Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 1,387 records · Page 77Linked to original sources

bioRxiv2023

Dorsal hippocampal oxytocin receptor regulates adult peer bonding in rats

Healthy social relationships are beneficial whereas their breakdown is often linked to psychiatric disorders. Parental care and bonding between sexual partners have been well studied both at the level of behavioral analysis and underlying neuronal mechanisms. By contrast, little is known about the neural and molecular basis of peer bonding, defined as social bonds formed between unrelated individuals of the same sex, due to the lack of a suitable experimental paradigm. We found that adult Sprague Dawley (SD) rats of the same sex form strong peer bonds with each other following co-housing. Peer bonded rats exhibit affiliative displays toward their cagemates who are distressed whereas they exhibit agonistic behaviors toward strangers in these situations. Using innovative, genetic strategies in rats, we show that both oxytocin receptor (OXTR) bearing neurons and Oxtr signaling in the dorsal hippocampus are essential for peer bonds to form. Together, we have developed a new platform for studying peer bonding and demonstrate a neural pathway that governs this behavior.

neuroscience↗

bioRxiv2023

Population suppression with dominant female-lethal alleles is boosted by homing gene drive

Methods to suppress pest insect populations using genetic constructs and repeated releases of male homozygotes have recently been shown to be an attractive alternative to older sterile insect technique based on radiation. Female-specific lethal alleles have substantially increased power, but still require large, sustained transgenic insect releases. Gene drive alleles bias their own inheritance to spread throughout populations, potentially allowing population suppression with a single, small-size release. However, suppression drives often suffer from efficiency issues, and the most well-studied type, homing drives, tend to spread without limit. In this study, we show that coupling female-specific lethal alleles with homing gene drive allowed substantial improvement in efficiency while still retaining the self-limiting nature (and thus confinement) of a lethal allele strategy. Using a mosquito model, we show the required releases sizes for population elimination in a variety of scenarios, including different density growth curves, with comparisons to other systems. Resistance alleles reduced the power of this method, but these could be overcome by targeting an essential gene with the drive while also providing rescue. A proof-of-principle demonstration of this system in Drosophila melanogaster was effective in both basing its inheritance and achieving high lethality among females that inherit the construct in the absence of antibiotic. Overall, our study shows that substantial improvements can be achieved in female-specific lethal systems for population suppression by combining them with a gene drive.

synthetic biology↗

bioRxiv2023

Single-molecule Ligand Response of Guanidine-IV riboswitch

Riboswitches represent a class of non-coding RNA that possess the unique ability to specifically bind ligands and, in response, regulate gene expression. A recent report unveiled a type of riboswitch, known as the guanidine-IV riboswitch, which responds to guanidine levels to regulate downstream genetic transcription. However, the precise molecular mechanism through which the riboswitch senses its target ligand and undergoes conformational changes remain elusive. This gap in understanding has impeded the potential applications of this riboswitch. To bridge this knowledge gap, our study investigated the conformational dynamics of the guanidine-IV riboswitch RNA upon ligand binding. We employed single-molecule fluorescence resonance energy transfer (smFRET) to dissect the behaviors of the aptamer, terminator, and full-length riboswitch. Our findings indicated that the aptamer portion exhibited higher sensitivity to guanidine compared to the terminator and full-length constructs. Additionally, we utilized Position-specific Labelling of RNA (PLOR) combined with smFRET to observe, at the single-nucleotide and single-molecule level, the structural transitions experienced by the guanidine-IV riboswitch during transcription. Notably, we discovered that the influence of guanidine on the riboswitch RNAs conformations was significantly reduced after the transcription of 88 nucleotides. Furthermore, we proposed a folding model for the guanidine-IV riboswitch in the absence and presence of guanidine, thereby providing insights into its ligand-response mechanism. Impact statementThe aptamer domain of the guanidine-IV riboswitch exhibits a greater sensitivity to guanidine, surpassing that observed in both the terminator and full-length riboswitch. A finely-tuned transcriptional window of the guanidine-IV riboswitch was detected to be responsive to ligand binding. Furthermore, a folding-function model for the guanidine-IV riboswitch under both guanidine-free and guanidine-present conditions offers valuable insights into its regulatory mechanism.

