Search bioRxiv⌕ Search

Biology subjects

Xia, X.

Publications and source records attributed to Xia, X..

At least 55 records · Page 3Linked to original sources

The Conserved Transcription Factor Kruppel Regulates the Survival and Neurogenesis ofMushroom Body Neuroblasts in Drosophila Adult Brains

In various metazoans, including Drosophila and humans, neural progenitors exit the cell cycle and are eliminated by the end of development, limiting adult neurogenesis. We demonstrate that in Drosophila, the conserved transcription factor Kruppel (Kr) controls neurogenic capacity of a specific subset of neuroblasts that forms the mushroom body (MBNBs), analogous to the mammalian hippocampus. The Irregular facet mutation, which alters Kr expression, and neuroblast-specific Kr depletion allow MBNBs, but not other neuroblasts, to persist beyond development and generate neurons in adult brains. Persisting MBNBs express Imp, an RNA-binding protein that promotes neuroblast proliferation and survival. Our results underscore a critical role for Kr in the developmental control of a specific progenitor population, uncovering a novel mechanism controlling adult neurogenesis.

developmental biology↗

Increased pathogenicity and transmission of SARS-CoV-2 Omicron XBB.1.9 sublineage, including HK.3 and EG.5.1

With the SARS-CoV-2 Omicron XBB.1.9 sublineage circulating worldwide, two XBB.1.9 variants, EG.5.1 and HK.3 spread rapidly and became dominant from middle 2023. However, the spike features, pathogenicity, and transmissibility of HK.3 are largely unknown. Here, we performed multiscale investigations to reveal the virological features of XBB.1.9 subvariants, especially the newly emerging HK.3. HK.3 revealed high replication efficiency in vitro. The HK.3 spike exhibited enhanced processing, although its infectivity, fusogenicity, and hACE2 binding affinity were comparable to those of the EG.5 and XBB.1 spikes. All XBB.1.9.1, EG.5.1 and HK.3 strains demonstrated efficient transmission in hamsters, although XBB.1.9.1 exhibited stronger fitness in the upper airways. HK.3 and EG.5.1 exhibited greater pathogenicity than XBB.1.9.1 and BA.2 in H11-K18-hACE2 hamsters. Our studies provide insight into the newly emerging pathogens HK.3 and EG.5.1. ImportanceIn animal models, the ongoing attenuated pathogenicity and poor transmission of Omicron subvariants seems to reach a consensus. However, our results revealed that Omicron XBB.1.9 subvariants, including one of the key variants of interest, EG.5 with its another key subvariant HK.3, universally exhibited both increased pathogenicity and highly transmission. This study reemphasized the importance of surveillance in characteristics of epidemic Omicron subvariants.

microbiology↗

Respiratory mucosal administration of DNA aptamer nanomaterials protects against antigenically diverse SARS-CoV-2 variants

The ongoing COVID-19 pandemic has highlighted the need for innovative therapeutic strategies to combat rapidly evolving pathogens that challenge the efficacy of traditional vaccines and monoclonal antibody treatments. Here, we explored the potential of TMSA52, a previously described homotrimeric DNA aptamer as a universal prophylactic and therapeutic agent against SARS-CoV-2. TMSA52 demonstrates exceptional binding affinities and broad neutralization against diverse SARS-CoV-2 variant spike proteins that are further enhanced through multimerization onto lamellar iridium nanoplates. Respiratory mucosal delivery of TMSA52 nanomaterials was well-tolerated. Surprisingly, TMSA52 offered potent protection from infection with ancestral SARS-CoV-2 on-par with monoclonal antibodies, and superior protection against antigenically distant SARS-CoV-2 variants. These findings establish DNA aptamers as a promising, cost-effective, and scalable alternative to traditional monoclonal antibody therapies. This study underscores the potential of aptamer-based platforms as a next-generation strategy to enhance global pandemic preparedness and expand our arsenal of infectious disease countermeasures.

immunology↗

A new GRAB sensor reveals differences in the dynamics and molecular regulation between neuropeptide and neurotransmitter release

