bioRxiv ScienceSearch

SEARCH · bioRxiv Science

Results for “pharmacology and toxicology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

299 records · Page 3Linked to original sources

Subcellular carbohydrate compartmentation and organic acid signatures reveal natural variation in cold acclimation of Arabidopsis thaliana

Plant cold acclimation emerges from coordinated adjustments in photosynthesis, primary metabolism, and intracellular carbon allocation. Yet, the regulatory role of subcellular metabolite compartmentation in natural variation of cold acclimation remains insufficiently understood. Here, we investigated four Arabidopsis thaliana accessions grown either individually or in bulk to determine how growth configuration and genotype shape the metabolism of sugars and organic acids during cold exposure. Using non-aqueous fractionation, we quantified plastidial, cytosolic, and vacuolar sugar pools alongside whole-cell carbohydrates, organic acids, enzyme activities, photosynthetic parameters, and stress markers. A neural-network classifier revealed that subcellular sugar distribution together with sugar amounts and organic acids provided the strongest discriminatory power among accessions, surpassing photosynthetic traits and enzyme activities. Our findings demonstrate that natural variation in cold acclimation is strongly determined by genotype-specific subcellular metabolite architectures, and that the cultivation strategy modulates these intracellular signatures. We conclude that subcellular compartmentation of metabolites represents a cellular control layer for natural variation of cold acclimation and resilience in Arabidopsis thaliana.

plant biology

A mutation-agnostic and allele-specific ASO strategy demonstrates potent functional rescue and retinal preservation in RHO-linked retinitis pigmentosa

Autosomal dominant retinitis pigmentosa (adRP) caused by RHO mutations is a leading form of inherited retinal degeneration. Extensive allelic heterogeneity of RHO pathogenic variants limits the translational applicability of mutation-specific gene therapies. To address this, we developed SNARE (SNP-guided Silencing of Aberrant RHO Expression), a mutation-independent, allele-specific antisense oligonucleotide (ASO) strategy. SNARE selectively suppresses mutant RHO transcripts by targeting the common, benign c.-26A/G single-nucleotide polymorphism (SNP) as an allelic discriminator. Candidate gapmer ASOs were screened in engineered reporter lines and validated in patient-derived retinal organoids, identifying RHOligo-A as the lead c.-26A-targeting candidate. In vitro, RHOligo-A achieved robust, preferential knockdown of the target allele, improving RHO localization in retinal organoids, and demonstrated a favorable safety profile with minimal transcriptomic off-target effects and no detectable immunostimulatory activity. Subsequent validation in a novel, humanized RHOP347L/WT mouse model, achieved sustained c.-26A-linked allele-selective suppression, retinal structure preservation, and significantly restored visual function, upon a single intravitreal administration. These findings establish RHOligo-A and SNARE as a scalable, mutation-independent therapeutic platform with strong translational potential and substantial clinical reach for RHO-associated adRP.

genetics

Phosphorylation of spleen tyrosine kinase Y130 positively regulates intracellular signaling and functional responses in platelets

Syk is a non-receptor type protein-tyrosine kinase (PTK), which is associated with platelets surface receptors, glycoprotein VI (GPVI) and C-type lectin-like receptor II-type (CLEC-2). Syk is also expressed in most hematopoietic lineage cells and other cells, such as fibroblasts and neuronal cells. Syk has two tandem SH2 motifs and a C-terminal kinase domain, which are interrupted by interdomains A and B containing multiple tyrosine residues playing a regulatory role upon phosphorylation. This study aims to evaluate the role of Y130 in Syk signaling in platelets. Syk(Y130F) knock-in (KI) mice we generated using the CRISPR-Cas9 technique represent the first in-vivo model harboring this mutation. Using this system, we compared the platelet signaling and responses in wild-type (WT) and Syk(Y130F) littermates. Platelets from homozygous Syk(Y130F) mice showed a decrease in functional responses after activation with CRP, a GPVI agonist, and CLEC-2 crosslinking compared to WT littermates with no significant differences in responses to PAR-4 or purinergic receptor agonists. Key signaling events triggered via both GPVI and CLEC-2, including phosphorylation LAT and PLC-2, were also reduced in Syk(Y130F) platelets at low agonist concentrations. Consistent with these findings, the time to occlusion in the FeCl3 injury model and bleeding time in the tail bleeding assay were significantly enhanced in Syk(Y130F) mice compared to WT littermates. Thus, phosphorylation of Syk Y130 enhances GPVI- and CLEC-2-mediated signaling and functional responses in platelets affecting thrombosis and hemostasis.

