Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 415 records · Page 23Linked to original sources

bioRxiv2024

Transcranial Brain Atlas Based on Photon Measurement Density Function in a Triple-Parameter Standard Channel Space

Functional near-infrared spectroscopy (fNIRS) is a widely used transcranial brain imaging technique in neuroscience research. Nevertheless, its lack of anatomical information poses challenges for designing appropriate optode montage and localizing fNIRS signals to underlying anatomical regions. The photon measurement density function (PMDF) is often employed to address these issues, as it accurately measures the sensitivity of a fNIRS signal channel to perturbations of absorption coefficients at any brain locations. However, existing PMDF-based localization methods have two limitations: a limited channel space, and PMDF estimation based on single standard head models, which differ anatomically from individual subjects. To overcome these limitations, this study proposes a continuous fNIRS standard channel space and constructs a PMDF-based transcranial brain atlas (PMDF-TBA) by calculating PMDFs based on MRI images of 48 adults. PMDF-TBA contains group-averaged sensitivities of channels to gray matter and brain regions of atlases, such as Brodmann, AAL2, and LPBA40. Through leave-one-out cross-validation, we evaluated the prediction ability of PMDF-TBA for sensitivity of unseen individuals and found that it outperformed PMDFs based on single standard head models. Thus, PMDF-TBA serves as a more generalizable fNIRS spatial localization tool. Therefore, PMDF-TBA can be utilized to optimize optode montage design, improve channel sensitivity to target brain regions, and assist in the source localization of fNIRS data, thereby promoting the application of fNIRS in neuroscience research.

neuroscience↗

bioRxiv2024

Contracted anterior-posterior systematic covariance of cortical thickness in early-onset schizophrenia

Background and HypothesisSchizophrenia is a neurodevelopmental condition with alterations in both sensory and association cortical areas. These alterations have been reported to follow structural connectivity patterning, and to occur in a system-level fashion. Here, we investigated whether pathological alterations of schizophrenia originated from an early disruption of cortical organization by using 7-17-years-old individuals with early-onset schizophrenia (EOS). Study DesignWe estimated cortical thickness using T1-weighted structural MRI data from 95 patients with antipsychotic-naive first-episode EOS and 99 typically developing (TD) controls. We then computed structural covariance of cortical thickness and estimated system-level organizational axes by performing nonlinear dimensionality reduction techniques on covariance matrices for the EOS and TD groups. Finally, we tested for group differences between EOS and TD individuals in terms of both structural covariance and covariance distances along the systematic axis. Study ResultsThe first covariance gradient differentiated motor regions from other cortical areas. Similar to the macrostructural axis in adults, the second gradient axis in young TD discriminated anterior from posterior regions and was compressed in EOS patients relative to TD controls. In addition, patients showed increased structural covariance between two ends of the systematic axis, with increased geodesic distance of covarying regions between two ends. ConclusionOur findings revealed a contracted organizational axis of cortical thickness in EOS patients, which was attributed to excessive distally coordinated changes between anterior and posterior regions of the cortex. Taken together, our study suggests a possible early disruption of system-level neurodevelopment in schizophrenia.

pathology↗

bioRxiv2024

Group identification drives brain integration for collective performance

Group identification may influence collective behaviors and result in variations in collective performance. However, the evidence for this hypothesis and the neural mechanisms involved remain elusive. To this end, we conducted a study using both single-brain activation and multi-brain synchronization analyses to investigate how group identification influences collective problem-solving in a murder mystery case. Our results showed that groups with high levels of identification performed better individually compared to those with low identification, as supported by single-brain activation in the dorsolateral prefrontal cortex (DLPFC). Furthermore, high-identification groups also showed enhanced collective performance, supported by within-group neural synchronization (GNS) in the orbitofrontal cortex (OFC). The DLPFC-OFC connectivity played a crucial role in linking individual and collective performance. Overall, our study provides a two-in-one neural model to explain how group identification affects collective decision-making processes, offering valuable insights into the dynamics of group interactions.

