Biology subjects

Tan, J.

Publications and source records attributed to Tan, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Biodegradable Intra-arterial Devices for Focal Drug Delivery to Targeted Organs

This study presents the development of biodegradable intra-arterial drug delivery (IADD) devices for the focal treatment of targeted organs. The IADD devices are fabricated using magnesium (Mg) and poly(glycerol sebacate) (PGS), leveraging their biocompatibility and tunable biodegradability, and are loaded with two model drugs, dexamethasone (DEX) or cisplatin (CIS). The IADD devices with helical and linear designs were fabricated for focal drug delivery to targeted organs and characterized for their microstructure and composition using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), thermogravimetric analysis (TGA), and Fourier-transform infrared spectroscopy (FTIR). The results confirmed the successful incorporation and stability of the drugs within the device. The IADD devices demonstrated in vitro release of DEX and CIS over 30 days, with drug-dependent and fabrication-dependent release profiles. The IADD devices demonstrated cytocompatibility with endothelial cells and sustained pharmacological activity against glioma cells throughout the in vitro release period. DEX-loaded IADD devices were implanted into the artery upstream of a target organ in rat models. The devices implanted into the renal artery to target the kidney and the carotid artery to target the brain achieved 109-fold and 68-fold improvements, respectively, in organ vs systemic drug levels compared to oral drug administration. Arterial histology and explanted-device analysis provided preliminary evidence of local vascular tolerability and device integrity over the examined implantation period. Overall, these results support IADD devices as a proof-of-concept approach for focal intra-arterial drug delivery to targeted organs, demonstrating substantially elevated target-organ drug levels relative to systemic exposure. HighlightsO_LIIntroduction of a novel intra-arterial drug delivery (IADD) platform C_LIO_LIIADD devices were fabricated from bioresorbable Mg and drug-loaded PGS C_LIO_LIDEX- and CIS-loaded IADD devices were evaluated for in vitro release and bioactivity C_LIO_LIIADD delivery achieved marked DEX enrichment in the kidney and brain C_LIO_LIPost-implantation studies support preliminary vascular safety C_LI

bioengineering↗

bioRxiv2026

PEhub resolves the hierarchical regulatory architecture of multi-way enhancer hubs in the human brain

Chromatin interaction assays capture regulatory architecture as stochastic pairwise contacts, limiting the ability to resolve how multiple enhancers cooperatively regulate transcription. Here we introduce a promoter-centric quantitative framework, termed PEhub, that resolves multi-way enhancer hubs as higher-order regulatory units from chromatin interaction data. By reparameterizing stochastic pairwise ligation events into promoter-conditioned enhancer networks, our approach explicitly models synergistic enhancer cooperation while accounting for distance-dependent interaction decay through a statistically principled null model. Using H3K27ac HiChIP data, we identify promoter-anchored enhancer hubs and validate their physical existence with single-molecule Pore-C, demonstrating that inferred hubs correspond to bona fide multi-way chromatin assemblies. Application to six human brain regions reveals that enhancer hubs are associated with elevated transcriptional output and exhibit a hierarchical organization spanning shared, circuit-specific, and region-restricted regulatory programs. This architecture hierarchically stratifies genetic risk and transcription factor deployment, linking three-dimensional genome organization to transcriptional control and disease-associated variation. Together, this promoter-centric framework provides a generalizable strategy for resolving higher-order regulatory architecture from 3D genome data and establishes multi-way enhancer hubs as a functionally and genetically meaningful layer of transcriptional regulation in complex tissues.

bioinformatics↗

bioRxiv2026

ACE-2-like Enzymatic Activity in Anti-SARS-CoV-2 Spike Protein Monoclonal Antibodies