molecular biology

Dynamic coupling of cell fate specification and cell sorting during mouse preimplantation development

During preimplantation development in mice, cells of the inner cell mass undergo a cell fate decision to become either Epiblast (Epi) or Primitive Endoderm (PrE) cells. Cell fate patterns during this stage range from an alternating pattern at the beginning to the separation of Epi and PrE at the end. Several mechanisms guiding this decision and pattern formation have been proposed, including intra- and intercellular signalling, cell division and cell sorting. The current understanding is that signalling generates the cell fates and subsequent sorting introduces the spatial cell fate separation. We used agent-based modelling to investigate whether cell differentiation and cell sorting can act concurrently and how their relative contributions to pattern formation may change over time. Comparing our model to experimental data for mouse blastocysts and ICM organoids, we find two mechanistic regimes that can produce the experimentally observed spatial separation: (i) simultaneous long-range intercellular signalling and cell sorting, and (ii) a gradual transition from short-range signalling to cell sorting, in which the timing is mediated via reducing cell fate plasticity. While the second agrees better with existing experimental evidence for late blastocysts, the first might still be relevant for early and mid blastocysts. Together, our results refine the sequential view of Epi/PrE patterning by showing that fate specification and cell sorting can be dynamically coupled, with their relative contributions changing over the course of blastocyst development.

developmental biology

Data coverage and model formulation reshape quantitative interpretations of bacterial transcriptional regulation

Thermodynamic models quantitatively describe interactions between transcription machinery and bacterial promoters. Contrary to conventional understanding, model analysis by Parisutham et al. (2025) attributes transcriptional inhibition by repressors to overstabilization of the RNA polymerase-promoter complex rather than prevention of its formation. Moreover, it suggests an inverse scaling relationship between basal promoter strength and transcriptional fold change, applicable to both repressor- and activator-mediated regulation. To reevaluate findings from this study, we systematically analyze empirical data and compare its framework with conventional thermodynamic models. In contrast to the inverse scaling relationship, data across multiple sources exhibit a peaked tradeoff between basal promoter strength and fold change, underscoring the importance of broad data coverage in revealing the full pattern required for reliable model inference. Furthermore, we identify the model assumption responsible for the apparent inverse scaling and misinterpretation of regulatory mechanisms. Relaxing this assumption enables the model to capture the peaked tradeoff and yield inferences consistent with established mechanisms of transcriptional repression and activation. We further derive a mathematical solution that connects basal expression to fold change for both repressor- and activator-regulated promoters. Our results underscore the importance of broad data coverage to avoid a blind-men-and-elephant interpretation and establish basal promoter strength as a key design parameter governing transcriptional regulation.

systems biology

Synaptic adhesion molecule signaling is activated and organized by tyrosine phosphorylation-induced biomolecular condensate formation

The precise formation of synapses ensures the proper wiring and function of nervous systems. Specific synapse formation is controlled by synaptic adhesion molecules, which link pre- and post-synaptic cells. Despite this central role, details of how adhesion molecules organize and signal intracellularly to build core synaptic structures are limited. Here, we identify multiple tyrosine phosphorylation sites on the cytoplasmic tail of the C. elegans SYG-1 synaptic adhesion molecule that are critical to initiate presynapse formation. We determine that SRC-1 and SRC-2 tyrosine kinases are redundantly responsible for SYG-1 phosphorylation and are consequently critical for presynapse assembly. The phosphorylated population of SYG-1 localizes in clusters within a larger SYG-1 pool and these clusters mark sites of presynaptic active zone assembly. Reconstitution of SYG-1 clusters in vitro with SH2-domain adapters and WSP-1 reveals a dynamic biomolecular condensate-forming system. Blocking phosphotyrosine adapters and condensate formation in vivo results in the loss of SYG-1 clusters, defective presynapse formation, and compromised neurotransmission. We conclude that phosphorylation of a subpopulation of synaptic adhesion molecules activates and organizes them into condensate-based clusters to initiate presynapse formation.

