Biology subjects

Li, D.

Publications and source records attributed to Li, D..

At least 361 records · Page 20Linked to original sources

bioRxiv2023

Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization

The hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA transcription to result in NAD-capped RNA (NAD-RNA). NAD-RNA that intimately connects metabolite with gene expression can be developed as novel biomarkers for aging and disease. Epitranscriptome-wide profiling of NAD-RNAs involves chemo-enzymatic labeling and affinity-based enrichment; yet currently available computational analysis cannot adequately remove variations associated with capture procedures. Here, we propose a spike-in-based normalization and data-driven evaluation framework, enONE, for the omic-level analysis of NAD-capped RNAs. We demonstrate that carefully designed spike-in RNAs, together with modular normalization procedures and evaluation metrics, can lead to the optimal normalization that maximally removes unwanted variations, empowering quantitative and comparative assessment of NAD-RNAs from different datasets. Using enONE and a human aging cohort, we reveal critical features of NAD-capped RNAs that occur with normal age. enONE facilitates the discovery of NAD-capped RNAs that are responsive to physiological changes, laying a critical foundation for functional investigations into this modification.

bioinformatics↗

bioRxiv2023

mRNA challenge predicts brain cancer immunogenicity and response to checkpoint inhibitors

To prospectively determine whether brain tumors will respond to immune checkpoint inhibitors (ICIs), we developed a novel mRNA vaccine as a viral mimic to elucidate cytokine release from brain cancer cells in vitro. Our results indicate that cytokine signatures following mRNA challenge differ substantially from ICI responsive versus non-responsive murine tumors. These findings allow for creation of a diagnostic assay to quickly assess brain tumor immunogenicity, allowing for informed treatment with ICI or lack thereof in poorly immunogenic settings.

cancer biology↗

bioRxiv2023

Dual role of striatal astrocytes in behavioral flexibility and metabolism in the context of obesity

Brain circuits involved in metabolic control and reward-associated behaviors are potent drivers of feeding behavior and are both dramatically altered in obesity, a multifactorial disease resulting from genetic and environmental factors. In both mice and human, exposure to calorie-dense food has been associated with increased astrocyte reactivity and pro-inflammatory response in the brain. Although our understanding of how astrocytes regulate brain circuits has recently flourish, whether and how striatal astrocytes contribute in regulating food-related behaviors and whole-body metabolism is still unknown. In this study, we show that exposure to enriched food leads to profound changes in neuronal activity and synchrony. Chemogenetic manipulation of astrocytes activity in the dorsal striatum was sufficient to restore the cognitive defect in flexible behaviors induced by obesity, while manipulation of astrocyte in the nucleus accumbens led to acute change in whole-body substrate utilization and energy expenditure. Altogether, this work reveals a yet unappreciated role for striatal astrocyte as a direct operator of reward-driven behavior and metabolic control.

physiology↗

bioRxiv2023

Lactococcus G423 Ameliorates the Growth Performance of Broilers by Modulation of Gut Microbiota- Metabolites

This study aimed to explore whether Lactococcus G423 could ameliorate growth performance of broilers by modulation of gut microbiota-metabolites based on the 16S ribosomal RNA (rRNA) and liquid chromatography-mass spectrometry (LC-MS). A total of 640 one-day-old AA broilers were randomly divided into 4 groups (Control (CON), Lac_L, Lac_H, and ABX). Average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) were calculated on the 42nd day. The ileum content was harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC-MS analyses. Then, the results of 16S rRNA analysis were confirmed by quantitative polymerase chain reaction (qPCR). Compared with the CON group, ADG significantly increased in the Lac_H group (P<0.05), and survival rate significantly decreased in the Lac_H, Lac_H, and ABX groups (all P<0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly risen (P<0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (P<0.05). The results of LC-MS demonstrated that Lactococcus could significantly improve the levels of some metabolites (6-hydroxy-5-methoxyindole glucuronide, 9,10-DiHOME, carbamazepine-O-quinone, N-Acetyl-L-phenylalanine, and kynurenine), and these metabolites were involved in 5 metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (P<0.05). Lactococcus improved wight and survival rate of broilers through the gut microbiota, regulating the pathways of amino acid metabolism, lipid metabolism, bile acid metabolism, and carbohydrate metabolism. However, antibiotics may negatively influence the gut microbiota. IMPORTANCEImprovements in the growth rate of broiler chickens can be achieved through dietary manipulation of the naturally occurring bacterial populations while mitigating the withdrawal of antibiotic growth promoters. Lactococcus is industrially crucial lactic acid bacteria, can be incorporated into the diets of chickens to improve their growth performance. This study investigated the key mechanisms behind this progression and pinpointed Lactococcus improved wight and survival rate of broilers through the gut microbiota, regulating the pathways of amino acid metabolism, lipid metabolism, bile acid metabolism, and carbohydrate metabolism.

