Biology subjects

Dong, Y.

Publications and source records attributed to Dong, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Bispecific antibody targeting of lipid nanoparticles

Lipid nanoparticles (LNP) are the most clinically advanced non-viral gene delivery system. While progress has been made for enhancing delivery, cell specific targeting remains a challenge. Targeting moieties such as antibodies can be chemically-conjugated to LNPs however, this approach is complex and has challenges for scaling up. Here, we developed an approach to generate antibody-conjugated LNPs that utilizes a bispecific antibody (bsAb) as the targeting bridge. As a docking site for the bsAb, we generated LNPs with a short epitope, derived from hemagglutinin antigen (HA), embedded in the PEG component of the particle (LNPHA). We generated bsAb in which one domain binds HA and the other binds different cell surface proteins, including PD-L1, CD4, CD5, and SunTag. Non-chemical conjugation of the bsAb and LNP resulted in a major increase in the efficiency and specificity of transfecting cells expressing the cognate target. LNP/bsAb mediated a 4-fold increase in in vivo transfection of PD-L1 expressing cancer cells, and a 26-fold increase in ex vivo transfection of quiescent primary human T cells. Additionally, we created a universal bsAb recognizing HA and anti-rat IgG2, enabling LNP tethering to off-the-shelf antibodies such as CD4, CD8, CD20, CD45, and CD3. By utilizing a molecular dock and bsAb technology, these studies demonstrate a simple and effective strategy to generate antibody-conjugated LNPs, enabling precise and efficient mRNA delivery.

bioengineering↗

bioRxiv2024

Fitness translocation: improving variant effect prediction with biologically-grounded data augmentation

Data scarcity limits the characterization of protein fitness landscapes and the development of accurate variant effect prediction models. To address this challenge, we introduce fitness translocation, a data augmentation strategy that generates synthetic variants for a target protein by leveraging variant fitness data previously measured in homologous proteins. Using embeddings from protein language models, the method computes the difference between each homolog variant and its wild type and applies these offsets to the target wild-type embedding to create synthetic variants in embedding space. We illustrate the utility of fitness translocation in the context of variant effect prediction on three protein families: IGPS, GFP, and SARS-CoV-2 spike proteins, across different models and training data sizes. Fitness translocation consistently improves predictive performance, particularly under limited training data, and is effective even when augmenting with remote homologs sharing as little as 35% sequence identity. These results illustrate how biologically grounded data augmentation can expand and diversify protein fitness landscapes, supporting more data-efficient protein engineering. The code is available at https://github.com/adrienmialland/ProtFitTrans.

bioinformatics↗

bioRxiv2024

BioMedGraphica: An All-in-One Platform for Biomedical Prior Knowledge and Omic Signaling Graph Generation

Multi-omic data analysis is essential for scientific discovery in precision medicine. However, translating statistical results of omic data analysis into novel scientific hypothesis remains a significant challenge. Human experts must manually review analysis results and generate new hypothesis based on extensive and inter-connected biomedical prior knowledge, which is subjective and not scalable. While large language models (LLMs) can accelerate the discovery, their reasoning improves when grounded in structured, auditable and comprehensive biomedical prior knowledge. Biomedical knowledge, however, is scattered across heterogeneous databases that use diverse and inconsistent nomenclature systems, making it difficult to integrate resources into a unified format for scalable analysis. This fragmentation limits the ability of AI systems to fully leverage biomedical data for scientific discovery. To address these challenges, we developed BioMedGraphica, an all-in-one platform that harmonizes fragmented biomedical resources by integrating 11 entity types and 30 relation types from 43 databases into a unified knowledge graph containing 2,306,921 entities and 27,232,091 relations. In addition, to the best of our knowledge, this is the first work to propose a novel Textual-Numeric Graph (TNG) data-structure for multi-omics data analysis. In TNG, textual information captures prior biological knowledge (e.g., transcription start sites, functions, mechanisms), while numeric values represent quantitative biomedical features, and the integrated relations can help uncover mechanisms. By bridging prior knowledge with user-specific data, TNG is a novel and ideal data-structure for the development of graph foundation models, with the potential to improve prediction performance and interpretability, while also augmenting LLMs by supplying graph-structured mechanistic context to strengthen reasoning. The details for BioMedGraphica code can be accessed by github link: https://github.com/FuhaiLiAiLab/BioMedGraphica and BioMedGraphica knowledge graph data can be downloaded from huggingface dataset: https://huggingface.co/datasets/FuhaiLiAiLab/BioMedGraphica