neuroscience

A Microneurosurgical Survival Platform for Elucidating Mechanisms of Brain Tumor Recurrence and Metastasis

Brain tumor recurrence remains the leading cause of mortality in neuro-oncology, and there is a lack of preclinical models replicating the clinical cycle of surgical resection and relapse. To bridge this gap, we developed a novel microneurosurgical survival platform in mice using the NICO Myriad system. We orthotopically implanted pediatric medulloblastoma cells into the mouse cerebral cortex or cerebellum, followed by longitudinal microneurosurgical resection. Bioluminescence imaging and gross fluorescence verified successful resection, local and distal recurrence and metastasis. Comparative bulk RNA sequencing revealed extensive stage-specific transcriptomic divergence alongside conserved core gene sets (2,702 genes in the cerebral cortex and 3,240 genes in the cerebellum) across primary, locally recurrent, and distally recurrent stages. Pathway analysis shows activation of cellular growth, second messenger signaling, and cellular stress adaptation pathways. Targeted qPCR validation demonstrated that post-surgical relapse is driven by a distinct molecular program: recurrent tumors downregulate primary developmental drivers (PTCH1, MYCBP2), canonical suppressors (FOS, PTEN), and chromatin regulators (HDAC2), while selectively upregulating post-transcriptional machinery (RBM8A), endosomal trafficking regulators (RAB5C), acetyltransferases (NAA15), and the m6A RNA demethylase ALKBH5. These findings reveal that medulloblastoma shifts from a primary oncogenic state toward post-transcriptional and transcriptomic survival mechanisms following surgery. Identifying persistent candidates within this conserved core framework provides a roadmap for next-generation precision immunotherapies.

cancer biology

The trade-off between parsimony and model complexity for understanding biomedical mechanisms from mathematical models

Mechanistic mathematical models have been used extensively to provide a deeper understanding of biological mechanisms, including unveiling the regulation of tumour growth and its response to various treatments. However, given the breadth of biological regulatory mechanisms, these models are frequently large and thus prone to potential issues with parameter identifiability. Statistical metrics like the Akaike and Bayesian information criteria can help identify a parsimonious model by balancing goodness of fit against model complexity. Yet simple models may fail to provide sufficient biological insight if they do not adequately capture known physiological processes or mechanisms. A modeller must therefore balance hypothesis generation and biological learning with model tractability. Here, we illustrate this balance using models of ovarian cancer growth and treatment response to cisplatin and immune checkpoint blockade in homologous recombination (HR)-deficient and HR-proficient immunocompetent mouse models. We develop a hierarchy of mathematical models of increasing complexity to describe tumour growth, treatment response, and immune dynamics. Our results highlight the limits of relying purely on statistical metrics for model selection, particularly when the goal is to obtain biological insight and underscore the importance of balancing model complexity to avoid overfitting and parameter unidentifiability.

systems biology

Spatial Transcriptomics Reveals Compartment-Specific Immune Activation Signatures in Ileal and Lymph Node Tissue in Treated HIV Infection

People with HIV (PWH) on long-term antiretroviral therapy (ART) continue to experience elevated rates of morbidities and mortality driven by persistent immune activation despite viral suppression. Known contributors include low-level HIV provirus activity, microbial translocation in part from epithelial barrier dysfunction, microbiome dysfunction, and co-infections. However, how these interact and where they predominate across tissue compartments remains incompletely defined. Here, we applied spatial transcriptomics to characterize compartment-specific transcriptional programs in ileum (epithelium, Peyer's patches, lamina propria) and inguinal lymph nodes (B Cell follicles and T cell zone) from ten PWH on long-term ART, stratified by CD4/CD8 ratio into low-ratio and high-ratio groups, with low-ratio as a proxy for immune activation and increased risk for non-AIDS related serious event. Comparison of global expression found significant differences between groups in four of five compartments. Differential expression analysis identified 483 differentially expressed genes across four of five compartments, with the greatest burden in the T-cell zone and none in the lamina propria. Gene set enrichment analysis identified 116 enriched pathways predominantly in the low-ratio group, spanning immune activation, infection-associated, and metabolic programs, with Peyer's patches showing the broadest transcriptional divergence of any compartment. Cross-compartment signals included higher expression of ORMDL3 and ARL17B in the low-ratio group implicating mitochondrial stress and inflammasome activation, lower expression of CCL3L3 and FCMR in the low-ratio group suggesting impaired immune execution, and divergent ribosomal protein programs between B-cell follicles and the T-cell zone. Cell deconvolution identified compartment-specific differences in estimated immune cell proportions, and T-cell zone gene expression showed significant associations with HIV reservoir measures and plasma markers of microbial translocation and immune activation. Together these findings support spatially heterogeneous immune activation as a feature of persistent immune dysregulation in treated HIV infection and provide compartment-resolved, hypothesis-generating evidence for the tissue-specific mechanisms driving inflammation in this population.