biochemistry↗

bioRxiv2023

Systematic comparison of sequencing-based spatial transcriptomic methods

Recent advancements of sequencing-based spatial transcriptomics (sST) have catalyzed significant advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare six sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, significantly impacting the effective resolutions. Furthermore, we observed that spatial transcriptomic data demonstrate unique attributes beyond merely adding a spatial axis to single-cell data, including an enhanced ability to capture patterned rare cell states along with specific markers, albeit being influenced by multiple factors including sequencing depth and resolution. Our study assists biologists in sST platform selection, and helps foster a consensus on evaluation standards and establish a framework for future benchmarking efforts that can be used as a gold standard for the development and benchmarking of computational tools for spatial transcriptomic analysis.

genomics↗

bioRxiv2023

The balance between ATR and DDK activities controls TopBP1-mediated locking of dormant origins at the pre-IC stage

Replication stress, a major hallmark of cancers, and ensuing genome instability source from impaired progression of replication forks. The first line of defense against fork slowing is compensation, a long-described process that elicits firing of otherwise dormant origins. It remains unclear whether compensation requires activation of the DNA replication checkpoint or passively results from lengthening of the window of time during which dormant origins can fire when fork progression slows, or both. Using molecular DNA combing we show here that a linear relationship ties inter-origin distances to fork speeds, independently of the checkpoint status. We called this line "stressline" and further show that its slope enables precise quantification of the compensation efficiency. Comparison of the slopes in different genetic backgrounds reveals that compensation requires ATR, not CHK1, while TopBP1 and CDC7/DBF4 repress dormant origin activation. These results strongly suggest that TopBP1 locks dormant origins at the pre-IC stage and that ATR and DDK oppose to control the conversion of dormant pre-ICs into functional salvage origins. Both passive and active processes thus contribute to compensation. Moreover, Repli-seq and OK-seq analyses confirm the activating role of ATR and permit development of ATRAP-seq, a new procedure allowing mapping of early constitutive origins.

genetics↗

bioRxiv2023

Complex ecosystems lose stability when resource consumption is out of niche

Natural communities exhibit diverse dynamics, encompassing global stability, multi-stability, periodic oscillations, and chaotic fluctuations in species abundances. Resource-consumer interactions provide a lens for mechanistic understanding of community behaviors, yet only a globally stable equilibrium can exist in the original MacArthur resource-consumer model. Here we find that diverse dynamics emerges when species consume resources that contribute little to their own growth. Key to understanding these results is comparison of niche range (difference between growth-promoting resources of similar species) and consumption range (difference between growth-promoting resources and the resources that are actually consumed). If the consumption range is small, we observe global stability as in the MacArthur model. But when consumption range increases to about the niche range, stability is lost, giving rise to emergent alternative stable states, globally stable states but with species extinction, and slightly later, persistent fluctuations. Given its importance in dictating stability, we define the ratio between consumption and niche ranges as encroachment, and find that it predicts key community properties like diversity and attractor basins even after the instability transition. In particular, after the loss of stability (encroachment greater than one), species extinction increases approximately linearly with encroachment. Since encroachment relies only on intrinsic species properties, community stability is resilient to environmental changes such as resource supply and mortality rate. Encroachment provides a framework for capturing resource competition due to growth-consumption inconsistency in complex communities as well as a robust quantitative characterization of the resulting emergent dynamics.

ecology↗

bioRxiv2023

Thalamic network controllability changes and cognitive impairment in multiple sclerosis

