Biology subjects

Dong, Z.

Publications and source records attributed to Dong, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Decoding Proteoforms with Single Acid Resolution Using a Sub-nanometer Diameter Pore

When a denatured protein isoform (i.e., a proteoform) immersed in electrolyte is impelled by an electric field through a sub-nanometer-diameter pore (i.e., a sub-nanopore) spanning a thin membrane, the sequence of amino acid (AA) residues constituting the proteoform can be directly "read" one at a time by measuring fluctuations in the electrolytic current. Corroborating this assertion, an analysis of the pore current with molecular dynamic (MD) simulations reveals that the fluctuations are correlated to the sequence of AA volumes, the water in the pore and affected by the acid mobility. After alignment to account for variations in the acid mobility, the simulated pore current is nearly perfectly correlated to the pattern of empirical fluctuations. To prove out the prospects for decoding proteoforms this way, site-specific post-translational modifications (PTMs) and point mutations in amyloid-beta (A{beta} 1-42) are analyzed with a sub-nanopore assay. The results show that single acids can be resolved in proteoforms with a dynamic range limited by the size of phenylalanine and glycine. With this sensitivity and single acid resolution, the sequence of a scrambled variant of A{beta} 1-42 was discriminated with a p-value < 10-5.

biophysics↗

bioRxiv2022

NSC-derived exosomes enhance therapeutic effects of NSC transplantation on cerebral ischemia in mice

AbstractTransplantation of neural stem cells (NSCs) has been proved to promote functional rehabilitation of brain lesions including ischemic stroke. However, the therapeutic effects of NSC transplantation is limited by the low survival and differentiation rates of NSCs due to the harsh environment in the brain after ischemic stroke. Here, we employed NSCs derived from human induced pluripotent stem cells (iPSCs) together with exosomes extracted from NSCs to treat cerebral ischemia induced by middle cerebral artery occlusion/reperfusion (MCAO/R) in mice. The results showed that NSC-derived exosomes significantly reduced the inflammatory response, alleviated oxidative stress after NSC transplantation, and facilitated NSCs differentiation in vivo. The combination of NSCs with exosomes ameliorated the injury of brain tissue including cerebral infarct, neuronal death and glial scarring, and promoted the motor function recovery. To explore the underlying mechanisms, we analyzed the miRNA profiles of NSC-derived exosomes and the potential downstream genes. Our study provided the rationale for the clinical application of NSC-derived exosomes as a supportive adjuvant for NSC transplantation after stroke.

neuroscience↗

bioRxiv2022

Macaque Brainnetome Atlas with Fine-grained Parcellations and Reliable Connections

The rhesus macaque (Macaca mulatta) is a crucial experimental animal that shares many genetic, brain organizational, and behavioral characteristics with humans. A macaque brain atlas that identifies anatomically and functionally distinct regions is fundamental to biomedical and evolutionary research. However, even though connectivity information is vital for understanding brain functions, a connectivity-based whole-brain atlas of the macaque has not previously been made. In this study, we created a new whole-brain map, the Macaque Brainnetome Atlas (MacBNA), based on the anatomical connectivity profiles provided by high angular and spatial resolution ex vivo diffusion MRI data. The new atlas consists of 248 cortical and 56 subcortical regions as well as their structural and functional connections. The parcellation and the diffusion-based tractography were comprehensively evaluated with multi-contrast MRI, invasive neuronal-tracing, and Nissl-stained images collected from a single subject and with open-access datasets from other cohorts. As a demonstrative application, the structural connectivity divergence between macaque and human brains was mapped using the Brainnetome atlases of those two species to uncover the genetic underpinnings of the evolutionary changes in brain structure. The resulting resource includes (1) the thoroughly delineated Macaque Brainnetome Atlas (MacBNA), (2) regional connectivity profiles, (3) the postmortem high resolution macaque diffusion and T2-weighted MRI dataset (Brainnetome-8), and (4) multi-contrast MRI, block-face, and section images collected from a single macaque. MacBNA can serve as a common reference frame for mapping multifaceted features across modalities and spatial scales and for integrative investigation and characterization of brain organization and function. Therefore, it will enrich the collaborative resource platform for nonhuman primates and facilitate translational and comparative neuroscience research.

