Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 541 records · Page 30Linked to original sources

bioRxiv2025

Increased aridity is associated with diversity and composition changes in the biocrust mycobiome

Drylands comprise 45% of Earths land area and contain ecologically critical soil surface communities known as biocrusts. Biocrusts are composed extremotolerant organisms including cyanobacteria, microfungi, algae, lichen, and bryophytes. Fungi in biocrusts help aggregate these communities and may form symbiotic relationships with nearby plants. Climate change threatens biocrusts, particularly moss biocrusts, but its effects on the biocrust mycobiome remain unknown. Here, we performed a culture-dependent and metabarcoding survey of the moss biocrust mycobiome across an aridity gradient to determine whether local climate influences fungal community composition. As the local aridity index increased, fungal communities exhibited greater homogeneity in beta diversity. At arid and hyper-arid sites, communities shifted toward more extremotolerant taxa. We identified a significant proportion of fungal reads and cultures from biocrusts that could not be classified. Rhodotorula mucilaginosa and R. paludigena were significantly enriched following surface sterilization of healthy biocrust mosses. This aligns with their known roles as plant endophytes. We also observed septate endophyte colonization in the photosynthetic tissues of mosses from arid climates. Collectively, these results suggest that the biocrust mycobiome will undergo significant shifts in diversity due to climate change, favoring extremotolerant taxa as climate conditions intensify. The survey results also highlight taxa with the potential to serve as bioinoculants for enhancing biocrust resilience to climate change. These findings offer valuable insights into the potential impacts of climate change on drylands and provide crucial information for biocrust conservation.

microbiology↗

bioRxiv2025

Structure, identification and characterization of the RibD-enolase complex in Francisella

Francisella tularensis is a highly infectious bacterium, a Tier 1-select agent, and the causative agent of tularemia, a potentially fatal zoonotic disease. In this study originally aiming to identify anti-tularemia drug targets, we serendipitously determined the atomic structures and identified their components of the native RibD-enolase protein complex in Francisella novicida; and subsequently systematically characterized the catalytic functions of the RibD-enolase complex. Originally discovered as individually protein in Escherichia coli and yeast, respectively, RibD and enolase are two essential enzymes involved in distinct metabolic pathways, both of which could serve as potential therapeutic targets for tularemia treatment and prevention. Our biochemical validation using pull-down assays confirmed the formation of this complex in vivo, revealing that all eluted RibD is bound to enolase, while the majority of enolase remained uncomplexed. Structural analysis reveals unique features of the Francisella complex, including key RibD-enolase interactions that mediate complex assembly and {beta}-strand swapping between RibD subunits. Furthermore, molecular dynamics simulations of the ligand-bound RibD-enolase complex highlight localized conformational changes within the substrate-binding sites and suggest a gating mechanism between RibDs substrate and cofactor-binding sites to ensure efficient uptake and turnover. Despite the physical association between RibD and enolase, enzymatic assays indicated their catalytic activities are independent of each other, thus the complex may have alternative functional roles that warrant further exploration. Our study provides the first structural and biochemical characterization of the RibD-enolase complex, establishing a foundation for further investigations into its functional significance in Francisella and potential antibacterial development. SignificanceFrancisella tularensis, a dangerous bacterium classified as a high-priority bioterrorism threat, causes tularemia, a severe and sometimes deadly disease spread from animals to humans. In a study originally aimed at finding new treatments, we accidentally uncovered a unique partnership between two enzymatic proteins--RibD and enolase--in Francisella. These proteins, previously known to work alone in other non-pathologic organisms, were found to form a heterodimer of RibD and enolase dimers in Francisella. Biochemical experiments confirmed that enolase works both alone and together with RibD in living cells. In addition to the novel heterodimer-of-homodimer configuration, the RibD subunits feature swapped {beta} strands for dimerization as compared to E. coli RibD homodimer. The results offer clues for designing future antibiotics against tularemia and beyond.

microbiology↗

bioRxiv2025

Thiazole substitution of a labile amide bond - a new option towards stable pantothenamide-mimics