Recent research suggests that individuals with multiple sclerosis (MS) and cognitive impairment exhibit more effortful and less efficient transitions in brain network activity. Previous studies further highlight the increased vulnerability of specific regions, particularly the thalamus, to disease-related damage. This study investigates whether MS affects the controllability of specific brain regions in driving network activity transitions across the brain and examines the relationship between these changes and cognitive impairment in patients. Resting-state functional MRI and neuropsychological data were collected from 102 MS and 27 healthy controls. Functional network controllability analysis was performed to quantify how specific regions influence transitions between brain activity patterns or states. Disease alterations in controllability were assessed in the main dataset and then replicated in an independent dataset of 95 MS and 45 healthy controls. Controllability metrics were then used to distinguish MS from healthy controls and predict cognitive status. MS-specific controllability changes were observed in the subcortical network, particularly the thalamus, which were further confirmed in the replication dataset. Cognitively impaired patients showed significantly greater difficulty in the thalamus steering brain transitions towards difficult-to-reach states, which are typically associated with high-energy-cost cognitive functions. Thalamic network controllability proved more effective than thalamic volume in distinguishing MS from healthy controls (AUC = 88.3%), and in predicting cognitive status in MS (AUC = 80.7%). This study builds on previous research highlighting early thalamic damage in MS, aiming to demonstrate how this damage disrupts activity transitions across the cerebrum and may predict cognitive deficits. Our findings suggest that the thalamus in MS becomes less capable of facilitating broader brain activity transitions essential for high-energy-cost cognitive functions, implying a potential pathological mechanism that links thalamic functional changes to cognitive impairment in MS.

neuroscience↗

bioRxiv2023

Single-cell 5' RNA sequencing of camelid peripheral B cells reveals cellular basis of heavy-chain antibody production

Camelids are capable of producing both conventional tetrameric antibodies (Abs) and dimeric heavy-chain antibodies (HCAbs). While B cells generating these two types of Abs exhibit distinct B-cell receptors (BCRs), it remains unclear whether these two B cell populations differ in their phenotypes and developmental processes. Here, we collected eight PBMC samples before and after immunization from four Bactrian camels and conducted single-cell 5 RNA sequencing. We characterized the functional subtypes and differentiation trajectories of circulating B cells in camels, including native B cells, memory B cells, intermediate B cells, atypical B cells, and plasma cells. Additionally, we reconstructed single-cell BCR sequences and revealed the IGHV and IGHC gene types. We found that B cells expressing variable genes of HACbs (VHH) were widely present in various functional subtypes and showed highly overlapping differentiation trajectories to B cells expressing variable genes of conventional Abs (VH). After immunization, the transcriptional changes in VHH+ and VH+ B cells were also largely consistent. Our study elucidates the cellular context of HCAb production in camels, and lays the foundation for the development of single B cell-based nanobody screening.

genomics↗

bioRxiv2023

Elucidating the Glycan-Binding Specificity and Structure of Cucumis melo Agglutinin, a New R-Type Lectin

Plant lectins have garnered attention for their roles as laboratory probes and potential therapeutics. Here, we report the discovery and characterization of Cucumis melo agglutinin (CMA1), a new R-type lectin from melon. Our findings reveal CMA1s unique glycan-binding profile, mechanistically explained by its 3D structure, augmenting our understanding of R-type lectins. We expressed CMA1 recombinantly and assessed its binding specificity using multiple glycan arrays, covering 1,046 unique sequences. This resulted in a complex binding profile, strongly preferring C2-substituted, beta-linked galactose (both GalNAc and Fuca1-2Gal), which we contrasted with the established R-type RCA1 lectin. We also report binding of specific glycosaminoglycan subtypes and a general enhancement of binding by sulfation. Further validation using agglutination, thermal shift assays, and surface plasmon resonance confirmed and quantified this binding specificity in solution. Finally, we solved the high-resolution structure of the CMA1 N-terminal domain using X-ray crystallography, supporting our functional findings at the molecular level. Our study provides a comprehensive understanding of CMA1, laying the groundwork for further exploration of its biological and therapeutic potential.