bioinformatics↗

bioRxiv2024

A lineage-resolved multimodal single-cell atlas reveals the genomic dynamics of early C. elegans development

Multimodal single-cell profiling provides a powerful approach for unravelling the gene regulatory mechanisms that drive development, by simultaneously capturing cell-type- specific transcriptional and chromatin states. However, its inherently destructive nature hampers the ability to trace regulatory dynamics between mother and daughter cells. Taking advantage of the invariant cell lineage of Caenorhabditis elegans, we constructed a lineage- resolved single-cell multimodal map of pre-gastrulation development, which allows the tracing of chromatin and gene expression changes across cell divisions and regulatory cascades. We characterise the early dynamics of genome regulation, revealing that zygotic genome activation occurs on an accessible chromatin landscape pre-patterned both maternally and zygotically, and we identify a redundant family of transcriptional regulators that drive a transient pre-gastrulation program. Our findings demonstrate the power of a lineage-resolved atlas for dissecting the genome regulatory events of development.

genomics↗

bioRxiv2024

Desmoplakin is a desmosomal mechanosensor

Desmosomes are essential cell-cell adhesion organelles that enable tension-prone tissue, like the skin and heart, to withstand mechanical stress. Desmosomal anomalies are associated with numerous epidermal disorders and cardiomyopathies. Despite their critical role in maintaining tissue resilience, an understanding of how desmosomes sense and respond to mechanical stimuli is lacking. Here, we use a combination of super-resolution imaging, FRET-based tension sensors, atomistic computer simulations, and biochemical assays to demonstrate that actomyosin forces induce a conformational change in desmoplakin, a critical cytoplasmic desmosomal protein. We show that in human breast cancer MCF7 cells, actomyosin contractility reorients keratin intermediate filaments and directs force to desmoplakin along the keratin filament backbone. These forces induce a conformational change in the N-terminal plakin domain of desmoplakin, converting this domain from a folded (closed) to an extended (open) conformation. Our findings establish that desmoplakin is mechanosensitive and responds to changes in cellular load by undergoing a force-induced conformational change.

cell biology↗

bioRxiv2024

Chronic intermittent ethanol produces nociception through endocannabinoid-independent mechanisms in mice

Alcohol use disorder (AUD) affects millions of people and represents a significant health and economic burden. Pain represents a frequently under-treated aspect of hyperkatifeia during alcohol withdrawal, yet to date no drugs have received FDA approval for the treatment of this indication in AUD patients. This study aims to evaluate the potential of targeting bioactive lipid signaling pathways as a therapeutic approach for treating alcohol withdrawal-related pain. We utilized a chronic intermittent ethanol (CIE) vapor exposure model in C57BL/6J mice of both sexes to establish alcohol dependence, and demonstrated that CIE mice developed robust tactile allodynia and thermal hyperalgesia during withdrawal that was independent of prior blood alcohol levels. Next, we evaluated four drugs for their efficacy in reversing tactile allodynia during abstinence from CIE using a cross-over treatment design that included FDA-approved naltrexone as well as commercially available inhibitors targeting inflammatory lipid signaling enzymes including fatty acid amide hydrolase (FAAH), monoacylglycerol lipase (MAGL), and 15-Lipoxygenase (LOX). None of these compounds produced significant therapeutic benefit in reversing established CIE-induced tactile allodynia, despite attenuating pain-like behaviors at these doses in other chronic pain models. Additionally, we assessed plasma endocannabinoid levels in both sexes during withdrawal. We found that there is an inherent sex difference in the endogenous anti-inflammatory endocannabinoid tone in naive mice and CIE treatment affected endocannabinoids levels in female mice only. These findings underscore the need to better understand the driving causes of AUD induced pain and to develop novel therapeutic approaches to mitigate pain in AUD patients.

