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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2024

Advances in culturing of the sea star Patiria miniata

The use of the sea star Patiria miniata as a model system has produced groundbreaking advances in a disparate set of biomedical research fields, including embryology, immunology, regeneration, cell biology and evolution of development. Nonetheless, the life cycle of P. miniata has not yet been closed in the laboratory, precluding the generation of stable transgenic and mutant lines, which would greatly expand the toolset for experimentation with this model system. Rearing P. miniata in the laboratory has been challenging due to limited knowledge about metamorphosis cues, feeding habits of juveniles and their relatively long generation time. Here we report protocols to rear P. miniata embryos through sexual maturity in a laboratory setting. We provide detailed staging of early embryonic development at different temperatures, and show that larvae can be raised to competence in as little as 15 days. We find that retinoic acid induces metamorphosis effectively and present methods to rear juveniles on commercially available foods. We show that in a flow-through system, juveniles double in size every 2 months and reach sexual maturity in approximately 2 years. We report the first example of P. miniata raised through sexual maturity in a laboratory setting, paving the way for the generation of stable mutant sea star lines.

developmental biology↗

bioRxiv2024

Quantitative Detection of Amyloid Fibrils using Fluorescence Resonance Energy Transfer (FRET) Between Engineered Yellow and Cyan Proteins

Over 20 human diseases are caused by or associated with amyloid formation. Developing diagnostic tools to understand the process of amyloid fibril formation is essential for creating therapeutic agents to combat these widespread and growing health problems. Here, we capitalize on our recent striking discovery that green fluorescent protein (GFP), one of the most used proteins in molecular and cell biology, has a high intrinsic binding affinity to various structural intermediates along the fibrillation pathway, independent of amyloid sequence. Using engineered GFP with the fluorescence properties of Aquamarine and mCitrine, we developed a FRET-based sensor to quantitatively monitor amyloid fibrils. The proof-of-principle characterization was performed on a test system consisting of PAPf39 fibrils.

biophysics↗

bioRxiv2024

SOD1 controls neutrophil oxidative burst and microbial killing

AbstractNeutrophils are immune cells specialized in producing large amounts of reactive oxygen species (ROS) to kill microbes. However, the mechanisms by which these cells regulate the balance of different ROS species and mitigate oxidative stress remain unclear. Here, we demonstrate that superoxide dismutase 1 (SOD1) plays a crucial role in ROS formation and antimicrobial activity in neutrophils. Our findings reveal that SOD1 modulates the ratio of superoxide (O2-) to hydrogen peroxide (H2O2) during the ROS burst, thereby supporting myeloperoxidase (MPO) enzymatic activity. By employing biochemical, cell biological, and genetic approaches, we show that SOD1 is crucial for ROS formation during NETosis and microbial infections, as it reduces oxidative stress and enables complete neutrophil activation. Impairment of SOD1 activity increases cysteine oxidation and lipid peroxidation. Neutrophils isolated from a patient with a SOD1 mutation exhibit decreased ROS production and impaired neutrophil extracellular trap (NET) formation. Our findings suggest that SOD1 is a novel regulatory factor in the oxidative burst that enables the full immunological response of neutrophils.

immunology↗

bioRxiv2024

Bipolar and schizophrenia risk gene AKAP11 encodes an autophagy receptor coupling the regulation of PKA kinase network homeostasis to synaptic transmission

Human genomic studies have identified protein-truncating variants in AKAP11 associated with both bipolar disorder (BD) and schizophrenia (SCZ), implicating a shared disease mechanism driven by loss-of-function. AKAP11, a protein kinase A (PKA) adaptor, plays a key role in degrading the PKA-RI complex through selective autophagy. However, the neuronal functions of AKAP11 and the impact of its loss-of-function remains largely uncharacterized. Through multi-omics approaches, cell biology, and electrophysiology analysis in mouse models and human induced neurons, we delineated a central role of AKAP11 in coupling PKA kinase network regulation to synaptic transmission. Loss of AKAP11 distorted compartment-specific PKA and GSK3/{beta} activities and impaired cellular functions that significantly overlap with pathways associated with BD and SCZ. Moreover, we identified interactions between AKAP11, the PKA-RI adaptor SPHKAP, and the ER-resident autophagy-related proteins VAPA/B, which co-adapt and mediate PKA-RI complex degradation in neurons. Notably, AKAP11 deficiency impaired neurotransmission, providing key insights into the mechanism underlying AKAP11-associated psychiatric diseases.