biochemistry↗

bioRxiv2023

Development of a Nanoparticle-Based Tendon-Targeting Drug Delivery System to Pharmacologically Modulate Tendon Healing

Tendon regeneration following acute injury is marred by a fibrotic healing response that prevents complete functional recovery. Despite the high frequency of tendon injuries and the poor outcomes, including functional deficits and elevated risk of re-injury, there are currently no pharmacological therapies in clinical use to enhance the healing process. Several promising pharmacotherapies have been identified; however, systemic treatments lack tendon specificity, resulting in poor tendon biodistribution and perhaps explaining the largely limited beneficial effects of these treatments on the tendon healing process. To address this major unmet need, we leveraged our existing spatial transcriptomics dataset of the tendon healing process to identify an area of the healing tendon that is enriched for expression of Acp5. Acp5 encodes tartrate-resistant acid phosphatase (TRAP), and we demonstrate robust TRAP activity in the healing tendon. This unexpected finding allowed us to refine and apply our existing TRAP binding peptide (TBP) functionalized nanoparticle (NP) drug delivery system (DDS) to facilitate improved delivery of systemic treatments to the healing tendon. To demonstrate the translational potential of this drug delivery system, we delivered the S100a4 inhibitor, Niclosamide to the healing tendon. We have previously shown that genetic knockdown of S100a4 enhances tendon healing. While systemic delivery of Niclosamide did not affect the healing process, relative to controls, TBP-NP delivery of Niclosamide enhanced both functional and mechanical outcome measures. Collectively, these data identify a novel tendon-targeting drug delivery system and demonstrate the translational potential of this approach to enhance the tendon healing process.

bioengineering↗

bioRxiv2023

Bi-parental graph strategy to represent and analyze hybrid plant genomes

Hybrid plants are universally existed in wild and often exhibit greater performance of complex traits compared with their parents and other selfing plants. This phenomenon, known as heterosis, has been extensively applied in plant breeding for decades. However, the process of decoding hybrid plant genomes has seriously lagged due to the challenges in their genome assembling and the lack of proper methods to further represent and analyze them. Here we report the assembly and analysis of two hybrids: an intraspecific hybrid between two maize inbred lines and an interspecific hybrid between maize and its wild relative teosinte, based on the combination of PacBio High Fidelity (HiFi) sequencing and chromatin conformation capture sequencing data. The haplotypic assemblies are well-phased at chromosomal scale, successfully resolving the complex loci with extensive parental structural variations (SVs). By integrating into a bi-parental genome graph, the haplotypic assemblies can facilitate downstream short-reads based SV calling and allele-specific gene expression analysis, demonstrating outstanding advantages over one single linear genome. Our work provides an entire workflow which hopefully can promote the deciphering of the large numbers of hybrid plant genomes, especially those whose parents are unknown or unavailable and help to understand genome evolution and heterosis.

bioinformatics↗

bioRxiv2023

Glycodiversification of gentamicins through in vivo glycosyltransferase swapping enabled the creation of novel hybrid aminoglycoside antibiotics with potent activity and low ototoxicity

Aminoglycosides (AGs) are a class of potent antibiotics with a broad spectrum of activity. However, their use is limited by safety concerns associated with nephrotoxicity and ototoxicity, as well as drug resistance. To address these issues, semi-synthetic approaches for modifying natural AGs have successfully generated new generations of AGs, however, with limited types of modification due to significant challenges in synthesis. This study explores a novel approach that harness the bacterial biosynthetic machinery of gentamicins and kanamycins to create hybrid AGs, installing extensive natural modifications from gentamicins onto kanamycins. This was achieved by glycodiversification of gentamicins via swapping the glycosyltransferase (GT) in their producer with the GT from kanamycins biosynthetic pathway and resulted in the creation of a series of novel AGs with combined structural features of two, therefore referred to as genkamicins (GKs). The manipulation of the hybrid metabolic pathway enabled the target accumulation of different GK species and the successful isolation and characterization of six GK components. These compounds display retained antimicrobial activity against a panel of World Health Organization (WHO) critical priority pathogens, and GK-C2a, in particular, demonstrates low ototoxicity compared to clinical drugs in zebrafish embryos. This study provides a new strategy for diversifying the structure of AGs and a potential avenue for developing less toxic AG drugs to combat infectious diseases.