Many people with acute COVID-19 have clinical disease not clearly attributable to viral replication and many COVID-19 convalescents are affected by post-acute sequelae of COVID-19 (PASC, or long COVID, LC). LC has severely affected public health and economies worldwide. Features of LC including blood pressure dysregulation, coagulopathies, high levels of inflammation, and neuropsychiatric complaints. The mechanisms responsible for the pathogenesis of some of COVID-19s clinical features and LC have not been well established. The host cell receptor for SARS-CoV-2 is human angiotensin converting enzyme 2 (ACE2), which binds the SARS-CoV-2 spike protein receptor-binding domain (RBD) to initiate infection. We hypothesized that some people may produce anti-RBD antibodies that sufficiently resemble ACE2 structure to have ACE2-like catalytic activity after infection. Those antibodies, ACE2-like abzymes, may contribute to the pathogenesis of LC. Our previous studies showed that ACE2-like activity was associated with immunoglobulin in some acute and convalescent COVID-19 patients. ACE2-like catalytic activity correlated with blood pressure changes following a moderate exercise challenge in people convalescing from COVID-19. To further establish that ACE2-like activity could be attributed to antibodies, we screened human monoclonal antibodies (mAbs) against SARS-CoV-2 spike protein from 3 different research centers and others purchased from a commercial source for ACE2-like catalytic activity. We identified 4 human monoclonal antibodies with ACE2-like catalytic activity. The ACE2-like catalytic activity of these mAbs was not inhibited by MLN-4760, a compound that inhibits native human ACE2 catalytic activity, nor by EDTA, unlike native ACE2, a Zinc metalloprotease, but was inhibited by an overlapping pool of spike peptides. Enzyme kinetic studies showed that the mAbs had substantially lower Vmax and Km values than native ACE2. The data therefore suggested that the antibodies cleave ACE2 substrate via a different mechanism than native ACE2. The identification of specific mAbs with ACE2-like catalytic activity supports the hypothesis that antibodies induced by SARS-CoV-2 infection could help mediate the pathogenesis of COVID-19 and LC, and more generally, the hypothesis that catalytic antibodies induced by infectious agents can contribute to disease pathogenesis.

microbiology↗

bioRxiv2025

Single-cell atlas of the developing Down syndrome brain cortex

Down syndrome (DS), caused by trisomy of chromosome 21, is the leading genetic cause of intellectual disability, yet the mechanisms disrupting fetal brain development remain unclear. We performed single-cell transcriptomic and chromatin accessibility profiling of approximately 250,000 cells from 15 DS and 15 control human fetal cortices (10-20 weeks post-conception). Our analysis revealed a subtype-specific reduction in RORB/FOXP1-expressing excitatory neurons and widespread disruption of neurodevelopmental transcriptional programs. Chromosome 21 transcription factors BACH1, PKNOX1, and GABPA emerged as dosage-sensitive hubs regulating genes linked to intellectual disability. Antisense oligonucleotide-mediated normalization of these factors in human neural progenitors in vitro partially rescued target gene expression. Benchmarking a humanized in vivo model captured additional molecular and cellular signatures of DS, complementing the in vitro model. Together, this resource defines the gene-regulatory landscape underlying cortical development in DS and highlights candidate molecular targets and preclinical models for future intervention studies. HighlightsO_LISingle-cell atlas of Down syndrome fetal cortex links transcriptional dysregulation to reduction of layer 4 neurons C_LIO_LIChromosome 21 transcription factors PKNOX1, BACH1, and GABPA drive intellectual disability gene dysregulation C_LIO_LITransplanted human cells model late-stage DS phenotypes, bypassing scarcity of fetal tissue C_LIO_LIASO targeting chromosome 21 transcription factors restores DS-associated molecular signatures C_LI

neuroscience↗

bioRxiv2025

High-throughput in silico screen uncovers key regulators of 3D genome architecture