neuroscience↗

bioRxiv2024

scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains in human and mice

The binding of T cell receptor (TCR)/B cell receptor (BCR) CDR3 with linear or conformational epitopes is a prerequisite for the adaptive immune response. The rules for CDR3 length pairing and the amino acid (AA) distributions in the prioritized rearrangement of the {beta} chain (or heavy chain) and subsequent rearrangement of the chain (or light chain) during the process of germline V(D)J gene rearrangement and self-tolerance selection to form the T- or B-cell CDR3 repertoire are currently unknown. Single-cell VDJ sequencing can provide abundant information on CDR3 sequences in paired chains. In this study, the paired-chain CDR3 sequences of central and peripheral T and B cells in humans and mice were analyzed according to single-cell VDJ sequencing data. This is the first study to find that T cells with {beta} chains longer than paired chains and B cells with heavy chains longer than paired light chains have absolute advantages. The proportion of T cells with length differences of three or more AAs between paired chains in CDR3 in humans was significantly higher than that in mice, and the proportion of B cells with length differences of six or more AAs between paired chains in CDR3 in humans was significantly higher than that in mice. The CDR3 length range of the {beta} chain was narrower than that of the chain, while the heavy chain had a much wider range than the light chain. The CDR3 length in human TCRs and BCRs was greater than that in mice. Extreme length differences were found between paired chains in both human and mouse T and B cells. There were significant differences in the range of pairing length, AA distribution, hydrophobicity, and polarity of the paired-chain CDR3 region in 5 chains ({beta}, , H, {kappa}, and {lambda}). Human TCR and BCR paired CDR3 sequences exhibited greater plasticity than those of mice. This study reveals new ideas about the molecular mechanisms of TCR and BCR responses to different antigenic epitopes. Our innovative findings offer novel perspectives and techniques for examining V(D)J rearrangement and selection mechanisms in T and B cells. These advancements enable us to analyze antigenic epitopes targeted by TCRs and BCRs, and further, to explore the genetic evolution of T and B cell responses across diverse animal species. Graphical AbstractscRNA-seq the TCR and BCR CDR3 repertoires of 35 samples from the central and peripheral tissues of humans and mice. It provides an opportunity to reveal the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/596201v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@11982edorg.highwire.dtl.DTLVardef@1e2d1aaorg.highwire.dtl.DTLVardef@33200dorg.highwire.dtl.DTLVardef@7d61b1_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Systemic mRNA transport depends on m5C methylation, nuclear mRNA export factors and developmental phase changes

In grafted plants mRNAs can be transported from shoot to root, however, how their mobility is regulated remains poorly understood. Recent work has shown that m5C methylation plays an essential role in systemic mRNA mobility in vegetative plants, but its role at later developmental stages remains unclear. To address this, we examined the mobility of three mobile mRNAs, TCTP1, HSC70.1 and GRP7 in mutants deficient in m5C mRNA methylation. By comparing vegetative and flowering stages, we found that in contrast to GRP7, the reduced mobility of TCTP1 and HSC70.1 observed in the vegetative growth phase is restored upon flowering, indicating that m5C-dependent regulation of RNA transport is developmentally controlled. We further identified two RNA-binding proteins, the nuclear mRNA export factors ALY2 and ALY4, as phloem mobile. ALY2 and ALY4 deficient plants show a similar developmental effect on mRNA mobility as m5C mRNA methylation mutants, suggesting that they contribute to the regulation of systemic mRNA transport. Notably, combined perturbation of m5C methylation and ALY2 or ALY4 results in reduced mRNA mobility even in flowering plants. Together, our findings reveal an unexpected developmental layer of control over mRNA transport and identify the nuclear mRNA export factors ALY2 and ALY4 as potential regulators of long-distance RNA movement. SIGNIFICANCE STATEMENTmRNA m5C methylation is essential for shoot-to-root mRNA transport during plant growth; however, whether and how mRNA mobility is regulated, and whether it changes during development remains unclear. We show that TCTP1 and HSC70.1 mRNA transport is reduced in vegetatively growing m5C-deficient mutants but remains unaffected upon flowering, and identify ALY2 and ALY4 proteins, two nuclear export factors, as additional regulators of long-distance mRNA transport, providing new layer of mRNA transport.