synthetic biology↗

bioRxiv2023

Metabolism-focused CRISPR screen unveils Mitochondrial Pyruvate Carrier 1 as a critical driver for PARP inhibitor resistance in lung cancer

Homologous recombination (HR) and poly ADP-ribosylation are partially redundant pathways for repair of DNA damage in normal and cancer cells. In cell lines that are deficient in HR, inhibition of poly (ADP-ribose) polymerase (PARP1/2) is a proven target with several PARP inhibitors (PARPi) currently in clinical use. Resistance to PARP inhibitors often develops, usually involving genetic alterations in DNA repair signaling cascades, but also metabolic rewiring particularly in HR-proficient cells. PARP1/2 utilize NAD+ (nicotinamide adenine dinucleotide), an essential substrate not only for PARPs but also for multiple pathways in cellular metabolism, TCA cycle and mitochondrial functions. Thus, NAD+ is central to many key cellular functions. Both activation of PARPs by DNA damage and their inhibition by drugs such as olaparib affect NAD+ consumption. We surmised that alterations in NAD+ metabolism by cancer drugs such as Olaparib might be involved in the development of resistance to drug therapy. To test this hypothesis, we conducted a metabolism-focused CRISPR knockout (KO) screen to identify genes which undergo alterations during treatment of tumor cells with PARP inhibitors. Of about 3000 genes in the screen, our data revealed that mitochondrial pyruvate carrier 1 (MPC1) is an essential factor in desensitizing NSCLC lung cancer lines to PARP inhibition. In contrast to NSCLC lung cancer cells, triple negative breast cancer cells do not exhibit such desensitization following MPC1 loss and reprogram the TCA cycle and oxidative phosphorylation pathways to overcome PARP inhibitor treatment. Our findings unveil a previously unknown synergistic response between MPC1 loss and PARP inhibition in lung cancer cells.

cancer biology↗

bioRxiv2023

Biosurfactant stabilized nanoemulsions as multifunctional magnetically targeted delivery vehicles

Nanoemulsions have been widely used for pharmaceutic applications. However, there remains a significant challenge to functionalize available pharmaceutical surfactants with targeting or reporter moieties to generate next-generation drug delivery systems. Herein, a designed biosurfactant platform technology, based on our library of -helical peptide AM1 derivatives, was used to prepare multifunctional magnetic nanoemulsion drug delivery systems. Key factors such as electrostatic and steric stabilization of the nanoemulsions were determined using this peptide library. Stabilization of the nanoemulsion was achieved by controlled and tunable loading of PEG-functionalized biosurfactant at the oil-water interface. A model drug and iron oxide nanoparticles were incorporated into the oil core to prepare multifunctional nanoemulsions. In vitro cell uptake experiments using an external magnetic field demonstrated controlled rapid uptake of iron oxide loaded nanoemulsions by SKOV3 cancer and RAW 264.7 macrophage cells. SKOV3 cells demonstrated a slower rate of uptake under a magnetic field when compared to RAW 264.7 cells. This work demonstrates a highly adaptable hierarchical nanoemulsion system that can provide a platform to develop effective multifunctional nanomedicines and tools for biomedical insights. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/568750v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@31c3f2org.highwire.dtl.DTLVardef@1376aecorg.highwire.dtl.DTLVardef@14cb0aeorg.highwire.dtl.DTLVardef@1e37a6e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Evolution-guided large language model is a predictor of virus mutation trends

