Biology subjects

Bai, K.

Publications and source records attributed to Bai, K..

11 recordsLinked to original sources

bioRxiv2026

Addiction-Like Severity Predicts Prolonged Oxycodone Withdrawal-Induced Allodynia in Genetically Diverse Rats

Opioid withdrawal is associated with heightened pain sensitivity, including allodynia. Although opioid-induced allodynia is well-documented in humans and animal models, the relationship between the severity of opioid withdrawal-induced allodynia and individual addiction-like behaviors remains poorly understood. To address this gap, Heterogeneous Stock rats underwent long access (12 hours/day) intravenous oxycodone self-administration, followed by measurement of mechanical sensitivity at six timepoints across three weeks of abstinence. Rats were stratified by an Addiction Index derived from individual differences in the escalation of oxycodone intake, motivation to consume oxycodone, tolerance to oxycodones analgesic effects, and acute withdrawal-induced mechanical pain sensitivity. Here, we show that oxycodone withdrawal induces significant and prolonged allodynia for up to three weeks, with High Addiction Index rats exhibiting greater intensity and longer duration of pain sensitivity than Low Addiction Index rats. Results remained consistent even when excluding allodynia from the Addiction Index, highlighting the robustness of the association between addiction-like severity and protracted allodynia. Linear regression associations revealed that self-administration behaviors, particularly oxycodone intake escalation and motivation to seek oxycodone, predicted subsequent withdrawal-induced allodynia severity. These findings demonstrate that greater addiction-like severity is associated with more intense and prolonged withdrawal-induced pain, supporting mechanical allodynia as a marker of addiction severity. These results motivate future work to define the mechanisms linking addiction severity to protracted opioid withdrawal-induced pain, with the goal of informing targeted clinical interventions for individuals most susceptible to severe abstinence-related allodynia.

pharmacology and toxicology↗

bioRxiv2026

A standardized atlas of human bronchoalveolar lavage cells built using scalable ensemble annotation and cross-study robust markers

BackgroundBronchoalveolar lavage (BAL) single-cell RNA sequencing (scRNA-seq) offers rich insights into pulmonary immune dynamics, yet consistent cell-type annotation remains elusive. Existing methods often rely on a single reference, risking inconsistency and domain shift across datasets. A BAL-specific, high-resolution annotation framework is critically needed. MethodsWe developed BAL-EA (BAL Ensemble Annotation), a BAL-centric automated annotation framework that integrates robust, cross-study marker discovery with ensemble machine learning. BAL-EA harmonizes BAL cell identities into a three-tier taxonomy (11 major lineages, 13 refined classes, 21 fine-grained subtypes) compatible with the Human Lung Cell Atlas (HLCA) while capturing lavage-enriched biology. Marker catalogues were derived via reproducibility-guided differential expression across at least 10 independent sub-studies, ensuring resilience to dataset-specific bias. Comparative benchmarking was performed against six leading annotation tools using independent BAL datasets. ResultsWe assembled the largest BAL scRNA-seq atlas to date, integrating more than 347,333 lung cells from HLCA, multiple public BAL datasets, and the largest inhouse BAL cohort ever reported (241,924 cells from 30 individuals). BAL-EA outperformed existing annotation tools, achieving balanced macro-F1 scores over 0.95 for key lineages such as alveolar macrophages (AM), non-alveolar macrophages, and epithelial cells. Application to Chronic Obstructive Pulmonary Disease (COPD) BAL samples revealed reproducible disease-associated shifts, including increased neutrophils and CCL2-positive macrophages alongside reduced AM in COPD patients, findings validated in independent COVID-19 BAL datasets. The released atlas includes harmonized multi-resolution annotations, robust marker panels, pretrained models. ConclusionsThis work contributes the most comprehensive BAL scRNA-seq atlas, introduces a novel BAL-specific annotation framework (BAL-EA), standardizes BAL taxonomy at three resolutions, and provides rigorously validated marker gene resources. Together, these advances deliver a powerful reference for reproducible BAL scRNA-seq analysis and lay the foundation for clinical and translational applications in respiratory disease research.