plant biology↗

bioRxiv2024

Use of machine learning for quantification of retinal pigment epithelium tight junctions improves assay sensitivity

The retinal pigment epithelium (RPE) is critical for maintaining outer retinal barrier homeostasis. In age-related macular degeneration (AMD), the RPE can undergo a dedifferentiation process that includes tight junction (TJ) loss and displacement of zonula occludens-1 (ZO-1), which may impair structural and functional integrity of the RPE barrier and contribute to disease pathogenesis. Our objective was to develop an automated and sensitive quantification method for TJ aberrations in an RPE immunofluorescence imaging assay, following treatment with TNF or TGF{beta}2. However, quantifying ZO-1 morphological changes in the RPE using standard image analysis methods did not provide a satisfactory assay window. To address this challenge, we developed an imaging assay to quantify ZO-1 changes using a machine learning approach, enabling enhanced phenotypic characterization of the ZO-1 changes in RPE cells and improved assay sensitivity. We were also able to capture and quantify the reversal of these changes using etanercept, an TNF inhibitor, with this imaging assay. Our findings indicated that this machine learning ZO-1 quantification assay could serve as a potential phenotypic readout for RPE dedifferentiation and enabling large-scale mechanistic studies.

bioinformatics↗

bioRxiv2024

Protective effect of P2Y receptors antagonism on stress-induced retinal degeneration

The death of retinal pigment epithelial (RPE) cells and photoreceptors (PR) is a hallmark of the progression of several degenerative ocular disorders. The precise molecular driver(s) behind RPE and PR cell death, however, remains unknown. Recent studies have suggested the involvement of ATP and purinergic signaling in the progression of age-related macular degeneration (AMD) and retinal degeneration. We have discovered that RPE cells release ATP when subjected to stress, which in turn exacerbates stress-related signaling via purinergic receptors that ultimately results in degeneration. Our findings demonstrate that blocking P2Y purinergic receptors using suramin can effectively prevent toxin-induced RPE cell death and dysfunction in vitro. Furthermore, we show efficacy of suramin in preventing photoreceptor degeneration in vivo using the RHO-P23H zebrafish model. This study reinforces the involvement of ATP and purinergic signaling in maintaining retinal health, and highlights the potential of purinergic receptor antagonism as a therapeutic strategy for retinal degeneration.

cell biology↗

bioRxiv2024

APOE Impacts Lipid Trafficking in Retinal Pigment Epithelium Cells

Age-related macular degeneration (AMD) is typified by the formation of lipid-rich drusen under the retinal pigment epithelium (RPE) layer. Apolipoprotein E (APOE) is a known genetic risk factor for AMD and a substantial component of drusen, however, the mechanism by which APOE variants contribute to AMD pathology remains unclear. APOE is the primary cholesterol and lipid transport protein of the central nervous system, as well as a component circulating lipoproteins. To better understand how APOE-dependent lipid transport may impact AMD risk, we generated isogenic APOE iPS-RPE cells expressing each of the common human APOE isoforms, as well as an APOE knockout line. APOE knockout cells showed significant morphological and barrier function deficits, suggesting that APOE is essential for RPE health. Furthermore, we observed that APOE abundance is isoform-dependent in RPE cells and that lipid transport is deficient in APOE knockout RPE cells, as well as in RPE cells expressing APOE2, a variant associated with higher risk of AMD. Contrastingly, cells expressing APOE4 seem to respond strongly to lipid challenges by upregulating APOE to support efficient lipid transport. Our results suggest that disease associated APOE variants may impact lipid transport in RPE, contributing to the formation of drusen and impairing cellular function.

