Biology subjects

Song, Z.

Publications and source records attributed to Song, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Early evolution of the ecdysozoan body plan

Extant ecdysozoans (moulting animals) are represented by a great variety of vermiform or articulated organisms. However, controversies remain about the nature of their ancestral body plan although the vermiform hypothesis seems to prevail. We describe here Beretella spinosa gen et sp. nov. a tiny ecdysozoan from the early Cambrian, Yanjiahe Formation, South China, with an unusual sack-like appearance, single opening, and spiny ornament. Beretella has no equivalent among animals, except Saccorhytus from the basal Cambrian. Phylogenetic analyses resolve both forms as a sister group (Saccorhytida) to all known Ecdysozoa, thus suggesting that ancestral ecdysozoans may have been non-vermiform animals. Saccorhytids are likely to represent an early dead-end off-shot along the stem-line Ecdysozoa that possibly evolved through anatomical simplification (e.g. lack of anus). Although extinct during the Cambrian, this animal lineage provides precious insight into the early evolution of Ecdysozoa and the nature (possibly non-vermiform) of the earliest representatives of the group.

paleontology↗

bioRxiv2023

Parallel Molecular Data Storage by Printing Epigenetic Bits on DNA

DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, lifetime and energy consumption. However, writing large-scale data directly into DNA sequences by de novo synthesis remains uneconomical in time and cost. Inspired by the natural genomic modifications, in this work, we report an alternative, parallel strategy that enables the writing of arbitrary data on DNA using premade nucleic acids. With epigenetic modifications as information bits, our system employed DNA self-assembly guided enzymatic methylation to perform movable-type printing on universal DNA templates. By programming with a finite set of 700 DNA movable types and 5 templates, we achieved the synthesis-free writing of [~]270000 bits on an automated platform with 350 bits written per reaction. The data encoded in complex epigenetic patterns were retrieved high-throughput by nanopore sequencing, and algorithms were developed to finely resolve 240 modification patterns per sequencing reaction. Our framework presents a new modality of DNA-based data storage that is parallel, programmable, stable and scalable. Such a modality opens up avenues towards practical data storage and dual-mode data functions in biomolecular systems.

biochemistry↗

bioRxiv2023

Differentiation SELEX approach identifies RNA aptamers with different specificities for HIV-1 capsid assembly forms

The HIV-1 capsid protein (CA) assumes distinct assembly forms during replication, each presenting unique, solvent-accessible surfaces that facilitate multifaceted functions and host factor interactions. However, contributions of individual CA assemblies remain unclear, as the evaluation of CA in cells presents several technical challenges. To address this need, we sought to identify CA assembly form-specific aptamers. Aptamer subsets with different specificities emerged from within a highly converged, pre-enriched aptamer library previously selected to bind the CA hexamer lattice. Subsets were either highly specific for CA lattice or bound both CA lattice and CA hexamer. We further evaluated four representatives to reveal aptamer structural features required for binding, highlighting interesting features and challenges in aptamer structure determination. Importantly, our aptamers bind biologically relevant forms of CA and we demonstrate aptamer-mediated affinity purification of CA from cell lysates without virus or host modification. Thus, we have identified CA assembly form-specific aptamers that represent exciting new tools for the study of CA.

molecular biology↗

bioRxiv2023

An Artificial Intelligence-Assisted Digital Microfluidic System for Multistate Droplet Control

AbstractDigital microfluidics (DMF) is a versatile technique for parallel and field-programmable control of individual droplets. Given the high freedom in droplet manipulation, it is essential to establish self-adaptive and intelligent control methods for DMF systems with informed of the transient state of droplets and their interactions. However, most related studies focus on the localization and shape recognition of droplets. Here, we develop an AI-assisted DMF framework named "DropAI" for multistate droplet control based on droplet morphology. Semantic segmentation model is integrated into our custom-designed DMF system to recognize the droplet states and their interactions for feedback control with a state machine. The proposed model has a strong generalization ability and can recognize droplets of different colors and shapes with an error rate of less than 0.63%. It enables control of droplets without user intervene. The proposed system will inspire the development of semantic-driven DMF systems which can interface with artificial general intelligence (AGl) models for fully automatic control.

