Biology subjects

Chen, S.

Publications and source records attributed to Chen, S..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

Tuned to explore: Increased phasic responses to auditory targets and novelty in children regardless of induced tonic arousal

The ability to focus on relevant information while ignoring distractions is critical during childhood, as it supports learning, social interaction, and adaptation to changing environments. This attentional balance is thought to depend in part on arousal regulation, mediated by the activity of the locus coeruleus norepinephrine (LC-NE) system. Moderate levels of arousal are typically associated with optimal cognitive performance. However, the interaction between arousal and attention remains poorly understood in humans, especially during development. In this study, we investigated whether experimentally modulating tonic arousal, the baseline level of physiological alertness, affects attentional processing in children (N = 44, aged 6-8) and adults (N = 46, aged 18-35). Participants performed an active auditory three-stimulus (standard, novel, target) oddball task, designed to assess selective attention to target tones and distraction by novel sounds. Prior to each task block, tonic arousal was manipulated using music or videos varying in arousing content. Physiological responses were recorded continuously (skin conductance, pupil dilation, heart rate) to index both tonic arousal and transient, phasic changes in arousal triggered by task events. While tonic arousal modulation was successful, as confirmed by skin conductance levels, Bayesian analyses provided evidence for no effect of this modulation on subsequent attentional processing. Importantly, children generally exhibited stronger phasic arousal responses, particularly to task-irrelevant novel sounds, reflecting less mature regulation of attention and arousal. These findings show developmental differences in physiological responses to unexpected environmental stimuli and provide physiological evidence of increased distractibility during childhood.

neuroscience↗

bioRxiv2025

Measurement of atomic scattering factors by cryo-electron microscopy

Determination of specimen structure from cryo-electron microscopy (cryo-EM) experiments relies on an accurate model of the electrostatic potential of the specimen. For biological macromolecules, the potential is strongly influenced by the presence of chemical bonds between atoms, a fact unaccounted for by models of electron scattering that are currently standard in the field. We propose a Bayesian approach to the estimation of atomic scattering factors which incorporates the effect of the molecular environment while remaining fast, interpretable and transferable between molecules. Our algorithm infers atomic scattering factors directly from maps of the electrostatic potential determined by cryo-EM single particle analysis, bypassing the need for computationally-intensive theoretical calculations. The algorithm is used to infer empirical scattering factors from high-resolution reconstructions of catalase enzymes. To illustrate its broad applicability, the algorithm is also applied to a training set of publicly-available cryo-EM data. The empirical scattering factors show improved agreement with a test set of cryo-EM reconstructions. The predictions are further validated by comparison with magnetic susceptibility values of organic compounds, as well as by application to the refinement of atomic models. Significance StatementUnderstanding the structure of biomolecules is key to explaining their function. Cryo-electron microscopy is a method for reconstructing the electrostatic potential distribution of a biological macro-molecule, a quantity which contains information about atomic positions and the redistribution of charge due to chemical bonding. These factors should be modelled when inferring the structure of the molecule from its electrostatic potential. We develop an improved model of the potential that takes into account chemical bonding while remaining computationally tractable. The parameters of the model are inferred from a selection of cryo-electron microscopy datasets using Bayesian methods.

biophysics↗

bioRxiv2025

Standardizing the mouse MCAO Stroke Model: Distinguishing Internal Carotid vs Pterygopalatine Artery Occlusion

BackgroundThe intraluminal middle cerebral artery occlusion (MCAO) model is widely used in preclinical stroke research, but outcomes remain inconsistent because of variable occlusion times and inadvertent filament placement into the pterygopalatine artery (PPA). MethodsWe applied a modified version of the Koizumi method to directly visualize the internal carotid artery (ICA)-PPA bifurcation and systematically compare targeted ICA versus PPA occlusion. We combined multiple complementary methods - survival studies, neurological scoring, 2,3,5-Triphenyltetrazolium chloride (TTC) infarct staining, Evans blue blood brain barrier (BBB) permeability assays, laser speckle cerebral blood flow imaging, small-animal magnetic resonance imaging (MRI), and evaluation of inflammatory gene expression through qPCR - to rigorously characterize injury patterns, survival, and inflammatory responses. ResultsICA occlusion approximately caused a rapid 70% reduction in cerebral blood flow, progressive infarction (15 min: smaller infarct with approximately 50% 7-day survival; 30 min: moderate infarct but >50% mortality), and cortical edema. In contrast, PPA occlusion produced only a gradual 44% decline in blood flow, small infarcts at 60 min) and preserved survival (80% at 7 days). Finally, magnetic resonance imaging in 15-minute ICA occluded mice identified the development of cortical edema which was not observed in sham, 15-minute PPA, or 60-minute PPA mice. ConclusionThese findings identify 15-minute ICA occlusion as the most practical balance between reproducible infarction and survival for long-term studies, while 30 minutes is best reserved for short-term infarct induction when survival is less critical. By resolving two critical sources of MCAO variability, occlusion duration and vascular targeting, this study provides a standardized protocol and evidence-based occlusion benchmarks that will improve reproducibility in preclinical stroke studies