cell biology↗

bioRxiv2024

Discovery and binding site identification of a single-stranded DNA-binding protein that interacts with double-stranded DNA

Scientists have conducted in-depth studies on single-stranded DNA (ssDNA) binding and protein interaction network of single-stranded DNA binding proteins (SSBs). SSBs are widely present in cells from lower prokaryotes to higher mammals and are important proteins for ssDNA protection. In-depth studies in recent years have revealed a wide range of interactions between SSBs and other proteins. Studies have shown that in addition to playing the role of ssDNA protector, SSBs are also important members of biochemical pathways such as DNA replication and recombination. In this study, a single-stranded DNA binding protein SSF encoded by E. coli F plasmid with highly conserved N-terminal region was demonstrated to have ssDNA binding ability similar to E. coli SSB through gel migration experiments. At the same time, the dsDNA binding ability of SSF was also demonstrated, and the dissociation constant of this interaction (in the range of microliters) was determined by Micro-scale Thermophoresis (MST). Through the above experiments, a previously unreported SSB with dsDNA binding ability was revealed, and the region interacting with dsDNA was determined to be the C-terminal unstructured region. This study lays a foundation for further understanding of the mechanism of bacterial conjugation conducted by F plasmid, as well as the potential dsDNA binding ability and biological significance of other SSBs.

biochemistry↗

bioRxiv2024

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle

Kinship and pedigree information, used for estimating inbreeding, heritability, selection, and gene flow, is useful for breeding and animal conservation. However, as the size of the crossbred population increases, inaccurate generation and parentage recoding in livestock farms increases. Restriction-site-associated DNA sequencing (RAD-Seq) is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for Angus and Xiangxi yellow cattle, which benefit from good meat quality and yields, providing a basis for livestock management. A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping. The identified SNPs panel included 7305 SNPs capturing the maximum difference between paternal and maternal genome information allowing us to distinguish between the F1 and F2 generation with 90% accuracy. In addition, parentage assignment software based on different strategies verified that the cross-assignments. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.

genomics↗

bioRxiv2024

scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular het-erogeneity in complex biological systems. However, analyzing and integrating scRNA-seq data poses unique computational challenges due to sparsity, high variability, and technical batch effects. Here, we propose a novel framework called scDecorr for robust representation learning and data integration for scRNA-seq analysis. Our approach leverages the idea of feature decorrelation-based self-supervised learning (SSL) to obtain efficient low-dimensional representations of individual cells without relying on negative samples. By maximizing similarity among distorted embeddings while decorrelating their components, scDecorr captures the biological signature while eliminating technical noise. Furthermore, scDecorr incorporates unsupervised domain adaptation to bridge the gap between batches with different probability distributions, enabling effective integration of scRNA-seq data from diverse sources. Our framework achieves domain-invariant representations by learning cell embeddings independently across domains and employing domain-specific batch normalization. We evaluate scDecorr on a variety of single cell datasets and demonstrate its ability to integrate batches without losing the inherent biological variance, thereby facilitating optimal clustering. The representations generated by scDecorr also exhibit robustness in label transfer tasks, allowing for effective transfer of cell-type labels from reference to query datasets. Overall, scDecorr offers a powerful tool for efficient analysis and integration of large and complex scRNA-seq datasets, advancing our understanding of cellular processes and disease mechanisms. The code is available here https://github.com/hayatlab/scdecorr.

