Biology subjects

Huang, C.

Publications and source records attributed to Huang, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Maternal humoral factors modulate offspring gut immune homeostasis to mitigate diabetes development

Environmental risk factors possess the potential to modulate the pathogenesis of type I diabetes (T1D). Foremost among these factors are early life influences impacting the gastrointestinal (GI) tract. During infancy, both the microbiota and immune system are influenced by maternal factors contributing to key events in the neonatal GI tract. Despite the well-known importance of maternal factors on infant immune development, whether maternal immune dysregulation and dysbiosis can perpetuate the same in offspring remains largely unknown. To explore how these maternal factors impact offspring disease development, we used IgA-deficiency induced maternal dysbiosis in Non-Obese Diabetic (NOD) dams to study T1D development in their progeny. We found that maternal dysbiosis and absence of IgA led to changes in IgA-sufficient offspring immune development resulting in heightened GI immune activity. Maternal dysbiosis also contributed to altered microbiome establishment in progeny, such that pups exhibited reduced colonic abundance of Akkermansia muciniphila and Clostridoides difficile. In adulthood, these mice exhibited a lowered incidence of T1D. This protection was replicated by fostering high incidence offspring to dysbiotic dams, prompting us to propose that altered breast milk composition in dysbiotic dams can influence immune development and microbiome establishment in offspring, contributing to T1D resistance.

immunology↗

bioRxiv2024

State modulation in spatial networks with three interneuron subtypes

Several inhibitory interneuron subtypes have been identified as critical in regulating sensory responses. However, the specific contribution of each interneuron subtype remains uncertain. In this work, we explore the contributions of cell-type specific activity and synaptic connections to dynamics of a spatially organized spiking neuron network. We find that the firing rates of the somatostatin (SOM) interneurons align closely with the level of network synchrony irrespective of the target of modulatory input. Further analysis reveals that inhibition from SOM to parvalbumin (PV) interneurons must be limited to allow gradual transitions from asynchrony to synchrony and that the strength of recurrent excitation onto SOM neurons determines the level of synchrony achievable in the network. Our results are consistent with recent experimental findings on cell-type specific manipulations. Overall, our results highlight common dynamic regimes achieved across modulations of different cell populations and identify SOM cells as the main driver of network synchrony.

neuroscience↗

bioRxiv2024

An autonomous robotic system for high-throughput phenotyping and behavioral studies of individual fruit flies

The fruit fly, Drosophila melanogaster, is a widely used model species in biomedical research. Despite its importance, conducting manual experiments with individual fruit flies can be challenging and time-consuming, especially for studies of individual fly behaviors. Such studies often involve cumbersome preparatory steps, such as manually tethering a fly and then positioning it within an experimental setup1,2. These procedures commonly require the fly to be anesthetized, and, before behavioral assessments begin, the fly must recover from anesthesia. Hence, the introduction of automated phenotyping and behavioral assays would expedite important aspects of fly research, by minimizing manual handling of flies and decreasing the net time needed for experiments. Here, we introduce FlyMAX (Fly Manipulation and Autonomous eXperimentation), an autonomous robotic system for manipulating adult flies without use of anesthesia. FlyMAX collects individual flies from a standard vial, analyzes them with computer vision, and achieves a throughput of >1,000 flies per day for high-throughput inspection and characterization assays. Robotic handling had no detectable adverse effects on fly longevity or our assessments of fly health. Moreover, the behavioral performance of flies, especially of males, was better and less variable than of flies handled manually. Our system employs deep learning-based machine vision for real-time assessments of picking quality and fly phenotypes. This enables fully pipelined, autonomous experimentation for behavioral assays with individual flies in controlled environments, which was previously infeasible. Overall, FlyMAX constitutes a promising technology to enhance the efficiency and reproducibility of research with flies and other insects in fields such as genetics, neuroscience, and drug screening.

neuroscience↗

bioRxiv2024

Sustained Strain Applied at High Rates Drives Dynamic Tensioning in Epithelial Cells