physiology↗

bioRxiv2025

Migration patterns and hybridization within the Asian stonechat complex in response to a major geographical barrier

Long-distance avian migration is thought to be under strong natural selection. Facing geographical barriers, migrants display various patterns considered to be adaptive. For example, they may detour along either side around the barrier or cross it, requiring specialized behavioral adaptations. Variations within closely related taxa are excellent sources for understanding the evolutionary background of migration and how barriers are shaping migration routes. In Asia, some species are assumed to have a migratory divide in response to the major geographical barrier, the Qinghai-Tibet Plateau (QTP), including the stonechat taxa (Siberian Stonechat Saxicola maurus maurus and Amur Stonechat S. stejnegeri). As they detour along either side of the QTP, these taxa are believed to disfavor a crossing over the highland. However, the more southernly distributed Tibetan Stonechat (S. m. przewalskii) breeds on the QTP, suggesting adaptation to high elevation. To investigate migration patterns and the potentially associated genetic differences, we studied migration routes and population genetics of four populations around the assumed migratory divide in Russia and Mongolia, and of one from the QTP in China. Our results confirmed the existence of a migratory divide between maurus and stejnegeri, albeit with extensive hybridization. We observed both the hypothesized western and eastern routes, but also found individuals employing intermediate routes crossing the QTP, of which two-thirds were clear hybrids. Meanwhile, przewalskii followed a highland-crossing route and was genetically differentiated from maurus and stejnegeri. The diverse migration routes among Asian stonechats show differential responses towards the geographical barrier. The intermediate route may be associated with hybridization, and its conditional viability may facilitate gene flow between maurus and stejnegeri. The Asian stonechat complex thus offers great opportunities for novel research of the genetics and evolution of migration. The specific evolutionary background associated with inhabiting and crossing the QTP can offer new perspectives in this field. Teaser textMigratory divides can arise in birds because alternative routes around migratory barriers would select for behaviors to restrict hybridization. Hybrids of parental types that employ alternative routes are hypothesized to embark on intermediate routes that would expose them to suboptimal conditions, resulting in post-zygotic reproductive isolation. However, this hypothesis is challenged when a sister taxon actually breeds on the geographical barrier. This is the case in the Asian stonechat complex that breeds near or on the Qinghai-Tibet Plateau (QTP), the roof of the world. We demonstrated a migratory divide in central Siberia to Mongolia for race maurus and stejnegeri, yet showed also evidence for extensive hybridization. Hybrids migrated along a newly discovered intermediate route, seemingly viable and overlaps with the migration trajectory of race przewalskii over the eastern part of the QTP. The Asian migratory divide relative to the QTP thus provided new insights to the evolution of landbird migration.

evolutionary biology↗

bioRxiv2025

Ptf1a robustly drives the gliogenic switch in the rodent embryonic cortex in a dosage-dependent manner by activating pro-glial gene expression programs