neuroscience↗

bioRxiv2025

Exploring the kinetics and mechanism of phase separation in ternary lipid mixtures containing APP C99 using atomistic vs coarse-grained MD simulations

The phase separation of lipid bilayers, composed of mixtures of saturated and unsaturated lipids and cholesterol, is a topic of fundamental importance in membrane biophysics and cell biology. The formation of lipid domains, including liquid-disordered domains enriched in unsaturated lipids and liquid-ordered domains enriched in saturated lipids and cholesterol is believed to be essential to the function of many membrane proteins. Experiment, theory, and simulation have been used to develop a general understanding of the thermodynamic driving forces underlying phase separation in ternary and quaternary lipid mixtures. However, the kinetics of early events in lipid phase separation in the presence of transmembrane proteins remain relatively understudied. Using large-scale all-atom and coarse-grained simulations, we explore the kinetics and phase separation of ternary lipid mixtures of saturated lipid, unsaturated lipid, and cholesterol. Order parameters employed in the Cahn-Hilliard theory provide insight into the kinetics and mechanism of lipid phase separation. We observe three distinct time regimes in the phase separation process: a shorter time exponential phase followed by a power law phase followed by a longer time plateau phase. Comparison of lipid, protein and lipid-protein dynamics between all-atom and coarse-grained models identifies both quantitative and qualitative differences and similarities in the phase separation kinetics. Moreover, timescaling of dynamics of AA and CG simulation yields a similar kinetic mechanism of phase separation. The findings of this study elucidate fundamental aspects of membrane biophysics and the ongoing efforts to define the role of lipid rafts in the structure and function of cellular membrane.

biophysics↗

bioRxiv2025

The C terminus of infectious bursal disease virus (IBDV) VP3 encodes a predicted intrinsically disordered region (IDR), which promotes the formation of cytoplasmic puncta and modulates their physical properties.

The virus factories (VFs) of infectious bursal disease virus (IBDV) form through liquid-liquid phase separation (LLPS). A major component of the IBDV VF is the nonstructural protein VP3. Here, we predicted the full-length structure of the VP3 monomer and homodimer and employed molecular dynamics simulations to characterize their behavior. We identified the 36 amino acid carboxy(C)-terminus as a highly dynamic intrinsically disordered region (IDR). We then compared the cytoplasmic puncta that were made in the presence of the wild type (wt) VP3 with those made with a VP3 that lacked the C-terminus (VP3{Delta}C). Using live-cell imaging with fluorescent reporter tagged proteins, we found that VP3{Delta}C puncta were significantly less numerous (p<0.0001), smaller (p<0.0001), and more irregular in shape than puncta formed in the presence of wt VP3, demonstrating that the VP3 C terminal IDR promoted their formation. Moreover, by fluorescence recovery after photobleaching (FRAP), the VP3{Delta}C puncta had a significantly reduced mobile fraction (0.29) as compared to full-length VP3 puncta (0.70) (p<0.001), demonstrating that the VP3 C terminal IDR modulated their physical properties. However, the VP3{Delta}C puncta still exhibited liquid-like fusion events in the cytoplasm and were sensitive to treatment with aliphatic diols. Moreover, VP3 did not form puncta when expressed alone, and the removal of the C terminus did not abolish puncta formation completely. We propose that VP3 forms part of a higher order complex with other biomolecules to drive LLPS, and that the VP3 C terminal IDR modulates the physical properties of the resultant LLPS structures. ImportanceLLPS is a phenomenon of growing interest in cell biology. It is a part of the replication cycles of diverse viruses, but our understanding of the molecular basis that underpins the mechanism of phase separation is incomplete. We previously demonstrated that the birnavirus IBDV, a major agricultural pathogen, exploits LLPS in the formation of its VFs. Here, we have characterized the C-terminal 36 amino acid region of IBDV VP3 bioinformatically and by molecular dynamics simulations and found that it encodes a highly dynamic intrinsically disordered region (IDR). Furthermore, we found this region to promote the formation of cytoplasmic puncta and modulate their physical properties. This work contributes to a more detailed understanding of birnavirus replication at the molecular level, and to the study of LLPS as a phenomenon.