Epithelial cells experience long lasting loads of different magnitudes and rates. How they adapt to these loads strongly impacts tissue health. Yet, much remains unknown about the evolution of cellular stress in response to sustained strain. Here, by subjecting cell pairs to sustained strain, we report a bimodal stress response, where in addition to the typically observed stress relaxation, a subset of cells exhibits a dynamic tensioning process with significant elevation in stress within 100s, resembling active pulling-back in muscle fibers. Strikingly, the fraction of cells exhibiting tensioning increases with increasing strain rate. The tensioning response is accompanied by actin remodeling, and perturbation to actin abrogates it, supporting cell contractilitys role in the response. Collectively, our data show that epithelial cells adjust their tensional states over short timescales in a strain-rate dependent manner to adapt to sustained strains, demonstrating that the active pulling-back behavior could be a common protective mechanism against environmental stress.

biophysics↗

bioRxiv2024

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

Experimental access to cell types within the mammalian spinal cord is severely limited by the availability of genetic tools. To enable access to lower motor neurons (LMNs) and LMN subtypes, we generated single cell multiome datasets from mouse and macaque spinal cords and discovered putative enhancers for each neuronal population. We cloned these enhancers into adeno-associated viral vectors (AAVs) driving a reporter fluorophore and functionally screened them in mouse. We extensively characterized the most promising candidate enhancers in rat and macaque and developed an optimized pan LMN enhancer virus. Additionally, we generated derivative viruses expressing iCre297T recombinase or ChR2-EYFP for labeling and functional studies, and we created a single vector with combined enhancer elements to achieve simultaneous labeling of layer 5 extratelencephalic projecting (ET) neurons and LMNs. This unprecedented LMN toolkit will enable future investigations of cell type function across species and potential therapeutic interventions for human neurodegenerative diseases.

neuroscience↗

bioRxiv2024

Avian-restrict Salmonella transition to endemicity is accompanied by localized resistome adaptation

Bacterial regional demonstration after global dissemination is an essential pathway for selecting distinct finesses. However, the evolution of the resistome during the transition to endemicity remains unaddressed. Using the most comprehensive whole-genome sequencing dataset of Salmonella enterica serovar Gallinarum (S. Gallinarum) collected from 15 countries, including 45 newly recovered samples from two related local regions, we established the relationship among avian-specific pathogen genetic profiles and localization patterns. Initially, we revealed the international transmission and evolutionary history of S. Gallinarum to recent endemicity through phylogenetic analysis conducted using a spatiotemporal Bayesian framework. Our findings indicate that the independent acquisition of the resistome via the mobilome, primarily through plasmids and transposons shapes a unique antimicrobial resistance profile among different lineages. Notably, the mobilome-resistome combination among distinct lineages exhibits a geographical-specific manner, further supporting a localized endemic mobilome-driven process. Collectively, this study elucidates resistome adaptation in the endemic transition of an avian-specific pathogen, likely driven by the localized farming style, and provides valuable insights for targeted interventions.

microbiology↗

bioRxiv2024

Different Roles of D1/D2 Medium Spiny Neurons in the Nucleus Accumbens in Pair Bond Formation of Male Mandarin Voles

The mesolimbic dopamine (DA) system has been implicated in pair bond formation. However, involvements of DA release, real time activities, and electrophysiological activities of D1/D2 medium spiny neurons (MSNs) in the nucleus accumbens (NAc) shell in pair bonding remain unclear. This work verified that male mandarin voles after pair bonding released higher levels of DA in the NAc shell and displayed higher levels of D1 MSNs activity and lower levels of D2 MSNs activity upon sniffing their partners compared to upon sniffing an unknown female. Moreover, pair bonding induced differential alterations in both synaptic plasticity and neuronal intrinsic excitability in both D1 MSNs and D2 MSNs. In addition, chemogenetic inhibition of ventral pallidum (VP) -projecting D2 MSNs in the NAc shell enhanced pair bond formation, while chemogenetic activation of VP-projecting D2 MSNs in the NAc shell inhibited pair bond formation. These findings suggest that different neuronal activity of NAc shell D1 MSNs / D2 MSNs regulated by increasing DA release after pair bonding may be a neurobiological mechanism underlying pair bond formation.