genomics↗

bioRxiv2025

Incentive Salience, not Psychomotor Sensitization or Tolerance, Drives Escalation of Cocaine Self-Administration in Heterogeneous Stock Rats

Sensitization and tolerance are two phenomena often studied independently despite overlapping neurobiological substrates. Each has extensive research showing their influence on the development and maintenance of addiction, but the degree to which they drive escalation in cocaine self-administration is poorly understood. Using self-administration, intravenous noncontingent infusions, and pose-estimation machine vision, we find that incentive salience, not psychomotor sensitization or tolerance, drives the escalation of cocaine self-administration in heterogenous stock rats. Individual differences in psychomotor sensitization or tolerance were found to have no effect on cocaine intake. Incentive salience as measured by locomotion and active lever entrances per meter traveled occurring before the self-administration session began (pre-lever activity measures) during Short Access (2-hours) was found to predict intake during Long Access (6-hours). Both pre-lever locomotion and active lever entrances per meter were found to increase during Long Access and after two-to-three days of abstinence. Critically, rats with low pre-lever activity during Short Access escalated both their intake and pre-lever measures by the end of Long Access to levels comparable with high pre-lever activity rats who maintained their elevated responding. These findings support the notion that incentive salience during Short Access is a catalyst to escalated use and an early marker of addiction vulnerability. Moreover, they suggest that individuals initially resistant to incentive salience can, with sufficient exposure, become sensitized and escalate cocaine use to the same level as more susceptible individuals. Analysis of pre-lever activity offers a novel longitudinal behavioral marker to predict vulnerability and provides a framework for understanding individual trajectories of addiction.

neuroscience↗

bioRxiv2025

An activated wheat CCG10-NLR immune receptor forms an octameric resistosome

Nucleotide-binding and leucine-rich repeat (LRR) receptors (NLRs) are widespread intracellular immune sensors across kingdoms. In plants, the G10-type coiled-coil (CCG10)-NLRs form a distinct phylogenetic clade that remains poorly characterized. Here, we identified a gain-of-function (GOF) mutant of Wheat Autoimmunity 3 (WAI3), designated WAI3GOF, which encodes a constitutively activated CCG10-NLR protein due to an amino acid substitution. Cryo-EM structural analysis revealed that activated WAI3 assembles into a distinctive octameric resistosome. Arabidopsis RPS2, another CCG10-NLR, also forms an octamer, indicating a conserved structural property across monocot and dicot plants. The WAI3 resistosome mediates a prolonged and sustained increase in cytosolic calcium influx, facilitated by a unique channel architecture arising from its divergent CC domain configuration. Notably, this domain arrangement may be shared by many plant NLRs that lack the conserved EDVID motif in their CC domains. Our findings uncover a previously uncharacterized resistosome structure and provide insights into plant immune receptor plasticity.

plant biology↗

bioRxiv2025

Single virus lipid mixing study of Sendai virus provides insight into fusion mechanism

Single virus studies have proven useful to interrogate the entry mechanism for several viral families. Here, we employ a fluorescence microscopy-based single virus assay to study the fusion (lipid mixing) of Sendai virus to model membranes, the first for any paramyxovirus to our knowledge. We find that fusion wait times following binding are exponentially distributed, suggesting a single rate-limiting step. Compared to previously studied viruses, fusion is relatively slow (tens of minutes) and inefficient (only a small fraction of virions undergo fusion). Trypsin treatment of the virus or different viral receptors in the target alter the efficiency, although the wait time distribution remains unchanged in both cases. This provides constraints on the fusion mechanism and the identity of the rate-limiting step. Together, our data paints a picture of Sendai virus as a comparatively inefficient and slow fusion "machine" and sets the stage for investigation of other paramyxoviruses.

biophysics↗

bioRxiv2025

High Incidence of Estrous Cycle Irregularities in Heterogeneous Stock (HS) Rats is Associated with Severe Cocaine Addiction-like Behaviors