The emergence and spread of artemisinin-resistant, malaria-causing P. falciparum provide the impetus for the development of novel antimalarials. Pantothenamides are potent inhibitors of malaria parasite proliferation, however their clinical use is hindered by pantetheinase-mediated degradation in human serum. Here we report the synthesis and biological activity of a series of pantothenamide-mimics in which the labile amide bond is replaced by a thiazole ring with various orientations. Out of 23 novel compounds generated and tested in the presence of pantetheinase, several display sub-micromolar antiplasmodial activity in vitro. A selection of compounds was studied in more detail and CoA biosynthesis and/or utilisation pathways were confirmed to be the target. Toxicity to human cells was not observed. Kinetic studies identified the selected compounds as substrates of the HsPanK3 enzyme, but with much lower affinity compared to that of the natural substrate pantothenate. The most potent thiazole-bearing antiplasmodial compound was found to bind to PfPanK with a 120-fold higher affinity compared to HsPanK, highlighting excellent selectivity, not only against the key first enzyme in the CoA biosynthesis pathway, but also at the whole-cell level. In conclusion, thiazole substitution of the labile amide bond represents a promising avenue for the development of antimalarial pantothenamide-mimics.

pharmacology and toxicology↗

bioRxiv2025

Characterizing trajectory-like chromatin architectures with Fun2

Chromatin is intricately folded into dynamic 3D structures, orchestrating key DNA metabolic processes. DNA replication, a core chromatin metabolic event, is tightly linked to these chromatin architectures. Recently, a replication-associated chromatin interaction structure was discovered as fountains via Replication-associated in situ Hi-C (Repli-HiC), supporting that replication forks remain spatially coupled from initiation to termination. Chromatin fountains are pivotal for understanding DNA replication within the complex chromatin landscape. However, the characteristics of these fountains can vary due to factors such as origin firing efficiency and local chromatin organization. In this study, we introduce a reinforcement learning-based computational framework, integrated with Monte Carlo Tree Search (MCTS) and value gradient optimization, to develop the Fun2 algorithm. Fun2 enables a comprehensive characterization of trajectory-like chromatin architectures, including both chromatin fountains and stripes, with enhanced adaptability and accuracy. This tool facilitates systematic investigation of the spatiotemporal dynamics of DNA replication and extends to other chromatin remodeling processes, such as Cohesin-mediated loop extrusion. The Fun2 algorithm provides a versatile computational tool for deciphering dynamic chromatin architectures, offering new insights into genome organization and its regulatory mechanisms.

bioinformatics↗

bioRxiv2025

Cultured endothelial cells present organ-specific RTK distributions: advancing receptor measurement and data standardization via quantitative flow cytometry

PurposeReceptor tyrosine kinase (RTK) concentrations on the plasma membrane correlate with angiogenic functions in vitro and in rodent models. The intracellular RTK pool also regulates plasma membrane receptor availability and signaling pathways. Organs have specialized angiogenic functions essential to their distinct roles, supporting the hypothesis that plasma membrane and intracellular RTK concentrations vary across endothelial cells (ECs) from different organs. MethodsUsing quantitative flow cytometry on human ECs derived from dermis, umbilical vein, kidney, liver, and brain, we measured and statistically analyzed the concentrations of selected RTKs within ECs and on their plasma membranes. ResultsVEGFR1 exhibited the lowest concentrations on the plasma membrane (300-900 VEGFR1/cell) among VEGFRs. HDMECs (dermis) showed the lowest VEGFR1 level among the examined EC types. Whole-cell VEGFR1 concentrations were 2500-7500 VEGFR1/cell, with 12-26% located on the plasma membrane. The proportion of VEGFR2 located on the plasma membrane was higher at > 30%, except in HGMECs (kidney) where it was 24%. Plasma membrane VEGFR2 was significantly lower in HDMECs and HGMECs compared with HBMECs (brain), whereas whole-cell VEGFR2 levels were consistently in the range of 14,100-22,500 molecules/cell. VEGFR3 was the least localized to the plasma membrane, from 2% in HGMECs to 14% in HDMECs at the highest level of 4400 VEGFR3/cell. Whole-cell VEGFR3 concentrations ranged from 32,400 in HDMECs to 62,000 VEGFR3/cell in HLiSMECs (liver), with no significant differences among EC types. NRP1 was most abundant on the plasma membrane of HUVECs (umbilical vein) at 39,700 NRP1/cell; other ECs displayed 26,000-29,900 NRP1/cell, approximately 5-fold higher than the numbers of VEGFRs. Across EC types, Axl was present on the plasma membrane at levels (6900-12,200 Axl/cell) similar to those of VEGFR2. ConclusionsWe quantified and statistically analyzed plasma membrane and whole-cell expression of angiogenic RTKs across cultured human ECs from five different organs. Our findings suggest that RTK protein distribution might not fully reflect the differential angiogenic capacities in cultured ECs. In vitro monoculture conditions might reduce EC organ-specific features essential for refining vascular models.