The co-existence and co-transmission of neuropeptides and small molecule neurotransmitters in the same neuron is a fundamental aspect of almost all neurons across various species. However, the differences regarding their in vivo spatiotemporal dynamics and underlying molecular regulation remain poorly understood. Here, we developed a GPCR-activation-based (GRAB) sensor for detecting short neuropeptide F (sNPF) with high sensitivity and spatiotemporal resolution. Furthermore, we explore the differences of in vivo dynamics and molecular regulation between sNPF and acetylcholine (ACh) from the same neurons. Interestingly, the release of sNPF and ACh shows different spatiotemporal dynamics. Notably, we found that distinct synaptotagmins (Syt) are involved in these two processes, as Syt7 and Syt for sNPF release, while Syt1 for ACh release. Thus, this new GRAB sensor provides a powerful tool for studying neuropeptide release and providing new insights into the distinct release dynamics and molecular regulation between neuropeptides and small molecule neurotransmitters.

neuroscience↗

BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow

Bioinformatics plays a crucial role in understanding biological phenomena, yet the exponential growth of biological data and rapid technological advancements have heightened the barriers to in-depth exploration of this domain. Thereby, we propose Bio-Informatics Agent (BIA), an intelligent agent leveraging Large Language Models (LLMs) technology, to facilitate autonomous bioinformatic analysis through natural language. The primary functionalities of BIA encompass extraction and processing of raw data and metadata, querying both locally deployed and public databases for information. It further undertakes the formulation of workflow designs, generates executable code, and delivers comprehensive reports. Focused on the single-cell RNA sequencing (scRNA-seq) data, this paper demonstrates BIAs remarkable proficiency in information processing and analysis, as well as executing sophisticated tasks and interactions. Additionally, we analyzed failed executions from the agent and demonstrate prospective enhancement strategies including selfrefinement and domain adaptation. The future outlook includes expanding BIAs practical implementations across multi-omics data, to alleviating the workload burden for the bioinformatics community and empowering more profound investigations into the mysteries of life sciences. BIA is available at: https://github.com/biagent-dev/biagent.

bioinformatics↗

Mechanical cues of extracellular matrix determines tumor innervation

Peripheral tumors can establish local autonomic and sensory nerve networks, termed as tumor innervation (TIN), to support tumorigenesis and metastasis. While nerve dependence in cancers is well-established, the mechanisms governing TIN remain unclear. Here, we report that extracellular matrix (ECM) stiffness, a major mechanical abnormality in the tumor microenvironment (TME), is an essential contributor of TIN. In preclinical models, reducing lysyl oxidase-mediated ECM crosslinking lowers tissue stiffness and TIN in pancreatic cancer, while inflammation-induced matrix stiffening boosts the hyperinnervation of the pancreatic precursor lesions. Mechanistically, {beta}1-containing integrins sense the mechanical cues exerted by ECM stiffness, and the translational co-activator YAP1 acts as an essential nuclear relay to induce the expression of neurotropic genes, particularly brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF). 3D imaging of the whole cleared pancreas reveals that blockade of mechanosensor integrin {beta}1 or pharmacological inhibition of the mechanotransducer YAP1 effectively reduces TIN. In clinical settings, tumor samples with a dense, crosslinked, and stiffened ECM exhibit significant TIN. In summary, these findings identify ECM stiffness as an important driver of TIN and suggest that targeting integrin {beta}1/YAP1-dependent mechanotransduction may counteract TIN.