bioengineering↗

bioRxiv2023

Conditioned Protein Structure Prediction

Deep learning based protein structure prediction has facilitated major breakthroughs in biological sciences. However, current methods struggle with alternative conformation prediction and offer limited integration of expert knowledge on protein dynamics. We introduce AFEXplorer, a generic approach that tailors AlphaFold predictions to user-defined constraints in coarse coordinate spaces by optimizing embedding features. Its effectiveness in generating functional protein conformations in accordance with predefined conditions were demonstrated through comprehensive examples. AFEXplorer serves as a versatile platform for conditioned protein structure prediction, bridging the gap between automated models and domain-specific insights.

bioinformatics↗

bioRxiv2023

Looming detection in complex dynamic visual scenes by interneuronal coordination of motion and feature pathways

Detecting looming signals for collision avoidance faces challenges in real-world scenarios due to interference from moving backgrounds. Astonishingly, animals, like insects with limited neural systems, adeptly respond to looming stimuli while moving at high speeds. Existing insect-inspired looming detection models integrate either motion-pathway or feature-pathway signals, remaining susceptible to dynamic visual scene interference. We propose that coordinating interneuron signals from the two pathways could elevate looming detection performance in dynamic conditions. We used artificial neural network (ANN) to build a combined-pathway model based on Drosophila anatomy. The model exhibits convergent neural dynamics with biological counterparts after training. In particular, a multiplicative interneuron operation enhances looming signal patterns. It reduces background interferences, boosting looming detection accuracy and enabling earlier warnings across various scenarios, such as 2D animated scenes, AirSim 3D environments, and real-world situations. Our work presents testable biological hypotheses and a promising bio-inspired solution for looming detection in dynamic visual environments.

neuroscience↗

bioRxiv2023

Estrogen prevents age-dependent beige adipogenesis failure through NAMPT-controlled ER stress pathway

Thermogenic beige adipocytes are recognized as potential therapeutic targets for combating metabolic diseases. However, the metabolic advantages they offer are compromised with aging. Here, we show that treating mice with estrogen (E2), a hormone that decreases with age, to mice can counteract the aging- related decline in beige adipocyte formation when subjected to cold, while concurrently enhancing energy expenditure and improving glucose tolerance. Mechanistically, we find that nicotinamide phosphoribosyltranferase (NAMPT) plays a pivotal role in facilitating the formation of E2-induced beige adipocytes, which subsequently suppresses the onset of age-related ER stress. Furthermore, we found that targeting NAMPT signaling, either genetically or pharmacologically, can restore the formation of beige adipocytes by increasing the number of perivascular adipocyte progenitor cells. Conversely, the absence of NAMPT signaling prevents this process. In conclusion, our findings shed light on the mechanisms governing the age-dependent impairment of beige adipocyte formation and underscore the E2-NAMPT controlled ER stress as a key regulator of this process. HighlightsO_LIEstrogen restores beige adipocyte failure along with improved energy metabolism in old mice. C_LIO_LIEstrogen enhances the thermogenic gene program by mitigating age-induced ER stress. C_LIO_LIEstrogen enhances the beige adipogenesis derived from SMA+ APCs. C_LIO_LIInhibiting the NAMPT signaling pathway abolishes estrogen-promoted beige adipogenesis. C_LI

physiology↗

bioRxiv2023

Aminomutation catalyzed by CO2 self-sufficient cascade amino acid decarboxylases

Molecular editing of an amino group from -position of amino acids to its {beta}-position is of scientific interest and could be economically appealing. Here we reconstructed an in vitro biotransformation pathway composed of two cascade decarboxylases, i.e., aspartate {beta}-decarboxylase and aspartate -decarboxylase, and implemented molecular editing to change -alanine into {beta}-alanine. In it, we discovered a new reaction of aspartate {beta}-decarboxylase that can fix CO2 directly. This cascade enzymatic pathway enabled an aminomutation reaction with 100% carbon atom economy. This work presented the first CO2-fixing biological reaction catalyzed by the amino acid decarboxylases and demonstrated a new means for the molecular editing of -amino acids.

biochemistry↗

bioRxiv2023

Shared and distinct molecular effects of regulatory genomic variants provide insight into mechanisms of distal enhancer-promoter communication