bioinformatics

DNA Sequence-Programmed Protein Coronas Determine Intracellular Fate and Proteostatic Stress of Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) show promise for optical biosensing, imaging, and drug delivery, but turning them into safe, precision nanomedicine tools requires understanding how nanotube surface chemistry dictates recognition and processing by cells. Like other nanomaterials, carbon nanotubes acquire a biomolecular corona on contact with biological fluids, and corona identity is increasingly recognized as central to sensor performance and drug delivery efficacy. However, whether corona identity also governs the intracellular fate of carbon nanotubes remains largely unknown. Here, we show that the single-stranded DNA wrapping of (6,5)-enriched single-walled carbon nanotubes reprograms their protein corona, intracellular trafficking, and macrophage response. By profiling (AT)15, (GT)15, and (CT)15 wrapped SWCNTs, we show that the wrapping sequence programs both the protein corona and the resulting proteostatic stress on macrophages. Photoluminescence imaging and confocal Raman measurements reported that (AT)15 is internalized the most yet leaves the proteome and nanotube structure largely undisturbed, whereas (CT)15, taken up the least, undergoes the most aggressive intracellular degradation and drives the highest oxidative and proteostatic stress. Corona proteomics indicated that all three tested nanotubes form coronas with distinct functional identities that are responsible for divergent intracellular routes. Time-resolved intracellular proteomics combined with functional assays resolved how the host cell reorganizes its biomolecular complexity over time, including oxidative outputs, aside from a sequence-independent core response involving particle engagement, phagosomal sorting, and lysosomal processing. These findings provide mechanistic insight into nanomaterial-cell interactions and the wrapping sequence as a tunable, nucleotide-level design handle for controlling the intracellular fate of carbon nanomaterials, with potential implications for safe and effective nanomedicine platforms.

bioengineering

Increased substrate complexity drives re-diversification and functional reorganization in simplified methanogenic consortia

Anaerobic digestion is a sustainable process for methane production that relies on complex microbial networks. While simplified enriched consortia offer a promising strategy to improve process control, excessive simplification can disrupt key functions and microbial partnerships, reducing community resilience. In this study, we investigated whether simplified methanogenic communities could re-diversify and maintain methane production when exposed to more complex substrates, namely butyrate and glucose. We also evaluated the effect of vitamin and amino acid supplementation on sustaining key methanogens and beneficial microbial partners. Three methanogenic communities were monitored over three months for methane production and microbial diversity while receiving butyrate and/or glucose, with different vitamin or amino acid supplements. Exposure to more complex substrates successfully restored the diversity of acidogenic and acetogenic populations, even after prolonged feeding with simple substrates, highlighting both the resilience of the simplified communities and the ecological importance of low-abundance taxa. However, the transition reduced process stability and methane production, likely due to substrate overloading. The results further suggest that substrate complexification should be introduced stepwise, promoting acetogenesis before acidogenesis. This fundamental study brings new light on which factors must be considered in the long-term goal of designing tailored-made consortia for anaerobic digestion.

bioengineering

A transcriptomic and spatial map of serotonin autoreceptor expression in Drosophila