neuroscience↗

Virological characteristics of SARS-CoV-2 Omicron BA.5.2.48

With the prevalence of sequentially-emerged sublineages including BA.1, BA.2 and BA.5, SARS-CoV-2 Omicron infection has transformed into a regional epidemic disease. As a sublineage of BA.5, the BA.5.2.48 outbreak and evolved into multi-subvariants in China without clearly established virological characteristics, especially the pathogenicity. Though reduced airborne transmission and pathogenicity of former Omicron sublineages have been revealed in animal models, the virological characteristics of BA.5.2.48 was unidentified. Here, we evaluated the in vitro and in vivo virological characteristics of two isolates of the prevalent BA.5.2.48 subvariant, DY.2 and DY.1.1 (a subvariant of DY.1). DY.2 replicates more efficiently than DY.1.1 in HelahACE2+ cells and Calu-3 cells. The A570S mutation (of DY.1) in a normal BA.5 spike protein (DY.2) leads to a 20% improvement in the hACE2 binding affinity, which is slightly reduced by a further K147E mutation (of DY.1.1). Compared to the normal BA.5 spike, the double-mutated protein demonstrates efficient cleavage and reduced fusogenicity. BA.5.2.48 demonstrated enhanced airborne transmission capacity in hamsters than BA.2. The pathogenicity of BA.5.2.48 is greater than BA.2, as revealed in K18-hACE2 rodents. Under immune selection pressure, DY.1.1 shows stronger fitness than DY.2 in hamster turbinates. Thus the outbreaking prevalent BA.5.2.48 multisubvariants exhibites divergent virological features. ImportanceOmicron continues to circulate and evolves novel sublineages with indistinguishable pathogenicity and transmission. Therefore humanized Omicron-sensitive animal models must be applied to evaluate the virological characteritics and antiviral therapeutics. By using multiple models including the Omicron-lethal H11-K18-hACE2 rodents, BA.5.2.48 revealed higher pathogenicity in the novel H11-K18-hACE2 rodent models than the previously epidemic BA.2, and thus the models are more adapted to Omicron studies. Moreover, the regional outbreaking of BA.5.2.48 promotes the multidirectional evolution of its subvariants, gaining either enhanced pathogenicity or a fitness in upper airways which is associated with higher transmission, highlighting the importance of surveillance and virological studies on regionally endemic sublineages which represents the short-run evolutionary direction of Omicron.

microbiology↗

BET inhibition induces GDH1-dependent glutamine metabolic remodeling and vulnerability in liver cancer

Bromodomain and extra-terminal domain (BET) proteins, which function partly through MYC, are critical epigenetic readers and emerging therapeutic targets in cancer. Whether and how BET inhibition simultaneously induces metabolic remodeling remains unclear. Here we find that even transient BET inhibition by JQ-1 and other pan-BET inhibitors blunts liver cancer cell proliferation and tumor growth. BET inhibition decreases glycolytic gene expression but enhances mitochondrial glucose and glutamine oxidative metabolism revealed by metabolomics and isotope labeling analysis. Specifically, BET inhibition downregulates miR-30a to upregulate glutamate dehydrogenase 1 (GDH1) independent of MYC, which produces -ketoglutarate for mitochondrial oxidative phosphorylation (OXPHOS). Targeting GDH1 or OXPHOS is synthetic lethal to BET inhibiton, and combined BET and OXPHOS inhibition therapeutically prevents liver tumor growth in vitro and in vivo. Together, we uncover an important epigenetic-metabolic crosstalk whereby BET inhibition induces MYC- independent and GDH1-dependendent glutamine metabolic remodeling that can be exploited for innovative combination therapy of liver cancer.

cancer biology↗

An octopamine-specific GRAB sensor reveals a monoamine relay circuitry that boosts aversive learning

Octopamine (OA), analogous to norepinephrine in vertebrates, is an essential monoamine neurotransmitter in invertebrates that plays a significant role in various biological functions, including olfactory associative learning. However, the spatial and temporal dynamics of OA in vivo remain poorly understood due to limitations associated with the currently available methods used to detect it. To overcome these limitations, we developed a genetically encoded GPCR activation-based (GRAB) OA sensor called GRABOA1.0. This sensor is highly selective for OA and exhibits a robust and rapid increase in fluorescence in response to extracellular OA. Using GRABOA1.0, we monitored OA release in the Drosophila mushroom body (MB), the flys learning center, and found that OA is released in response to both odor and shock stimuli in an aversive learning model. This OA release requires acetylcholine (ACh) released from Kenyon cells, signaling via nicotinic ACh receptors. Finally, we discovered that OA amplifies aversive learning behavior by augmenting dopamine-mediated punishment signals via Oct{beta}1R in dopaminergic neurons, leading to alterations in synaptic plasticity within the MB. Thus, our new GRABOA1.0 sensor can be used to monitor OA release in real-time under physiological conditions, providing valuable insights into the cellular and circuit mechanisms that underlie OA signaling.

neuroscience↗

General Capillary Endothelial Cells Undergo Reprogramming into Arterial Endothelial Cells in Pulmonary Hypertension through HIF-2a/Notch4 Pathway