neuroscience↗

bioRxiv2022

Super-resolution ultrasound imaging of cerebrovascular impairment in a mouse model of Alzheimer's disease

Increasing evidence has suggested a link between cerebrovascular disease and the cognitive impairment of patients with Alzheimers disease. However, cerebrovascular disease and Alzheimers disease share several risk factors making it unclear whether cerebrovascular deficiency and Alzheimers disease pathology have additive effects on cognition or if cerebrovascular impairment merely exacerbates existing Alzheimers disease-associated cognitive decline. Additionally, early-stage Alzheimers disease typically involves hippocampal atrophy, complicating most efforts to elucidate the interplay between cerebral microvascular function and Alzheimers disease progression due to the necessity of probing deep-brain structures. The purpose of this study was to demonstrate the use of ultrasound localization microscopy on the 5xFAD mouse model of Alzheimers disease (3-month and 6-month-old cohorts) in comparison to age-matched wild-type controls, revealing microvascular scale reconstructions throughout the whole brain depth, to visualize and quantify Alzheimers disease-associated vascular impairments. We found that functional decreases in hippocampal and entorhinal flow velocity preceded structural derangements in regional vascular density. In addition to providing global vascular quantifications of deep brain structures with a high local resolution, this technology also permitted hierarchical analysis of individual vessels and, in some cases, potentially allowed for decoupling of arteriole and venous flow contributions. Co-registered histological sectioning confirmed the regionalized hypo-perfusion deficits seen on ultrasound imaging, which were co-localized with amyloid beta plaque deposition. Significance statementThe study of the impact of cerebrovascular disease on Alzheimers disease pathology is complicated by the need to image deep-brain structures with high vascular fidelity. We demonstrate that ultrasound localization microscopy, a super-resolution acoustic imaging technique, is capable of imaging cerebrovasculature throughout the entire depth of the brain at a microvascular scale. This technology was applied to the 5xFAD mouse model of Alzheimers disease, where it was found that 5xFAD animals have significant impairments in vascular function in the entorhinal cortex and hippocampal region in comparison to age matched controls at the 3-month timepoint. Structural derangements in cerebrovasculature were only observed in the 6-month-old animal cohorts, with a maintained impairment in vascular function.

neuroscience↗

bioRxiv2022

Contrast-free Super-resolution Doppler (CS Doppler) based on Deep Generative Neural Networks

Super-resolution ultrasound microvessel imaging based on ultrasound localization microscopy (ULM) is an emerging imaging modality that is capable of resolving micron-scaled vessels deep into tissue. In practice, ULM is limited by the need for contrast injection, long data acquisition, and computationally expensive post-processing times. In this study, we present a contrast-free super-resolution Doppler (CS Doppler) technique that uses deep generative networks to achieve super-resolution with short data acquisition. The training dataset is comprised of spatiotemporal ultrafast ultrasound signals acquired from in vivo mouse brains, while the testing dataset includes in vivo mouse brain, chicken embryo chorioallantoic membrane (CAM), and healthy human subjects. The in vivo mouse imaging studies demonstrate that CS Doppler could achieve an approximate 2-fold improvement in spatial resolution when compared with conventional power Doppler. In addition, the microvascular images generated by CS Doppler showed good agreement with the corresponding ULM images as indicated by a structural similarity index of 0.7837 and a peak signal-to-noise ratio of 25.52. Moreover, CS Doppler was able to preserve the temporal profile of the blood flow (e.g., pulsatility) that is similar to conventional power Doppler. Finally, the generalizability of CS Doppler was demonstrated on testing data of different tissues using different imaging settings. The fast inference time of the proposed deep generative network also allows CS Doppler to be implemented for real-time imaging. These features of CS Doppler offer a practical, fast, and robust microvascular imaging solution for many preclinical and clinical applications of Doppler ultrasound.

bioengineering↗

bioRxiv2022

Determination of expression profiles for Drosophila ovarian Follicle Stem Cells (FSCs) using single-cell RNA sequencing