neuroscience↗

bioRxiv2024

scCancerExplorer: a comprehensive database for interactively exploring single-cell multi-omics data of human pan-cancer

Genomic, epigenomic, and transcriptomic alterations are hallmarks of cancer cells, and are closely connected. Especially, epigenetic regulation plays a critical role in tumorigenesis and progression. The growing single-cell epigenome data in cancer research provide new opportunities for data mining from a more comprehensive perspective. However, there is still a lack of databases designed for interactively exploring the single-cell multi-omics data of human pan-cancer, especially for the single-cell epigenome data. To fill in the gap, we developed scCancerExplorer, a comprehensive and user-friendly database to facilitate the exploration of the single-cell genome, epigenome (chromatin accessibility and DNA methylation), and transcriptome data of 50 cancer types. Five major modules were provided to explore those data interactively, including "integrated multi-omics analysis", "single-cell transcriptome", "single-cell epigenome", "single-cell genome", and "TCGA analysis". By simple clicking, users can easily investigate gene expression features, chromatin accessibility patterns, transcription factor activities, DNA methylation states, copy number variations, and TCGA survival analysis results. Taken together, scCancerExplorer is distinguished from previous databases with rich and interactive functions for exploring the single-cell multi-omics data of human pan-cancer. It bridges the gap between single-cell multi-omics data and the end-users, and will facilitate progress in the field of cancer research. scCancerExplorer is freely accessible via https://bianlab.cn/scCancerExplorer.

cancer biology↗

bioRxiv2024

The effects of L-carnitine and fructose in improved Ham's F10 on sperm culture in idiopathic severe asthenospermia within 24h

Trial designTo study the effects of L-carnitine and fructose on semen parameters of severe asthenospermia patients by sperm culturing in vitro within 24h. We optimized the energy composition and antioxidant substances of sperm culture medium in vitro (based on Hams F10 culture medium) by orthogonal test for preparing high quality culture medium. Sperms of 60 patients with idiopathic severe asthenospermia were collected, and cultured in vitro within 24h, by Hams F10 culture medium added to different concentrations of L-carnitine and fructose and culture temperature, whose effects on sperm motility were observed to determine which is the most appropriate concentration and temperature. MethodsFor determining the appropriate concentration of L-carnitine and fructose and the suitable culture temperature in Hams F10 culture medium, the orthogonal experiments were carried out to optimize above three factors, which had great influence on sperm viability, survival rate, deformity rate and DNA fragmentation index (DFI). ResultsThe final concentration of L-carnitine and fructose was determined in terms of initial tests to assess the effects of different concentrations (4, 8, 12, and 16 mg/ml L-carnitine and 0.125, 0.250, 0.375, and 0.50 mg/ml fructose) on sperm viability and motility in culture. During the operation of processing and culturing sperms in vitro within 24h, orthogonal test showed that sperm viability was better at the final concentration of 8 mg/ml L-carnitine and 0.375 mg/mL fructose in improved Hams F10 culture medium at 36.5 . ConclusionIdiopathic severe asthenospermia sperm can be effectively improved by the modified Hams F10 culture medium of the final concentration of 8 mg/ml L- carnitine and 0.375 mg/mL fructose in at 36.5 within 24h, which has shown better culture effect and is superior to Hams F10 basic medium.

biochemistry↗

bioRxiv2024

Cyclic di-GMP as an Antitoxin Regulates Bacterial Genome Stability and Antibiotic Persistence in Biofilms

Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.

