozEb simultaneously in S. aureus resulted in severely defective cell division phenotypes, reminiscent of cell lacking lipoteichoic acid (LTA). Indeed, we demonstrate that there is an intricate interplay between CozE, biosynthesis of LTA, and membrane homeostasis in S. aureus. By screening for potential genetic links, we establish that there is synthetic lethal relationship between CozE and UgtP, the enzyme synthesizing the LTA glycolipid anchor Glc2DAG. On the contrary, in cells lacking LtaA, the flippase of Glc2DAG, the essentiality of CozEa and CozEb was alleviated. Furthermore, by immunoblotting, we found that CozEb plays a unique role in controlling LTA polymer length and stability. Using reconstituted proteoliposomes, we also demonstrated that CozE proteins modulate the glycolipid flipping activity of LtaA in vitro. Together, the results demonstrate a new function of CozE proteins, facilitating proper membrane homeostasis and LTA biosynthesis in S. aureus.

microbiology↗

bioRxiv2023

The DeMixSC deconvolution framework uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples

Bulk deconvolution with single-cell/nucleus RNA-seq data is critical for understanding heterogeneity in complex biological samples, yet the technological discrepancy across sequencing platforms limits deconvolution accuracy. To address this, we introduce an experimental design to match inter-platform biological signals, hence revealing the technological discrepancy, and then develop a deconvolution framework called DeMixSC using the better-matched, i.e., benchmark, data. Built upon a novel weighted nonnegative least-squares framework, DeMixSC identifies and adjusts genes with high technological discrepancy and aligns the benchmark data with large patient cohorts of matched-tissue-type for large-scale deconvolution. Our results using a benchmark dataset of healthy retinas suggest much-improved deconvolution accuracy. Further analysis of a cohort of 453 patients with age-related macular degeneration supports the broad applicability of DeMixSC. Our findings reveal the impact of technological discrepancy on deconvolution performance and underscore the importance of a well-matched dataset to resolve this challenge. The developed DeMixSC framework is generally applicable for deconvolving large cohorts of disease tissues, and potentially cancer.

bioinformatics↗

bioRxiv2023

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries

Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.

synthetic biology↗

bioRxiv2023

Oncogenic KEAP1 mutations activate TRAF2-NFκB signaling to prevent apoptosis in lung cancer cells

The Kelch-like ECH-associated protein 1 (KEAP1) - Nuclear factor erythroid 2-related factor 2 (NRF2) pathway is the major transcriptional stress response system in cells against oxidative and electrophilic stress. NRF2 is frequently constitutively active in many cancers, rendering the cells resistant to chemo- and radiotherapy. Loss-of-function (LOF) mutations in the repressor protein KEAP1 are common in non-small cell lung cancer, particularly adenocarcinoma. While the mutations can occur throughout the gene, they are enriched in certain areas, indicating that these may have unique functional importance. In this study, we show that in the GSEA analysis of TCGA lung adenocarcinoma RNA-seq data, the KEAP1 mutations in R320 and R470 were associated with enhanced Tumor Necrosis Factor alpha (TNF) - Nuclear Factor kappa subunit B (NF{kappa}B) signaling as well as MYC and MTORC1 pathways. To address the functional role of these hotspot mutations, affinity purification and mass spectrometry (AP-MS) analysis of wild type (wt) KEAP1 and the mutants was employed to interrogate differences in the protein interactome. We identified TNF receptor associated factor 2 (TRAF2) as a putative protein interaction partner. Both mutant KEAP1 forms showed increased interaction with TRAF2 and other anti-apoptotic proteins, suggesting that apoptosis signalling could be affected by the protein interactions. A549 lung adenocarcinoma cells overexpressing mutant KEAP1 showed high TRAF2-mediated NF{kappa}B activity and increased protection against apoptosis, XIAP being one of the key proteins involved in anti-apoptotic signalling. To conclude, KEAP1 R320Q and R470C and its interaction with TRAF2 leads to activation of NF{kappa}B pathway, thereby protecting against apoptosis.

cancer biology↗

bioRxiv2023

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.

Understanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement program and unleashing their substantial potentials in human biomedicine research. Here, we conducted a meta-GWAS analysis for 232 complex traits with 28.3 million imputed whole-genome sequence variants in 70,328 individuals from 14 pig breeds. We identified a total of 6,878 genomic regions associated with 139 complex traits. By integrating with the Pig Genotype-Tissue Expression (PigGTEx) resource, we systemically explored the biological context and regulatory circuits through which these trait-associated variants act and finally prioritized 16,664 variant-gene-tissue-trait circuits. For instance, rs344053754 regulates the expression of UGT2B31 in the liver by affecting the activity of regulatory elements and ultimately influences litter weight at weaning. Furthermore, we investigated the conservation of genetic and regulatory mechanisms underlying 136 human traits and 232 pig traits. Overall, our multi-breed meta-GWAS in pigs provides invaluable resources and novel insights for understanding the regulatory and evolutionary mechanisms of complex traits in both pigs and humans.

genetics↗

bioRxiv2023

Landscape of Large-Scale Somatic Genomic Insertions in Non-Small Cell Lung Carcinoma Revealed by Nanopore Sequencing

Previous NSCLC genomic studies were mostly based on the next-generation sequencing of short reads, which is an efficient approach for identifying single nucleotide variants and small indels but ineffective for identifying structural variants, especially large-scale insertions. Here, we studied 151 lung adenocarcinoma (LUAD) and 106 lung squamous cell carcinoma (LUSC) samples and paired blood samples using nanopore sequencing technology. We developed a rigorous computational pipeline and characterized the landscape of large-scale somatic insertions in NSCLC. Combining other omics data, we report three findings: 1. we identified an LUSC-enriched somatic simple repeat expansion shared by approximately 40% of LUSC patients that regulates PTPRZ1 gene expression through distal enhancers; 2. the somatic insertion of transposable elements (TEs) in NSCLC were mostly complex TEs consisting of multiple TE elements; and 3. the insertion of short interspersed nuclear elements, especially from the Alu family in young lineages, is a frequent somatic mutation type that shapes the transcriptome of NSCLC through the expression of these elements.

genomics↗

bioRxiv2023

PRIME-BSPre: A genome-wide protein-RNA binding sites prediction method based on templates

Identification of RNA binding sites that potentially interact with RNA-binding proteins facilitates a comprehensive analysis of protein-RNA interactions and enables further investigation into the mechanisms underlying RNA splicing and modification. However, the current experimental data remains limited in comparison to the vast family of RBPs, and deep learning prediction methods are inadequate for those RBPs lacking sufficient interaction data for training. Therefore, we present PRIME-BSPre, a genome-wide method for predicting protein-RNA binding sites based on templates that incorporate both RNA sequence and secondary structure as well as the tertiary structure of corresponding RBPs. We have successfully benchmarked our method on the human genome, demonstrating excellent prediction performance on RBP datasets beyond our library and robustness across cell lines. Additionally, we are pioneers in introducing the low Shannon entropy algorithm to describe binding preferences of RNA motifs. Our predicted results further support the hypothesis that RBPs preferentially bind RNA motifs with low complexity.

bioinformatics↗