Drosophila ovarian Follicle Stem Cells (FSC) present an excellent paradigm for understanding how a community of active stem cells maintained by population asymmetry is regulated. Here we describe single-cell RNA sequencing studies of a pre-sorted population of cells that include FSCs and the neighboring cell types, Escort Cells (ECs) and Follicle Cells (FCs), which they support. Cell-type assignment relies on anterior-posterior (AP) location within the germarium. We clarify the previously determined location of FSCs and use spatially targeted lineage studies as further confirmation. The scRNA profiles among four clusters are consistent with an AP progression from anterior ECs through posterior ECs and then FSCs, to early FCs. Several genes with graded profiles from ECs to FCs are highlighted as candidate effectors of the inverse gradients of the two principal signaling pathways, Wnt and JAK-STAT, that guide FSC differentiation and division.

developmental biology↗

bioRxiv2022

Metabolic control of histone acetylation for precise and timely regulation of minor ZGA in early mammalian embryos

Metabolism feeds into the regulation of epigenetics via metabolic enzymes and metabolites. However, metabolic features, and their impact on epigenetic remodeling during mammalian pre-implantation development, remain poorly understood. In this study, we established the metabolic landscape of mouse pre-implantation embryos from zygote to blastocyst, and quantified some absolute carbohydrate metabolites. We integrated these data with transcriptomic and proteomic data, and discovered the metabolic characteristics of the development process, including the activation of methionine cycle from 8-cell embryo to blastocyst, high glutaminolysis metabolism at blastocyst stage, enhanced TCA cycle activity from the 8-cell embryo stage, and active glycolysis in the blastocyst. We further demonstrated that oxidized nicotinamide adenine dinucleotide (NAD+) synthesis is indispensable for mouse pre-implantation development. Mechanistically, in part, NAD+ is required for the exit of minor zygotic gene activation (ZGA) by cooperating with SIRT1 to remove zygotic H3K27ac. In human, NAD+ supplement can promote the removal of zygotic H3K27ac and benefit pre-implantation development. Our findings demonstrate that precise and timely regulation of minor ZGA is controlled by metabolic dynamics, and enhance our understanding of the metabolism of mammalian early embryos. HighlightsO_LIWe identified the metabolic features of mouse pre-implantation embryo development. C_LIO_LINAD+ synthesis is indispensable for mouse embryo pre-implantation development. C_LIO_LINAD+-mediated erasure of zygotic H3K27ac is required for the exit of minor ZGA. C_LIO_LINAD+ supplement promotes the removal of zygotic H3K27ac and benefits preimplantation development of human embryos. C_LI

developmental biology↗

bioRxiv2022

Ensemble remodeling supports memory-updating

Memory-updating is critical in dynamic environments because updating memories with new information promotes versatility. However, little is known about how memories are updated with new information. To study how neuronal ensembles might support memory-updating, we used a hippocampus-dependent spatial reversal task to measure hippocampal ensemble dynamics when mice switched navigational goals. Using Miniscope calcium imaging, we identified neuronal ensembles (co-active neurons) in dorsal CA1 that were spatially tuned and stable across training sessions. When reward locations were moved during a reversal session, a subset of these ensembles decreased their activation strength, correlating with memory-updating. These "remodeling" ensembles were a result of weakly-connected neurons becoming less co-active with their peers. Middle-aged mice were impaired in reversal learning, and the prevalence of their remodeling ensembles correlated with their memory-updating performance. Therefore, we have identified a mechanism where the hippocampus breaks down ensembles to support memory-updating.

neuroscience↗

bioRxiv2022

Invigorating human MSCs for transplantation therapy via Nrf2/DKK1 co- stimulation in a mice acute-on-chronic liver failure model