Gene enhancers often form long-range contacts with promoters, but it remains unclear if enhancer activity and their chromosomal contacts are mediated by the same DNA sequences and recruited factors. We studied the effects of expression quantitative trait loci (eQTLs) on enhancer activity and promoter contacts in primary monocytes isolated from 34 individuals. Using eQTL-Capture Hi-C and a Bayesian approach considering both intra- and inter-individual variation, we initially detected 19 eQTLs associated with enhancer-eGene promoter contacts, most of which also associated with enhancer accessibility and activity. Capitalising on these shared effects, we devised a multi-modality Bayesian strategy, which identified 629 "trimodal QTLs" jointly associated with enhancer accessibility, eGene promoter contact, and gene expression. Causal mediation analysis and CRISPR interference revealed causal relationships between these three modalities. Many detected QTLs overlapped disease susceptibility loci and influenced the predicted binding of myeloid transcription factors, including SPI1, GABPB and STAT3. Additionally, a variant associated with PCK2 promoter contact directly disrupted a CTCF binding motif and impacted promoter insulation from downstream enhancers. Jointly, our findings suggest an inherent genetic link between the activity and connectivity of enhancers with relevance for human disease, and highlight the role of genetically-determined chromatin boundaries in gene control.

genetics↗

bioRxiv2023

Anti-PD-1-iRGD Peptide Conjugate Boosts Antitumor Efficacy via Engagement Augmentation and Penetration Enhancement of T cells

Despite the important breakthroughs of immune-checkpoint inhibitors (ICIs) in recent years, the overall objective response rate (ORR) remains limited in various cancers. Here, we synthesized programmed cell death protein-1 (PD-1) antibody iRGD conjugate (PD-1-(iRGD)2) through glycoengineering and bio-orthogonal reaction. PD-1-(iRGD)2 exhibited extra iRGD receptor dependent affinity to several cancer cell lines rather than normal cell lines. Via dual targeting, PD-1-(iRGD)2 engageed tumor cells and T cells thus mediating T cell activation and facilitating tumor elimination. Besides, the attachment of iRGD impressively improved the penetrability of both PD-1 antibody and PD-1+ T cells. In multiple syngeneic mouse models, PD-1-(iRGD)2 effectively reduced tumor growth with satisfactory biosafety. Moreover, results of flow cytometry and single-cell RNA-seq revealed that PD-1-(iRGD)2 remodeled the tumor microenvironment (TME) and expanded a unique population of "better effector" CD8+ tumor infiltrating T cells (TILs) expressing stem and memory associated genes including Tcf7, Il7r, Lef1 and Bach2. Conclusively, PD-1-(iRGD)2 could be a novel and promising therapeutic approach for cancer immunotherapy. Statement of significanceDesigned against the clinical dilemma of unsatisfied response rate after contemporary cancer immunotherapy, PD-1-(iRGD)2 engages T cells and tumor cells, promotes T cell infiltration and expands a unique population of "better effectors" with enhanced therapeutic potential for the treatment of cancer.

immunology↗

bioRxiv2023

Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis.

Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation (FMT) treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase (GAD) and putrescine aminotransferase (PAT), in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.

microbiology↗

bioRxiv2023

The Notch-Pdgfr beta axis suppresses brown adipocyte progenitor differentiation in early postnatal mice

De novo brown adipogenesis holds potential in combating the epidemics of obesity and diabetes. However, the identity of brown adipocyte progenitor cells (APCs) and their regulation have not been extensively studied. Here through in vivo lineage tracing, we observed that PDGFR{beta}+ pericytes give rise to developmental brown adipocytes, but not to those in adult homeostasis. In contrast, TBX18+ pericytes contribute to brown adipogenesis throughout both developmental and adult stages, though in a depot-specific manner. Mechanistically, Notch inhibition in PDGFR{beta}+ pericytes promotes brown adipogenesis through the downregulation of PDGFR{beta}. Furthermore, inhibition of Notch signaling in PDGFR{beta}+ pericytes mitigates HFHS (high-fat, high-sucrose) induced glucose and metabolic impairment in both developmental and adult stages. Collectively, these findings show that the Notch/PDGFR{beta} axis negatively regulates developmental brown adipogenesis, and its repression promotes brown adipose tissue expansion and improves metabolic health. HighlightsO_LIPDGFR{beta}+ pericytes act as an essential developmental brown APC. C_LIO_LITBX18+ pericytes contribute to brown adipogenesis in a depot-specific manner. C_LIO_LIInhibiting Notch-Pdgfr{beta} axis promotes brown APC adipogenesis. C_LIO_LIEnhanced postnatal brown adipogenesis improves metabolic health in adult stage. C_LI