Hormonal fluctuations throughout the estrous cycle have been hypothesized to influence drug-related behaviors. Preclinical models show that some cocaine-related behaviors are influenced by the estrous cycle. However, the extent to which the estrous cycle modulates cocaine self-administration in outbred heterogeneous stock (HS) rats, a population that captures human genetic diversity, is unknown. This study aimed to examine the relationship between estrous phases and cocaine self-administration behavior in HS rats using a model of extended access to cocaine self-administration. We focused on the escalation of intake, breaking point, and resistance to foot shock. Using vaginal swabbing and lavage techniques, we first characterized the relationship between estrous phase and cocaine intake. We then comprehensively evaluated estrous cycling patterns in young adult and adult HS rats, comparing them with Wistar rats. Contrary to our hypothesis, estrous phase showed no association with cocaine self-administration in HS rats. HS rats exhibited irregular estrous cycling with variability to the phase length, even in the absence of drug exposure, a phenomenon not observed in the Wistar strain. Irregular estrous cycle was associated with high cocaine-related behaviors. This study provides the first evidence that some female HS rats exhibit irregular estrous cycling. Moreover, rats with severe addiction-like behaviors had more instances of irregular cycling. These results demonstrate that, in HS rats, the estrous phase per se has no major influence on cocaine self-administration, but that the severity of addiction-like behaviors are associated with more irregularity of the estrus cycle. As HS rats gain popularity in behavioral and genome-wide studies, understanding these cycle disruptions is crucial as they may reveal genetic links into female vulnerability to drugs.

neuroscience↗

bioRxiv2022

Tumor microenvironments impair T cell receptor affinity and function

CD8+ T cells underpin effective anti-tumor immune responses in melanoma; however, their functions are attenuated due to various immunosuppressive factors in the tumor microenvironment (TME), resulting in disease progression. T cell function is elicited by the T cell receptor (TCR), which recognizes antigen peptide-major histocompatibility complex (pMHC) expressed on tumor cells via direct physical contact, i.e., two-dimensional (2D) interaction. TCR-pMHC 2D affinity plays a central role in antigen recognition and discrimination, and is sensitive to both the conditions of the T cell and the microenvironment in which it resides. Herein, we demonstrate that CD8+ T cells residing in TME have lower 2D TCR-pMHC bimolecular affinity and TCR-pMHC-CD8 trimolecular avidity, pull fewer TCR-pMHC bonds by endogenous forces, flux lower level of intracellular calcium in response to antigen stimulation, exhibit impaired in vivo activation, and show diminished anti-tumor effector function. These detrimental effects are localized in the tumor and tumor draining lymph node (TdLN), and affect both antigen-inexperienced and antigen-experienced CD8+ T cells irrespective of their TCR specificities. These findings implicate impaired antigen recognition as a mechanism of T cell dysfunction in the TME.

immunology↗

bioRxiv2022

scAnnotate: an automated cell type annotation tool for single-cell RNA-sequencing data

MotivationSingle-cell RNA-sequencing (scRNA-seq) technology enables researchers to investigate a genome at the cellular level with unprecedented resolution. An organism consists of a heterogeneous collection of cell types, each of which plays a distinct role in various biological processes. Hence, the first step of scRNA-seq data analysis is often to distinguish cell types so they can be investigated separately. Researchers have recently developed several automated cell type annotation tools, requiring neither biological knowledge nor subjective human decisions. Dropout is a crucial characteristic of scRNA-seq data widely used in differential expression analysis. However, dropout information is not explicitly used by any current cell annotation method. Fully utilizing dropout information for cell type annotation motivated this work. ResultsWe present scAnnotate, a cell annotation tool that fully utilizes dropout information. We model every genes marginal distribution using a mixture model, which describes both the dropout proportion and the distribution of the non-dropout expression levels. Then, using an ensemble machine learning approach, we combine the mixture models of all genes into a single model for cell-type annotation. This combining approach can avoid estimating numerous parameters in the high-dimensional joint distribution of all genes. Using fourteen real scRNA-seq datasets, we demonstrate that scAnnotate is competitive against nine existing annotation methods. Furthermore, because of its distinct modelling strategy, scAnnotates misclassified cells are very different from competitor methods. This suggests using scAnnotate together with other methods could further improve annotation accuracy. AvailabilityWe implemented scAnnotate as an R package and made it publicly available from CRAN. ContactXuekui Zhang: xuekui@uvic.ca and Li Xing: li.xing@math.usask.ca

