Biology subjects

Zheng, X.

Publications and source records attributed to Zheng, X..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Role of microglia in stress-induced alcohol intake in female and male mice

Rates of alcohol use disorder (AUD) have escalated in recent years, with a particular increase among women. Women are more susceptible to stress-induced alcohol drinking, and preclinical data suggest that stress can increase alcohol intake in female rodents; however, a comprehensive understanding of sex-specific neurobiological substrates underlying this phenomenon is still emerging. Microglia, the resident macrophages of the brain, are essential for reshaping neuronal processes, and microglial activity contributes to overall neuronal plasticity. We investigated microglial dynamics and morphology in limbic brain structures of male and female mice following exposure to stress, alcohol or both challenges. In a modified paradigm of intermittent binge drinking (repeated "drinking in the dark"), we determined that female, but not male, mice increased their alcohol consumption after exposure to a physical stressor and re-exposure trials in the stress-paired context. Ethanol (EtOH) drinking and stress altered a number of microglial parameters, including overall number, in subregions of the amygdala and hippocampus, with effects that were somewhat more pronounced in female mice. We used the CSF1R antagonist PLX3397 to deplete microglia in female mice to determine whether microglia contribute to stress-induced escalation of EtOH intake. We observed that microglial depletion attenuated stress-induced alcohol intake with no effect in the unstressed group. These findings suggest that microglial activity can contribute to alcohol intake under stressful conditions, and highlight the importance of evaluating sex-specific mechanisms that could result in tailored interventions for AUD in women.

neuroscience↗

bioRxiv2024

Soybean PHR1-regulated low phosphorus-responsive GmRALF22 increases uptake of phosphate via stimulating GmPTs expression

Phosphorus (P) is one of essential macronutrients for plant growth and development. Rapid Alkalization Factors (RALFs) play crucial roles in plant responses to nutrient stresses, however, the functions of Glycine max RALFs (GmRALFs) under low P (LP) stress remain elusive. In this study, we first identified 27 GmRALFs in soybean, then we revealed that GmRALF10, GmRALF11, and GmRALF22 are induced in both roots and leaves, while only GmRALF5, GmRALF6, and GmRALF25 are up-regulated in leaves in LP conditions. Furthermore, GmRALF22 was found to be the target gene of transcription factor GmPHR1, which binds the P1BS cis-element in the promoter of GmRALF22 via electrophoretic mobility shift assay (EMSA) and DUAL-LUC experiment. Colonization of Bacillus subtilis that deliver GmRALF22 increases the expression of high affinity phosphate (Pi) transporter gene GmPT2, GmPT11, GmPT13 and GmPT14, thus increases the total amount of dry matter and soluble Pi in soybean. RNA-sequencing uncovered that GmRALF22 alleviates LP stress by regulating the expression of JA-, SA- and immune-related genes. Finally, we verified that GmRALF22 is dependent on FERONIA to promote Arabidopsis primary root growth under LP conditions. In summary, GmPHR1-GmRALF22 module positively regulates soybeans tolerance to LP. HighlightsO_LISoybean genome has 27 GmRALFs. GmRALF5, GmRALF6, GmRALF10, GmRALF11, GmRALF22 and GmRALF25 are induced in low phosphorus (LP). C_LIO_LIGmPHR1 directly regulate the transcription of GmRALF22 via binding the promoter P1BS cis-element. C_LIO_LISecretion of GmRALF22 protein by Bacillus subtilis promoted soybean growth under LP conditions by improving soybean P nutrition through increased expression of high affinity phosphate (Pi) transporter gene. C_LIO_LIGmRALF22 regulates soybean P nutrition by JA-, SA- and immune-related genes expression at transcriptome level. That application of GmRALF22 promoted primary root growth in Arabidopsis in LP is dependent on FER receptor. C_LI