microbiology↗

bioRxiv2024

Unraveling factors responsible for pathogenic differences in Lassa virus strains

Lassa virus (LASV) is the etiological agent of Lassa fever (LF), a severe hemorrhagic disease with potential for lethal outcomes. Apart from acute symptoms, LF survivors often endure long-term complications, notably hearing loss, which significantly impacts their quality of life and socioeconomic status in endemic regions of West Africa. Classified as a Risk Group 4 agent, LASV poses a substantial public health threat in affected areas. Our laboratory previously developed a novel lethal guinea pig model of LF utilizing the clinical isolate LASV strain LF2384. However, the specific pathogenic factors underlying LF2384 infection in guinea pigs remained elusive. In this study, we aimed to elucidate the differences in the immunological response induced by LF2384 and LF2350, another LASV isolate from a non-lethal LF case within the same outbreak. Through comprehensive immunological gene profiling, we compared the expression kinetics of key genes in guinea pigs infected with LASV LF2384 and LF2350. Our analysis revealed differential expression patterns for several immunological genes, including CD94, CD19-2, CD23, IL-7, and CIITA, during LF2384 and LF2350 infection. Moreover, through the generation of recombinant LASVs, we sought to identify the specific viral genes responsible for the observed pathogenic differences between LF2384 and LF2350. Our investigations pinpointed the L protein as a crucial determinant of pathogenicity in guinea pigs infected with LASV LF2384. Author summaryLassa virus (LASV) is known to cause lethal hemorrhagic fever, Lassa fever, and is classified as a Risk Group-4 agent, which need to be handled in the highest biocontainment laboratories, biosafety level-4 (BSL-4), due to its high pathogenicity and the lack of preventive or treatment methods. LASV infection has a huge impact on public health and socioeconomics in endemic areas, however, its pathogenic mechanism is still largely unknown. In order to unveil the mechanisms of LASV pathogenesis, we compared the pathogenicity of two LASV isolates, which have opposite phenotypes in guinea pigs. Additionally, we determined the viral factor responsible for pathogenic differences between LASV isolates using reverse genetics. In summary, our study provides valuable insights into the immunological and virological factors underlying the pathogenic differences between LASV strains associated with lethal and non-lethal LF cases. Understanding these distinctions is essential for informing strategies for the diagnosis, treatment, and prevention of LF.

microbiology↗

bioRxiv2024

Modeling Repertoire Behavior within the Energy-Based Framework: A Study on Cell Proliferation and Somatic Hypermutation during the Adaptive Immune Response

Monitoring and describing the adaptive immune repertoire(IR) for disease detection and diagnosis is essential in healthcare research. Many phenomenon have been observed to generalize the static property of IR, but the mathematical description of the formation and dynamic changes of IR still lacks research. Here, we present a mathematical and physical model to interpret the cell proliferation and somatic hypermutation(SHM) process in IR, difficulties to generate different clones in IR are computed, and IR distance is calculated as the minimum effort required to transform one IR distribution to another. IR distribution and distance can be detected from samples containing 104 cells. The validity of our method is confirmed by the unsupervised clustering of data from mice spleen and clinical PBMC samples including various immune stages and diseases. Our work dynamically characterize and quantify IR process, enabling a macroscopic immunoevaluation by sensitive immune fluctuation detection from minute samples.

biophysics↗

bioRxiv2024

Desmosomal Cadherin Tension Loss in Pemphigus Vulgaris Mediated by the Inhibition of Active RhoA at Cell-Cell Adhesions