Boosting stem cell resilience against an extrinsically harsh recipient environment is critical to therapeutic efficiency of stem cell-based transplantation innovations in liver disease contexts. We aimed to establish the efficacy of a transient plasmid-based preconditioning strategy to boost mesenchymal stromal cells (MSCs) capacity for anti-inflammation/antioxidant defense and paracrine actions on recipient hepatocytes. In MSCs, the master antioxidant regulator Nrf2 was found to bind directly to the antioxidant response element in the DKK1 promoter region. Activation of Nrf2 and DKK1 enhanced the anti-stress capacities of MSCs in vitro. In an acute-on-chronic liver failure (ACLF) murine model, transient co-overexpression of Nrf2 and DKK1 via plasmid transfection markedly improved MSC resilience against inflammatory and oxidative assaults, boosted MSC transplantation efficacy and promoted recipient liver regeneration because of a shift from the activation of the anti-regenerative IFN-{gamma}/STAT1 pathway to the pro-regenerative IL-6/STAT3 pathway in the liver. Moreover, specific ablation of DKK1 receptor CKAP4 but not LRP6 in recipient hepatocytes nullified therapeutic benefits from MSC transplantation. In long-term observations, tumorigenicity was undetected in mice following transplantation of such transiently preconditioned MCSs. In conclusion, co-stimulation of Nrf2/DKK1 signaling decisively and safely improves the efficacy of human MSC-based therapies in mouse ACLF models through apparently CKAP4-dependent paracrine mechanisms.

molecular biology↗

bioRxiv2022

Arbidol inhibits esophageal squamous cell carcinoma growth in vitro and in vivo through suppressing ataxia telangiectasia and Rad3-related protein kinase

BackgroundEsophageal cancer has a global impact on human health due to its high incidence and mortality. Therefore, there is an urgent need to develop new drugs to treat or prevent the prominent pathological subtype of esophageal cancer, esophageal squamous cell carcinoma. Based upon a screening of drugs approved by the Food and Drug Administration, we discovered that Arbidol could effectively inhibit the proliferation of esophageal squamous cell carcinoma in vitro and in vivo. MethodWe first conducted a series of cell-based assays and found that Arbidol treatment inhibited the proliferation and colony formation ability of ESCC cells and promoted G1 phase cell cycle arrest. Phospho-proteomics experiments and in vitro kinase assays were subsequently performed using cell lysates derived from Arbidol-treated cells in order to identify the underlying growth inhibitory mechanism. Finally, a PDX model was used to verify the inhibitory effect of Arbidol in vivo. FindingArbidol inhibits proliferation of ESCC in vitro and in vivo through the DNA replication pathway and is associated with the cell cycle. InterpretationArbidol is a potential ATR inhibitor via binding to ATR kinase to reduce the phosphorylation and activation of MCM2 at Ser108. FundingThis research was supported by the National Natural Science Foundation of China (grant number 81872335), the National Natural Science Youth Foundation (grant number 81902486), and the Natural Science Foundation of Henan (grant number 161100510300).

cancer biology↗

bioRxiv2022

Single-cell transcriptome landscape of zebrafish liver reveals hepatocytes and immune cell interactions in understanding nonalcoholic fatty liver disease

Zebrafish have emerged as an attractive animal model for studying nonalcoholic fatty liver disease (NAFLD). However, little is known about the cell types and intercellular interactions in zebrafish liver. Here, we established a liver atlas that consists of 10 cell types using single-cell RNA sequencing. By examining the heterogeneity of hepatocytes and analyzing the expression of NAFLD-associated genes in the specific cluster, we provide a potential target cell model to study NAFLD. Additionally, our analysis identified two distinct resident macrophages with inflammatory and noninflammatory functions and characterized the successive stepwise development of T cell subtypes in the liver. Importantly, we uncovered possible molecular mechanisms and revealed the central regulation of macrophages on target cells of fatty liver by analyzing the cellular interaction between hepatocytes and immune cells. Our data provide valuable information for future research on NAFLD in zebrafish.

immunology↗

bioRxiv2022

Curvelet Transform-based Sparsity Promoting Algorithm for Fast Ultrasound Localization Microscopy