pharmacology and toxicology↗

bioRxiv2024

Projections between the globus pallidus externa and cortex span motor and non-motor regions

The globus pallidus externa (GPe) is a heterogenous nucleus of the basal ganglia, with intricate connections to other basal ganglia nuclei, as well as direct connections to the cortex. The anatomic, molecular and electrophysiologic properties of cortex-projecting pallidocortical neurons are not well characterized. Here we show that pallidocortical neurons project to diverse motor and non-motor cortical regions, are organized topographically in the GPe, and segregate into two distinct electrophysiological and molecular phenotypes. In addition, we find that the GPe receives direct synaptic input back from deep layers of diverse motor and non-motor cortical regions, some of which form reciprocal connections onto pallidocortical neurons. These results demonstrate the existence of a fast, closed-loop circuit between the GPe and the cortex which is ideally positioned to integrate information about behavioral goals, internal states, and environmental cues to rapidly modulate behavior.

neuroscience↗

bioRxiv2024

BMP4 is sufficient to induce a caudal organizer

The caudal part of a vertebrate embryo consists of somites, neural tube, lateral plate mesoderm derivatives and the tailbud. However, the minimal conditions and factors sufficient to induce the caudal region, particularly in humans, remain unresolved. Here, we show that BMP4 alone, when administered at appropriate dosage, is sufficient to induce the formation of an organizer for caudal induction. This organizer induces caudal cell fate specification and morphogenesis in zebrafish embryos. In 3D human pluripotent stem cells (hPSCs) aggregates, BMP4 can induce an elongated embryonic structure characterized by caudal fates. Importantly, hPSCs instructed by BMP4 are sufficient to induce a secondary caudal region when grafted into the animal pole of the zebrafish embryo. Our study thus uncovers BMP4 as the inducer in the formation of a caudal organizer in the vertebrate embryo. Significance statementWe demonstrate that BMP4 alone can induce the formation of a caudal organizer, a critical structure that guides the development of the caudal region in vertebrates. Using zebrafish embryos, embryonic explants, human pluripotent stem cell xenografts, and 3D human stem cell aggregates, we show that this organizer replicates morphogenesis and key differentiation pathways seen in natural development. Our findings uncover a novel role for BMP4 and define the minimal requirements for inducing this organizer, offering new insights into vertebrate development and potential applications in regenerative medicine.

developmental biology↗

bioRxiv2024

Systems metabolic engineering of Corynebacterium glutamicum for efficient L-tryptophan production

Corynebacterium glutamicum is a versatile industrial microorganism for producing various amino acids. However, there have been no reports of well-defined C. glutamicum strains capable of hyperproducing L-tryptophan. This study presents a comprehensive metabolic engineering approach to establish robust C. glutamicum strains for L-tryptophan biosynthesis, including: (1) identification of potential targets by enzyme-constrained genome-scale modeling; (2) enhancement of the L-tryptophan biosynthetic pathway; (3) reconfiguration of central metabolic pathways; (4) identification of metabolic bottlenecks through comparative metabolome analysis; (5) engineering of the transport system, shikimate pathway, and precursor supply; and (6) repression of competing pathways and iterative optimization of key targets. The resulting C. glutamicum strain achieved a remarkable L-tryptophan titer of 50.5 g/L in 48h with a yield of 0.17 g/g glucose in fed-batch fermentation. This study highlights the efficacy of integrating computational modeling with systems metabolic engineering for significantly enhancing the production capabilities of industrial microorganisms.