Binding of autoantibodies to keratinocyte surface antigens, primarily desmoglein 3 (Dsg3) of the desmosomal complex, leads to the dissociation of cell-cell adhesion in the blistering disorder pemphigus vulgaris (PV). After the initial disassembly of desmosomes, cell-cell adhesions actively remodel in association with the cytoskeleton and focal adhesions. Growing evidence highlights the role of adhesion mechanics and mechanotransduction at cell-cell adhesions in this remodeling process, as their active participation may direct autoimmune pathogenicity. However, a large part of the biophysical transformations after antibody binding remains underexplored. Specifically, it is unclear how tension in desmosomes and cell-cell adhesions changes in response to antibodies, and how the altered tensional states translate to cellular responses. Here, we showed a tension loss at Dsg3 using fluorescence resonance energy transfer (FRET)-based tension sensors, a tension loss at the entire cell-cell adhesion, and a potentially compensatory increase in junctional traction force at cell-extracellular matrix adhesions after PV antibody binding. Further, our data indicate that this tension loss is mediated by the inhibition of RhoA at cell-cell contacts, and the extent of RhoA inhibition may be crucial in determining the severity of pathogenicity among different PV antibodies. More importantly, this tension loss can be partially restored by altering actomyosin based cell contractility. Collectively, these findings provide previously unattainable details in our understanding of the mechanisms that govern cell-cell interactions under physiological and autoimmune conditions, which may open the window to entirely new therapeutics aimed at restoring physiological balance to tension dynamics that regulates the maintenance of cell-cell adhesion.

biophysics↗

bioRxiv2024

Directed evolution for cell separation in budding yeast

Natural isolates of the yeast Saccharomyces cerevisiae were evolved under a transfer protocol that selected for cell separation and against clumpy growth. Whole-genome sequencing of haploid populations revealed strong selection to deactivate AMN1, a known regulator of post-mitotic cell separation, as well as multiple instances of loss-of-function mutations on the Rim101 pathway, pointing to a previously unknown role of the Rim101 pathway in regulating cell separation. In diploid populations, we observed repeated large partial deletions of chromosome III caused by fusions of the mating type loci MAT and HMR (Hawthornes deletion) or MAT and HML (Stratherns circle). We measured the spontaneous rate of Hawthornes deletion and found that it is within an order of magnitude of previously measured rates of whole-chromosome aneuploidy. A diploid population in which neither large deletion was detected instead fixed a heterozygous nonsynonymous mutation to the calcium channel CCH1, also pointing to a novel role for this gene in relation to cell separation.

evolutionary biology↗

bioRxiv2024

hESCs-derived organoids achieve liver zonation by LSEC modulation

Liver zonation, essential for diverse physiological functions, is lacking in existing organoid models, hindering their ability to recapitulate liver development and pathogenesis. Addressing this gap, we explored the feasibility of achieving zonated organoid by co-culturing human embryonic stem cells (hESCs) derived hepatocytes with hESCs derived liver sinusoidal endothelial cells (LSECs) exhibiting characteristics of either the liver lobules pericentral (PC) or periportal (PP) regions. Introducing zonated LSECs with variable WNT2 signaling subtly regulate hepatocyte zonation, resulting in noticeable metabolic function changes. Considering the lipid metabolism variations in PC and PP organoids, we constructed biomimetic zonated non-alcoholic fatty liver disease (NAFLD) organoids and revealed that glucagon-like peptide-1 receptor agonist (GLP-1RA) target LSECs, but not hepatocytes, indicating potential therapeutic mechanisms of GLP-1RA in NAFLD alleviation. This study highlights the crucial role of non-parenchymal cells in organoids for recapitulating niche heterogeneity, offering further insights for drug discovery and in vitro modeling of organ heterogeneity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/592562v1_figu1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@1907c9eorg.highwire.dtl.DTLVardef@e5a76borg.highwire.dtl.DTLVardef@152a1dcorg.highwire.dtl.DTLVardef@981f_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractSchematic of hESCs-derived liver zonation organoids C_FIG