microbiology↗

bioRxiv2023

Optics-aware super-resolution light-field microscopy for long-term volumetric imaging of dynamic intracellular processes at millisecond timescales

Long-term and high-spatiotemporal-resolution 3D imaging of living cells remains an unmet challenge for super-resolution microscopy, owing to the noticeable phototoxicity and limited scanning speed. While emerging light-field microscopy can mitigate this issue through three-dimensionally capturing biological dynamics with merely single snapshot, it suffers from suboptimal resolution insufficient for resolving subcellular structures. Here we propose an Adaptive Learning PHysics-Aware Light-Field Microscopy (Alpha-LFM) with a physics-aware deep learning framework and adaptive-tuning strategies capable for highly-generalizable light-field reconstruction of diverse subcellular dynamics. Alpha-LFM delivers sub-diffraction-limit spatial resolution ([~]120 nm) while maintaining high temporal resolution and low phototoxicity. It enables rapid (at hundreds of volumes per second), long-term (up to 60 hours) 3D super-resolution imaging of diverse intracellular dynamics with exceptional details. Using Alpha-LFM approach, we finely resolve the lysosome-mitochondrial interactions, capture rapid motion of peroxisome and the endoplasmic reticulum, and reveal the variations in mitochondrial fission activity throughout two complete cell cycles.

microbiology↗

bioRxiv2023

Dysregulation of Prefrontal Oligodendrocyte Lineage Cells Across Mouse Models of Adversity and Human Major Depressive Disorder

Animal models of adversity have yielded few molecular mechanisms that translate to human stress-related diseases like major depressive disorder (MDD). We congruently analyze publicly available bulk-tissue transcriptomic data from prefrontal cortex (PFC) in multiple mouse models of adversity and in MDD. We apply strategies, to quantify cell-type specific enrichment from bulk-tissue transcriptomics, utilizing reference single cell RNA sequencing datasets. These analyses reveal conserved patterns of oligodendrocyte (OL) dysregulation across animal experiments, including susceptibility to social defeat, acute cocaine withdrawal, chronic unpredictable stress, early life stress, and adolescent social isolation. Using unbiased methodologies, we further identify a dysregulation of layer 6 neurons that associate with deficits in goal-directed behavior after social isolation. Human post-mortem brains with MDD show similar OL transcriptome changes in Brodmann Areas 8/9 in both male and female patients. This work assesses cell type involvement in an unbiased manner from differential expression analyses across animal models of adversity and human MDD and finds a common signature of OL dysfunction in the frontal cortex.

neuroscience↗

bioRxiv2023

Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy

Computational super-resolution (SR) methods, including conventional analytical algorithms and deep learning models, have substantially improved optical microscopy. Among them, supervised deep neural networks have demonstrated outstanding SR performance, however, demanding abundant high-quality training data, which are laborious and even impractical to acquire due to the high dynamics of living cells. Here, we develop zero-shot deconvolution networks (ZS-DeconvNet) that instantly enhance the resolution of microscope images by more than 1.5-fold over the diffraction limit with 10-fold lower fluorescence than ordinary SR imaging conditions in an unsupervised manner without the need for either ground truths or additional data acquisition. We demonstrate the versatile applicability of ZS-DeconvNet on multiple imaging modalities, including total internal reflection fluorescence microscopy, three-dimensional (3D) wide-field microscopy, confocal microscopy, lattice light-sheet microscopy, and multimodal structured illumination microscopy (SIM), which enables multi-color, long-term, super-resolution 2D/3D imaging of subcellular bioprocesses from mitotic single cells to multicellular embryos of mouse and C. elegans.

bioengineering↗

bioRxiv2023

The pluripotency factor Tex10 finetunes Wnt signaling for PGC and male germline development

Testis-specific transcript 10 (Tex10) is a critical factor for pluripotent stem cell maintenance and preimplantation development. Here, we dissect its late developmental roles in primordial germ cell (PGC) specification and spermatogenesis using cellular and animal models. We discover that Tex10 binds the Wnt negative regulator genes, marked by H3K4me3, at the PGC-like cell (PGCLC) stage in restraining Wnt signaling. Depletion and overexpression of Tex10 hyperactivate and attenuate the Wnt signaling, resulting in compromised and enhanced PGCLC specification efficiency, respectively. Using the Tex10 conditional knockout mouse models combined with single-cell RNA sequencing, we further uncover critical roles of Tex10 in spermatogenesis with Tex10 loss causing reduced sperm number and motility associated with compromised round spermatid formation. Notably, defective spermatogenesis in Tex10 knockout mice correlates with aberrant Wnt signaling upregulation. Therefore, our study establishes Tex10 as a previously unappreciated player in PGC specification and male germline development by fine-tuning Wnt signaling.