Pulmonary arterial hypertension (PAH) is characterized by a progressive increase of pulmonary vascular resistance and obliterative pulmonary vascular remodeling that result in right heart hypertrophy, failure, and premature death. The underlying mechanisms of loss of distal capillary endothelial cells (ECs) and obliterative vascular lesion formation remain unclear. Our recent single-cell RNA sequencing, spatial transcriptomics analysis, RNASCOPE, and immunostaining analysis showed that arterial ECs accumulation and loss of capillary ECs were evident in human PAH patients and pulmonary hypertension (PH) rodents. Pseudotime trajectory analysis of the single-cell RNA sequencing data suggest that lung capillary ECs transit to arterial ECs during the development of PH. Our study also identified CXCL12 as the marker for arterial ECs in PH. Capillary EC lineage tracing approach using capillary specific-Dre;Tdtomato reporter mice demonstrated that capillary ECs gave rise to arterial ECs during PH development. Genetic deletion of HIF-2a or pharmacological inhibition of Notch4 normalized the arterial programming in PH. In conclusion, our study demonstrates that capillary endothelium transits to arterial endothelium through the HIF-2a-Notch4 pathway during the development of PAH. Thus, targeting arterial EC transition might be a novel approach for treating PAH patients.

physiology↗

Endothelial fatty acid-binding proteins contribute to the pathogenesis of pulmonary hypertension

Pulmonary arterial hypertension (PAH) is a devastating disease characterized by obliterative vascular remodeling and persistent increase of vascular resistance, leading to right heart failure and premature death. Understanding the cellular and molecular mechanisms will help develop novel therapeutic approaches for PAH patients. Single-cell RNA sequencing (scRNAseq) analysis found that both FABP4 and FABP5 were highly induced in endothelial cells (ECs) of Egln1Tie2Cre (CKO) mice, which was also observed in pulmonary arterial ECs (PAECs) from idiopathic PAH (IPAH) patients, and in whole lungs of pulmonary hypertension (PH) rats. Plasma levels of FABP4/5 were upregulated in IPAH patients and directly correlated with severity of hemodynamics and biochemical parameters using plasma proteome analysis. Genetic deletion of both Fabp4 and 5 in CKO mice (Egln1Tie2Cre/Fabp4-5-/-, TKO) caused a reduction of right ventricular systolic pressure (RVSP) and RV hypertrophy, attenuated pulmonary vascular remodeling and prevented the right heart failure assessed by echocardiography, hemodynamic and histological analysis. Employing bulk RNA-seq and scRNA-seq, and spatial transcriptomic analysis, we showed that Fabp4/5 deletion also inhibited EC glycolysis and distal arterial programming, reduced ROS and HIF-2 expression in PH lungs. Thus, PH causes aberrant expression of FABP4/5 in pulmonary ECs which leads to enhanced ECs glycolysis and distal arterial programming, contributing to the accumulation of arterial ECs and vascular remodeling and exacerbating the disease.

molecular biology↗

Genomic insights into photosymbiotic evolution in Tridacna squamosa

Photosymbiosis is fundamental driving force for ecological success of benthic coral reef ecosystems, and contributing to their biodiversity and resilience. As a benchmark organism indicative of reef health, the fluted giant clam (Tridacna squamosa) forms an exemplary photosymbiotic relationship with the symbiont Symbiodiniaceae dinoflagellates, whose initiation and maturation require finely coordinated interactions. However, much of the origin and dynamics of this reciprocal interplay remains unclarified. Here, we report the first complete whole genome of T. squamosa, in conjunction with integrated multi-omics data, to illuminate the key evolutionary innovations and molecular events supporting the establishment and maintenance of photosymbiotic lifestyle in the giant clam. Programmed regulation of symbiont recognition, host immune system and GPCRs signaling activation co-contributed to dinoflagellates acquisition in T. squamosa larvae. Adaptive metabolic remodeling in the host siphonal mantle, a photosymbiotic niche, is critical to maintain the robustness of phtosymbiosis. T. squamosa has expanded light sensing gene family and evolved sophisticated signaling pathways to protect against UV photo-damage. Evidence also supports significant contribution of positive selection to host DNA-repair. Overall, our study here offers fresh mechanistic insights into the parallel evolution and molecular machinery of photosymbiosis in the giant clam-dinoflagellates duet, with implications for devising solutions to sustainable conservation.