bioengineering↗

bioRxiv2025

PACAP alleviates the defective epididymis and sperm function in LPS-induced acute mice epididymitis

BackgroundTo investigate the molecular mechanisms by which PACAP alleviates LPS-induced epididymitis, focusing on its anti-inflammatory and antioxidant pathways in the epididymal microenvironment. MethodsA mouse model of acute epididymitis was induced by LPS injection. The study assessed the levels of inflammatory markers (IL-6 and TNF- mRNA) in the cauda epididymis, sperm motility and morphology, morphological alterations in the epididymis, and the expression of inflammation and antioxidant-related genes. PACAP treatment was administered to evaluate its effects on these parameters. ResultsResults showed elevated levels of IL-6 and TNF- mRNA in the cauda epididymis due to LPS injection. PACAP treatment effectively reduced these inflammatory markers and improved compromised sperm motility and morphology. PACAP also ameliorated morphological changes in the epididymis and mitigated the LPS-induced increase in leukocyte and macrophage markers. Gene expression analysis revealed that PACAP co-treatment suppressed LPS-induced upregulation of Il-6 and Tnf- in caput tissues. In cauda tissues, PACAP significantly reduced the expression of LPS-elevated Tnf- and IL-1{beta}. PACAP up-regulated the antioxidant genes Cat and Sod1, which were down-regulated by LPS. IVF experiments demonstrated that PACAP restored the effects of LPS on sperm-egg fusion and embryo development. In conclusion: PACAP played a crucial role in maintaining epididymal function and sperm quality in the presence of inflammation.

molecular biology↗

bioRxiv2025

Decoding the neural basis of sensory phenotypes in Autism

BackgroundDifferences in sensory processing are a defining characteristic of autism, affecting up to 87% of autistic individuals. These differences cause widespread perceptual changes that can negatively impact cognition, development, and daily functioning. Recent research identified five sensory processing phenotypes with varied behavioural presentations; however, their neural basis remains unclear. This study aims to ground these sensory phenotypes in unique patterns of functional connectivity. MethodsWe analyzed data from 146 autistic participants in the Province of Ontario Neurodevelopmental Network. We classified participants into sensory phenotypes using k-means clustering of scores from the Short Sensory Profile. We then computed a connectivity matrix from 200 cortical and 32 subcortical regions and calculated graph-theoretic measures (betweenness centrality, strength, local efficiency, clustering coefficient) to assess information exchange between these regions. We then trained machine learning models to use these measures to classify between all pairs of sensory phenotypes. ResultsWe replicated that our sample of autistic participants was best categorized into five sensory phenotypes. The machine learning models distinguished 7/10 phenotype pairs using graph-theoretic measures (p < 0.005). Information exchange within and between the somatomotor network, orbitofrontal cortex, posterior parietal cortex, prefrontal cortex and subcortical areas were highly predictive of sensory phenotype. ConclusionsThis study shows that distinct sensory phenotypes in autism correspond with unique patterns of functional connectivity. Cortical, subcortical, and network-level connectivity all play a role in shaping distinct sensory processing styles in autism. These findings lay the groundwork for understanding these phenotypes and highlight opportunities to develop interventions in cases of maladaptive sensory processing.

neuroscience↗

bioRxiv2025

Basic-Leucine-Zipper Transcription Factors Regulate Selective Molecular Phenotypes in Regulatory T Cells During IL-2-Induced Activation