Serotonin is an evolutionarily ancient neurotransmitter that modulates an array of behaviors such as mood, sleep, and appetite across species. Serotonin acts primarily by binding to serotonin receptors, which are expressed in post-synaptic neurons (heteroreceptors) and serotonergic neurons themselves (autoreceptors). Serotonin autoreceptors modulate serotonergic tone, the foundational principles of which have been excellently demonstrated in vertebrate and invertebrate models. However, many aspects of the mechanisms and contexts in which this modulation occurs are still unclear. Drosophila melanogaster is a powerful model organism that can provide unique insights into autoreceptor function by the ability to perform precise spatial and temporal genetic manipulation with structural and functional readouts / behaviors of serotonin systems. However, a systematic characterization of serotonin autoreceptor expression in Drosophila has not been conducted. Here we use single-cell sequencing and genetic labeling to show that all five serotonin receptors are expressed in serotonergic neurons and map their expression at both the larval and adult stages of development. This is the first evidence of 5-HT2A and 5-HT7 expression in serotonergic neurons in any organism. Moreover, the unique combinations of autoreceptor expression in specific neuronal clusters will aid in the development of novel hypotheses for autoreceptor function, and demonstrates the utility of Drosophila as a model organism to study the function of serotonin autoreceptors.

neuroscience

Low-Density Lipoprotein Modulates Plasma Fibrin Network Architecture and Impairs Fibrinolysis

Low-density lipoprotein (LDL) is a major atherogenic lipoprotein, yet its potential to directly modify the fibrin scaffold of blood clots is incompletely understood. Here, we investigated how LDL alters plasma fibrin network architecture and internal fibrinolysis across defined fibrinogen/thrombin conditions. Pooled normal human plasma was supplemented with LDL and clotted with controlled concentrations of fibrinogen and thrombin. Fibrin architecture was visualized by confocal microscopy and quantified by pore-size analysis; clot formation and lysis were monitored turbidimetrically in the presence of tissue plasminogen activator (tPA). Increasing LDL produced a pronounced reduction in fibrin-network pore size across the tested fibrinogen/thrombin conditions. The LDL dependence of pore diameter was well described by a power-law relationship, D_pore=(6.54 +/- 0.11)[LDL]^(-0.12 +/- 0.02) , (R^2 = 0.90), with a significant negative LDL exponent (p = 4 x 10^5). Increasing LDL also prolonged clot lysis time and altered turbidity kinetics. These findings extend epidemiologic and clinical associations between ApoB-containing lipoproteins and hypofibrinolytic clot phenotypes by demonstrating, in a controlled plasma system, that LDL itself can modify fibrin network architecture and fibrinolytic susceptibility. The results support a structure-function role for LDL within the fibrin biomaterial and motivate direct tests of LDL incorporation, protofibril packing, fibrinolytic-protein binding, and single-fiber mechanics.

biophysics

Polymicrobial catheter biofilms sustain susceptible Enterococcus faecalis and Escherichia coli during β-lactam treatment

Broad-spectrum {beta}-lactam exposure can select for Enterococcus-dominated urinary communities in catheterized intensive-care patients, even when co-colonizing Escherichia coli remains susceptible. We investigated paired E. faecalis and E. coli isolates recovered before and after piperacillin-tazobactam (TZP) treatment using a catheter biofilm model and showed that their survival depends on mutualism and biofilm-dependent persistence. Without antibiotics, E. faecalis reduced E. coli biofilm formation yet promoted pre-attachment co-aggregation and reorganized mixed-biofilm architecture on the catheter. Despite TZP susceptibility and the absence of resistance determinants, catheter-associated biofilms and biofilm-dispersed cells survived concentrations 250- to 1000-fold above their MICs, whereas planktonic cells were eliminated. Survivors retained susceptibility but showed delayed regrowth, consistent with a transient persister-like state. In the post-treatment pair, each species sustained the other during recovery, coinciding with a nonsynonymous substitution in the enterococcal surface adhesin Esp. These findings show that antagonistic and cooperative interactions can coexist within catheter biofilms and enable susceptible polymicrobial communities to withstand {beta}-lactam treatment without {beta}-lactam resistance.

microbiology

Whole-body Super-resolution Functional and Molecular Imaging with Panoramic Photoacoustic-Ultrasound Tomography