The increasing frequency of emerging viral infections necessitates a rapid human response, highlighting the cost-effectiveness of computational methods. However, existing computational approaches are limited by their input forms or incomplete functionalities, preventing a unified prediction of diverse viral variation drivers and hindering in-depth applications. To address this issue, we propose a unified evolution-driven framework for predicting virus variation drivers, named E2VD, which is guided by virus evolutionary traits priors. With evolution-inspired design, E2VD comprehensively and significantly outperforms state-of-the-art methods across various virus variation drivers prediction tasks. Moreover, E2VD effectively captures the fundamental patterns of virus evolution. It not only distinguishes different types of mutations but also accurately identifies rare beneficial mutations that are critical for virus to survival, while maintains generalization capabilities on different viral lineages. Importantly, with predicted biological drivers, E2VD perceives virus evolutionary trends, in which potential high-risk mutation sites are accurately recommended. Overall, E2VD represents a unified, structure-free, and interpretable approach for analyzing and predicting viral evolutionary fitness, providing an ideal alternative to costly wet-lab measurements to accelerate responses to emerging viral infections.

bioinformatics↗

bioRxiv2023

Deep Learning Model Imputes Missing Stains in Multiplex Images

Multiplex staining enables simultaneous detection of multiple protein markers within a tissue sample. However, the increased marker count increased the likelihood of staining and imaging failure, leading to higher resource usage in multiplex staining and imaging. We address this by proposing a deep learning-based MArker imputation model for multipleX IMages (MAXIM) that accurately impute protein markers by leveraging latent biological relationships between markers. The models imputation ability is extensively evaluated at pixel and cell levels across various cancer types. Additionally, we present a comparison between imputed and actual marker images within the context of a downstream cell classification task. The MAXIM models interpretability is enhanced by gaining insights into the contribution of individual markers in the imputation process. In practice, MAXIM can reduce the cost and time of multiplex staining and image acquisition by accurately imputing protein markers affected by staining issues.

pathology↗

bioRxiv2023

A "suicide" BCG strain provides enhanced immunogenicity and robust protection against Mycobacterium tuberculosis in macaques

Intravenous (IV) BCG delivery provides robust protection against Mycobacterium tuberculosis (Mtb) in macaques but poses safety challenges. Here, we constructed two BCG strains (BCG-TetON-DL and BCG-TetOFF-DL) in which tetracyclines regulate two phage lysin operons. Once the lysins are expressed, these strains are killed in immunocompetent and immunocompromised mice yet induced similar immune responses and provided similar protection against Mtb challenge as wild type BCG. Lysin induction resulted in release of intracellular BCG antigens and enhanced cytokine production by macrophages. In macaques, cessation of doxycycline administration resulted in rapid elimination of BCG-TetOFF-DL. However, IV BCG-TetOFF-DL induced increased pulmonary CD4 T cell responses compared to WT BCG and provided robust protection against Mtb challenge, with sterilizing immunity in 6 of 8 macaques, compared to 2 of 8 macaques immunized with WT BCG. Thus, a "suicide" BCG strain provides an additional measure of safety when delivered intravenously and robust protection against Mtb infection.

immunology↗

bioRxiv2023

Development of an Engineered Mycobacterium tuberculosis Strain for a Safe and Effective Tuberculosis Human Challenge Model

Human challenge experiments could greatly accelerate the development of a tuberculosis (TB) vaccine. Human challenge for tuberculosis requires a strain that can both replicate in the host and be reliably cleared. To accomplish this, we designed Mycobacterium tuberculosis (Mtb) strains featuring up to three orthogonal kill switches, tightly regulated by exogenous tetracyclines and trimethoprim. The resultant strains displayed immunogenicity and antibiotic susceptibility similar to wild-type Mtb under permissive conditions. In the absence of supplementary exogenous compounds, the strains were rapidly killed in axenic culture, mice and nonhuman primates. Notably, the strain that contained three kill switches had an escape rate of less than 10-10 per genome per generation and displayed no relapse in a SCID mouse model. Collectively, these findings suggest that this engineered Mtb strain could be a safe and effective candidate for a human challenge model.

microbiology↗