The vertebrate genome is spatially organized into topologically associating domains (TADs), primarily via cohesin-mediated loop extrusion which typically halts at convergent CTCF binding sites to establish domain boundaries. However, despite the essential roles of CTCF and cohesin in establishing TADs, a long-standing paradox persists: CTCF and cohesin binding sites dramatically outnumber observed TAD boundaries, suggesting the existence of undiscovered architectural factors. To identify such missing factors, we conducted high-resolution in silico screens using C.Origami, a multi-modal AI model for predicting chromatin interactions. Remarkably, we identified ZNF654 and JMJD6 as novel factors uniquely defining TAD boundaries. Experimental validation confirmed that ZNF654, an uncharacterized vertebrate-specific zinc-finger protein, interacts with CTCF to form an architectural protein complex that demarcates chromatin domains. Genetic knockout of ZNF654 weakens TAD boundary strength without influencing other CTCF or cohesin binding sites. JMJD6, a deeply conserved jmjC-family dioxygenase, marks the anchors of the strongest chromatin stripes at both TAD boundaries and enhancer-promoter sites, while deleting JMJD6 weakens or diminishes such interaction signature. These results revealed the long-sought factors that uniquely mark TAD boundary and chromatin interaction anchors which, together with CTCF and cohesin, demarcate chromatin domains during 3D genome organization. Last, the evolutionary trajectory of ZNF654 and JMJD6 offers key insight into the evolutionary origins of 3D genome organization across metazoan species.

genomics↗

bioRxiv2025

Molecular basis of high-torque transmission of the Vibrio polar flagellar motor

The bacterial flagellar motors are huge protein nanomachines that drive rotation of the flagellum for bacterial motility, and have considerable diversity in structure among bacterial species, which enables the transmission of different torques to the flagellar filaments to propel bacteria and renders various swimming abilities. Relative to the bacterial peritrichous flagellar motors, the polar flagellar motors are the faster rotational machines and transmit high torque to drive bacterial high-speed motility in liquid and empower swimming in viscous environments. However, the structural basis of high-torque transmission of the polar flagellar motors is still unclear. Here we present an atomic-resolution cryo-electron microscope structure of the polar flagellar motor in complex with the hook from Vibrio alginolyticus, comprising 295 subunits from 18 proteins. Extensive inter-subunit interactions and additional phospholipids generate the higher rigidity of the rod. The LP ring utilizes more electrostatic charges on the inner surface and less physical contacts to facility the higher-speed rotation of the rod. The additional HT ring tightly binds to the outer surface of the LP ring to enhance the LP-ring stability. A previously function-unknown component FlrP enhances the interactions of 15 FliF peptides of the MS ring with the rod and stabilizes the LPHT and MS rings. The hook has two different states, L- and R-state, which provides structural flexibility of the hook to drive the unique forward-reverse-flick motility of the bacteria in the flicking process. This study provides unprecedented molecular insights into evolution and structural adaptions of the bacterial polar flagellar motors for high-torque transmission.

microbiology↗

bioRxiv2025

Transcriptome profiles of telocytes along the intestinal crypt-villus axis

Background & aimsIntestinal epithelial cells rely on a complex array of signals from the stromal microenvironment to determine their fate and function along the crypt-villus axis, but the precise cellular sources and combinations of signals regulating each position remain poorly defined. MethodsHere, we present a high-resolution atlas of a unique mesenchymal cell type previously identified as telocytes, mapped along the crypt-villus axis using single-cell RNA sequencing integrated with in-situ approaches and reporter mouse models. ResultsWe identify four spatially distinct telocyte subtypes: crypt, villus base, villus mid and villus tip, each with a unique gene expression profile. Crypt telocytes are enriched for canonical Wnt signaling components that support stem and progenitor cell maintenance, while villus base telocytes are a source of Bmps (bone morphogenic proteins) and express contractility-associated genes, suggesting a role in tissue architecture. Villus mid telocytes display signatures of immune regulation and inflammation, while villus tip telocytes are specialized for the regulation of ribonucleoprotein complexes and nutrient sensing. ConclusionsThis atlas provides a foundational resource for understanding how diverse telocyte populations coordinate signaling environments and shape intestinal homeostasis through both epithelial interactions and extensive crosstalk among themselves.

cell biology↗

bioRxiv2025

A cholinergic mechanism orchestrating task-dependent computation across the cortex