molecular biology↗

bioRxiv2024

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we developed a novel approach integrating highly multiplexed imaging, laser microdissection, and deep visual proteomics (DVP) to spatially profile the proteomes of 21 distinct cell populations in human colorectal and tonsil cancers with high sensitivity. We selected colorectal tumor as an example of a cold tumor, uncovering an immunosuppressive macrophage barrier impeding T cell infiltration and regionally altering lymphocyte proteomes. Spatial proteomic analysis revealed distinct functional states of T cells in different tumor compartments. In tonsil cancer - a hot tumor, we identified significant heterogeneity of cell proteomes influenced by proximity to cytotoxic T cell subtypes. Tumor-infiltrating T cells exhibited metabolic adaptations and enhanced stress resilience, enabling migration into hypoxic regions. Our spatially-resolved, highly multiplexed strategy deciphers the complex cellular interplay within the tumor microenvironment, with implications for identifying new immunotherapy targets and signatures. HighlightsO_LINovel approach integrates multiplexed imaging and deep proteomics to profile the tumor microenvironment C_LIO_LIIdentified 21 distinct cell populations and thousands of proteins from single cell types C_LIO_LIMacrophage barrier impedes T cell tumor infiltration and T cells adapt to hypoxia C_LIO_LISpatial insights may guide new immunotherapy targets and personalized oncology C_LI

cancer biology↗

bioRxiv2024

Interleukin-1 prevents SARS-CoV-2-induced membrane fusion to restrict viral transmission via induction of actin bundles

Innate immune responses triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection play pivotal roles in the pathogenesis of COVID-19, while host factors including pro-inflammatory cytokines are critical for viral containment. By utilizing quantitative and qualitative models, we discovered that soluble factors secreted by human monocytes potently inhibit SARS-CoV-2-induced cell-cell fusion in viral-infected cells. Through cytokine screening, we identified that interleukin-1{beta} (IL-1{beta}), a key mediator of inflammation, inhibits syncytia formation mediated by various SARS-CoV-2 strains. Mechanistically, IL-1{beta} activates RhoA/ROCK signaling through a non-canonical IL-1 receptor-dependent pathway, which drives the enrichment of actin bundles at the cell-cell junctions, thus prevents syncytia formation. Notably, in vivo infection experiments in mice confirms that IL-1{beta} significantly restricted SARS-CoV-2 spreading in the lung epithelia. Together, by revealing the function and underlying mechanism of IL-1{beta} on SARS-CoV-2-induced cell-cell fusion, our study highlights an unprecedented antiviral function for cytokines during viral infection.

immunology↗

bioRxiv2024

Kynurenine monooxygenase blockade reduces endometriosis-like lesions, improves visceral hyperalgia, and rescues mice from a negative behavioural phenotype in experimental endometriosis

Endometriosis is a common and debilitating neuro-inflammatory disorder that is associated with chronic pain. Definitive diagnosis is based on the presence of endometrial-like tissue (lesions) in sites outside the uterus. Kynurenine monooxygenase (KMO) is a mitochondrial enzyme of tryptophan metabolism that regulates inflammation and immunity. Here, we show that KMO is expressed in epithelial cells in human endometriosis tissue lesions and in corresponding lesions in a mouse model of endometriosis. In mice, oral treatment with the potent KMO inhibitor KNS898 induced a biochemical state of KMO blockade with accumulation of kynurenine, diversion to kynurenic acid and ablation of 3-hydroxykynurenine production. In the mouse model of endometriosis, KMO inhibition improved histological outcomes and endometriosis pain-like behaviours, even when KNS898 treatment commenced one week after initiation of lesions. Taken together, these results suggest that KMO blockade is a promising new non-hormonal therapeutic modality for endometriosis.

pathology↗

bioRxiv2024

Super Enhancer-driven LncRNA UNC5B-AS1 Inhibits Inflammatory Phenotypic Transition in Smooth Muscle Cells via Lactylation Modification