bioinformatics↗

bioRxiv2024

Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes

Cancer-associated fibroblast (CAF) subpopulations in pancreatic ductal adenocarcinoma (PDAC) have been identified using single-cell RNA sequencing (scRNAseq) with divergent characteristics, but their clinical relevance remains unclear. We translate scRNAseq-derived CAF cell-subpopulation-specific marker genes to bulk RNAseq data, and develop a single- sample classifier, DeCAF, for the classification of clinically restraining and permissive CAF subtypes. We validate DeCAF in 19 independent bulk transcriptomic datasets across four tumor types (PDAC, mesothelioma, bladder and renal cell carcinoma). DeCAF subtypes have distinct histology features, immune landscapes, and are prognostic and predict response to therapy across cancer types. We demonstrate that DeCAF is clinically replicable and robust for the classification of CAF subtypes in patients for multiple tumor types, providing a better framework for the future development and translation of therapies against permissive CAF subtypes and preservation of restraining CAF subtypes. SignificanceWe introduce a replicable and robust classifier, DeCAF, that delineates the significance of the role of permissive and restraining CAF subtypes in cancer patients. DeCAF is clinically tractable, prognostic and predictive of treatment response in multiple cancer types and lays the translational groundwork for the preclinical and clinical development of CAF subtype specific therapies.

genomics↗

bioRxiv2024

Epithelial NSD2 maintains FMOs-mediated taurine biosynthesis to prevent intestinal barrier disruption

Inflammatory bowel disease (IBD) poses a significant challenge due to its intricate pathogenesis. NSD2, a histone methyltransferase responsible for dimethylating histone 3 at lysine 36, is associated with transcriptional activation. However, the precise role of NSD2 in IBD remains unexplored. In this study, we discovered a downregulation of NSD2 in both the intestinal epithelial cells (IECs) of patients and the IBD mouse model. Deficiency of NSD2 in mouse IECs aggravated epithelial barrier disruption and inflammatory response in IBD. Mechanically, NSD2 loss downregulated H3K36me2 and FMO (taurine-synthesis enzyme) mRNA in IECs, resulting in decreased taurine biosynthesis in IECs. Importantly, supplementation with taurine significantly attenuated the symptoms of NSD2 deficiency-induced IBD. These data demonstrate that NSD2 plays a pivotal role in maintaining FMOs-mediated taurine biosynthesis to prevent intestinal inflammation. Our findings also underscore the importance of NSD2-H3K36me2-mediated taurine biosynthesis in maintaining intestinal mucosal barrier homeostasis.

cell biology↗

bioRxiv2024

The dual resistance mechanism of CYP325G4 and CYP6AA9 in Culex pipiens pallens legs according to transcriptome and proteome analysis