Regulatory T (Treg) cells have long been recognized as modulators of immunological tolerance and homeostasis. Previously, we used scRNA-seq to reveal significant Treg heterogeneity in response to IL-2-induced activation. Herein, we leveraged enrichment analyses, as well as bulk and single-nucleus multi-omics in splenic and lung Tregs, to uncover and confirm the importance of transcription factors (TFs) and chromatin remodeling in Treg activation. Multiple bZIP TF motifs showed increased chromatin accessibility post IL-2 treatment, with correlated transcriptional changes resembling Th1 and Th2 molecular phenotypes, further confirmed by spatial ATAC-seq. By combining gene perturbation and CUT&RUN assays before and after Treg stimulation, we show that bZIP TFs, such as BATF and BACH1, are critical to IL-2-induced Treg activation, coordinating epigenetic and transcriptional changes that selectively drive T-helper phenotypes and metabolic pathways.

genomics↗

bioRxiv2025

Excavating Podocyte-Protective Targets of phloroglucinol-terpene hybrids Utilizing AI Models and Omics Analysis

Lupus nephritis (LN) is a multifactorial autoimmune inflammatory disorder, with podocyte dysfunction or structural abnormalities playing a pivotal role in its pathogenesis. Eucalyptus leaves, traditionally employed in folk medicine, have demonstrated notable efficacy in managing non-infectious inflammations. Eucarbwenstols D (R14) is a novel phloroglucinol-terpene that has been isolated from Eucalyptus robusta. To further refine potential targets, we utilized an AI scoring system and successfully identified the epidermal growth factor receptor (EGFR) as the novel target of R14. This discovery was built upon the foundation of transcriptome and connectivity mapping (CMap) analysis. Molecular docking and molecular dynamics simulations were employed to analyze the interaction between R14 and EGFR, surface plasmon resonance (SPR) and homogeneous time-resolved fluorescence (HTRF) assays were utilized to accurately quantify the binding affinity between R14 and EGFR. Western blot (WB) and immunofluorescence assays were then conducted to explore the downstream signaling pathways initiated by EGFR, specifically the PI3K/AKT/mTOR pathway. These assays demonstrated that R14 modulates the expression of apoptotic proteins Bax and Bcl-2 through this pathway, thereby exerting a protective effect on podocytes from undergoing apoptosis. The modulation of key podocyte proteins, nephrin and podocin, further substantiates this protective effect. Overall, we have applied a novel AI algorithm model that transcends bioinformatics analysis to precise identification of the novel podocyte target of R14. In this study, R14 was identified for the first time as a novel scaffold compound for EGFR inhibition. Moreover, R14 has demonstrated its capacity to inhibit podocyte apoptosis, thereby protecting these critical cells. This discovery establishes a robust theoretical foundation for the use of phloroglucinol-terpene hybrids (PTHs) in the treatment of LN.

cell biology↗

bioRxiv2025

Layered stomatal immunity contributes to resistance of Vitis riparia against downy mildew Plasmopara viticola

Downy mildew (DM), caused by Plasmopara viticola, is one of the most serious grapevine diseases. Resistant grapevines are a well-known tool for mitigating pathogen-caused damage. We evaluated 29 global grapevine cultivars from 7 species for the sensitivity to P. viticola. Chardonnay belonging to the sensitive species V. vinifera and Qingdahean belonging to the well-known resistant species V. riparia were chosen for further investigation on the resistance mechanism against DM. Unlike Chardonnay, Qingdahean exerted an inhibitory effect on stomatal targeting, suppression of stomatal closure, stomatal penetration of P. viticola, and the development of primary hyphae and haustoria during the early phase of infection, and contained higher levels of malondialdehyde (MDA), which was significantly increased by P. viticola infection, toxic to the pathogen and had an interfering effect on the stomatal targeting. Furthermore, Qingdahean resisted pathogen invasion through the rapid induction of guard cell death and the hypersensitive responses (HR) of other cell types. These findings suggest that resistance to P. viticola consists of layered stomatal immunity in addition to the well-known HR in V. riparia, which is overcome by the pathogen in V. vinifera.

plant biology↗

bioRxiv2025

The novel SCN5A-P1891A mutation is associated with left ventricular hypertrabeculation and links Nav1.5 to cardiomyocyte proliferation and disrupted 3D cardiac tissue formation