developmental biology↗

bioRxiv2023

Neutralization of SARS-CoV-2 BQ.1.1 and XBB.1.5 by Breakthrough Infection Sera from Previous and Current Waves in China

SARS-CoV-2 is continuing to evolve and diversify, with an array of various Omicron sub-lineages, including BA.5, BA.2.75, BN.1, BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5, now circulating globally at recent time. In this study, we evaluated the neutralization sensitivity of a comprehensive panel of Omicron subvariants to sera from different clinical cohorts, including individuals who received homologous or heterologous booster vaccinations, vaccinated people who had Delta or BA.2 breakthrough infection in previous waves, and patients who had BA.5 or BF.7 breakthrough infection in the current wave in China. All the Omicron subvariants exhibited substantial neutralization evasion, with BQ.1, BQ.1.1, XBB.1, and XBB.1.5 being the strongest escaped subvariants. Sera from Omicron breakthrough infection, especially the recent BA.5 or BF.7 breakthrough infection, exhibited higher neutralizing activity against all Omicron sub-lineages, indicating the chance of BA.5 and BF.7 being entirely replaced by BQ or XBB subvariants in China in a short-term might be low. We also demonstrated that the BQ and XBB subvariants were the most resistant viruses to monoclonal antibodies. Continuing to monitor the immune escape of SARS-CoV-2 emerging variants and developing novel broad-spectrum vaccines and antibodies are still crucial.

immunology↗

bioRxiv2023

Vaccinia virus induces EMT-like transformation and RhoA-mediated mesenchymal migration

The emerging outbreak of monkeypox is closely associated with the viral infection and spreading, threatening global public health. Virus-induced cell migration facilitates viral transmission. However, high-resolution dynamics and mechanisms underlying this type of cell migration remain unclear. Here, we investigate the motility of cells infected by vaccinia virus (VACV), a close relative of monkeypox, through combining multi-omics analyses and high-resolution live-cell imaging. We find that, upon VACV infection, the epithelial cells undergo EMT-like transformation, during which they lose intercellular junctions and acquire the migratory capacity to promote viral spreading. After transformation, VACV-induced mesenchymal migration is highly dependent on the actin cytoskeleton and RhoA signaling, which is responsible for the depolymerization of robust actin stress fibers, the leading-edge protrusion formation, and the rear-edge recontraction. Our study reveals how poxviruses alter the epithelial phenotype and regulate RhoA signaling to induce fast migration, providing a unique perspective to understand the pathogenesis of poxviruses.

cell biology↗

bioRxiv2023

Host-microbe interactions mediate doramectin-promoted metabolic reprogramming of CD8+ T-cells and amplify antitumor immunity

The intestinal microbiota and its metabolites influence the host metabolic environment and CD8+ T-cell function. Metabolic changes in T-cells are thought to enhance the antitumor immune response. Here, we show that doramectin (DOR), a macrocyclic lactone (ML) of the avermectin (AVM) family, can modify CD8+ T-cell metabolism to increase and accelerate effector function. However, the functional capability of DOR depends mainly on the accessibility of gut microbiota. Using metagenomic and metabolomic techniques, we describe for the first time the interplay between gut microbiota and host metabolism involved in metabolic reprogramming of CD8+-T cells following DOR administration. Interestingly, we found that, after DOR administration, Firmicutes phylum not only impact DOR transport and absorption, but also boost amino acid levels in CD8+ T-cells, consistent with increased production of tumor necrosis factor alpha (TNF-) and, in particular, interferon gamma (IFN-{gamma}), which together play an important role in antitumor immunity. In contrast, the dysbiotic microbial community may abrogate the anticancer efficacy of DOR and lead to enhanced tumor growth and decreased survival. This finding likely supports the view that the presence of certain bacteria in the gut governs extra-intestinal immune responses and may be associated with metabolic adaptations necessary for efficient function of CD8+ T-cells upon DOR administration.