synthetic biology↗

bioRxiv2024

Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity

Recent advancements in probe-based, full-transcriptome, high-resolution technologies for Formalin-Fixed Paraffin-Embedded (FFPE) tissues, such as Visium CytAssist, Chromium Flex (10X Genomics), and GeoMx DSP (Nanostring), have opened new opportunities for studying decades-old archival samples in biobanks, facilitating the generation of data from extensive cohorts. However, the experimental protocols can be labor-intensive and costly; therefore, it is thus essential for researchers to carefully evaluate the strengths and limitations of each technology in relation to their specific research objectives. Here, we report the results of a comparative analysis of the three methods mentioned above on FFPE archival tumor samples from four non-small cell lung cancer, four breast cancer and six diffuse large B-cell lymphoma. We highlight some relative advantages and disadvantages of each method in the context of operational challenges, bioinformatic analysis and biological discovery. Our results show that: 1) all three methods yielded good-quality, highly reproducible transcriptomic data from serial sections of the same FFPE block; 2) GeoMx data contained mixtures of cell types, even when pre-selecting areas with cell type-specific markers; 3) high-throughput spot-level (Visium) or cell-level (Chromium) data enabled the identification of tumor heterogeneity within and between patients, which could be used to identify targeted therapies. Our data support the use of Visium and Chromium for high-throughput and discovery-driven projects, while the GeoMx platform could be suited for addressing specialized questions on targeted regions. All data generated from this study, including GeoMx, Visium, Chromium, H&E, and expert annotations are publicly available.

bioinformatics↗

bioRxiv2024

Structural Basis of GPCR-G Protein Pre-coupling and Activation: Insights from CCR1-Gi Complex

GPCR-mediated G protein activation cycle contains obligated step of the receptor-G protein assembly before G protein activation (pre-coupling state). However, transient nature of this pre-coupling state has prevented structural and mechanistic understanding of this essential step of G protein activation cycle. In this study, we discover that CCR1 has high level of pre-coupling state, which allows its rapid response to chemokines. Taking advantage of this observation, we uncover molecular mechanism of the pre-coupling state by solving the cryo-electron microscopy structure of the chemokine receptor CCR1 in complex with its cognate G protein (Gi) in a pre-coupled, inactivated state. This structure reveals that CCR1 adopts a conformation distinct from both its fully active and inactive states, with the G proteins 5 helix partially inserted into the receptors intracellular cavity. Notably, the C-terminal four residues of the G subunit are disordered in this pre-coupled state, contrasting with their well-defined -helical structure in the fully active complex. Functional assays demonstrate that while deletion of these four C-terminal G residues does not affect pre-coupling, it abolishes G protein activation upon agonist binding. This finding highlights the critical role of these residues in GPCR-mediated G protein activation, but not in initial recruitment. Furthermore, our studies indicate that the ability to form pre-coupled complexes is conserved among chemokine receptors, suggesting a common mechanism for rapid signal transduction in this GPCR subfamily. These results provide the first structural evidence for GPCR-G protein pre-coupling and offer molecular insights into the transition from inactive to active states. Our findings fill the long-missing gap in understanding GPCR-mediated G protein activated cycle.

biophysics↗

bioRxiv2024

Microbial succession, community assembly and adaptation over five years in a newly discovered deep-sea cold seep