It is widely believed that the gliogenic switch during rodent embryonic development is governed by the orchestrated crosstalk between a cohort of genes and extracellular cues. Here we report that ectopic expression of the single bHLH factor, pancreas transcription factor 1 (PTF1A), is sufficient to drive radial glial progenitors (RGPs)-regardless of progenitor heterogeneity and developmental stage-to differentiate into glial cells. Ptf1a- expressing RGPs exhibit progenitor behaviors indicative of a neurogenic-to-gliogenic fate transition, resembling endogenous progenitors at the late stages of embryonic development, and preferentially produce OLIG2+ oligodendrocytes in vivo, some of which are positive for PDGFR or CC1. This robust gliogenic competency depends on the dosage of stable Ptf1a expression in RGPs. RNAseq reveals the glial transcriptome, including upregulated expression of several notch signaling components and the endothelin receptors in Ptf1a RGPs. We further identify Ednrb as one of the downstream targets of Ptf1a that directs RGPs toward gliogenesis via the ERK1/2 signaling pathway. In summary, our study uncovers a novel and robust role for Ptf1a in glial fate specification, offering a potential strategy for generating human oligodendrocytes in vitro.

neuroscience↗

bioRxiv2025

Cytosolic mannosyltransferases involved in the ER N-glycosylation pathway exhibit bacterial ancestry

N-glycosylation in eukaryotes begins with the assembly of a lipid-linked oligosaccharide on the endoplasmic reticulum membrane. As a pivotal post-translational protein modification, it is conserved across all three domains of life. However, the evolutionary origins of the N-glycosylation pathway remain a subject of ongoing debate in evolutionary biology, largely due to the limited availability of robust data regarding the evolutionary trajectories of the glycosyltransferases involved in this process. Here, we present phylogenetic analyses of the eukaryotic ALG1 and ALG2 mannosyltransferases (MTases), which are crucial for constructing the core trimannosyl Man3GlcNAc2 structure conserved in eukaryotic N-glycans. Our comprehensive phylogenetic study, combined with functional and structural analyses, suggests that the ALG2 MTase likely originated from a bacterial ancestor. This inference is further supported by the identification of sequential and functional ALG1 homologs exclusively within bacterial lineages, rather than in Asgard archaea or other archaeal groups. Our findings challenge the prevailing hypothesis that the eukaryotic N-glycosylation pathway primarily evolved from archaeal ancestors, instead suggesting a chimeric origin involving contributions from both bacterial and archaeal lineages. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/682550v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1ac81a8org.highwire.dtl.DTLVardef@746054org.highwire.dtl.DTLVardef@604bdborg.highwire.dtl.DTLVardef@14235d_HPS_FORMAT_FIGEXP M_FIG C_FIG The ALG glycosyltransferase (GTases) involved in the initial stage of eukaryotic N-glycosylation on the cytosolic side of the ER membrane exhibit chimeric evolutionary origins. LUCA: Last Universal Common Ancestor; LECA: Last Eukaryotic Common Ancestor. HighlightsO_LIThe evolutionary trajectories of cytosolic ALG mannosyltransferases (MTases) were studied C_LIO_LIThe ancestor of ALG2 exhibited in the LUCA but evolved its MTase activity in bacterial lineages C_LIO_LIThe ALG1 MTase originated from bacterial lineages C_LI

molecular biology↗

bioRxiv2025

Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in dedifferentiated endometrial carcinomas

The mammalian SWI/SNF (mSWI/SNF) family of chromatin remodelers govern cell type-specific chromatin accessibility and gene expression and assemble as three distinct complexes: canonical BAF (cBAF), Polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF). ARID1A and ARID1B are paralog subunits that specifically nucleate the assembly of cBAF complexes and are frequently co-mutated in highly aggressive dedifferentiated/undifferentiated endometrial carcinomas (DDEC/UECs). Here, in cellular models and primary human tumors, we find that ARID1A/B deficiency-mediated cBAF loss results in increased ncBAF and PBAF biochemical abundance and chromatin-level functions to maintain the DDEC oncogenic state. Further, treatment with clinical-grade SMARCA4/2 ATPase inhibitors markedly attenuates DDEC cell proliferation and tumor growth in vivo and synergizes with carboplatin-based chemotherapy to extend survival. These findings reveal the oncogenic contributions of shifted mSWI/SNF family complex stoichiometry and resulting gene regulatory dysregulation and suggest therapeutic utility of mSWI/SNF small molecule inhibitors in DDEC/UEC and other cBAF-disrupted cancer types.