BackgroundThe phenotypic transition of pulmonary artery smooth muscle cells (PASMCs) is a central pathological alteration in pulmonary artery remodeling that contributes to pulmonary hypertension (PH). The specific role of long noncoding RNAs (lncRNAs), especially super enhancer (SE)-driven lncRNAs, in the phenotypic transformation of PASMCs induced by hypoxia remains unclear. The objective of this study is to determine the mechanistic role of the super enhancer-driven LncRNA UNC5B-AS1 in phenotypic transformation of PASMCs and hypoxia-induced vascular remodeling. MethodsThe lncRNA UNC5B-AS1 regulated by super-enhancers was identified in hypoxic human PASMCs through RNA sequencing and H3K27ac ChIP sequencing. Overexpression of lncRNA UNC5B-AS1 in human PASMCs was performed to elucidate its role in the pathogenesis of PH. A conserved functional fragment of lncRNA UNC5B-AS1 was used for the treatment of mouse PH. ResultsIn PASMCs, we have identified a SE-driven lncRNA called UNC5B-AS1 that regulates phenotype transition. It is transcriptionally activated by the transcription factor FOXP3. We demonstrate that UNC5B-AS1, as a molecular scaffold in mitochondria, stabilizes the interaction between LRPPRC, which is rich in leucine, and oxidative respiratory chain complex IV. This complex regulates the lactylation modification level of upstream promoter regions of inflammatory genes IL-1{beta}, IL-6, and TNF- by influencing the glycolytic pathway in PASMCs under hypoxic conditions, ultimately affecting the inflammatory phenotype transition of PASMCs. ConclusionsOur findings identify the SE-driven lncRNA UNC5B-AS1 as a novel regulatory factor in hypoxia-induced phenotypic switch of PASMCs, and suggest that overexpression of UNC5B-AS1 may represent a promising therapeutic strategy for PH. HighlightsThe long non-coding RNA UNC5B-AS1, regulated by super-enhancers (SE), is downregulated in hypoxic PASMCs, and regulates PASMC phenotype transition through glycolysis. The super-enhancer region of lncRNA UNC5B-AS1 recruits the transcription factor FOXP3 to its promoter region, forming a chromatin loop to regulate its expression. The lncRNA UNC5B-AS1 acts as a molecular scaffold stabilizing the interaction between LRPPRC and mitochondrial complex IV. The lactate generated by glycolysis activation induces lactylation modification of histones at the IL-1{beta}, IL-6, and TNF- promoters, leading to the inflammatory phenotype transition of PASMCs. Overexpression of lncRNA UNC5B-AS1 conserved fragment reversed SuHx-induced PH in mice. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/593065v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@864576org.highwire.dtl.DTLVardef@13a5fe4org.highwire.dtl.DTLVardef@16d7884org.highwire.dtl.DTLVardef@35d50_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Functional and multi-omic aging rejuvenation with GLP-1R agonism

Identifying readily implementable methods that can effectively counteract aging is urgently needed for tackling age-related degenerative disorders. Here, we conducted functional assessments and deep molecular phenotyping in the aging mouse to demonstrate that glucagon-like peptide-1 receptor agonist (GLP-1RA) treatment attenuates body-wide age-related changes. Apart from improvements in physical and cognitive performance, the age-counteracting effects are prominently evident at multiple omic levels. These span the transcriptomes and DNA methylomes of various tissues, organs and circulating white blood cells, as well as the plasma metabolome. Importantly, the beneficial effects are specific to aged mice, not young adults, and are achieved with a low dosage of GLP-1RA which has a negligible impact on food consumption and body weight. The molecular rejuvenation effects exhibit organ-specific characteristics, which are generally heavily dependent on hypothalamic GLP-1R. We benchmarked the GLP-1RA age-counteracting effects against those of mTOR inhibition, a well-established anti-aging intervention, observing a strong resemblance across the two strategies. Our findings have broad implications for understanding the mechanistic basis of the clinically observed pleiotropic effects of GLP-1RAs, the design of intervention trials for age-related diseases, and the development of anti-aging-based therapeutics.

systems biology↗

bioRxiv2024

Biodiversity increases the forecastability of species abundances in changing environments