Photoacoustic (PA) and ultrasound (US) imaging provide complementary molecular, functional, and anatomical contrasts. Here, we present a panoramic PA-US imaging platform that integrates multispectral PA computed tomography (PACT) along with reflection-mode and transmission-mode US imaging through a single shared full-ring ultrasound array. We employ an ultrafast planewave transmission scheme in reflection-mode US for power Doppler (PWD) imaging and ultrasound localization microscopy (ULM). Additionally, we use the transmission-mode US to reconstruct a spatially resolved speed of sound (SoS) map that corrects both PA and US reconstruction. Such correction sharpens the resolution of PACT, suppresses the artifacts of PWD, and improves microbubble localization of ULM. Elevational scanning further enables whole-body volumetric imaging with co-registered PA and US contrasts. The integrated system maps photoswitchable DrBphP1-expressing tumors alongside their blood perfusion and oxygenation environment. Applying the platform to monitor unilateral renal ischemia-reperfusion injury, we report that microvascular perfusion and renal oxygenation recover at different rates. Collectively, we demonstrate that the integrated PA-US imaging platform provides a unified framework for multiparametric study of anatomy, perfusion, microvascular flow, oxygenation, and molecular activities.

bioengineering

Germ granules act as repositories for RNA and protein molecules essential for zebrafish germline development

Germ granules are conserved, phase-separated ribonucleoprotein condensates enriched in germline determinants, yet their precise function remains unclear. Using quantitative live imaging, translational reporters, and targeted disruption of germ granule assembly in zebrafish primordial germ cells, we show that germ granules are dispensable for germ cell fate, migration, and gamete production. Instead, granules act as reservoirs, sequestering transcripts and releasing them gradually for cytoplasmic translation. Under heat stress or translational inhibition, granules further accumulate mRNAs and canonical stress granule factors, indicating a role in buffering RNA and regulatory protein availability rather than serving as sites of localized translation, as previously proposed. Consistent with this reservoir model, cytoplasmic expression of the germline determinants Nanos3 and Dead end is sufficient to direct somatic cells toward a germline fate even in the absence of germ granules. Correspondingly, germ cells lacking granules develop normally but show reduced persistence of germline RNA expression and impaired fertility. Together, these findings establish zebrafish germ granules as protective condensates that safeguard germline determinants and enhance developmental robustness by buffering the timing and rate of RNA translation.

cell biology

Evolution and Human Neural Individuality

Individuality is a defining feature of human biology. The functional network architecture of the human brain harbors person-specific qualities and forms individualized connectivity profiles that function as a neural fingerprint, both stable and unique across time. Here, using fMRI data from 431 Human Connectome Project participants, we examined whether neural individuality is more strongly exhibited in brain regions bearing signatures of recent human evolution. We calculated region-wise fingerprinting accuracy and associated it with four properties of evolutionary cortical organization: cortical expansion, myelin content estimate (T1w/T2w), human-specific gene-expression profiles, and functional homology to other primates. Across all four measures, neural individuality was strongest in cortical areas showing greater evolutionary novelty in humans, particularly frontoparietal control and default mode networks, and weaker in more conserved primary regions. Our findings connect evolutionary variation across species with stable functional variation among individuals.

neuroscience

Designing antimicrobials with programmable mechanism and safety

Antimicrobial peptides (AMPs) are a promising solution to antimicrobial resistance, yet generative models for their design cannot control the physicochemical properties and motifs that shape activity and selectivity. Here, we present OmegAMP, a conditional diffusion framework controlling net charge, mean hydrophobicity, and sequence length, supporting de novo, analog, and motif-guided design. Across 204 wet-lab characterized peptides, de novo generation yielded antimicrobials with broad activity against multidrug-resistant Gram-negative isolates. Analog generation converted six inactive prototypes into antimicrobials, with the prototype determining each analog's membrane-disruption mode and mammalian-cell safety. Motif-guided analog generation preserved lipopolysaccharide engagement of active prototypes, and a redesigned non-antimicrobial leucine zipper acquired antimicrobial activity while retaining DNA-perturbing character in vitro. In murine skin and thigh infection models, leads reduced bacterial burden, with a motif-guided DNA-perturbing lead matching the fluoroquinolone control systemically. OmegAMP opens a programmable route to new peptide antibiotics whose mechanism and safety follow from the chosen prototype.

bioinformatics