cancer biology↗

bioRxiv2023

Optimizing the design of spatial genomic studies

Spatially-resolved genomic technologies have shown promise for studying the relationship between the structural arrangement of cells and their functional behavior. While numerous sequencing and imaging platforms exist for performing spatial transcriptomics and spatial proteomics profiling, these experiments remain expensive and labor-intensive. Thus, when performing spatial genomics experiments using multiple tissue slices, there is a need to select the tissue cross sections that will be maximally informative for the purposes of the experiment. In this work, we formalize the problem of experimental design for spatial genomics experiments, which we generalize into a problem class that we call structured batch experimental design. We propose approaches for optimizing these designs in two types of spatial genomics studies: one in which the goal is to construct a spatially-resolved genomic atlas of a tissue and another in which the goal is to localize a region of interest in a tissue, such as a tumor. We demonstrate the utility of these optimal designs, where each slice is a two-dimensional plane, on several spatial genomics datasets.

bioinformatics↗

bioRxiv2023

Cell segmentation for high-resolution spatial transcriptomics

Spatial transcriptomics promises to greatly improve our understanding of tissue organization and cell-cell interactions. While most current platforms for spatial transcriptomics only offer multi-cellular resolution, with 10-15 cells per spot, recent technologies provide a much denser spot placement leading to sub-cellular resolution. A key challenge for these newer methods is cell segmentation and the assignment of spots to cells. Traditional image-based segmentation methods are limited and do not make full use of the information profiled by spatial transcrip-tomics. Here we present SCS, which combines imaging data with sequencing data to improve cell segmentation accuracy. SCS assigns spots to cells by adaptively learning the position of each spot relative to the center of its cell using a transformer neural network. SCS was tested on two new sub-cellular spatial transcriptomics technologies and outperformed traditional image-based segmentation methods. SCS achieved better accuracy, identified more cells, and provided more realistic cell size estimation. Sub-cellular analysis of RNAs using SCS spots assignments provides information on RNA localization and further supports the segmentation results.

bioinformatics↗

bioRxiv2023

Identification and Characterization of a Novel Major Facilitator Superfamily (MFS) Efflux Pump SA09310 Mediating Tetracycline Resistance in Staphylococcus aureus

Drug efflux systems have recently been recognized as an important mechanism of multidrug resistance in bacteria. Here, we described the identification and characterization of a novel chromosomally encoded multidrug efflux pump (SA09310) in Staphylococcus aureus. SA09310 is a 43-kDa protein with 12 transmembrane helices. The conserved amino acid sequence motifs of the major facilitator superfamily (MFS) were identified in the protein SA09310, which indicated SA09310 belonged to MFS transporters. Expression of the sa09310 gene was induced by different types of antibiotics, including aminoglycoside, tetracycline, macrolides, and chloramphenicol. The sa09310 gene knockout mutant ({Delta}sa09310) was constructed, and its susceptibility to 30 different antibiotics was evaluated. Mutant{bigtriangleup} sa09310 exhibited increased sensitivity to tetracycline and doxycycline, with 64-fold and 8-fold decreased MICs, respectively. The mechanism of SA09310 mediating tetracycline resistance was demonstrated by its ability to extrude intracellular tetracycline from within the cells into the environment. The efflux activity of SA09310 was further confirmed by EtBr accumulation and efflux assays. In addition, the efflux activity of SA09310 was observed to be blocked by the known efflux pump inhibitor carbonyl cyanide-chlorophenylhydrazone (CCCP), which provided direct evidence that suggested the H+-dependent activity of SA09310 efflux pump. The conservation of SA09310 homologs in Staphylococcus indicated the universal function of these SA09310-like protein clusters. In conclusion, the function-unknown protein SA09310 has been identified and characterized as a tetracycline efflux pump, thereby mediating tetracycline resistance in S. aureus.

microbiology↗

bioRxiv2023

Cross-β helical filaments of Tau and TMEM106B in Gray and White Matter of Multiple System Tauopathy with presenile Dementia