evolutionary biology↗

Threshold-Free Network-Oriented Statistics in Neuroscience

Network neuroscience has emerged as an indispensable tool for studying brain structure and function. Currently, the network-based statistic (NBS) procedure is widely used for dealing with massive multiple testing/comparison problems in brain networks. However, the NBS requires choosing a hard cluster-forming threshold, lacking objective rules. A powerful and flexible statistical framework is urgently needed with growing interest in finer-grained network explorations across modalities and scales. Here, we introduce a permutation-based framework--"Threshold-Free Network-Oriented Statistics" (TFNOS). It integrates two "threshold-free" pathways: traversing all cluster-forming thresholds (TT) and using predefined clusters (PC). The TT procedure, building upon the threshold-free network-based statistics, requires setting additional parameters. The PC procedures comprise six variants given the degree of freedom in pooling data, null distribution construction, and controlled error rate. Using numerical simulations, we evaluated the performance of the TT procedure under 600 parameter combinations, then benchmarked TFNOS procedures and baselines across different topologies of effects, sample sizes, and effect sizes, and finally provided illustrative examples with real data. We offer recommended parameter values that allow the TT procedure to stably maintain leading power, while empirically controlling the false discovery rate (FDR) beyond only weakly controlling the familywise error rate (FWER). Notably, the relevant parameters commonly employed in the field appear overly liberal. Furthermore, for the PC procedures, FDR-controlling variants showed improved power compared to FWER-controlling variants, and some of them are simple but do not compromise power. The nonparametric PC procedures allow the selection of any test statistics considered appropriate. Overall, the TFNOS is a generalized framework for inference on edges/nodes of undirected/directed brain networks. We provide empirical and principled criteria for selecting appropriate procedures and may enhance the reproducibility and sensitivity of future brain research.

neuroscience↗

Rapid and Highly Sensitive Detection of Fentanyl and its Analogs by a Novel Chemiluminescence Immunoassay

A highly sensitive immunoassay with sub-picogram limit of detection for fentanyl and a wide range of fentanyl analogs has been developed, using a novel high affinity antibody fused with NanoLuc, a small-size luciferase that can emit strong and stable luminescence. When applied to unaltered clinical human urine samples, the assay has sub-picogram limit of detection for fentanyl, with results fully concordant with gold standard liquid chromatography-mass spectrometry. When applied to environmental samples, the assay can detect as low as 0.25 pg fentanyl per inch2 environment surface. Assay turn-around-time is less than 1 hour, with inexpensive equipment needed and potential for high throughput automation or in-field screening. This novel assay has broad potential applications in clinical, environmental, occupational and forensic scenarios by detecting trace amount of fentanyl and its analogs to keep frontline workers safe.

pharmacology and toxicology↗

Asynchronous Detection of Erroneous Behaviors in Human-Robot Interaction with EEG: A Comparative Analysis of Machine Learning Models.

We present a comparative analysis of two distinct machine-learning models designed to detect asynchronous errors during Human-Robot Interaction (HRI). The models under scrutiny are a customized ResNet model and an ensemble model, both trained and validated using EEG data. The ResNet model is a unique adaptation of the Residual Network, comprising a one-dimensional convolutional layer followed by batch normalization and ReLU activation. It also features a custom Residual Block structure and an adaptive average pooling layer, concluding with a fully connected linear layer for binary classification. The ensemble model, on the other hand, incorporates various machine learning models such as MLP, logistic regression, SVM, random forest, and XGBoost, unified in a pipeline with feature extraction and transformation steps. A critical component of our research is the innovative probability map, which maintains a granularity of 0.1 seconds. This map forecasts the likelihood of forthcoming one-second intervals being classified as either Error or Non-error. Our comparative analysis reveals significant variations in the performance of the two models, both of which exhibit promising results in detecting erroneous behaviors during HRI. We provide detailed validation results, including the accuracy, F1 score, and confusion matrix for each model. This study offers valuable insights into the potential of machine learning in enhancing HRI efficiency and accuracy, indicating promising directions for future research.