In an ever-changing environment, animals often need to switch between performing different tasks involving distinct sets of cognitive processes. Many such tasks involve neural activity distributed across the cortex, with dynamics that depend on both task demands and behavioral strategy1-17. A fundamental but unanswered question is what circuit mechanisms orchestrate these task-dependent dynamics. Here, we hypothesized that acetylcholine release in the cortex plays a key role. The cortexs only long-range source of this neuromodulator is the basal forebrain cholinergic system, which targets the entire cortical sheet and can individually modulate single regions on sub-second timescales18-26. To test our hypothesis, we first imaged cholinergic axons innervating the cortex while mice switched frequently between two navigational decision-making tasks in virtual reality (VR), only one of which required gradual accumulation of sensory evidence. We found that cholinergic input to the cortex is spatiotemporally heterogeneous and multiplexes sensory, motor, arousal, and cognitive signals in a task- and strategy-dependent fashion, with overall higher activity during evidence accumulation. Crucially, beyond contextual variables, cholinergic activity directly tracked task computations themselves, encoding an evidence-dependent decision variable only in the accumulation task. To test if acetylcholine release is causal to the performance of each task, we optogenetically silenced cholinergic terminals in the cortex while simultaneously imaging excitatory cortical activity. We found that this input is selectively required for evidence accumulation, and for large-scale cortical coding of evidence and choice during the accumulation task. Thus, we have identified a new cholinergic mechanism that orchestrates cortex-wide activity in a task-dependent manner and serves as a key node in the distributed brain network underlying the accumulation of sensory evidence.

neuroscience↗

bioRxiv2025

Spatio-Temporal Multi-Omics Profiling of Mechanisms and Biomarkers in Inhaled Drug-Induced Lung Toxicity

Comprehensive understanding and early detection of drug-induced lung toxicity remain critical challenges in respiratory drug development. In this study, we propose a multi-omics framework that integrates spatial and temporal tissue-specific transcriptomic signatures with proteomics from minimally invasive biofluids to understand mechanisms and identify safety biomarkers associated with lung toxicity. Using this framework, we identified a panel of candidate biomarkers in bronchoalveolar lavage fluid and plasma, including LCN2/NGAL, RETNLA, SP-D, SPP1/osteopontin, and MMP7, that correlate with histopathological features (e.g., inflammation and epithelial remodeling). We confirmed that these molecular biomarkers were consistently dysregulated across a range of inhaled lung toxicants, human disease (IPF), and environmental exposures (smoke, Alternaria), demonstrating broad applicability across different toxic exposures and translatability. Collectively, this study establishes a robust workflow for mechanism-guided biomarker discovery and proposes a panel of candidates for monitoring drug-induced lung injury in humans.

systems biology↗

bioRxiv2025

Breaking the ''one nucleus, one whole genome'' rule: Neurospora crassa separates its haploid chromosomes into different nuclei

The nucleus is a defining feature of eukaryotic cells, compartmentalizing the genome to enable precise regulation of diverse cellular processes. The long-standing paradigm in textbooks states that each nucleus carries at least a complete haploid genome --the "one nucleus, one whole genome" rule. A striking exception was recently uncovered: in two sclerotia-forming plant pathogenic fungi in the Sclerotiniaceae family, Sclerotinia sclerotiorum and Botrytis cinerea, haploid chromosomes are irregularly distributed across multiple nuclei. However, whether such phenomenon occurs in other eukaryotes, particularly in non-pathogenic fungi, is unclear. Through a literature survey, we identified many fungi that can potentially also separate their haploid chromosomes across different nuclei. Interestingly, Neurospora crassa, a foundational fungal genetics model, came out as a candidate. Its conidia, typically containing two or three nuclei, were believed to harbor a complete haploid genome within each nucleus. However, using approaches including chromosome counting, flow cytometry, and fluorescence in situ hybridization, we found that haploid chromosomes in N. crassa can be unevenly distributed among multiple nuclei. These findings challenge longstanding assumptions in fungal genetics and provide new directions for investigating genome organization. Our results indicate that the organisms violating the "one nucleus, one whole genome" rule are beyond sclerotia-forming pathogenic fungi. Since over 90% of fungi have not even been described, we propose that many more of them may likewise partition their genomes non-uniformly across nuclei, a process that could facilitate their adaptation and evolution.

microbiology↗

bioRxiv2025

Computational Discovery of Core Protein - Targeted Therapeutics Against Ginger Wilt Pathogen Ralstonia solanacearum

