Biology subjects

Li, V. W.

Publications and source records attributed to Li, V. W..

7 recordsLinked to original sources

bioRxiv2026

Disease progression shapes circadian and locomotor disruption in a model of multiple sclerosis

Multiple sclerosis (MS) is an autoimmune demyelinating disease of the central nervous system featuring a wide range of debilitating symptoms. Wearable activity recording devices have recently been adopted to improve symptom monitoring in MS, capturing symptoms related to sleep/wake cycles, circadian disruption, and fatigue. However, comparable measures of activity have yet been established in pre-clinical models of MS, the most widely used being experimental autoimmune encephalomyelitis (EAE). We therefore sought to characterize changes in continual home-cage activity over the course of EAE, and establish whether home-cage monitoring can be used as an observer-independent measure of disease progression. Our results showed that locomotor activity in the mid-active/dark phase was most severely affected by EAE. Disrupted circadian (24-hour) activity was observed during the peak and onset stages of disease. Bout activity analysis revealed >40-minute long activity bouts as a sensitive indicator of non-motor symptoms independent of clinical score-based motor deficits. Current assessment of disease progression in EAE relies on clinical scores, which primarily assess motor deficits through visual observation prone to observer bias. Various computed activity parameters were found to be altered during key disease stages, suggesting that a combination of activity measures can serve as objective indicators of disease progression. Overall, our results show that home-cage activity effectively captures signs of non-motor symptoms in the EAE model of MS and can serve as an observer-independent measure of EAE disease progression.

animal behavior and cognition↗

bioRxiv2026

Hidden drivers of restoration: Persistent divergence in soil microbiome functional capacity post-habitat reconstruction

Ecosystems today are facing unprecedented environmental stress, leading to large-scale losses of habitat and ecosystem services. To address this, reconstructive efforts aim to restore habitat features and their natural complexity, biodiversity, and function. However, many reconstructive efforts fail to consider microbial communities, even though they play key roles in decomposition, nutrient cycling, and plant and animal health. Here, we use shotgun metagenomic sequencing to compare the structure and functional capacity of soil microbial communities from natural Everglades tree islands and islands constructed within a landscape-scale experimental Everglades restoration effort, followed by a manipulative greenhouse experiment to link tree sapling traits with microbiome functional genetic divergence. We found that constructed and natural island microbiomes exhibited strong, robust, and persistent divergence in both taxonomic and functional composition, with natural island microbial communities having greater functional genetic diversity and redundancy. Furthermore, we identified enrichment in functional pathways in constructed island microbiomes such as those involved in pollutant degradation that may reflect continued disturbance leading to shifts in microbiome functional profiles. Despite their capacity for functions such as nitrogen cycling we found to be important for supporting sapling growth, constructed island microbiomes displayed reduced functional genetic diversity and redundancy and were enriched in pathways associated with environmental disturbance, suggesting a potentially diminished capacity for long-term resilience. Overall, our assessment of soil microbial communities in reconstructed and natural habitats emphasizes how reconstructive restoration can impact microbial functional repertoires and highlights the importance of these hidden players in management and restoration of ecosystem health.

ecology↗

bioRxiv2025

Climate variability disrupts mutualism-driven increases in population persistence

Understanding how species interactions impact population dynamics and long-term persistence over broad temporal and spatial scales is crucial for predicting species distributions and responses to global change. Here, we integrate range-wide field surveys of [~]90 grass host populations spanning 13 years with demographic modeling based on six-year common garden experiments conducted across the host range to demonstrate that mutualistic fungal endophytes promote population-level persistence and growth of their native host grass across its distribution, with non-mutualistic populations four times more likely to go locally extinct. Despite providing population-level benefits, endophyte prevalence declined eight-fold more in historically mutualistic populations that experienced high climate variability. Thus, mutualisms can underpin population persistence and buffer hosts against environmental stress, but may themselves be vulnerable to global change, with concerning implications for long-term population viability and, ultimately, species distributions under an increasingly uncertain climate.

ecology↗

bioRxiv2025

Spatial Transcriptomics Using Archived Formalin-Fixed Paraffin-Embedded Core Needle Biopsy Tissues Revealed Unique Transcriptomic Signatures in Kidney Transplant Rejections

Clinical core needle biopsies present challenges for transcriptomic analysis due to limited tissue volume. In this study, we determined the feasibility of using spatial transcriptomics to evaluate rejection on formalin-fixed paraffin-embedded (FFPE) core needle biopsies from human kidney allografts. We demonstrated that non-rejection, active antibody mediated rejection (AMR), acute cell mediated rejection (TCMR) and chronic active AMR have distinct transcriptomic signatures. Subclusters of monocytes/macrophages with high Fc gamma receptor IIIA (FCGR3A) expression were identified in C4d-positive active AMR and acute TCMR, and the spatial distribution of these cells corresponded to the characteristic histopathological features. Key markers related to monocyte/macrophage activation and innate alloantigen recognition were upregulated, along with metabolic pathways associated with trained immunity in AMR and TCMR. The discovery of unique transcriptomic signatures associated with AMR and TCMR facilitates the differentiation of acute kidney allograft rejections using spatial transcriptomic data derived from FFPE core needle biopsies.

immunology↗

bioRxiv2024

Mass spectrometric profiling of estrogen and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling

Estrogen and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no reports of estrogen measured in human stool. This methodological limitation in turn limits our understanding of the relationship between systemic and intestinal estrogen. We thus developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method for measuring free and conjugated forms of 15 estrogens and estrogen metabolites in human stool and plasma. We first investigated human stool and plasma estrogen in healthy control males; follicular and luteal phase premenopausal females; and postmenopausal females. Most estrogens were present in the plasma and stool of all groups, and plasma estrogen levels correlated with stool estrogen levels. In stool, estrogens were higher in premenopausal females, with estrogen levels rising across the menstrual cycle. We further combined these measures with shotgun metagenomic sequencing of the stool microbiomes. The level of estrogen deconjugation enzyme gene copy number (beta-glucuronidase + arylsulfatase) was higher in premenopausal females; while the gene copy numbers of beta-glucuronidase + arylsulfatase, but not beta-glucuronidase alone, correlated with reactivated stool estrogen in all groups. Moreover, deconjugation enzyme gene copy number correlated with plasma total estrogen in males and with individual plasma estrogen metabolites in all groups. These results support the hypothesis that gut microbial beta-glucuronidase and arylsulfatase control the reactivation of gut estrogen while modulating systemic levels through the uptake and recirculation of reactivated estrogen.

molecular biology↗

bioRxiv2024

Analyzing RNA-Seq Data from Chlamydia with Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems

MotivationRNA sequencing (RNA-Seq) offers profound insights into the complex transcriptomes of diverse biological systems. However, standard differential expression analysis pipelines based on DESeq2 and edgeR encounter challenges when applied to the immediate early transcriptomes of Chlamydia spp., obligate intracellular bacteria. These challenges arise from their reliance on assumptions that do not hold in scenarios characterized by extensive transcriptomic activation and limited repression. Standard analyses using unique chlamydial RNA-Seq reads alone identify nearly 300 upregulated and about 300 downregulated genes, significantly deviating from actual RNA-Seq read trends. ResultsBy incorporating both chlamydial and host reads or adjusting for total sequencing depth, the revised normalization methods each detected over 700 upregulated genes and 30 or fewer downregulated genes, closely aligned with observed RNA-Seq data. Further validation through qRT-PCR analysis confirmed the effectiveness of these adjusted approaches in capturing the true extent of transcriptomic activation during the immediate early phase of chlamydial infection. While the strategies employed are developed in the context of Chlamydia, the principles of flexible and context-aware normalization may inform adjustments in other systems with unbalanced gene expression dynamics, such as bacterial spore germination. Availability and implementationThe code for reproducing the presented bioinformatic analysis is available at https://zenodo.org/records/11201379.

bioinformatics↗

bioRxiv2023

Requirement of GrgA for Chlamydia infectious progeny production, optimal growth, and efficient plasmid maintenance

Chlamydia, an obligate intracellular bacterial pathogen, has a unique developmental cycle involving the differentiation of invading elementary bodies (EBs) to noninfectious reticulate bodies (RBs), replication of RBs, and redifferentiation of RBs into progeny EBs. Progression of this cycle is regulated by three sigma factors, which direct the RNA polymerase to their respective target gene promoters. We hypothesized that the Chlamydia-specific transcriptional regulator GrgA, previously shown to activate {sigma}66 and {sigma}28, plays an essential role in chlamydial development and growth. To test this hypothesis, we applied a novel genetic tool known as dependence on plasmid-mediated expression (DOPE) to create Chlamydia trachomatis with conditional GrgA-deficiency. We show that GrgA-deficient C. trachomatis RBs have a growth rate that is approximately half of the normal rate and fail to transition into progeny EBs. In addition, GrgA-deficient C. trachomatis fail to maintain its virulence plasmid. Results of RNA-seq analysis indicate that GrgA promotes RB growth by optimizing tRNA synthesis and expression of nutrient-acquisition genes, while it enables RB-to-EB conversion by facilitating the expression of a histone and outer membrane proteins required for EB morphogenesis. GrgA also regulates numerous other late genes required for host cell exit and subsequent EB invasion into host cells. Importantly, GrgA stimulates the expression of {sigma}54, the third and last sigma factor, and its activator AtoC, and thereby indirectly upregulating the expression of {sigma}54-dependent genes. In conclusion, our work demonstrates that GrgA is a master transcriptional regulator in Chlamydia and plays multiple essential roles in chlamydial pathogenicity. IMPORTANCEHallmarks of the developmental cycle of the obligate intracellular pathogenic bacterium Chlamydia are the primary differentiation of the infectious elementary body (EB) into the proliferative reticulate body (RB) and the secondary differentiation of RBs back into EBs. The mechanisms regulating these transitions remain unclear. In this report, we developed an effective novel strategy termed DOPE that allows for the knockdown of essential genes in Chlamydia. We demonstrate that GrgA, a Chlamydia-specific transcription factor, is essential for the secondary differentiation and optimal growth of RBs. We also show that GrgA, a chromosome-encoded regulatory protein, controls the maintenance of the chlamydial virulence plasmid. Transcriptomic analysis further indicates that GrgA functions as a critical regulator of all three sigma factors that recognize different promoter sets at developmental stages. The DOPE strategy outlined here should provide a valuable tool for future studies examining chlamydial growth, development, and pathogenicity.

microbiology↗