molecular biology↗

bioRxiv2025

Leptin-Associated Sex Difference in TMJ OA Induced by Metabolic Endotoxemia

Background: Temporomandibular joint (TMJ) osteoarthritis (OA) is a degenerative disease affecting the whole synovial joint, with a higher prevalence in women. Obesity is recognised as a risk factor for knee OA, but its association with TMJ degeneration remains controversial. Lipopolysaccharide (LPS), or endotoxin, has increasingly been proposed as a mediator of obesity-related knee OA. In parallel, adipose-derived leptin played a role in the development of metabolic OA. This study investigated whether chronic LPS exposure induces TMJ OA and whether leptin is involved in this process. Methods: Six-month-old female and male Wistar rats received continuous subcutaneous LPS infusion to induce TMJ OA. At 10 weeks, peripheral blood, white adipose tissue, and TMJs were harvested for biochemical, histological, micro-computed tomography and gene expression analyses. Primary TMJ chondrocytes isolated from healthy rats were used to investigate sex-specific cellular responses to leptin and LPS in vitro. Results: Chronic LPS exposure induced mild, sex-divergent TMJ changes. Compared to same-sex healthy controls, LPS-treated females showed a marginally worse Mankin score (P = 0.053) with greater cartilage glycosaminoglycan loss (P = 0.032), synovitis and subchondral bone deterioration, whereas LPS-treated males only showed worse cartilage surface fibrillation. Both sexes showed subcutaneous adipocyte hypertrophy in response to LPS. Only females progressed to adipose inflammation and plasma leptin elevation (P = 0.018), which correlated strongly with total Mankin score (Spearman rho=+0.773, P = 0.024). Leptin was detected in the joint on chondrocytes co-expressing leptin receptor (OB-R) and inducible nitric oxide synthase (iNOS). The percentage of cells positive for leptin, OB-R and iNOS was differentially abundant in LPS-treated females than in sex-matched controls and LPS-treated males. In vitro, at the same leptin dose, female chondrocytes exhibited lower metabolic activity and greater oxidative stress than male chondrocytes. Notably, leptin upregulated matrix metallopeptidase (MMP)-13 expression only in LPS-primed female chondrocytes. Conclusion: Chronic systemic LPS exposure induced sex-divergent TMJ osteoarthritic pathology, adipose dysfunction and altered leptin signalling. The tissue-level changes were associated with leptin-linked inflammatory cascades amplified in female chondrocytes. These findings suggest that leptin is involved in the pathogenesis of systemic endotoxin-triggered TMJ OA and may partly explain sex differences in OA development.

pathology↗

bioRxiv2025

Bioinformatic analysis and experimental validation of ursolic acid's effects on Staphylococcus aureus-induced osteomyelitis

Osteomyelitis (OM), particularly methicillin-resistant Staphylococcus aureus (MRSA)-induced OM, remains a serious clinical challenge due to complex pathogenesis and rising antibiotic resistance. This study aimed to elucidate the therapeutic mechanism of ursolic acid (UA) against MRSA- induced OM using integrated network pharmacology, bioinformatics, and experimental validation. Through target prediction and multi-database mining, we identified 57 common targets of UA and OM. ML algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) and random forest, pinpointed three core genes: Neutrophil Elastase (ELANE), Lactoferrin (LTF), and S100A12. Enrichment analyses revealed significant involvement in neutrophil extracellular trap (NET) formation, inflammatory response, and immune regulation. Molecular docking and dynamics simulations confirmed stable binding between UA and ELANE. In vitro, UA exhibited antibacterial activity against clinical MRSA isolates (MIC = 16-64 g/mL) and showed synergistic effects with Penicillin (FICI = 0.125-0.5). These results demonstrate that UA combats OM through immunomodulation, anti-inflammatory actions, and direct antibacterial activity, providing a foundation for its use as an adjuvant therapy against MRSA-related OM.

microbiology↗

bioRxiv2025

Diel rhythms shape viral community structure and activity across the host domains of life