Bacterial wilt caused by Ralstonia solanacearum poses a severe threat to ginger production worldwide, as no consistently effective control measures exist. Here, we present a comprehensive strategy integrating pangenome analysis, functional enrichment, molecular docking, and state-of-the-art protein structure prediction to identify antibacterial agents targeting this phytopathogen. By prioritizing core, evolutionarily conserved proteins in R. solanacearum, we utilized AutoDock Vina and the recently developed AlphaFold3 to assess the binding affinity and validate protein-ligand interactions of key candidates from commercially available antibacterial pesticides. In vitro antibacterial assays confirmed strong inhibitory effects for several compounds, notably streptomycin sulfate, phellodendrine chloride, chlorogenic acid, and allicin. Our results highlight the power of combining large-scale computational screening with experimental validation for accelerating the discovery of novel antibacterial agents against highly divergent, recalcitrant plant pathogens. ImportanceThe indiscriminate use of broad-spectrum agrochemicals causes pollution and antimicrobial resistance. Our study proposes a targeted strategy against Ralstonia solanacearum by focusing on essential core proteins. This approach aims to develop specific agents that minimize harm to soil microbiota and reduce resistance selection. Our in silico framework aligns with green chemistry, offering a sustainable path for crop protection with a lower environmental footprint.

bioinformatics↗

bioRxiv2025

LRP8 is a Receptor for Yellow Fever Virus

Yellow fever virus (YFV), an arbovirus causing substantial human morbidity and mortality, was the first human virus discovered over a century ago. The live-attenuated 17D vaccine is among the most successful vaccines in medicine. Despite the importance of YFV, its receptor has remained unknown. Here, we performed a barcoded, genome-wide human ORF library screen and identified LRP8 (also named APOER2) as a receptor for YFV. We show that LRP8 expression specifically boosts YFV infection in cell lines by promoting entry. AAV-mediated expression of human LRP8 in mouse liver aggravates infection and pathology. LRP8 knockdown abolishes YFV infection in brain cells, primary human hepatocytes, and notably in mosquitoes. Biochemically, LRP8 directly interacts with YFV particles via the viral envelope protein. This function of LRP8 is conserved across species, particularly in mosquitoes and primates. A soluble LRP8 decoy protein can block YFV infection in vitro and in mice, providing a potential therapeutic or prophylactic strategy. Our findings provide groundwork for understanding YFV entry, tropism, and pathogenesis, and may enable development of novel therapeutics to treat YFV infection.

microbiology↗

bioRxiv2025

Deep learning for mass extinction detection on fossilized phylogenies: power, limitations, and lessons for simulation-based phylodynamic inference

Detecting mass extinction events from phylogenies is a fundamental yet challenging task. While traditional likelihood-based methods are available, deep learning offers a powerful, simulation-based alternative. Here, we evaluate a deep learning approach using a novel hybrid model that combines Graph Neural Networks with Long Short-Term Memory networks. This model analyzes phylogenies--containing both extant species and fossils--simulated under a complex skyline Fossilized Birth-Death model that incorporates mass extinctions and fluctuating background rates. We validate the architectures effectiveness through ablation studies. Our investigation revealed that the stochasticity of the simulation was a primary obstacle, creating significant "label noise" that initially limited performance. A direct comparison showed our deep learning approach performed slightly better than Bayesian methods. It is robust to uncertainty in phylogenetic branch lengths and topology and generalizes to larger trees, but its performance degrades under model mismatch with higher background extinction rates. However, our work highlights a critical limitation: the model is highly specific to the definition of mass extinction it was trained on. Consequently, any modification to this definition necessitates retraining a new model from scratch. We conclude by summarizing the challenges and lessons learned for simulation-based inference in phylodynamics.

evolutionary biology↗

bioRxiv2025

Serological evidence of SARS-CoV-2 infection in red and fallow deer in Great Britain.