molecular biology↗

bioRxiv2025

Nucleoplasmic Lamin A/C controls replication fork restart upon stress by modulating local H3K9me3 and ADP-ribosylation levels

Mild replication interference is a consolidated strategy for cancer chemotherapy. Tolerance to mild replication stress (RS) relies on active fork slowing, mediated by transient fork reversal and RECQ1-assisted restart, and modulated by PARP1 and nuclear architectural components via yet-elusive mechanisms. We combined acute protein inactivation with cell biology and single-molecule approaches to investigate the role of Lamin A/C upon mild RS. We found that Lamin A/C dynamically interacts with replication factories throughout the nucleus and, together with its nucleoplasmic partner LAP2, is required to induce active fork slowing and maintain chromosome stability upon mild genotoxic treatments. Inactivating nucleoplasmic Lamin A/C reduces poly-ADP-ribosylation (PAR) levels at nascent DNA, triggering deregulated RECQ1-mediated restart of reversed forks. Moreover, we found that the heterochromatin mark H3K9me3, previously reported at stalled forks, also accumulates in response to mild RS. H3K9me3 accumulation requires Lamin A/C, which prevents its premature removal by the histone demethylase JMJD1A/KDM3A. H3K9me3 loss per se phenocopies Lamin A/C inactivation, reducing PAR levels and deregulating RECQ1 activity at forks. Hence, nucleoplasmic Lamin A/C, H3K9me3 and PARylation levels are crucial, mechanistically-linked modulators of fork slowing, remodelling and restart upon mild RS, with important implications for chemotherapy response and Lamin A/C deregulation in human disease.

molecular biology↗

bioRxiv2025

Multi-scale simulations of membrane adhesion mediated by CD47-SIRPα complexes

Adhesion of biological cells is essential for various processes, including tissue formation, immune responses, and signaling. It involves multiple length scales, ranging from nanometers to micrometers, which are characteristic of (a) the intercellular receptor-ligand binding that mediates the cell adhesion, (b) the spatial distribution of the receptor and lignad proteins in the membranes of adhering cells, (c) adhesion-induced deformations and thermal undulations of the membranes, (d) the overall size of the interface between adhering cells. Therefore, computer simulations of cell membrane adhesion require multi-scale modeling and suitable approximations that capture the essential physics of the system under study. Here, we introduce such a multi-scale approach to study membrane adhesion mediated by the CD47-SIRP binding, which is an immunologically relevant process. The synergetic use of coarse-grained molecular dynamics simulations and mesoscale kinetic Monte Carlo simulations allows us to explore both equilibrium properties and dynamical behavior of adhering membranes on the relevant length scales between 1 nm and 1 {micro}m on time scales ranging from 0.1 ns all the way up to about 20 s. The multi-scale simulations not only reproduce available experimental data but also give quantitative predictions on binding-induced conformational changes of SIRP and membrane-mediated cooperativity of the CD47-SIRP binding as well as fluctuation-induced interactions between the CD47-SIRP complexes. Our approach is applicable to various membrane proteins and provides invaluable data for comparison with experimental findings.

biophysics↗

bioRxiv2025

Safe focused ultrasound-mediated blood-brain barrier opening is driven primarily by transient reorganization of tight junctions