Circadian rhythms, driven by endogenous clocks and synchronized with environmental cues, are fundamental to life on Earth. While extensively studied in diverse organisms, their influence on viral ecology remains largely unexplored. This study takes the temporal dynamics of viruses in Daya Bay as an example to uncover the rhythmic control of viral replication and activity. Using a high-resolution time-series dataset collected every 2 hours over a 3-day period, we identified a total of 22,151 viral operational taxonomic units (vOTUs) and 414 Nucleocytoplasmic Large DNA Virus (NCLDV) genomes. Our analysis revealed significant diel fluctuations, with 14.48% of vOTUs exhibiting diel patterns in metagenomic abundance and 1.97% showing diel transcriptional activity. We found that these abundant diel viruses infect hosts across the domains of life, including cyanobacteria, pelagibacteria, Marine Group II (MGII) archaea and protists, all known for their diel metabolism. The expanded spectrum of host diversity with diel viral interactions significantly broadens our understanding of virus-host rhythmic dynamics in natural environmental settings. A strong positive correlation was detected between the transcriptional activities of these diel viruses and their respective hosts. Contrary to bacteriophages, which mostly peaked during the day, we demonstrated that NCLDVs showed nocturnal diel abundance with a co-fluctuating diel transcriptomic activity pattern tightly hitched to their hosts, peaking at night and declining during the day. Furthermore, we identified a rich compendium of viral genes with significant diel expression patterns, including those related to structural protein production, DNA replication, and stress response. Notably, several essential viral genes involved in stress response and repair were found to be diel transcribed for the first time, including UV-endonuclease (UvdE), peroxidase, chaperones, and early light-induced protein (ELIP). Our findings suggest that viruses across host domains actively synchronize with environmental cues to optimize their replication and transmission, despite their dependence on host metabolism. This study provides novel insights into the rhythmic control of viral communities and their intricate interactions with hosts, with profound implications for microbial community succession and biogeochemical cycles.

ecology↗

bioRxiv2025

Preselection CD4+CD8+ thymocytes modulate TCR responsiveness following TCRβ selection

Modulation of TCR sensitivity during positive selection is critical to avoid negative selection and direct thymocytes into their appropriate lineage. Thymocytes just prior to positive selection (preselection) are highly responsive to low affinity self-ligands and are also actively rearranging their TCR locus as they await a positive selection signal. Preselection DP thymocytes were thought to be relatively homogeneous and TCR modulation during this stage had not been previously described. Here we provide evidence for progressive gene expression changes within the preselection DP thymocyte population that correlates with a gradual loss of TCR responsiveness and a defect in upregulating TCR target genes associated with the CD4 fate. We relate these observations to the link between positive selection and T cell lineage commitment.

immunology↗

bioRxiv2025

Absolute hand determination of glycofibrils from natural sources in cryo-EM

Glycans are one of the four fundamental macromolecules that constitute life. However, compared with proteins and nucleic acids, our understanding of the structures and functional mechanisms of glycans remains limited. Moreover, it is generally challenging to obtain high-resolution three-dimensional structures of glycans. Recent studies have demonstrated the potential of the CryoSeek strategy in enabling high-throughput structural determination of glycans, thereby presenting novel avenues for their structural investigation. Meanwhhile, unlike proteins, near atomic resolution density maps of glycofibrils do not inherently facilitate the determination of absolute hand, which is a prerequisite for building atomic models of glycofibrils. Existing absolute hand determination methods have severe limitations in the cases of glycofibrils from natural sources. In this study, we introduce Ahaha, a straightforward and efficient method for determining such absolute hand in cryo-EM. With their absolute hand measured by Ahaha, we built atomic models of four glycofibrils derived from a natural water sample, facilitating the study of glycans. The online service of Ahaha is available at https://cryoseek.org/ahaha.

biophysics↗

bioRxiv2025

Contralateral-Ipsilateral Segregation as a Conserved Principle of the Visual Corpus Callosum

How the brain maintains distinct information streams within dense white matter is a fundamental question. We investigated whether the visual corpus callosum transmits information via segregated "parallel wires" or mixed pathways. This distinction is critical: a mixed architecture would render the signals origin ambiguous, whereas a segregated arrangement implies that spatial position tracks the direction of information flow. Using high-field fMRI and Bayesian modeling in humans, we demonstrate a segregated architecture featuring distinct contralateral and ipsilateral channels. This functional segregation mirrors a precise anatomical arrangement in mice, where dual-color viral tracing and light-sheet microscopy reveal that callosal axons remain spatially segregated in distinct laminae after crossing the midline. Our findings establish a conserved "parallel wires" principle of callosal organization, providing a new framework to decode directional information flow and assess pathway-specific damage in neurological disease.