SARS-CoV-2 is the viral agent of COVID-19 disease in humans and has been shown to infect a wide range of mammals, including white-tailed deer in North America and fallow deer in the Republic of Ireland. There are six species of deer in the UK which inhabit both urban and rural areas, providing a broad interface for human-deer interaction. Little is known if British deer species act as a reservoir for zoonotic spread of consequence to human health. Here, we report a high seroprevalence of SARS-CoV-2 neutralising antibodies in British deer, adding native red deer to the list of susceptible species. 62% of fallow and 25% of red deer sampled between 2024 and 2025 from one British deer park were positive for SARS-CoV-2 infection by serology. Data suggest that deer may function as permissive, reservoir-capable hosts and highlight the risks of anthroponosis and zoonosis from unregulated human-deer contact. While there is currently no evidence to suggest that these viruses are persisting within deer populations in Great Britain, the animal origins of SARS-CoV-2 highlight the importance of appropriate and limited interactions with wildlife, to minimise transmission risks and safeguard both animal and human health.

microbiology↗

bioRxiv2025

Characterization and deorphanization of RYamide signaling in Aedes aegypti: a potential regulator of hindgut-associated physiology

Neuropeptide Y-related signaling, consisting of various neuropeptides and their receptors including, for example, the mammalian neuropeptide Y (NPY), pancreatic polypeptide (PP), and peptide YY (PYY) families, along with neuropeptide Y-like peptides in insects, is evolutionarily conserved across vertebrates and invertebrate organisms. Vertebrate NPY is known as an important regulator of energy homeostasis and feeding behaviour, while studies on one NPY-associated signaling system in arthropods, known as RYamide, have mainly focused on functions regulating feeding-related behaviours. The current study aimed to begin exploring an additional functional role of RYamide signaling related to excretory physiology in Aedes aegypti given that a candidate RYamide receptor, RYaR2, is enriched in the hindgut of adult mosquitoes based on publicly available RNA-seq databases. Herein, we report that the RYamide transcript is expressed in all post-embryonic stages with greatest abundance in adult male mosquitoes. Specifically, the central nervous system and the ventral nerve cord were demonstrated as the major sources of RYamide, as supported by RT-qPCR and intense RYamide immunoreactivity observed in the protocerebral posterior dorsomedial neurons and protocerebral anterolateral neurons in the mushroom body region, along with an intensively stained pair of neurons in the terminal abdominal ganglion (TAG). The pair of immunoreactive neurons in the TAG contain elaborate processes extending onto the hindgut, with a branch extending posteriorly over the rectum where fine processes are in close proximity to the rectal papillae (pads) while an anterior branch extends over the ileum terminating at the midgut-hindgut junction forming a fine circular plexus over the pyloric valve. Importantly, two orphan GPCRs, previously referred to as NPYLRs, were functionally deorphanized as bona fide RYamide receptors. Their responses to diverse peptidergic ligands were assessed, revealing that RYamides elicited the strongest receptor activation, with half maximal effective concentrations in the pico- to nanomolar range. Notably, our phylogenetic analysis revealed that while only a single RYaR is commonly found across most arthropods, culicine mosquito species including A. aegypti possess two RYaRs. The characterization of RYamide signaling with respect to excretory physiology involving the hindgut, particularly in species having two receptor isoforms such as culicine mosquitos, may provide valuable insights for development of novel, species-specific pest control strategies.

zoology↗

bioRxiv2025

Evaluating the impact and detectability of mass extinctions on total-evidence dating