Focused ultrasound (FUS) with microbubbles opens the blood-brain barrier (BBB) to allow targeted drug delivery into the brain. The mechanisms by which endothelial cells (ECs) respond to either low acoustic pressures known to open the BBB transiently, or high acoustic pressures that cause brain damage, remain incompletely characterized. Here, we use a mouse strain where tight junctions between ECs are labelled with eGFP and apply FUS at low (450 kPa) and high (750 kPa) acoustic pressures, after which mice are sacrificed at 1 or 72 hours. We find that the EC response leading to FUS-mediated BBB opening at low pressures is localized primarily in arterioles and capillaries, and characterized by a transient loss and reorganization of tight junctions. BBB opening still occurs at low safe pressures in mice lacking caveolae, suggesting that it is driven primarily by transient dismantlement and reorganization of tight junctions. In contrast, BBB opening at high pressures is associated with obliteration of EC tight junctions that remain unrepaired even after 72 hours, allowing continuous fibrinogen passage and persistent microglial activation. Single-cell RNA-sequencing of arteriole, capillary and venule ECs from FUS mice reveals that the transcriptomic responses of ECs exposed to high pressure are dominated by genes belonging to the stress response and cell junction disassembly at both 1 and 72 hours, while lower pressures induce primarily genes responsible for intracellular repair responses in ECs. Our findings suggest that at low pressures transient reorganization of tight junctions and repair responses mediate safe BBB opening for therapeutic delivery. Significance StatementFocused ultrasound with microbubbles is used as a noninvasive method to safely open the BBB at low acoustic pressures for therapeutic delivery into the CNS, but the mechanisms mediating this process remain unclear. Kugelman et al., demonstrate that FUS-mediated BBB opening at low pressures occurs primarily in arterioles and capillaries due to transient reorganization of tight junctions. BBB opening still occurs at low safe pressures in mice lacking caveolae, suggesting a transcellular route-independent mechanism. At high unsafe pressures, cell junctions are obliterated and remain unrepaired even after 72 hours, allowing fibrinogen passage and persistent microglial activation. Single-cell RNA-sequencing supports cell biological findings that safe, FUS-mediated BBB opening may be driven by transient reorganization and repair of EC tight junctions.

bioengineering↗

bioRxiv2025

Microscopic and structural observations of actin filament capping and severing by Cytochalasin D

Cytochalasin D (CytoD) is widely used to inhibit actin polymerization, but the underlying regulatory mechanism is unclear. We addressed this using Total Internal Reflection Fluorescence (TIRF) microscopy. Our time course depolymerization assay of individual actin filaments showed that CytoD tightly caps the barbed end, with an estimated Km value for inhibition of 4.1 nM and a duration time of [~]1 min. Consistently, in polymerization assays, CytoD at concentrations near the Km value completely suppressed barbed end elongation. Interestingly, at lower concentrations, CytoD acted as a leaky capper, allowing actin monomer addition by rapidly binding to and dissociating from barbed ends. We interpreted this contradictory behavior as arising from differences in binding modes: capping one strand (fast dissociation) or both strands (slow dissociation). CytoD severs actin filaments at micromolar levels, a concentration range commonly used in cell biological studies. Although the severing rate is slower than cofilin, the frequency is higher, resulting in the fragmentation of filaments into shorter pieces. Severing activity was suppressed by inorganic phosphate or cofilin. We determined the crystal structure of CytoD bound to filamentous conformation (F-form) actin and found that CytoD fits better in the hydrophobic cleft of F-form actin than in the monomeric conformation actin, explaining the preferential binding towards barbed end subunits. The structure further indicates that CytoD prevents barbed end depolymerization by stabilizing the terminal subunits in the F-form, which is supported by our MD simulations. Collectively, our results demonstrate how CytoD regulates actin dynamics at the molecular level.

biophysics↗

bioRxiv2025

Hyperlipidemia drives tumor growth in a mouse model of obesity-accelerated breast cancer growth.

Obesity is an established risk factor for breast cancer (BC), yet the specific mechanisms driving this association remain unclear. Dysregulated lipid metabolism has emerged as a key factor in cancer cell biology. While obesity is often accompanied by hyperlipidemia, the isolated impact of elevated lipid levels on BC growth has not been experimentally tested. Using the E0771 orthotopic model of obesity-accelerated BC growth in immune-competent mice, we investigated the direct role of systemic lipids in tumor growth. Combining dietary and genetic mouse models, we show that elevated circulating lipids are sufficient to accelerate BC tumor growth even in the absence of obesity or alterations in blood glucose and/or insulin levels. Pharmacological lowering of systemic lipid levels attenuates BC growth in obese mice, suggesting a direct role for lipids in fueling tumor expansion. Notably, we also show that weight loss alone, without a corresponding reduction in lipid levels such as that induced by a ketogenic diet, fails to protect against BC, highlighting the necessity of targeting lipid metabolism in obesity-associated BC. Our findings establish hyperlipidemia as a critical driver of BC progression and suggest that lipid-lowering interventions may be a promising strategy to mitigate BC risk in obese individuals.