Mosquitoes within the Culex pipiens complex play a crucial role in human disease transmission. Insecticides, especially pyrethroids, are used to control these vectors. Mosquito legs are the main entry point and barrier for insecticides to gain their neuronal targets. However, the resistance mechanism in mosquito legs is unclear. Herein, we employed transcriptomic analyses and isobaric tags for relative and absolute quantitation techniques to investigate the resistance mechanism, focusing on Cx. pipiens legs. We discovered 2346 differentially expressed genes (DEGs) between deltamethrin-resistant (DR) and deltamethrin-sensitive (DS) mosquito legs, including 41 cytochrome P450 genes. In the same comparison, we identified 228 differentially expressed proteins (DEPs), including six cytochrome P450 proteins). Combined transcriptome and proteome analysis revealed only two upregulated P450 genes, CYP325G4 and CYP6AA9. The main clusters of DEGs and DEPs were associated with metabolic processes, such as cytochrome P450-mediated metabolism of drugs and xenobiotics. Transcription analysis revealed high CYP325G4 and CYP6AA9 expression in the DR strain at 72 hours post-eclosion compared with that in the DS strain, particularly in the legs. Mosquitoes knocked down for CYP325G4 were more sensitive to deltamethrin than the controls. CYP325G4 knockdown reduced the expression of several chlorinated hydrocarbon (CHC)-related genes, which altered the cuticle thickness and structure. Conversely, CYP6AA9 knockdown increased CHC gene expression without altering cuticle thickness and structure. P450 activity analysis demonstrated that CYP325G4 and CYP6AA9 contributed to metabolic resistance in the midgut and legs. This study identified CYP325G4 as a novel mosquito deltamethrin resistance factor, being involved in both metabolic and cuticular resistance mechanisms. The previously identified CYP6AA9 was investigated for its involvement in metabolic resistance and potential cuticular resistance in mosquito legs. These findings enhance our comprehension of resistance mechanisms, identifying P450s as promising targets for the future management of mosquito vector resistance, and laying a theoretical groundwork for mosquito resistance management. Author SummaryCulex pipiens mosquitoes are the primary vector of the filamentous nematode, Wuchereria bancrofti and also involved in the transmission of other pathogens, such as West Nile virus (WNV), avian malarias, and avian pox virus. Insecticides, particularly pyrethroids, continue to be the primary method to control these significant vectors. Worryingly, resistance to insecticides has become widespread and is rapidly intensifying in Culex mosquitoes throughout China, posing a threat to the efficacy of insecticides. Legs are the main sites of contact with ITNs and sprayed insecticides, and the insecticides have to penetrate the leg cuticle to reach their targets.Therefore, the resistance mechanisms in mosquito legs deserve further investigation. Several reports have found a certain amount of P450 in insect legs. Unfortunately, none of the above reports have conducted further functional studies on P450s in the legs. Here, we have identified two P450 enzymes, CYP325G4 and CYP6AA9, through the integrated analysis of transcriptomics and proteomics. CYP325G4 enriched in the cuticle of resistant mosquitoes might possess a dual resistance mechanism involving metabolic resistance and cuticle resistance. CYP6AA9 was slightly different, possibly exerting metabolic resistance as its main function and also being involved in cuticle synthesis. Understanding the dual resistance mechanism of P450s in the metabolism of pyrethroid insecticides will have an important role in optimizing vector control strategies.

physiology↗

bioRxiv2024

Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine

SARS-CoV-2 ancestral strain-induced immune imprinting poses great challenges to vaccine updates. Studies showed that repeated Omicron exposures could override immune imprinting induced by inactivated vaccines but not mRNA vaccines, a disparity yet to be understood. Here, we analyzed the underlying mechanism of immune imprinting alleviation in inactivated vaccine (CoronaVac) cohorts. We observed in CoronaVac-vaccinated individuals who experienced BA.5/BF.7 breakthrough infection (BTI), the proportion of Omicron-specific memory B cells (MBCs) substantially increased after an extended period post-Omicron BTI, with their antibodies displaying enhanced somatic hypermutation and neutralizing potency. Consequently, the neutralizing antibody epitope distribution encoded by MBCs post-BA.5/BF.7 BTI after prolonged maturation closely mirrors that in BA.5/BF.7-infected unvaccinated individuals. Together, these results indicate the activation and expansion of Omicron-specific naive B cells generated by first-time Omicron exposure helped to alleviate CoronaVac-induced immune imprinting, and the absence of this process should have caused the persistent immune imprinting seen in mRNA vaccine recipients. HighlightsO_LILongitudinal MBC profiling of CoronaVac-vaccinated individuals following BA.5 BTI C_LIO_LIOmicron-specific MBC proportion rises greatly after extended period post-BA.5 BTI C_LIO_LIOmicron-specific naive B cell maturation reduces ancestral strain immune imprinting C_LI

immunology↗

bioRxiv2024

Roles and mechanisms of leptomeningeal collaterals in human distal MCA territory ischemia