Deep-sea cold seeps, characterized by the release of hydrocarbon-rich fluids such as methane from the seafloor, create unique ecosystems with evolving biological communities. Microorganisms serve as pioneers, initially colonizing early-stage cold seeps and providing essential matter and energy for subsequent colonizers. However, microbial succession, community assembly, and adaptation in these environments remain largely unexplored due to challenges associated with locating early-stage cold seeps. Here, we collected sediment samples from a newly discovered early-stage cold seep site, QDN-W07, in the South China Sea at varying depths over five years. We also sampled two previously reported cold seep sites, QDN-S18 and HM-ROV01, for comparative analysis. Amplicon sequencing revealed a high relative abundance of ANME-3 (up to 99%) and Methylomonadaceae (up to 83%) in surface sediments, and indicated changes in microbial community structures over time. Dispersal limitation dominated community assembly, while the contribution of homogeneous selection decreased over time, accompanied by a declined in the intensity of microbial association. Metagenomic analysis of core microbiome, comprising 172 metagenomic-assembled genomes at QDN-W07, revealed tolerance to low temperatures and oxygen. Core microbiome genomes were enriched with genes related to aerobic methane oxidation, urea metabolism, and the oxidation of sulfur, ammonia and carbon monoxide. These results indicate that core microorganisms obtain energy from the oxidation of inorganic compounds, allowing them to thrive in cold, methane-rich and unstable conditions. Overall, this study enhances our understanding of deep biosphere life, biogeochemical cycling, and the ecological management of cold seep environments.

microbiology↗

bioRxiv2024

Comparative spatiotemporal single cell transcriptomes reveal rewiring of pre-existing regulations during emergence of Kranz anatomy in C4 grasses

Many of the worlds most productive food and bioenergy crops use C4 photosynthesis, which have high photosynthetic efficiency due to a Kranz anatomy-based CO2 concentrating mechanism. Here, we took a comparative transcriptomics approach using single cell spatial transcriptomes of leaf primordia for maize (Zea mays) and single cell RNA-seq (scRNA-seq) atlases of corresponding leaf tissues for three C4 species (Zea mays, Sorghum bicolor, Setaria viridis) and one C3 rice (Oryza sativa) to study regulatory networks involved in the development and evolution of Kranz anatomy. We show that the formation of Kranz anatomy involves extensive recruitment and modification of pre-existing regulatory modules, especially the SHR-SCR module and the auxin signaling pathway. Members of the INDETERMINATE DOMAIN (IDD) family transcription factors, including IDD7 and IDDP1, contribute to the modification of the involved modules. These extensive recruitment and modification of existing genetic regulatory programs underlie the repeated emergence of C4 photosynthesis during evolution.

plant biology↗

bioRxiv2024

scAGCI: an anchor graph-based method for cell clustering from integrated scRNA-seq and scATAC-seq data

Cell clustering plays a crucial role in the analysis of single-cell multi-omics research. Despite many methods for multi-omics integrated clustering, challenges such as noise, data sparsity, and biointerpretability analysis hider effective clustering. Recent studies have demonstrated that anchor graph learning clustering in the multiview graph domain can help alleviate sparsity and high noise, reducing runtime costs. However, addressing the heterogeneity and high noise levels in multi-omics data is crucial for obtaining a more representative anchor graph. Furthermore, the existing methods often directly obtain surface information from multi-omics for clustering purposes, neglecting the mining and utilization of higher-order correlations among different features within shared information. In response to these challenges, we propose scAGCI, a cell clustering method based on anchor graphs that integrates both scRNA-seq and scATAC-seq data. Our method captures specific and shared anchor graphs representing the properties of omics data in the process of dynamic anchor unification, and mines high-order shared information to complete the omics representation. Subsequently, clustering results are obtained by integrating the specific and shared omics representation. Extensive experiments show that our method not only outperforms 13 state-of-the-art methods in terms of clustering metrics and running time, but also that the completed omics retains the biological meaning of the original omics.

bioinformatics↗

bioRxiv2024

Manipulation of the brown glume and internode 1 gene leads to alterations in lignified tissue coloration, lignification, and pathogen resistance in wheat

Lignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defense. In this study, we identified an ethyl methanesulfonate (EMS)-derived Aegilops tauschii mutant named brown glume and internode 1 (bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes, and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identified AET6Gv20438400 (BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon in BGI1. We validated the function of BGI1 using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues. BGI1 knockout mutants exhibited reduced lignin content and shearing force relative to wild type, while BGI1 overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot and Fusarium crown rot. We confirmed that BGI1 exhibits CAD activity both in vitro and in vivo, playing an important role in lignin biosynthesis. BGI1 was highly expressed in the stem and spike and localized in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated with BGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signaling pathway. The identification and functional characterization of BGI1 significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defense against pathogen infection in wheat.