BackgroundLeft ventricular hypertrabeculation (LVHT) is a heterogenous cardiac condition with a complex and poorly understood aetiology. We comprehensively characterised the effect of a novel P1891A mutation in the SCN5A gene, which encodes the voltage-gated sodium channel Nav1.5, identified in a Finnish family diagnosed with LVHT. MethodsWe generated SCN5A-P1891A mutation-carrying human induced pluripotent stem cell-derived cardiomyocytes (P1891A-hiPSC-CMs) and performed electrophysiological assessments, including patch-clamp studies, and fluorescent calcium imaging, to determine the mutations effect on hiPSC-CM electrophysiology. We also evaluated the impact of the mutation on the proliferative capacity in response to mitogenic stimuli and on the hypertrophic response following cyclic mechanical stretch or endothelin-1 treatment. Further, we assessed the effect on contractile parameters in three-dimensional (3D) contractile hydrogels (engineered heart tissues, EHTs) and conducted advanced proteomics to understand the consequences of the mutation on Nav1.5 protein-protein interactions. ResultsThe SCN5A-P1891A mutation reduced the sodium current densities and increased both the sodium window current and arrhythmogenicity; however, action potential parameters were unaffected. Advanced proteomics characterised, for the first time, the complete Nav1.5 interactome and revealed that the SCN5A-P1891A mutation negated interactions with fibroblast growth factor 12 (FGF12) and FGF13, that are known to modulate sodium channel activity. Baseline proliferation was unchanged, although aged P1891A-hiPSC-CMs demonstrated enhanced proliferative capacity following mitogenic stimulation. Further, P1891A-hiPSC-CMs exhibited a heightened stress response upon mechanical stretch, resulting in the upregulation of heart failure-associated genes. Strikingly, EHTs derived from P1891A-hiPSC-CMs yielded disparate phenotypes. Whilst the majority condensed only partially and failed to beat synchronously, a small subset condensed fully yet exhibited weak contractile properties, alongside age-associated functional decline. In contrast, EHTs derived from healthy control hiPSC-CMs consistently condensed fully and demonstrated a positive correlation between post-fabrication age and contractile properties ConclusionsOur study presents a unique aetiology of LVHT and reveals a novel association between SCN5A mutations and enhanced human cardiomyocyte proliferation. Further, the inability of P1891A-hiPSC-CMs to consistently form fully condensed 3D cardiac tissues may be linked to their abnormal response to mechanical stretch and provides a powerful 3D model for future mechanistic research and drug development studies to better understand and treat LVHT.

molecular biology↗

bioRxiv2025

A distinctive subset of microglia positioned at the paraventricular zone are dedicated to cleaning the cerebrospinal fluid

The interconnected ventricles in the central nervous system are filled with cerebrospinal fluid (CSF) which serves multifaceted roles including bring away metabolic wastes. However, whether there is an inherent "dislodging" mechanism, in addition to CSF drainage and reabsorption, at play for the removal of microparticles in the CSF is unclear. In this study, we identified a subset of microglia distributed in close proximity to the ependymal wall of ventricles. They differed from parenchymal microglia in morphology, behaviors and transcriptomes. In particular, the paraventricular microglia extended transependymal dendrites into the lumen of ventricles and were proficient in sequestering and phagocytosing intraventricular exogenous particles when present. A specific removal of the paraventricular microglia led to an acute ventriculomegaly due to an increased colloid osmotic pressure in the CSF resulting from protein accumulation. Thus, we identified the paraventricular microglia as specific guardians in monitoring and cleaning the CSF.

immunology↗

bioRxiv2025

Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than gene expression diversity. The strategy of using single genome reference for RNA-seq analysis could not handle introgression bias, especially for hexaploidy wheat. Here, we conducted RNA-seq for 328 wheat lines, including representative diverse landraces and elite cultivars from China and the United States, to investigate the role of gene expression variation in shaping agronomic traits. Using pan-genome resources, we identified 20,615 more transcripts than using the Chinese Spring reference genome alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed from wild relatives were under tight genetic control. Genes responding to environmental stress show higher activity after introgressed into the wheat genome, demonstrating how long-term breeding selection impacted the gene expression regulation of targeted introgression. Multi-omics modeling identified 231 high-confidence candidate genes for 34 field agronomic traits and the seedling resistance phenotypes of 8 powdery mildew isolates. More than one fifth of those candidates have no homolog in Chinese Spring reference genome. By utilizing the indexed KN9204 EMS library, 80% candidates showed significant trait difference between wild type and mutant lines. Furthermore, directional shifts in genes of which expression were changed by breeding improvement demonstrated distinct adaptations to local environments. Our study constructed a pan-gene atlas to correct the reference bias of reads mapping in RNA-seq studies and revealed the expression patterns of introgressed genes within the wheat genome and their regulatory mechanisms, which highlighted the impact of breeding selection on gene expression of the worlds most important crop.