Accurate forecasts of ecological dynamics are critical for ecosystem management and conservation, yet the drivers of forecastability are poorly understood. Environmental change and diversity are considered major challenges to ecological forecasting. This assumption, however, has never been tested experimentally because forecasts have high data requirements. In a long-term microcosm experiment, we manipulated species richness of 30 experimental protist communities and exposed them to constant or gradually decreasing light levels. We collected finely-resolved time series (123 sampling dates over 41 weeks) of species abundances, community biomass, and oxygen concentrations. We then employed data-driven forecasting methods to forecast these variables. We found that species richness and light had a weak interactive effect on forecasts of species abundances: richness tended to reduce forecast accuracy in constant light but tended to increase forecast accuracy in declining light. These effects could partially be explained by differences among time series in variability and autocorrelation. Forecasts of aggregate properties (community biomass, oxygen), however, were unaffected by richness and light, and were not more accurate than those of species abundances. Our forecasts were based on time series that were detrended and standardized. Since real-world forecasting applications require predictions at the original scale of the forecasted variable, it is important to note that the results were qualitatively identical when back-transforming the forecasts to the original scale. Taken together, we found no strong evidence that higher diversity results in lower forecastability. Rather, our results imply that promoting diversity could make populations more predictable when environmental conditions change. From a conservation and management perspective, our findings suggest that diversity conservation might have beneficial effects on decision-taking by increasing the forecastability of species abundances in changing environments.

ecology↗

bioRxiv2024

scCaT: an explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing

Sepsis is a life-threatening condition characterized by an exaggerated immune response to pathogens, leading to organ damage and high mortality rates in the intensive care unit. Although deep learning has achieved impressive performance on prediction and classification tasks in medicine, it requires large amounts of data and lacks explainability, which hinder its application to sepsis diagnosis. We introduce a deep learning framework, called scCaT, which blends the capsulating architecture with Transformer to develop a sepsis diagnostic model using single-cell RNA sequencing data and transfers it to bulk RNA data. The capsulating architecture effectively groups genes into capsules based on biological functions, which provides explainability in encoding gene expressions. The Transformer serves as a decoder to classify sepsis patients and controls. Our model achieves high accuracy with an AUROC of 0.93 on the single-cell test set and an average AUROC of 0.98 on seven bulk RNA cohorts. Additionally, the capsules can recognize different cell types and distinguish sepsis from control samples based on their biological pathways. This study presents a novel approach for learning gene modules and transferring the model to other data types, offering potential benefits in diagnosing rare diseases with limited subjects. Author summaryDeep learning models used in disease diagnosis usually suffer from insufficient data for training and the lack of explainability, especially in rare diseases. These shortages hinder their application to sepsis diagnosis. Here we propose a diagnostic framework name scCaT(https://github.com/Kimxbzheng/CaT), which transfers knowledge learned from single-cell RNA-seq, for diseases with insufficient bulk data. The framework uses capsulating architecture to group genes into capsules and provide explainability to the deep learning model for sepsis diagnosis. ScCaT achieves robust and outstanding performance for sepsis diagnosis in both scRNA-seq and bulk RNA datasets. This architecture offers potential approaches in diagnosing rare diseases with limited subjects with explainability.

bioinformatics↗

bioRxiv2024

Decoding Missense Variants by Incorporating Phase Separation via Machine Learning

Computational models have made significant progress in predicting the effect of protein variants. However, deciphering numerous variants of unknown significance (VUS) located within intrinsically disordered regions (IDRs) remains challenging. To address this issue, we introduced phase separation (PS), which is tightly linked to IDRs, into the investigation of missense variants. Phase separation is vital for multiple physiological processes. By leveraging missense variants that alter phase separation propensity, we developed a machine learning approach named PSMutPred to predict the impact of missense mutations on phase separation. PSMutPred demonstrated robust performance in predicting missense variants that affect natural phase separation. In vitro experimental findings further underscore its validity. By applying PSMutPred on over 522,000 ClinVar missense variants, it significantly contributes to decoding the pathogenesis of disease variants, especially those in IDRs. Our work provides unique insights into the understanding of a vast number of VUSs in IDRs, thereby expediting clinical interpretation and diagnosis of disease variants.

bioinformatics↗

bioRxiv2024

The minimal SUF system can substitute for the canonical iron-sulfur cluster biosynthesis systems by using inorganic sulfide as the sulfur source.