BackgroundLeptomeningeal collaterals (LMCs) provided hemodynamic support and reperfusion during acute ischemic stroke (AIS). Although regulation details have been deeply acquired from animal models, human cortex may share limited hemodynamic patterns due to larger physical scale that needs further investigation. MethodsWe performed sequential hierarchical blocking during awake craniotomy on fourteen human subjects to mimic AIS in middle cerebral artery (MCA) M4 segment territory. Widefield microscope was applied to reveal microcirculation of LMCs. Relative flow rate (RFR) was measured to evaluate the impact of LMCs hierarchy on microcirculation maintenance. Single-cell sequencing and spatial transcriptomics were further performed to analyze the mechanism of different LMCs recruitment abilities. ResultsLMCs RFR decreased to 30.75% immediately (95% CI, 6.64 - 54.86%, P < 0.001), and about 80.25% RFR was finally recovered within 5 minutes (95% CI, 55.2 - 105.3%, P = 0.0034) during M4 occlusion. For M5 and pial branches occlusion, RFR decreased to 55.78% with no further recovery (95% CI, 22.50-89.05%, P = 0.014), and 4 in 11 subjects had no valid microcirculation. For subjects with better recruitment ability, the proportion of arteriole is much higher in leptomeninx (76 - 79% vs. 36 - 56%). There were more significant interaction pairs associated with key signaling pathways between arteriole and neuron/astrocyte (TGF-beta signaling pathway, ECM-receptor interaction) ConclusionsAbundant LMCs supported hemodynamic stability during AIS in human subjects. The proportion of arteriole is much higher in leptomeninx for subjects with better recruitment ability. The Active neuron/astrocyte - arteriole interaction may improve LMCs recruitment. GRAPH ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/594043v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@eb7fb8org.highwire.dtl.DTLVardef@10e10aforg.highwire.dtl.DTLVardef@6954c7org.highwire.dtl.DTLVardef@13ceb98_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure

The small molecule epiberberine (EPI) is a natural alkaloid with versatile bioactivities against several diseases, including cancer and bacterial infection. EPI can induce the formation of a unique binding pocket at the 5' side of a human telomeric G-quadruplex (HTG) sequence Q4, resulting in a nanomolar binding affinity (KD approximately 26 nM) with significant fluorescence enhancement upon binding. It is important to understand (1) how EPI binding affects HTG structural stability and (2) how enhanced EPI binding may be achieved through the engineering of the DNA binding pocket. In this work, the EPI binding-induced HTG structure stabilization effect was probed by a peptide nucleic acid (PNA) invasion assay in combination with a series of biophysical techniques. We show that the PNA invasion-based method may be useful for the characterization of compounds binding to DNA (and RNA) structures in physiological conditions without the need to vary the solution temperature or buffer components, which are typically needed for structural stability characterization. Importantly, the combination of theoretical modeling and experimental quantification allows us to successfully engineer the Q4 derivative Q4-ds-A by a simple extension of a duplex structure to Q4 at the 5' end. Q4-ds-A is a superb EPI binder with a KD of 8 nM, with the binding enhancement achieved through the preformation of a binding pocket and a reduced dissociation rate. The tight binding of Q4 and Q4-ds-A with EPI allows us to develop a novel magnetic bead-based affinity purification system to effectively extract EPI from Rhizoma coptidis (Huang Lian) extracts.

biochemistry↗

bioRxiv2024

Asymmetric binding of coactivator SRC1 to FXR-RXR and allosteric communication within the complex

Farnesoid X receptor (FXR) is a promising target for treatment of metabolic associated fatty liver disease (MAFLD). In this study, we employed an integrative approach to investigate the interaction between FXR-RXR-hSHP-1 complex and the entire coactivator SRC1-NRID (nuclear receptor interaction domain). We constructed a multi-domain model of FXR120-RXR98-hSHP-1, highlighting the interface between FXR-DBD and LBD. Using HDX-MS, XL-MS, and biochemical assays, we revealed the allosteric communications in FXR-RXR-hSHP-1 upon agonist and DNA binding. We then demonstrated that SRC1 binds only to the coactivator binding surface of FXR within the FXR-RXR heterodimer, with the NR-box2 and NR-box3 of SRC1 as the key binding motifs. Our findings, which provide the first model of SRC1-NRID in complex with FXR-RXR-hSHP-1, shed light on the molecular mechanism through which the coactivator asymmetrically interacts with nuclear receptors and provide structural basis for further understanding the function of FXR and its implications in diseases.

biophysics↗