Ultrasound localization microscopy (ULM) based on microbubble (MB) localization was recently introduced to overcome the resolution limit of conventional ultrasound. However, ULM is currently challenged by the requirement for long data acquisition times to accumulate adequate MB events to fully reconstruct vasculature. In this study, we present a curvelet transform-based sparsity promoting (CTSP) algorithm that improves ULM imaging speed by recovering missing MB localization signal from data with very short acquisition times. CTSP was first validated in a simulated microvessel model, followed by the chicken embryo chorioallantoic membrane (CAM), and finally, in the mouse brain. In the simulated microvessel study, CTSP robustly recovered the vessel model to achieve an 86.94% vessel filling percentage from a corrupted image with only 4.78% of the true vessel pixels. In the chicken embryo CAM study, CTSP effectively recovered the missing MB signal within the vasculature, leading to marked improvement in ULM imaging quality with a very short data acquisition. Taking the optical image as reference, the vessel filling percentage increased from 2.7% to 42.2% using 50ms of data acquisition after applying CTSP. CTSP used 80% less time to achieve the same 90% maximum saturation level as compared with conventional MB localization. We also applied CTSP on the microvessel flow speed maps and found that CTSP was able to use only 1.6s of microbubble data to recover flow speed images that have similar qualities as those constructed using 33.6s of data. In the mouse brain study, CTSP was able to reconstruct the majority of the cerebral vasculature using 1-2s of data acquisition. Additionally, CTSP only needed 3.2s of microbubble data to generate flow velocity maps that are comparable to those using 129.6s of data. These results suggest that CTSP can facilitate fast and robust ULM imaging especially under the circumstances of inadequate microbubble localizations.

bioengineering↗

bioRxiv2022

Deep Learning-based Microbubble Localization for Ultrasound Localization Microscopy

Ultrasound localization microscopy (ULM) is an emerging vascular imaging technique that overcomes the resolution-penetration compromise of ultrasound imaging. Accurate and robust microbubble (MB) localization is essential for successful ULM. In this study, we present a deep learning (DL)- based localization technique that uses both Field-II simulation and in vivo chicken embryo chorioallantoic membrane (CAM) data for training. Both radiofrequency (RF) and in-phase quadrature (IQ) data were tested in this study. The simulation experiment shows that the proposed DL-based localization was able to reduce both missing MB localization rate and MB localization error. In general, RF data showed better performance than IQ. For the in vivo CAM study with high MB concentration, DL-based localization was able to reduce the vessel MB saturation time by more than 50% as compared to conventional localization. Additionally, we propose a DL-based framework for real-time visualization of the high-resolution microvasculature. The findings of the paper support the use of DL for more robust and faster MB localization, especially under high MB concentrations. The results indicate that further improvement could be achieved by incorporating temporal information of the MB data.

bioengineering↗

bioRxiv2022

A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

We present a multiomic cell atlas of human lung development that combines single cell RNA and ATAC sequencing, high throughput spatial transcriptomics and single cell imaging. Coupling single cell methods with spatial analysis has allowed a comprehensive cellular survey of the epithelial, mesenchymal, endothelial and erythrocyte/leukocyte compartments from 5-22 post conception weeks. We identify new cell states in all compartments. These include developmental-specific secretory progenitors and a new subtype of neuroendocrine cell related to human small cell lung cancer. Our datasets are available through our web interface (https://lungcellatlas.org). Finally, to illustrate its general utility, we use our cell atlas to generate predictions about cell-cell signalling and transcription factor hierarchies which we test using organoid models. HighlightsO_LISpatiotemporal atlas of human lung development from 5-22 post conception weeks identifies 144 cell types/states. C_LIO_LITracking the developmental origins of multiple cell compartments, including new progenitor states. C_LIO_LIFunctional diversity of fibroblasts in distinct anatomical signalling niches. C_LIO_LIResource applied to interrogate and experimentally test the transcription factor code controlling neuroendocrine cell heterogeneity and the origins of small cell lung cancer. C_LI

developmental biology↗

bioRxiv2021

Three-dimensional Shear Wave Elastography Using a 2D Row Column Addressing (RCA) Array