cancer biology↗

bioRxiv2025

Multi-alignment framework - consider and detect genomic and transcriptomic sequence alignment variability by comparing different techniques

DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) provided in this study offers a user-friendly platform for sequence alignment and quantification. It is adaptable to various research needs and can incorporate different tools and parameters for in-depth analysis, especially in low read rate scenarios. This framework can be used to compare results from different alignment programs and algorithms on the same dataset, allowing for a comprehensive analysis of subtle to significant differences. This concept is demonstrated in a small RNA case study. MAF is specifically designed for the Linux platform, commonly used in bioinformatics. Its script structure streamlines processing steps, saving time when repeating procedures with various data sets. While the focus is on microRNA analysis, the templates provided can be adapted for all transcriptomic and genomic analyses. The template structure allows for flexible integration of pre- and post-processing steps. MicroRNA analysis indicates that STAR and Bowtie2 alignment programs are more effective than BBMap. Combining STAR with the Salmon quantifier, or with some limitations, the Samtools quantification, appears to be the most reliable approach. This method is ideal for scientists who want to thoroughly analyze their alignment results to ensure quality. The detailed microRNA analysis demonstrates the quality of three alignment and two quantification methods, offering guidance on assessing result quality and reducing false positives.

bioinformatics↗

bioRxiv2025

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

Building predictive models of the cell requires systematically mapping how perturbations reshape each cells state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas of 100 million transcriptomic profiles measuring how each of 1,100 small-molecule perturbations impact cells across 50 cancer cell lines. Our high-throughput Mosaic platform, composed of a highly diverse and optimally balanced "cell village", reduces batch effects and enables parallel profiling of thousands of conditions at single-cell resolution at an unprecedented scale. As the largest single-cell dataset to date, Tahoe-100M enables artificial-intelligence (AI)-driven models to learn context-dependent functions, capturing fundamental principles of gene regulation and network dynamics. Although we leverage cancer models and pharmacological compounds to create this resource, Tahoe-100M is fundamentally designed as a broadly applicable perturbation atlas and supports deeper insights into cell biology across multiple tissues and contexts. By publicly releasing this atlas, we aim to accelerate the creation and development of robust AI frameworks for systems biology, ultimately improving our ability to predict and manipulate cellular behaviors across a wide range of applications.

genomics↗

bioRxiv2025

Capsule-mediated O-antigen masking protects hypervirulent Klebsiella pneumoniae from neutrophil killing

Klebsiella pneumoniae is listed as a critical priority pathogen by the WHO due to prevalent extended-spectrum {beta}-lactamase and carbapenem resistance and high mortality rates Hypervirulent K. pneumoniae (hvKp) causes life-threatening infections in immunocompetent individuals, while classical K. pneumoniae (cKp) causes nosocomial infections in immunosuppressed patients. The convergence of hypervirulence with antibiotic resistance is now a major global health threat. Using a murine pulmonary infection model, we show that hvKp resisted clearance despite significant neutrophil recruitment. Using clinical hvKp and cKp isolates, bone marrow derived neutrophils, cell biology, pharmacology and imaging (both light and electron microscopy) in ex vivo assays revealed that the hvKp hypermucoviscous capsule prevents bacterial recognition and neutrophil activation, blocking ROS production, degranulation, and neutrophil extracellular traps (NETs) formation. In the absence of capsule ({Delta}wcaJ) or hypermucoid capsule determinants ({Delta}rmpADC), hvKp activates neutrophils, leading to degranulation, NET formation and bacterial killing. While superimposing the absence of O-antigen ({Delta}rfb) on the {Delta}wcaJ abrogates degranulation, neutrophils still elaborate NETs that eliminate the {Delta}wcaJ/{Delta}rfb mutant at high efficiency. This suggests that O-antigen is a double-edged sword, functioning as a PAMP triggering neutrophil degranulation yet assisting the pathogen to evade NET-mediated destruction. These findings shed light on the mechanism underpinning immune evasion by the hypervirulent capsule in hvKp.