plant biology↗

bioRxiv2024

Temporal Dynamics of Nucleus Accumbens Neurons in Male Mice During Reward Seeking

The nucleus accumbens (NAc) regulates reward-motivated behavior, but the temporal dynamics of NAc neurons that enable "free-willed" animals to obtain rewards remain elusive. Here, we recorded Ca2+ activity from individual NAc neurons when mice performed self-paced lever-presses for sucrose. NAc neurons exhibited three temporally-sequenced clusters, defined by times at which they exhibited increased Ca2+ activity: approximately 0, -2.5 or -5 sec relative to the lever-pressing. Dopamine D1 receptor (D1)-expressing neurons and D2-neurons formed the majority of the -5-sec versus -2.5-sec clusters, respectively, while both neuronal subtypes were represented in the 0-sec cluster. We found that pre-press activity patterns of D1- or D2-neurons could predict subsequent lever-presses. Inhibiting D1-neurons at -5 sec or D2-neurons at -2.5 sec, but not at other timepoints, reduced sucrose-motivated lever-pressing. We propose that the time-specific activity of D1- and D2-neurons mediate key temporal features of the NAc through which reward motivation initiates reward-seeking behavior.

neuroscience↗

bioRxiv2024

Dietary L-3,4-dihydroxyphenylalanine (L-DOPA) augments cuticular melanization in Anopheles mosquitos while reducing their lifespan and malaria parasite burden

L-3,4-dihydroxyphenylalanine (L-DOPA), a naturally occurring tyrosine derivative, is prevalent in environments that include mosquito habitats, potentially serving as part of their diet. Given its role as a precursor for melanin synthesis we investigate the effect of dietary L-DOPA on mosquito physiology and immunity to Plasmodium falciparum and Cryptococcus neoformans infection. Dietary L-DOPA is incorporated into mosquito melanin via a non-canonical pathway and has a profound transcriptional effect associated with enhanced immunity, increased pigmentation, and reduced lifespan. Increased melanization results in an enhanced capacity to absorb electromagnetic radiation that affects mosquito temperatures. Bacteria in the mosquito microbiome act as sources of dopamine, a substrate for melanization. Our results illustrate how an environmentally abundant amino acid analogue can affect mosquito physiology and suggest its potential usefulness as an environmentally friendly vector control agent to reduce malaria transmission, warranting further research and field studies.

microbiology↗

bioRxiv2024

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

BackgroundThe agamid dragon lizard Pogona vitticeps is one of the most popular domesticated reptiles to be kept as pets worldwide. The capacity of breeding in captivity also makes it emerging as a model species for a range of scientific research, especially for the studies of sex chromosome origin and sex determination mechanisms. ResultsBy leveraging the CycloneSEQ and DNBSEQ sequencing technologies, we conducted whole genome and long-range sequencing for a captive-bred ZZ male to construct a chromosome-scale reference genome for P. vitticeps. The new reference genome is [~]1.8 Gb in length, with a contig N50 of 202.5 Mb and all contigs anchored onto 16 chromosomes. Genome annotation assisted by long-read RNA sequencing greatly expanded the P. vitticeps lncRNA catalog. With the chromosome-scale genome, we were able to characterize the whole Z sex chromosome for the first time. We found that over 80% of the Z chromosome remains as pseudo-autosomal region (PAR) where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2 and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of the SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes which considered the Z-linked AMH as the master sex-determining gene. ConclusionsOur study provides novel insights into the sex chromosome origin and sex determination of this model lizard. The near-complete P. vitticeps reference genome will also benefit future study of amniote evolution and may facilitate genome-assisted breeding.

genomics↗