neuroscience↗

bioRxiv2025

Specialization of ubiquitin ligases to distinct nucleic acid sensors

Innate immune sensors rely on ubiquitin ligases to calibrate antiviral responses, yet the rules governing substrate recognition by SPRY-containing ligases remain poorly defined. Here, we establish a large-scale structure-based screening pipeline using AlphaFold to systematically predict interactions between human nucleic acid sensors and SPRY-containing proteins. Our approach uncovered novel transient or degradation-sensitive interactions that are typically missed by proteomic methods, including a labile TRIM58-OAS1 complex. We show that SPRY domains dictate substrate specificity: TRIM25 preferentially engages ZAP, whereas Riplet favors RIG-I. Domain-swapping experiments demonstrated that SPRY domains are sufficient to reprogram ligase specificity and antiviral activity. Phylogenetic and structural analyses revealed that TRIM25 and Riplet evolved from a common ancestor but diverged in coiled-coil architecture and oligomeric state, while retaining conserved substrate preferences. Residue-level modeling identified hypervariable SPRY loops as critical determinants of recognition, a prediction validated by targeted mutagenesis of the TRIM25-ZAP interface. Finally, we show that distinct SPRY-containing ligases surveil self-amplifying RNA (saRNA) vaccines: Riplet-RIG-I primarily responds when RNA is delivered by lipofection, whereas TRIM25-ZAP is engaged upon lipid nanoparticle delivery, with functional consequences for vaccine expression. Together, these findings demonstrate that SPRY domains encode recognition logic for ubiquitin ligases, that AlphaFold enables discovery of otherwise hidden interactions and that these principles have direct implications for RNA-based therapeutics.

molecular biology↗

bioRxiv2025

Network pharmacology, bioinformatics, molecular docking and experimental verification of the mechanism of HXZTS treatment on osteoarthritis synovium

BackgroundOsteoarthritis (OA) is a prevalent joint disease characterized by synovial inflammation and synovial fibroblast dysfunction. Elucidating the molecular mechanisms underlying synovial tissue impairment in OA is crucial for developing targeted therapeutic interventions. Huoxuezhitongsan (HXZTS), a traditional Chinese medicine formula, has shown promising therapeutic effects in treating OA, but its mechanisms of action on synovial tissue remain unclear. MethodThis study integrated network pharmacology, bioinformatics analysis, molecular docking, and experimental validation to elucidate the potential targets, pathways, and mechanisms by which HXZTS exert therapeutic effects on osteoarthritic synovial tissue. ResultsNetwork analysis identified 21 active ingredients and 111 common targets of HXZTS for OA, with key compounds like quercetin, {beta}-sitosterol, and stigmasterol. Enrichment analysis revealed HXZTS modulates inflammation through TNF, IL-17, and MAPK signaling pathways, oxidative stress, apoptosis, angiogenesis, and metabolic regulation. Molecular docking demonstrated strong binding affinities of HXZTS compounds with targets like AKT1, TNF, TP53, IL6, and VEGFA. RT-qPCR validation confirmed the downregulation of inflammatory mediators like IL6 and PTGS2, alongside the upregulation of genes associated with potential cartilage repair effects, such as MMP1 and MMP3, upon HXZTS treatment. ConclusionsHXZTS exerts therapeutic effects on osteoarthritic synovial tissue through a multifaceted mechanism involving modulation of inflammation, oxidative stress, apoptosis, angiogenesis, and metabolic regulation. These findings provide insights into the potential application of HXZTS as a complementary or alternative therapeutic approach for managing OA and a foundation for developing novel targeted therapies.

bioinformatics↗

bioRxiv2025

Hemodynamic and electrophysiological progression of the Rose Bengal photothrombotic stroke model in mice: vasoactive properties of Rose Bengal, tissue heating, wavelength optimization, and sex differences in lesion volume