developmental biology↗

bioRxiv2023

P-tau Inflicts Intracellular Stress Responses That Are Mitigated by Apomorphine

BackgroundAbnormal phosphorylation of the microtubule-binding protein tau in the brain is a key pathological marker for Alzheimers disease and additional neurodegenerative tauopathies. However, how hyperphosphorylated tau causes cellular dysfunction or death that underlie neurodegeneration remains an unsolved question critical for the understanding of disease mechanism and the design of efficacious drugs. MethodsUsing a recombinant hyperphosphorylated tau protein (p-tau) synthesized by the PIMAX approach, we examined how cells responded to the cytotoxic tau and explored means to enhance cellular resistance to tau attack. ResultsUpon p-tau uptake, the intracellular calcium levels rose promptly. Gene expression analyses revealed that p-tau potently triggered endoplasmic reticulum (ER) stress, Unfolded Protein Response (UPR), ER stress-associated apoptosis, and pro-inflammation in cells. Proteomics studies showed that p-tau diminished heme oxygenase-1 (HO-1), an ER stress associated anti-inflammation and anti-oxidative stress regulator, while stimulated the accumulation of MIOS and other proteins. P-tau-induced ER stress-associated apoptosis and pro-inflammation are ameliorated by apomorphine, a brain-permeable prescription drug widely used to treat Parkinsons disease symptoms, and by overexpression of HO-1. ConclusionOur results reveal probable cellular functions targeted by hyperphosphorylated tau. Some of these dysfunctions and stress responses have been linked to neurodegeneration in Alzheimers disease. The observations that the ill effects of p-tau can be mitigated by a small compound and by overexpressing HO-1 that is otherwise diminished in the treated cells inform new directions of Alzheimers disease drug discovery.

biochemistry↗

bioRxiv2023

Multiscale Model for Ion Transport in Cellular Media and Applications in Smooth Muscle Cells

Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like the smooth muscles on vessel walls, can be treated as periodic bi-domain structures consisting of the intracellular space (ICS) and extracellular space (ECS) with semipermeable membranes in between. In this work, we first use a multi-scale asymptotic method to derive a macroscopic homogenized bidomain model from the microscopic electro-neutral (EN) model with different diffusion coefficients and nonlinear interface conditions. Then, the obtained homogenized model is applied to study ion transportation and micro-circulation in multi-celluar tissues under the impact of agonists, an internal calcium source, and extracellular potassium. Our model serves as a useful bridge between existing ordinary differential equation models and partial differential models that take into consideration spatial variation. On the one hand, numerical results show that ECS variables are almost invariant in the first two scenarios and confirm the validity of existing single-domain models, which treat variables in the ECS as constants. On the other hand, only the bidomain model is applicable to consider the effect of local extracellular potassium. Finally, the membrane potential of syncytia formed by connected cells is found to play an important role in the propagation of oscillation from the stimulus region to the non-stimulus region. Author summarySmooth muscle cells (SMCs) play a vital role in neurovascular coupling, which is the mechanism by which changes in neural activity are linked to alterations in blood flow. Dysfunctional SMCs can have significant implications for human health. The activation of SMCs is primarily regulated by the intracellular concentration of calcium ions (Ca2+). A multi-scale model for ion transport in multicellular tissue with varying connectivity has been proposed to investigate SMC activation under different stimuli. The simulation results confirm the critical role of gap junctions in wave propagation and vasoconstriction in the vessel wall. The blockage of gap junctions prevents the spread of the wave. Furthermore, the propagation of membrane potential is the primary cause of wave propagation.