plant biology↗

bioRxiv2025

Graph-based Contrastive Learning Enables Unified Integration and Niche Transfer Across Single-Cell and Spatial Multi-Omics

The rapid growth of single-cell and spatial omics has outpaced computational methods capable of unifying these data into a cohesive framework for tissue atlas construction and cross-sample analysis. A critical bottleneck lies in the inability of existing tools to co-embed cells from diverse technologies--spanning transcriptomics, epigenomics, and proteomics--into a shared reference space while preserving spatial architecture and molecular specificity. Here, we present Garfield (Graph-based Contrastive Learning Enables Fast Single-Cell Embedding), a geometric deep-learning framework that addresses these challenges through spatially or molecularly aware cell embedding. Leveraging a graph contrastive learning framework, Garfield learns a shared embedding space for data generated by diverse technologies, enabling seamless construction and querying of spatial reference atlases. Our results show that Garfield consistently outperforms state-of-the-art benchmark models in identifying spatial niches across multiple datasets. We further demonstrate Garfields versatility by applying it to multi-modal spatial data, including gene expression and chromatin accessibility, where it successfully identifies distinct niches in the mouse brain. Notably, Garfield reveals tumor microenvironment heterogeneity in non-small cell lung cancer and breast cancer, uncovered conserved, barrier-like immune niches at tumor margins orchestrating CD80-mediated T cell-B cell-dendritic cell interactions and IFN-/B cell activation pathways, forming spatially coordinated immune surveillance hubs. These findings underscore Garfields potential to advance spatial omics research by offering a robust, scalable solution for integrating and interpreting complex spatial data across diverse tissue types and modalities.

bioinformatics↗

bioRxiv2025

Somatic repetitive element insertions Define New Biomarkers in Pan-cancer genome

Repetitive elements insertions (REIs), including tandem repeat insertions (TRIs) and transposable element insertions (TEIs), constitute >90% of large-scale (>50bp) somatic insertions and are linked to diseases and cancer biomarkers. However, the genomic landscape of large-scale REIs in pan-cancer has not been well-characterized due to short-read sequencing limitations. Here, we detected somatic REIs in 325 cancer genomes across 12 cancer types using long-read whole-genome sequencing and customized algorithms. The diverse sequence patterns of somatic TRIs and the insertion mechanisms of somatic TEIs were characterized across different cancer types. We identified 152 high-frequency somatic TRIs, with 10 showing pan-cancer characteristics, including TRIs in SHROOM2, PALMD, and the enhancer of PTPRZ1. The MHC class II gene cluster exhibited the highest somatic TEI abundance, affecting [~]40% tumors. Adenocarcinomas and squamous cell carcinomas exhibited differing TEI distributions within this region. Our study highlights REIs as important but under-explored markers for personalized cancer diagnosis and immunotherapy.

genomics↗

bioRxiv2025

Parallel adaptation to geothermally-warmed habitats due to common structural variation and functional developmental pathways

Climate change is causing rapid increases in temperature which drives genomic changes tied to adaptation. However, predicting the outcomes of climate change presents challenges as the anticipated conditions have yet to be experienced by natural populations. Modelling and lab experiments suggest that natural populations will experience shifts in life history, physiology, phenology, and ecology, but the underlying genomic mechanisms involved are unknown. However, some contemporary natural populations experience habitat warming through geothermal activity and can provide valuable insights into evolutionary responses. Geothermally warmed habitats should impose strong selection on ectotherms compared to ambient habitats as they increase metabolic demands, alter developmental processes, and offer novel ecological conditions. We leveraged Icelandic threespine sticklebacks (Gasterosteus aculeatus) from populations that have adaptively diverged along a geothermal/ambient habitat axis. We obtained 173,485 single nucleotide polymorphisms (SNPs) across four independent instances of population divergence using whole genome sequencing. While the majority of genomic differentiation between geothermal/ambient ecotypes was non-parallel, the MAPK signalling pathway appeared across all ecotype pairs. We also identified a putative inversion located on chromosome XXI which appears to drive parallel genomic differentiation between geothermal and ambient ecotypes. Candidate genes within the putative inversion correspond to metabolic adaptations, including regulation of appetite and fat content. Appetite level showed strong heritable divergence between ecotypes, while the rate of weight loss during starvation and fat levels differed between ecotypes. Overall, both polygenic adaptation and parallel structural variation appeared to be key genomic mechanisms for adaptation to geothermally warmed environments. While allelic divergence was largely unique across populations, it resulted in similar functional phenotypic outcomes. Thus, structural and allelic variation both operate to facilitate adaptation to warming environments. Therefore, while management from a genomic perspective will play a role in mitigating the effects of climate change, this study suggests that consideration of functional molecular pathways will be key to conservation but with precise changes being difficult to predict due to the highly polygenic nature of thermal adaptation.