The photothrombotic stroke model is gaining popularity due to its relative simplicity, minimal invasiveness, and clinical relevance. Photothrombosis involves the delivery of an intravascular photosensitizer (Rose Bengal) followed by its photoactivation, resulting in vessel occlusion and ischemia. Using a combination of complementary optical and non-optical techniques, we characterized the physiological changes in mice undergoing photothrombosis. We report that Rose Bengal acts as a rapid vasoconstrictor, inducing hypoemia both in the brain and periphery even in the absence of its photoactivation. Conversely, we find that light, when used at photothrombosis-appropriate intensities and durations, induces large amounts of tissue heating and hyperemia even in the distal non-illuminated hemisphere. Furthermore, we show that use of the optimal photothrombotic wavelength based on the Rose Bengal absorption spectrum (yellow-561nm) produces a more consistent and pronounced drop in blood flow, and a shorter latency to the initial spreading depolarization (SD), ultimately resulting in a larger stroke. Similarly, when yellow light is used to induce a stroke in ChR2-expressing mice, the electrophysiological and hemodynamic confounds from green light cross activation of ChR2 are eliminated. Finally, we observe across cohorts that male mice have larger strokes than females. Altogether, we extensively describe important caveats and confounds concerning photothrombosis and provide a detailed characterization of its early ischemic events. Significance statementPhotothrombosis is a powerful model of ischemic stroke which uses light to photoactivate an intravascular dye (Rose Bengal). However, little is known about the independent effects of both the Rose Bengal and the light used to activate it. We show that both manipulations introduce separate confounds relevant to stroke outcomes, something which should be considered and accounted for when using this technique. In addition, we demonstrate that by using the optimal Rose Bengal excitation wavelength, the blood flow drop is more pronounced and consistent, resulting in larger strokes and perhaps better modelling human injury. Furthermore, we show that precautions can be taken to avoid spectral overlap when integrating photothrombosis in optogenetic experiments. Finally, we explore sex differences in lesion volume.

neuroscience↗

bioRxiv2025

Bridging biology and statistics with hybrid Bayesian experimental design for drug dose-response assays

Dose-response cytotoxicity assays are central to evaluating drug potency, yet selecting concentrations that capture both the full response range and key parameters such as the half-maximal inhibitory concentration (IC50) and Hill slope remains challenging. Practical constraints, including limited replicates, variability across culture conditions, and the trial-and-error nature of current practice, make assays time- and resource-intensive. To address this, we introduce a Bayesian inference framework that quantifies uncertainty, incorporates prior knowledge, and extend it with a Bayesian optimal experimental design (OED) strategy to systematically refine concentration selection. We further propose a hybrid OED approach that integrates information-theoretic design with space-filling principles, aligning statistical rigor with biological intuition. Applied to ER+ breast cancer cells in monoculture and co-culture with stromal cells, this framework revealed differential drug responses while improving information efficiency. More broadly, our results highlight how Bayesian OED can bridge computational and biological perspectives, offering a path toward more efficient, reproducible, and interpretable experimental design in cancer research and beyond. Author summaryWe present a statistical framework that systematically captures uncertainty in drug cytotoxicity assays, which are standard laboratory tests that measure how sensitive cells are to drug treatments. Applying this approach to breast cancer cells grown with and without supportive bone marrow cells, we revealed how the surrounding environment can protect cancer cells from therapy. By guiding the selection of drug concentrations, our framework reduces trial-and-error, thereby saving time and resources. Beyond cancer research, this strategy offers a general way to design more efficient biological experiments, ultimately supporting the development of new treatments.

cancer biology↗

bioRxiv2025

Spatial transcriptomics reveals injury responsive compartments and coordinated immune fibrotic signaling in ANCA associated renal vasculitis

ANCA-associated vasculitis (AAV) often presents with rapidly progressive glomerulonephritis, yet how immune and stromal programmes are organised within kidney tissue remains unclear. We applied spatial transcriptomics to renal cortex biopsies from patients with AAV of varying disease severity and normal-histology controls, generating a spatial map that localizes disease programmes in situ. Four disease-responsive compartments--immune/interstitial fibroblasts (IM/Fib), glomeruli, myofibroblasts, and vascular compartments--showed distinct compartment-specific signatures that correlated with histopathology at the patient level. We also identify coordinated immune-fibrotic signaling linked to severity. Within IM/Fib, the CXCR4-CD74 receptor complex co-localised with IgM cells, and lumican (LUM) co-localised with collagen I/III; both were validated by immunofluorescence and associated with fibrotic injury. These tissue-anchored signatures constitute candidate diagnostic/prognostic biomarkers, and show the utility of this foundational spatial transcriptomics map to generate testable hypotheses which will guide validation in larger, stratified, treatment-annotated cohorts.

bioinformatics↗