cell biology↗

bioRxiv2023

Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation

Van Gogh-like 2 (Vangl2), a core planar cell polarity (PCP) component, plays an important role in polarized cellular and tissue morphology induction, growth development and cancer. However, its role in regulating inflammatory responses remains elusive. Here, we report that Vangl2 is upregulated in patients with sepsis and identify Vangl2 as a negative regulator of NF-{kappa}B signaling by regulating the protein stability and activation of the core transcription component p65. Mice with myeloid-specific deletion of Vangl2 (Vangl2{Delta}M) are hypersusceptible to lipopolysaccharide (LPS)-induced septic shock. Vangl2 deficient myeloid cells exhibit enhanced phosphorylation and expression of p65, therefore, promoting the secretion of pro-inflammatory cytokines after LPS stimulation. Mechanistically, NF-{kappa}B signaling-induced-Vangl2 recruits E3 ubiquitin ligase PDLIM2 to catalyze K63-linked ubiquitination on p65, which serves as a recognition signal for cargo receptor NDP52-mediated selective autophagic degradation. Taken together, these findings demonstrate Vangl2 as a suppressor of NF-{kappa}B mediated inflammation and provide insights into the crosstalk between autophagy and inflammatory diseases.

immunology↗

bioRxiv2022

Cdkn2a regulates beige fat maintenance through BECN1-mediated autophagy

A potential therapeutic target to curb the obesity and diabetes epidemic is thermogenic beige adipocytes. However, beige adipocytes quickly transition into white adipocytes upon removing stimuli. Here, we define the critical role of Cdkn2a as a molecular pedal for the beige-to-white transition. Beige adipocytes lacking Cdkn2a exhibit prolonged lifespan, and mice are more resistant to diet-induced obesity, along with enhanced energy expenditure and improved glucose tolerance. Mechanistic studies demonstrate that Cdkn2a promotes the expression and activity of BECN1 by directly binding to its mRNA and its negative regulator BCL2L1, activating autophagy and accelerating the beige-to-white transition. Notably, reactivating autophagy by pharmacological or genetic methods abolishes beige adipocyte maintenance induced by Cdkn2a-ablation. Furthermore, hyperactive BECN1 alone significantly accelerates the beige-to-white transition. Collectively, these findings show that Cdkn2a-mediated autophagy serves as a brake system for beige adipocyte maintenance and is a highly promising target for anti-obesity and anti-diabetes therapy. HighlightsO_LICdkn2a ablation promotes beige fat maintenance and ameliorates diet-induced obesity C_LIO_LILoss of Cdkn2a retains beige adipocytes by inhibiting BECN1-mediated autophagy C_LIO_LICdkn2a modulates BECN1 by binding to its mRNA and its inhibitor BCL2L1, respectively C_LIO_LIHyperactive BECN1 is sufficient to accelerate the beige-to-white transition C_LI

cell biology↗

bioRxiv2022

An HBV mRNA vaccine with favorable virological suppression and superior immunity

BRIEF ABSTRACTHere we report on the development and comprehensive evaluations of an mRNA vaccine for chronic hepatitis B (CHB) treatment. In two different HBV carrier mouse models generated by viral vector-mediated HBV transfection (pAAV-HBV1.2 and rAAV8-HBV1.3), this vaccine demonstrates sufficient and persistent virological suppression, and robust immunogenicity in terms of induction of strong innate immune activation, high-level virus-specific antibodies, memory B cells and T cells. mRNA platform therefore holds prospects for therapeutic vaccine development to combat CHB.

immunology↗

bioRxiv2022

Divorce rate in birds increases with male promiscuity and migration distance

Socially monogamous animals may break up their partnership after one breeding season by a so-called divorce behaviour. Divorce rate immensely varies across avian taxa that have a predominantly monogamous social mating system. Although a range of factors associated with divorce have been tested, there is not a consensus regarding the large-scale variation and relationships among associated factors. Moreover, the impact of sexual roles in divorce still needs further investigation. Here, we applied phylogenetic comparative methods to analyze one of the largest datasets ever compiled that included divorce rates from published case studies of 232 avian species from 25 orders and 61 families. We tested correlations between divorce rate and a group of factors that are closely related to pair bond strength: promiscuity of both sexes, migration distance, and adult mortality. Our results showed that only male promiscuity, but not female promiscuity, had a critical relationship with divorce rate. Furthermore, migration distance was positively correlated with divorce rate and indirectly affected divorce rate via male promiscuity. These findings indicated that divorce might not be simply explained as an adaptive strategy or neutral occurrence, but could be a mixed response to sexual conflict and stress from the ambient environment.

ecology↗