neuroscience↗

Use of Large Language Models to Aid Analysis of Textual Data

The increasing use of machine learning and Large Language Models (LLMs) opens up opportunities to use these artificially intelligent algorithms in novel ways. This article proposes a methodology using LLMs to support traditional deductive coding in qualitative research. We began our analysis with three different sample texts taken from existing interviews. Next, we created a codebook and inputted the sample text and codebook into an LLM. We asked the LLM to determine if the codes were present in a sample text provided and requested evidence to support the coding. The sample texts were inputted 160 times to record changes between iterations of the LLM response. Each iteration was analogous to a new coder deductively analyzing the text with the codebook information. In our results, we present the outputs for these recursive analyses, along with a comparison of the LLM coding to evaluations made by human coders using traditional coding methods. We argue that LLM analysis can aid qualitative researchers by deductively coding transcripts, providing a systematic and reliable platform for code identification, and offering a means of avoiding analysis misalignment. Implications of using LLM in research praxis are discussed, along with current limitations.

scientific communication and education↗

Dual-color GRAB sensors for monitoring spatiotemporal serotonin release in vivo

The serotonergic system plays important roles in both physiological and pathological processes, and is a widely used therapeutic target for many psychiatric disorders. Although several genetically encoded GFP-based serotonin (5-HT) sensors were recently developed, their sensitivities and spectral profiles are relatively limited. To overcome these limitations, we optimized green fluorescent G-protein-coupled receptor (GPCR)-activation-based 5-HT (GRAB5-HT) sensors and developed a new red fluorescent GRAB5-HT sensor. These sensors have excellent cell surface trafficking, high specificity, sensitivity, and spatiotemporal resolution, making them suitable for monitoring 5-HT dynamics in vivo. Besides recording subcortical 5-HT release in freely moving mice, we observed both uniform and gradient 5-HT release in the mouse dorsal cortex with mesoscopic imaging. Finally, we performed dual-color imaging and observed seizure-induced waves of 5-HT release throughout the cortex following calcium and endocannabinoid waves. In summary, these 5-HT sensors can offer valuable insights regarding the serotonergic system in both physiological and pathological states.

neuroscience↗

Consecutive treatments of methamphetamine promote the 4 development of cardiac pathological symptoms in zebrafish

Chronic methamphetamine use, a widespread drug epidemic, has been associated with cardiac morphological and electrical remodeling, leading to the development of numerous cardiovascular diseases. While methamphetamine has been documented to induce arrhythmia, most results originate from clinical trials from users who experienced different durations of methamphetamine abuse, providing no documentation on the use of methamphetamine in standardized settings. Additionally, the underlying molecular mechanism on how methamphetamine affects the cardiovascular system remains elusive. A relationship was sought between cardiotoxicity and arrhythmia with associated methamphetamine abuse in zebrafish to identify and to understand the adverse cardiac symptoms associated with methamphetamine. Zebrafish were first treated with methamphetamine 3 times a week over a 2-week duration. Immediately after treatment, zebrafish underwent electrocardiogram (ECG) measurement using an in-house developed acquisition system for electrophysiological analysis. Subsequent analyses of cAMP expression and Ca2+ regulation in zebrafish cardiomyocytes were conducted. cAMP is vital to development of myocardial fibrosis and arrhythmia, prominent symptoms in the development of cardiovascular diseases. Ca2+ dysregulation is also a factor in inducing arrhythmias. During the first week of treatment, zebrafish that were administered with methamphetamine displayed a decrease in heart rate, which persisted throughout the second week and remained significantly lower than the heart rate of untreated fish. Results also indicate an increased heart rate variability during the early stage of treatment followed by a decrease in the late stage for methamphetamine-treated fish over the duration of the experiment, suggesting a biphasic response to methamphetamine exposure. Methamphetamine-treated fish also exhibited reduced QTc intervals throughout the experiment. Results from the cAMP and Ca2+ assays demonstrate that cAMP was upregulated and Ca2+ was dysregulated in response to methamphetamine treatment. Collagenic assays indicated significant fibrotic response to methamphetamine treatment. These results provide potential insight into the role of methamphetamine in the development of fibrosis and arrhythmia due to downstream effectors of cAMP.

physiology↗