BackgroundThe Microtubule-Associated Protein Tau (MAPT) is one of the proteins that are central to neurodegenerative diseases. The nature of intracellular tau aggregates is determined by the cell types whether neuronal or glial, the participating tau isoforms, and the structure of the amyloid filament. The transmembrane protein 106B (TMEM106B) has recently emerged as another significant player in neurodegeneration and aging. In the central nervous system, the composition of the gray and white matter differs considerably. The gray matter consists of nerve cell bodies, dendrites, unmyelinated axons, synaptic terminals, astrocytes, oligodendrocytes (satellite cells) and microglia. The white matter differs from the gray for the presence of axonal tracts as the only neuronal component and for the absence of nerve cell bodies, dendrites and synaptic terminals. Cryogenic electron microscopy (cryo-EM) studies have unveiled the structure of tau and TMEM106B, from the cerebral cortex, in several neurodegenerative diseases; however, whether tau and TMEM106B filaments from the gray and white matter share a common fold requires additional investigation. MethodsWe isolated tau and TMEM106B from the cerebral cortex and white matter of the frontal lobes of two individuals affected by multiple system tauopathy with presenile dementia (MSTD), a disease caused by the MAPT intron 10 mutation +3. We used immunostaining, biochemical, genetics and cryo-EM methods to characterize tau and TMEM106B. ResultsWe determined that tau filaments in the gray and the white matter of MSTD individuals can induce tau aggregation and have identical AGD type 2 folds. TMEM106B amyloid filaments were also found in the gray and white matter of MSTD; the filament folds were identical in the two anatomical regions. ConclusionsOur findings show for the first time that in MSTD two types of amyloid filaments extracted from the gray matter have identical folds to those extracted from the white matter. Whether in this genetic disorder there is a relationship in the pathogenesis of the tau and TMEM106B filaments, remains to be determined. Furthermore, additional studies are needed for other proteins and other neurodegenerative diseases to establish whether filaments extracted from the gray and white matter would have identical folds.

neuroscience↗

bioRxiv2023

The mechanosensitive ion channel Piezo1 contributes to ultrasound neuromodulation

Transcranial low-intensity ultrasound is a promising neuromodulation modality, with the advantages of non-invasiveness, deep penetration, and high spatiotemporal accuracy. However, the underlying biological mechanism of ultrasonic neuromodulation remains unclear, hindering the development of efficacious treatments. Here, the well-known Piezo1, was studied through a conditional knockout mouse model as a major molecule for ultrasound neuromodulation ex vivo and in vivo. We showed that Piezo1 knockout in the right motor cortex of mice significantly reduced ultrasound-induced neuronal calcium responses, limb movement and muscle EMG responses. We also detected higher Piezo1 in the central amygdala (CEA) which were found more sensitive to ultrasound stimulation than that of cortex. Knocking out the Piezo1 in CEA neurons showed a significant reduction of response under ultrasound stimulation while knocking out astrocytic Piezo1 showed no obvious changes in neuronal responses. Additionally, we excluded an auditory confound by monitoring auditory cortical activation and using smooth waveform ultrasound with randomized parameters to stimulate P1KO ipsilateral and contralateral regions of the same brain and recording evoked movement in the corresponding limb. Thus, we demonstrate that Piezo1 is functionally expressed in different brain regions, and that it is an important mediator of ultrasound neuromodulation in the brain, laying the ground for further mechanistic studies of ultrasound.

neuroscience↗

bioRxiv2022

The compact CasPi (Cas12l) bracelet "provides" a unique structural platform for DNA manipulation

CRISPR-Cas modules serve as the adaptive nucleic-acid immune systems for prokaryotes, and provide versatile tools for nucleic-acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Cas{pi} (Cas12l) ([~]860 aa), from the environmental metagenome. Complexed with a large guide-RNA ([~]170 nt) comprising the tracrRNA and crRNA, Cas{pi} (Cas12l) recognizes a unique 5 C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a bracelet architecture of Cas{pi} effector encircling the DNA target at 3.4-[A] resolution, substantially different from the canonical two-lobe architectures of Cas12 and Cas9 nucleases. And the large guide-RNA serves as a two-arm scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulations.

biophysics↗

bioRxiv2022

Comparing Genomic and Epigenomic Features across Species Using the WashU Comparative Epigenome Browser

Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers that help users visualize alignment, mismatch, and rearrangement between syntenic regions. However, there is a growing need for a comparative epigenome browser that can display genomic and epigenomic datasets across different species and enable users to compare them between syntenic regions. Here, we present the WashU Comparative Epigenome Browser (http://comparativegateway.wustl.edu). It allows users to load functional genomic datasets/annotations mapped to different genomes and display them over syntenic regions simultaneously. The browser also displays genetic differences between the genomes from single nucleotide variants (SNVs) to structural variants (SVs) to visualize the association between epigenomic differences and genetic differences. Instead of anchoring all datasets to the reference genome coordinates, it creates independent coordinates of different genome assemblies to faithfully present features and data mapped to different genomes. It uses a simple, intuitive genome-align track to illustrate the syntenic relationship between different species. It extends the widely used WashU Epigenome Browser infrastructure and can be expanded to support multiple species. This new browser function will greatly facilitate comparative genomic/epigenomic research, as well as support the recent growing needs to directly compare and benchmark the T2T CHM13 assembly and other human genome assemblies.

genomics↗