ObjectiveTo develop a 3D shear wave elastography (SWE) technique using a 2D row column addressing (RCA) array, with either external vibration or acoustic radiation force (ARF) as the shear wave source. Impact StatementThe proposed method paves the way for clinical translation of 3D-SWE based on the 2D RCA, providing a low-cost and high volume-rate solution that is compatible with existing clinical systems. IntroductionSWE is an established ultrasound imaging modality that provides a direct and quantitative assessment of tissue stiffness, which is significant for a wide range of clinical applications including cancer and liver fibrosis. SWE requires high frame-rate imaging for robust shear wave tracking. Due to the technical challenges associated with high volume-rate imaging in 3D, current SWE techniques are typically confined to 2D. Advancing SWE from 2D to 3D is significant because of the heterogeneous nature of tissue, which demands 3D imaging for accurate and comprehensive evaluation. MethodsA 3D SWE method using a 2D RCA array was developed with a volume-rate up to 2000 Hz. The performance of the proposed method was systematically evaluated on tissue-mimicking elasticity phantoms. Results3D shear wave motion induced by either external vibration or ARF was successfully detected with the proposed method. Robust 3D shear wave speed maps were reconstructed for both homogeneous and heterogeneous phantoms with inclusions. ConclusionThe high volume-rate 3D imaging provided by the 2D RCA array provides a robust and practical solution for 3D SWE with a clear pathway for future clinical translation.

bioengineering↗

bioRxiv2021

HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial Peptides

Identifying the targets of an antimicrobial peptide is a fundamental step in studying the innate immune response and combating antibiotic resistance, and more broadly, precision medicine and public health. There have been extensive studies on the statistical and computational approaches to identify (i) whether a peptide is an antimicrobial peptide (AMP) or a non-AMP and (ii) which targets are these sequences effective to (Gram-positive, Gram-negative, etc.). Despite the existing deep learning methods on this problem, most of them are unable to handle the small AMP classes (anti-insect, anti-parasite, etc.). And more importantly, some AMPs can have multiple targets, which the previous methods fail to consider. In this study, we build a diverse and comprehensive multi-label protein sequence database by collecting and cleaning amino acids from various AMP databases. To generate efficient representations and features for the small classes dataset, we take advantage of a protein language model trained on 250 million protein sequences. Based on that, we develop an end-to-end hierarchical multi-label deep forest framework, HMD-AMP, to annotate AMP comprehensively. After identifying an AMP, it will further predict what targets the AMP can effectively kill from eleven available classes. Extensive experiments suggest that our framework outperforms state-of-the-art models in both the binary classification task and the multi-label classification task, especially on the minor classes. Compared with the previous deep learning methods, our method improves the performance on macro-AUROC by 11%. The model is robust against reduced features and small perturbations and produces promising results. We believe HMD-AMP will both contribute to the future wet-lab investigations of the innate structural properties of different antimicrobial peptides and build promising empirical underpinnings for precise medicine with antibiotics.

bioinformatics↗

bioRxiv2021

Chitin and cuticle proteins form the cuticular layer in the spinning duct of silk-spinning arthropods

Chitin is found in the exoskeleton and peritrophic matrix of arthropods, but recent studies have also identified chitin in the spinning duct of silk-spinning arthropods. Here, we report the presence and function of chitin and cuticle proteins ASSCP1 and ASSCP2 in the spinning duct of silkworms. We show that chitin and these proteins are co-located in the cuticular layer of the spinning duct. Ultrastructural analysis indicates that the cuticular layer has a multilayer structure by layered stacking of the chitin laminae. After knocking down ASSCP1 and ASSCP2, the fine structure of this layer was disrupted, which had negative impacts on the mechanical properties of silk. This work clarifies the function of chitin in the spinning duct of silk-spinning arthropods. Chitin and cuticle proteins are the main components of the hard and rigid cuticular layer, providing the shearing stress during silk fibrillogenesis and regulating the final mechanical properties of silk.

molecular biology↗

bioRxiv2021

Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period of time. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell fate decisions. Here, we employed Stereo-seq, a high-definition spatially resolved transcriptomic technology, to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 139,391 spots at cellular size ([~]100 m2) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrative analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs for major signaling pathways and identified novel interactions that potentially crosstalk with the Notch signaling pathway during zebrafish development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

developmental biology↗