bioinformatics↗

bioRxiv2022

Rapid Selectivity to Natural Images Across Layers of Primate V1

Visual systems are thought to have adapted to the statistical properties of natural scenes. However, the extent to which visual neurons respond selectively to natural images, and the stage at which that selectivity emerges remains unclear. To address these questions, we recorded the visual activity of neurons in macaque V1 using high-density electrode arrays (Neuropixels), and compared neuronal responses to images presented at three levels of naturalness. We found that within 60 ms of stimulus onset, neurons in all cortical layers, including input layers 4C alpha and beta, responded more vigorously to natural images than to statistically matched naturalistic texture and noise images. The result remained when residual variations in the local image statistics were factored out. V1 neurons also showed high population and lifetime sparseness for natural images. Across the population of V1 neurons, sensitivity to natural images exceeded the sensitivity to other image categories. The results reveal a rapid and pervasive preference for natural images is present at the earliest stages of cortical processing.

neuroscience↗

bioRxiv2018

Polyacrylamide Bead Sensors for in vivo Quantification of Cell-Scale Stress in Zebrafish Development

Mechanical stress exerted and experienced by cells during tissue morphogenesis and organ formation plays an important role in embryonic development. While techniques to quantify mechanical stresses in vitro are available, few methods exist for studying stresses in living organisms. Here, we describe and characterize cell-like polyacrylamide (PAAm) bead sensors with well-defined elastic properties and size for in vivo quantification of cell-scale stresses. The beads were injected into developing zebrafish embryos and their deformations were computationally analyzed to delineate spatio-temporal local acting stresses. With this computational analysis-based cell-scale stress sensing (COMPAX) we are able to detect pulsatile pressure propagation in the developing neural rod potentially originating from polarized midline cell divisions and continuous tissue flow. COMPAX is expected to provide novel spatiotemporal insight into developmental processes at the local tissue level and to facilitate quantitative investigation and a better understanding of morphogenetic processes.

biophysics↗

bioRxiv2017

A synthetic stroma-free germinal center niche using material-surface driven polyvalent signaling efficiently induces antigen-specific humoral immunity ex vivo

B cells play a major role in the adaptive immune response by producing antigen-specific antibodies against pathogens and imparting immunological memory. Following infection or vaccination, antibody-secreting B cells and memory B cells are generated in specialized regions of lymph nodes and spleens, called germinal centers. Here, we report a fully synthetic ex-vivo system that recapitulates the generation of antigen-specific germinal-center (GC) like B cells using material-surface driven polyvalent signaling. This synthetic germinal center (sGC) reaction was effectively induced using biomaterial-based artificial \"follicular T helper cells (TFH)\" that provided both natural CD40-CD40L ligation as well as crosslinking of CD40; and by mimicking artificial \"follicular dendritic cells (FDC)\" to provide efficient, polyvalent antigen presentation. The artificial sGC reaction resulted in efficient B cell expansion, immunoglobulin (Ig) class switching, and expression of germinal center phenotypes. Antigen presentation during sGC reaction selectively enhanced the antigen-specific B cell population and induced somatic hyper-mutations for potential affinity maturation. The resulting B cell population consisted primarily of GC-like B cells (centrocytes) as well as some plasma-like B cells expressing CD138. With concurrent cell sorting, we successfully created highly enriched populations of antigen-specific B cells. Adoptive transfer of these GC-like B cells into non-irradiated isogeneic or non-lethally irradiated congenic recipient mice showed successful engraftment and survival of the donor cells for the 4 week test period. We show that this material-surface driven sGC reaction can be successfully applied to not only splenic B cells but also B cells isolated from more therapeutically relevant sources such as peripheral blood mononuclear cells (PBMCs), thus making our current work an exciting prospect in the new era of personalized medicine and custom-immunotherapy.

bioengineering↗