microbiology↗

bioRxiv2025

Unraveling new characteristics of γδT cells using scRNA-seq in TCR KO chicken

The characterization of T cells in chickens has proven to be challenging, primarily due to the lack of specific markers to differentiate classical Th1, Th2, and Th17 subsets. Furthermore, chickens possess a notably high proportion of {gamma}{delta} T cells, making them a unique model for investigating the poorly understood role of these cells not only in chickens but also in mammals. To gain deeper insights into the functions and characteristics of the {beta} and {gamma}{delta} T cell subsets in chickens, whole transcriptome analysis (WTA) on CD3+ single cells isolated from wild type (WT), TCR C{beta} knockout (KO) and TCR C{gamma} KO chickens at embryonic day (ED) 18, day (d) 3, and d14 post-hatch was conducted. The results indicate that {gamma}{delta} T cells exhibit cytolytic activity in both TCR C{beta} KO and WT chickens. A distinct cluster of {gamma}{delta} T cells expressing genes associated with the interferon pathway was revealed in TCR C{beta} KO chickens, which may contribute to the severe phenotype in these chickens, which is characterized by severe inflammation of spleen, gut and stomach. Additionally, novel gene markers were identified that precisely define the {beta} and {gamma}{delta} T cell subsets. These findings provide new insights into chicken T cell biology and contribute to a better understanding of the mechanisms underlying the severe phenotype observed in TCR C{beta} KO chickens.

immunology↗

bioRxiv2025

Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies

Protists are polyphyletic singled-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterised photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterised the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9 was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesise half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate (DMSP) biosynthesis. Biosynthesis of this important stress-protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not before been identified in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.

microbiology↗

bioRxiv2025

Reconstructing Noisy Gene Regulation Dynamics UsingExtrinsic-Noise-Driven Neural Stochastic Differential Equations

Proper regulation of cell signaling and gene expression is crucial for maintaining cellular function, development, and adaptation to environmental changes. Reaction dynamics in cell populations is often noisy because of (i) inherent stochasticity of intracellular biochemical reactions ("intrinsic noise") and (ii) heterogeneity of cellular states across different cells that are influenced by external factors ("extrinsic noise"). In this work, we introduce an extrinsic-noise-driven neural stochastic differential equation (END-nSDE) framework that utilizes the Wasserstein distance to accurately reconstruct SDEs from trajectory data from a heterogeneous population of cells (extrinsic noise). We demonstrate the effectiveness of our approach using both simulated and experimental data from three different systems in cell biology: (i) circadian rhythms, (ii) RPA-DNA binding dynamics, and (iii) NF{kappa}B signaling process. Our END-nSDE reconstruction method can model how cellular heterogeneity (extrinsic noise) modulates reaction dynamics in the presence of intrinsic noise. It also outperforms existing time-series analysis methods such as recurrent neural networks (RNNs) and long short-term memory networks (LSTMs). By inferring cellular heterogeneities from data, our END-nSDE reconstruction method can reproduce noisy dynamics observed in experiments. In summary, the reconstruction method we propose offers a useful surrogate modeling approach for complex biophysical processes, where high-fidelity mechanistic models may be impractical.

molecular biology↗

bioRxiv2025

Structural bases for Nuclear Factor 1-X activation and DNA recognition. Prototypic insight into the NFI transcription factor family

Nuclear Factor I (NFI) proteins were first identified in adenovirus DNA replication and later as regulators of gene transcription, stem cell proliferation, and differentiation. They play key roles in development, cancer and congenital disorders. Within the NFI family, NFI-X is critical for neural stem cell biology, hematopoiesis, muscle development, muscular dystrophies and oncogenesis. Here, we present the first structural characterization of the NFI transcription factor, NFI-X, both alone and bound to its consensus palindromic DNA site. Our analyses reveal a novel, MH1-like fold within NFI-X DNA-binding domain (DBD) and identify crucial structural determinants for activity, such as a Zn{superscript 2} binding site, dimeric assembly, activation mechanism and DNA-binding specificity. Given the >95% sequence identity within the NFI DBDs, our structural data are prototypic for the entire family; a NFI Rosetta Stone that allows decoding a wealth of biochemical and functional data and provides a precise target for drug design in a wider disease context.

biochemistry↗