evolutionary biology↗

bioRxiv2025

Integrative Analysis of Single-cell and Bulk RNA Sequencing Reveals Macrophage Heterogeneity in Lyme Arthritis

IntroductionLyme arthritis (LA) is a common late-stage manifestation of Lyme disease caused by Borrelia burgdorferi (Bb) infection. Macrophages play a crucial role in LA pathogenesis, yet their heterogeneity and functional states within the arthritic microenvironment remain poorly understood. MethodsWe integrated single-cell RNA sequencing data from ankle joint tissues of Bb-infected C57BL/6 mice with bulk RNA sequencing data from both infected ankle joints and bone marrow-derived macrophages. We developed a LA mouse model and validated key findings through histopathological examination and RT-qPCR analysis. ResultsWe identified nine distinct cell types in the joint microenvironment with significant compositional shifts during disease progression. Analysis of 16,617 Macrophages/Monocytes revealed seven functionally distinct subpopulations with differential responses to infection. Pseudo-time trajectory analysis demonstrated three principal differentiation pathways from monocyte-derived macrophages toward anti-inflammatory, TNF+, and IL1b+ inflammatory phenotypes. Cell-cell communication analysis revealed significantly altered TGF-{beta} signaling networks in LA, with the Tgfb1-(Tglbr1+TgIbr2) axis playing a critical role. GSVA and pathway analyses showed metabolic reprogramming from oxidative phosphorylation toward glycolysis in macrophages during infection. Through integrated analysis and LASSO regression, we identified four characteristic genes (SIRPB1C, FABP5, MMP14, and EGR1) as potential LA biomarkers and developed a diagnostic nomogram with high predictive accuracy. ConclusionOur integrative analysis provides comprehensive insights into macrophage heterogeneity and functional plasticity in LA, identifying characteristic biomarkers and potential therapeutic targets. The metabolic reprogramming and altered TGF-{beta} signaling networks we identified may contribute to disease pathogenesis and offer new avenues for intervention strategies.

genomics↗

bioRxiv2025

Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport

Deriving the sequence of transitions between cell types, or differentiation events, that occur during organismal development is one of the fundamental challenges in developmental biology. Single-cell and spatial sequencing of samples from different developmental timepoints provide data to investigate differentiation but inferring a sequence of differentiation events requires: (1) finding trajectories, or ancestor:descendant relationships, between cells from consecutive timepoints; (2) coarse-graining these trajectories into a differentiation map, or collection of transitions between cell types, rather than individual cells. We introduce Hidden-Markov Optimal Transport (HM -OT), an algorithm that simultaneously groups cells into cell types and learns transitions between these cell types from developmental transcriptomics time series. HM -OT uses low-rank optimal transport to simultaneously align samples in a time series and learn a sequence of clusterings and a differentiation map with minimal total transport cost. We assume that the law governing cell-type trajectories is characterized by the joint law on consecutive time points, tantamount to a Markov assumption on these latent trajectories. HM -OT can learn these clusterings in a fully unsupervised manner or can generate the least-cost cell type differentiation map consistent with a given set of cell type labels. We validate the unsupervised clusters and cell type differentiation map output by HM -OT on a Stereo-seq dataset of zebrafish development, and we demonstrate the scalability of HM -OT to a massive Stereo-seq dataset of mouse embryonic development. Code availabilitySoftware is available at https://github.com/raphael-group/HM-OT

bioinformatics↗