bioengineering↗

bioRxiv2024

Pinging the Hidden Attentional Priority Map: Suppression Needs Attention

Attentional capture by an irrelevant salient distractor is attenuated when the distractor is presented more frequently in one location compared to other locations, suggesting that people learn to suppress an irrelevant salient location. However, to date it is unclear whether this suppression is proactive, applied before attention has been directed to the distractor location, or reactive, occurring after attention has been directed to that specific location. The aim of the present study is to investigate how suppression is accomplished by using the pinging technique, which allows one to probe how attention is distributed across the visual field prior to the presentation of the search display. In an EEG experiment, participants performed a visual search task wherein they were tasked with identifying a shape singleton in the presence of an irrelevant color singleton. Compared to all other locations, this color singleton appeared more frequently at a specific location, which was termed the high-probability location. Prior to the search task, we introduced a continuous recall spatial memory task to reveal the hidden attentional priority map. Participants had to memorize the location of a memory cue continuously and report this location after the visual search task. Critically, after the presentation of the memory cue but before the onset of the search display, a neutral placeholder display was presented to probe how the hidden priority map is reconfigured by the learned distractor suppression. Behaviorally, there was clear evidence that the high-probability location was suppressed, as search was more efficient when the distractor appeared at this location. To examine the priority map prior to search, we adopted an inverted encoding approach to reconstruct the tuning profile of the memorized position in the spatial memory task. Inverted modeling resulted in reliable tuning profiles during memory maintenance that gradually decayed and that were revived again by the onset of a neutral placeholder display preceding search. After the onset of the placeholders, the tuning profile observed was characterized by a spatial gradient centered over the high-probability location, with tuning being most pronounced at the-to-be suppressed location. This finding suggests that while learned suppression is initiated prior to search display onset, it is preceded by an initial phase of spatial selection, which is in line with a reactive suppression account. Together these results further our understanding of the mechanism of spatial distractor suppression.

neuroscience↗

bioRxiv2024

Comprehensive evaluation and prediction of editing outcomes for near-PAMless adenine and cytosine base editors

Base editors enable the direct conversion of target bases without inducing double-strand breaks, showing great potential for disease modeling and gene therapy. Yet, their applicability has been constrained by the necessity for specific protospacer adjacent motif (PAM). We generated four versions of near-PAMless base editors and systematically evaluated their editing patterns and efficiencies using an sgRNA-target library of 45,747 sequences. Near-PAMless base editors significantly expanded the targeting scope, with both PAM and target flanking sequences as determinants for editing outcomes. We developed BEguider, a deep learning model to accurately predict editing results for near-PAMless base editors. We also provided experimentally measured editing outcomes of 20,541 ClinVar sites, demonstrating that variants previously inaccessible by NGG PAM base editors can now be precisely generated or corrected. We have made our predictive tool and data available online to facilitate development and application of near-PAMless base editors in both research and clinical settings.

bioinformatics↗

bioRxiv2024

An EEG Signature of MCH Neuron Activities Predicts Cocaine Seeking

BackgroundIdentifying biomarkers that predict substance use disorder (SUD) propensity may better strategize anti-addiction treatment. The melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus (LH) critically mediates interactions between sleep and substance use; however, their activities are largely obscured in surface electroencephalogram (EEG) measures, hindering the development of biomarkers. MethodsSurface EEG signals and real-time Ca2+ activities of LH MCH neurons (Ca2+MCH) were simultaneously recorded in male and female adult rats. Mathematical modeling and machine learning were then applied to predict Ca2+MCH using EEG derivatives. The robustness of the predictions was tested across sex and treatment conditions. Finally, features extracted from the EEG-predicted Ca2+MCH either before or after cocaine experience were used to predict future drug-seeking behaviors. ResultsAn EEG waveform derivative - a modified theta-to-delta ratio (EEG Ratio) - accurately tracks real-time Ca2+MCH in rats. The prediction was robust during rapid eye movement sleep (REMS), persisted through REMS manipulations, wakefulness, circadian phases, and was consistent across sex. Moreover, cocaine self-administration and long-term withdrawal altered EEG Ratio suggesting shortening and circadian redistribution of synchronous MCH neuron activities. In addition, features of EEG Ratio indicative of prolonged synchronous MCH neuron activities predicted lower subsequent cocaine seeking. EEG Ratio also exhibited advantages over conventional REMS measures for the predictions. ConclusionsThe identified EEG Ratio may serve as a non-invasive measure for assessing MCH neuron activities in vivo and evaluating REMS; it may also serve as a potential biomarker predicting drug use propensity.

neuroscience↗