Biosynthesis of iron-sulfur (Fe-S) clusters is indispensable for living cells. Three biosynthesis systems termed NIF, ISC and SUF have been extensively characterized in both bacteria and eukarya. For these L-cysteine is the sulfur source. A bioinformatic survey suggested the presence of a minimal SUF system composed of only two components, SufB* (a putative ancestral form of SufB and SufD) and SufC, in anaerobic archaea and bacteria. Here, we report the successful complementation of an Escherichia coli mutant devoid of the usual ISC and SUF systems upon expression of the archaeal sufB*C genes. Strikingly, this heterologous complementation occurred under anaerobic conditions only when sulfide was supplemented to the culture media. Mutational analysis and structural predictions suggest that the archaeal SufB*C most likely forms a SufB*2C2 complex and serves as the scaffold for de novo Fe-S cluster assembly using the essential Cys and Glu residues conserved between SufB* and SufB, in conjunction with a His residue shared between SufB* and SufD. We also demonstrate artificial conversion of the SufB*2C2 structure to the SufBC2D type by introducing several mutations to the two copies of sufB*. Our study thus elucidates the molecular function of this minimal SUF system and suggests that it is the evolutionary prototype of the canonical SUF system.

microbiology↗

bioRxiv2024

Decoding Continuous Character-based Language from Non-invasive Brain Recordings

Deciphering natural language from brain activity through non-invasive devices remains a formidable challenge. Previous non-invasive decoders either require multiple experiments with identical stimuli to pinpoint cortical regions and enhance signal-to-noise ratios in brain activity, or they are limited to discerning basic linguistic elements such as letters and words. We propose a novel approach to decoding continuous language from single-trial non-invasive fMRI recordings, in which a three-dimensional convolutional network augmented with information bottleneck is developed to automatically identify responsive voxels to stimuli, and a character-based decoder is designed for the semantic reconstruction of continuous language characterized by inherent character structures. The resulting decoder can produce intelligible textual sequences that faithfully capture the meaning of perceived speech both within and across subjects, while existing decoders exhibit significantly inferior performance in cross-subject contexts. The ability to decode continuous language from single trials across subjects demonstrates the promising applications of non-invasive language brain-computer interfaces in both healthcare and neuroscience.

neuroscience↗

bioRxiv2024

Bioorthogonal labeling and enrichment of histone monoaminylation reveal its accumulation and regulatory function in cancer cell chromatin

Histone monoaminylation (i.e., serotonylation and dopaminylation) is an emerging category of epigenetic mark occurring on the fifth glutamine (Q5) residue of H3 N-terminal tail, which plays significant roles in gene transcription. Current analysis of histone monoaminylation is mainly based on site-specific antibodies and mass spectrometry, which either lacks high resolution or is time-consuming. In this study, we report the development of chemical probes for bioorthogonal labeling and enrichment of histone serotonylation and dopaminylation. These probes were successfully applied for the monoaminylation analysis of in vitro biochemical assays, cells, and tissue samples. The enrichment of monoaminylated histones by the probes further confirmed the crosstalk between H3Q5 monoaminylation and H3K4 methylation. Finally, combining the ex vivo and in vitro analyses based on the developed probes, we have shown that both histone serotonylation and dopaminylation are highly enriched in tumor tissues that overexpress transglutaminase 2 (TGM2) and regulate the three-dimensional architecture of cellular chromatin. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/586010v3_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1bee3f7org.highwire.dtl.DTLVardef@1687013org.highwire.dtl.DTLVardef@1960bd0org.highwire.dtl.DTLVardef@1e19a04_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Normative growth modeling of brain morphology reveals neuroanatomical heterogeneity and biological subtypes in children with ADHD