Fossils are crucial for accurately dating phylogenetic trees because their ages provide vital constraints on the timing of macroevolutionary events, and their morphological characters offer key information on evolutionary rates and phylogenetic positions. The fossilized birth-death (FBD) process is a diversification model that incorporates both extant and extinct species, serving as a tree prior that seamlessly integrates fossils into phylogenetic inference. While the FBD model can account for mass extinctions, which caused rapid, widespread organismal loss, few studies have utilized FBD models incorporating these events in phylogenetic inference. This is likely because the detectability of mass extinctions and their impact on phylogenetic inference remain unclear. Through simulations, we assessed the influence of mass extinctions on divergence time and topology inference and evaluated the detectability of mass extinction signals in total-evidence dating. We examined three FBD tree priors: without mass extinction, with known mass extinction time and survival probability, and with known mass extinction time but unknown survival probability. Our results show that the FBD model with known mass extinction time and unknown survival probability was able to reliably detect mass extinctions when they occurred, and correctly refrained from detecting mass extinctions when they were absent. Moreover different FBD models generate similar divergence time and tree topology errors. Even when the FBD model used for tree inference did not explicitly account for mass extinction events, signals of mass extinction were still detectable on the resulting MCC trees. The accuracy of the detection was similar to the one obtained from MCC trees inferred using an FBD model that includes mass extinction parameters. We also reduced the fossilization rate and the number of morphological characters, obtaining results consistent with the aforementioned findings. However, reducing the fossilization rate decreased the accuracy of detecting mass extinctions when they occurred, and reducing the number of morphological characters decreased the accuracy of divergence time inference. Furthermore, we adjusted the priors for the existence of mass extinction and the survival probability of mass extinction. We found that the prior for the existence of mass extinction had no effect on inference, whereas the prior for the survival probability of mass extinction significantly influenced both the detection of mass extinctions and the estimation of survival probabilities. Finally, we applied these models to empirical datasets of tetraodontiform fishes and crinoids and found that, consistent with our simulation results, the inclusion of a mass extinction event in the tree prior had a negligible impact on the inferred topologies and divergence times.

evolutionary biology↗

bioRxiv2025

High-throughput 3D super-resolution ultrasound imaging

Capturing fast hemodynamics in deep organs is essential for understanding microvascular regulation of organ responses to physiological demands and pathological stress. However, non-invasive three-dimensional (3D) imaging of these microscale processes remains challenging due to trade-offs between spatial resolution, imaging speed, and penetration depth. Here, we present fluctuation-based high-order super-resolution acoustic microscope (FLAME), a tracking-free 3D ultrasound imaging technology capable of fast microvascular angiography and flow measurement. Using as few as 30 volumes, FLAME improves 3D ultrasound resolution by 8-fold ([~]50 m) and shortens data acquisition time by over two orders of magnitude, from tens of seconds to tens of milliseconds, compared with conventional tracking-based super-resolution approaches1-6. This high-throughput capability supports high-fidelity imaging of tissue functions under flexible experimental settings. FLAME achieves an unprecedented 3D super-resolution frame rate of [~]40 Hz, capturing transient hemodynamic responses to various physiological and pathological stimuli in different mouse organs, from the microvascular level to the whole-body scale. With open-sourced implementation, FLAME provides an accessible platform for real-time, in-depth hemodynamic monitoring across diverse biomedical applications and clinical translation.

bioengineering↗

bioRxiv2025

SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis

BackgroundAlternative promoter usage regulates isoform diversity in mammals, playing critical roles in development, disease, and cellular reprogramming. While Cap Analysis of Gene Expression (CAGE) enables precise transcription start site mapping, its high cost and limited coverage hinder scalability. In contrast, RNA-seq is abundant across biological contexts; several algorithms (ProActiv, Salmon, DEXSeq) infer promoter activity from these data, yet no unified, reproducible framework exists to execute, benchmark, and compare them or to scale alternative promoter analyses across large compendia. ResultsWe developed snakeAltPromoter, an end-to-end Snakemake workflow that ingests raw FASTQ files, performs quality control and alignment, quantifies promoter activity using three complementary strategies (junction-based, transcript-based, and first-exon-based), classifies promoters into major, minor/alternative, and inactive categories, and conducts both differential promoter activity and usage analysis. Crucially, snakeAltPromoter integrates a systematic benchmarking module against matched CAGE profiles to reveal method-specific strengths and limitations. ProActiv showed the highest concordance with CAGE in promoter classification, activity and differential analysis, Salmon was robust at low coverage and intronless cases. Overall, the complete workflow recovered a majority of CAGE-validated active promoters and processed a 50 M-read RNA-seq sample in around 2h on a 32-core node, demonstrating both accuracy and scalability. ConclusionssnakeAltPromoter is, to our knowledge, the first reproducible framework that pairs comparative method evaluation with scalable differential alternative promoter analysis. It provides concrete guidance for method selection under different experimental scenarios and enables high-throughput mining of promoter-level regulation from public RNA-seq repositories. Code and example data are freely available at https://github.com/YidanSunResearchLab/SnakeAltPromoter.git.

bioinformatics↗