BackgroundNeuroimaging studies suggest substantial individual heterogeneity in brain phenotypes in attention-deficit/hyperactivity disorder (ADHD). However, how these individual-level brain phenotypes contribute to the identification of ADHD biotypes and whether these biotypes have different treatment outcomes and neurobiological underpinnings remain largely unknown. MethodsWe collected multisite, high-quality structural magnetic resonance imaging data from 1,006 children aged 6-14 years, including 351 children with ADHD and 655 typically developing children. Normative growth models of cortical thickness were established for 219 regions in the typically developing children. Individual-level deviations from these normal references were quantified and clustered to identify ADHD biotypes. We validated the replicability and generalizability of the ADHD biotypes using two independent datasets and evaluated the associations of the biotypes with symptomatic, cognitive, and gene expression profiles, as well as follow-up treatment outcomes. FindingsNo more than 10% of children with ADHD had extreme deviations in cortical thickness in a single region, suggesting high heterogeneity among individuals with ADHD. On the basis of the brain deviation maps, we discovered two robust ADHD biotypes, an infra-normal subtype with cortical thinning associated with ADHD symptoms and a supranormal subtype with cortical thickening associated with cognition. Patients with the infra-normal subtype responded better to methylphenidate than to atomoxetine, although both subtypes showed treatment efficacy. Brain deviations in the infra-normal subtype were explained by the expression levels of genes enriched in presynaptic and axonal development and polygenic risk of ADHD. InterpretationWe identified anatomically distinct, clinically valuable, and biologically informed ADHD subtypes, providing insight into the neurobiological basis of clinical heterogeneity and facilitating a personalized medication strategy for ADHD patients. Panel: Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSubstantial individual heterogeneity in brain phenotypes in attention-deficit/hyperactivity disorder (ADHD) motivates the need to discover homogeneous biotypes. We searched PubMed for research articles on ADHD biotypes using brain MRI published before December 1, 2023, using the search terms ((attention deficit hyperactivity disorder [Title/Abstract]) OR (ADHD [Title/Abstract])) AND ((subtypes [Title/Abstract]) OR (subgroups [Title/Abstract]) OR (subtyping [Title/Abstract])) AND ((MRI [Title/Abstract]) OR (neuroimaging [Title/Abstract]) OR (brain [Title/Abstract])) without language restrictions. Of the eight included studies, two identified ADHD biotypes using structural morphology, four used functional activity, and two used multimodal features. However, none of these studies considered the developmental effect of the brain phenotypes, examined treatment response, or investigated the genetic correlates of the biotypes. Added value of this studyThis study is the first to use individualized brain measures extracted from normative models to investigate ADHD biotypes in a large sample of more than 1,000 children. We identified two reproducible ADHD biotypes, characterized by distinct symptomatic, cognitive, and gene expression profiles, as well as differential treatment responses. This study advances our understanding of the neurobiological basis underlying the clinical heterogeneity of ADHD and highlights the critical need to discover ADHD biotypes using an unbiased and individualized approach. Implications of all the available evidenceThis study revealed remarkable neuroanatomical heterogeneity in ADHD patients and identified anatomically distinct, clinically valuable, and biologically informed ADHD biotypes. Our findings have potential value for the investigation of data-driven biotypes to evaluate treatment efficacy and facilitate personalized treatment. We also highlight the need for future studies to move beyond the understanding of ADHD solely based on the "average patient" perspective.

neuroscience↗

bioRxiv2024

Rapid High-Throughput Isolation and purification of Chicken Myoblasts Based on Deterministic Lateral Displacement Microfluidic Chips

Myoblasts are defined as stem cells containing skeletal muscle cell precursors. However, there are some challenges associated with the purification of myoblast samples, including long culture times and ease of bacterial contamination. In this study, we propose a microfluidic myoblast cell enrichment and purification platform based on the principle of deterministic lateral displacement (DLD). To achieve this, we designed a DLD chip with three outlets and tested it on 11-day-old Wenchang chicken pectoral muscle tissue. A cell suspension was prepared using the collagenase method, pretreated, and then passed into the designed DLD chip for myoblast enrichment and purification. In this study, the number of myoblasts and the diameter of myoblasts increased slowly before E9, and the diameter of myofibers decreased and the number of myofibers increased rapidly after E9. The period when the number of muscle fibers is highest is E12, and the period when the diameter of muscle fibers increases again after the lowest point is also E12. After E12, the diameter of the muscle fibers increased and the number of muscle fibers decreased. At E12, myoblasts clustered and fused, and the proliferation of myoblasts was greatly reduced. E12 is both intact myoblasts and the most vigorous proliferation period, so the best time to determine isolation is E12. We attained a myoblast cell recovery rate of 80%, a target outlet collection purity of 99%, and a chip throughput of 50 m/min. This study provides a novel and effective method for the isolation and purification of skeletal muscle myoblasts.

cell biology↗

bioRxiv2024

The Diversified Astrocyte Developmental Programs are Modulated by Primary Ciliary Signaling

Astrocyte diversity is greatly influenced by local environmental modulation. Here, we report that the vast majority of brain astrocytes across the entire brain possess a singular primary cilium, a specialized signaling antenna localized to cell soma. Comparative single-cell transcriptomics reveals that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Independent of canonical Shh signaling, primary cilia are important regulators for astrocyte morphology and intracellular signaling balance. Dendritic spine analysis and transcriptomics reveal that perturbation of astrocytic cilia leads to disruption of neuronal development and global intercellular connectomes in the brain. Ultimately, mice with primary ciliary deficient astrocytes show behavioral deficits in sensorimotor function, sociability, learning and memory. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain.

neuroscience↗

bioRxiv2024

Interpretable antibody-antigen interaction prediction by bridging structure to sequence

With the application of personalized and precision medicine, more precise and efficient antibody drug development technology is urgently needed. Identification of antibody-antigen interactions is crucial to antibody engineering. The time-consuming and expensive nature of wet-lab experiments calls for efficient computational methods. Taking into account the non-overlapping advantage of current structure-dependent and sequence-only computational methods, we propose an interpretable antibody-antigen interaction prediction method, S3AI. The introduction of structural knowledge, combined with explicit modeling of chemical rules, establishes a sequence-to-function route in S3AI, thereby facilitating its perception of intricate molecular interactions through providing route and priors guidance. S3AI significantly and comprehensively outperforms the state-of-the-art models and exhibits excellent generalization when predicting unknown antibody-antigen pairs, surpassing specialized prediction methods designed for out-of-distribution generalization in fair comparisons. More importantly, S3AI captures the universal pattern of antibody-antigen interactions, which not only identifies the CDRs responsible for specific binding to the antigen but also unearths the importance of CDR-H3 for the interaction. Structure-free design and superior performance make S3AI ideal for large-scale, parallelized antibody optimization and screening, enabling the rapid and precise identification of promising candidates within the extensive antibody space.

bioinformatics↗

bioRxiv2024

Fertilization-induced synergid cell death by RALF12-triggered ROS production and ethylene signaling

Fertilization-dependent elimination of the persistent synergid cell is essential to block supernumerary pollen tubes and thus to avoid polyspermy in flowering plants. Little is known about the molecular mechanisms ensuring timely induction and execution of synergid cell death. We analysed manually isolated maize synergid cells along their degeneration and show that they are gland cells expressing batteries of genes encoding small secreted proteins under control of the MYB98 transcription factor. This network is down-regulated after fertilization, while genes involved in reactive oxygen species (ROS) production, ethylene biosynthesis and response, senescence, and oxidative stress regulation are induced before synergid elimination and its ultimate fusion with the endosperm. We further show that fertilization-induced RALF12 peptide specifically triggers mitochondrial ROS and apoptosis, while ethylene promotes synergid degeneration. In conclusion, this study sheds light on developmental programmed cell death (dPCD) in plants and provides a unique resource to discover novel PCD regulators.

cell biology↗