Biology subjects

Lee, T.

Publications and source records attributed to Lee, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Causal evidence for the role of dorsolateral prefrontal cortex in the implementation of cognitive control adjustments

Cognitive control processes enable us to use recent contextual information to flexibly adapt to current task demands. This ability to adapt control processes is exhibited in response conflict tasks. In these tasks, participants must respond to a relevant piece of information while overcoming the tendency to respond to task-irrelevant information that cues an automatic or habitual response. Control demands can be updated in these tasks via two separate routes. Both errors and conflict between task-irrelevant and task-relevant information affect performance on subsequent trials. A body of work has implicated dorsolateral prefrontal cortex (DLPFC) in implementing these control adjustments. However, this work has primarily relied on correlational techniques or focused on a single index of control adaptation. Here, we combine inhibitory transcranial magnetic stimulation (TMS) over DLPFC with computational modeling of behavior to test the causal role of DLPFC in control adaptation. We show that inhibitory TMS to DLPFC reduces the effect of previous trial conflict, and committing an error on the previous trial further reduces adaptive effects. This result provides causal evidence for DLPFC playing a general role in implementing trial-to-trial control adjustments.

neuroscience↗

bioRxiv2026

Surfactant-Assisted Colorimetric Signal Enhancement in Paper-Based Glucose Sensing

Paper-based colorimetric sensors offer a low-cost and accessible platform for point-of-care (POC) analysis, but enzyme activity loss during coating and drying can weaken analytical signals and require high enzyme loadings or complex immobilization procedures. Although surfactants are widely used to improve wettability in paper-based assays, their potential contribution to colorimetric performance beyond these effects remains unclear. Here, we investigated surfactant-assisted colorimetric signal enhancement in a glucose assay implemented on a 96-puddle paper plate (96-PPP) and identified Tween 20 as the most effective surfactant. Its effect on detection performance became more pronounced as glucose oxidase (GOx) loading decreased; at 0.1 mg/mL GOx, Tween 20 lowered the limit of detection (LoD) from 0.113 to 0.034 mg/mL (approximately 3.3-fold) over a working range of 0-5 mg/mL, despite no statistically significant change in the measured contact angle at this loading. Tween 20 had no appreciable effect on the reaction in solution but preserved 95% of the apparent reaction rate constant after drying, compared with 11% without it, and atomic force microscopy (AFM) revealed a more dispersed dried enzyme morphology on mica. Tween 20-containing sensors also showed slower signal decay during repeated wetting-drying cycles and thermal stress, retained 77% (vs 26%) of the response at 400 mM NaCl, and exhibited within-PPP and between-batch coefficients of variation (CVs) below 10% (vs 12.3-19.5%), while maintaining glucose selectivity over potentially interfering molecules. These results indicate that Tween 20 enhances paper-based glucose sensing beyond wettability, in part by retaining enzyme cascade activity during drying, although the contributions of the individual enzymes and the underlying mechanism remain to be established.

bioengineering↗

bioRxiv2026

What an atlas-fitted connectome can and cannot do: evolutionary search over interneuron stimulation in a whole-body C. elegans model

The C. elegans connectome is complete, but which behaviours its wiring can produce, and which it cannot, is unknown. We asked this question in a whole-body simulation whose only adaptive element is a learning agent outside the nervous system. The agent may inject current into a short whitelist of interneurons, never into motor neurons or muscles; the 302-neuron OpenWorm c302 network, with dynamics fitted once to a signal-propagation atlas, a literature-based motor layer and a viscoelastic body on agar do the rest. Every hypothesis was pre-registered with its judgement criterion. Stimulating five command and steering interneurons (AVB, AVA, SMDD, SMDV, RIV) was sufficient for chemotaxis to a source 2.5 mm away (91 % of trials; four of five training seeds), whereas stimulating eight sensory neurons was no better than chance, reproducing at the behavioural level the silence of the sensory-to-command step in the fitted network. Evolution rediscovered the pirouette rule, reversing and executing a deep bend when concentration fell, and ablations showed that reversal, deep bend and steering were all necessary. Shuffling the wiring while preserving weights, counts and signs cut performance to a fifth; in the atlas-fitted dynamics this loss was carried by the gap-junction layer. In corridors four body widths wide, corners were passed by a deep bend pressed against the wall, so the dorsal or ventral direction of the bend fixed the direction of the turn. With ventral bends only, right turns almost never occurred and the worm entered the ventral arm of a T-maze first. Because temporal sensing cannot distinguish the arms at a junction, the learned strategy was to enter one arm and reverse when the odour faded; a left-right concentration difference was needed before the bend direction followed the source. The model yields three testable predictions for narrow-maze assays and separates what the wiring contributes to navigation from what sensing and the body must supply.

neuroscience↗

bioRxiv2026

Frontal stimulation reshapes SCAN connectivity and improves motor function in Parkinson's disease

Parkinson's disease is a neurodegenerative disorder with characteristic motor deficits of bradykinesia and impaired coordination, and non-motor deficits affecting cognitive abilities such as attention and executive functions. Recent evidence suggests that some canonical motor deficits in Parkinson's disease (e.g., freezing of gait) are associated with abnormalities in frontal cortical processing typically thought to underlie executive functions such as cognitive control. The evidence from human research linking frontal cognitive disruption and motor deficits in people with Parkinson's disease is correlational. Individuals with cognitive impairments often also display gait and balance deficits, but causal evidence remains lacking. We combined non-invasive brain stimulation with functional MRI (fMRI) to ascertain whether dorsolateral prefrontal cortex (DLPFC) exerts a causal influence modulating motor function and to test the hypothesis that an excitatory stimulation protocol applied to a cognitive control network can improve motor performance in Parkinson disease. Participants with Parkinson's disease performed a precision force-tracking task shown to track with gait impairment while undergoing functional neuroimaging scans. On half of trials, participants were required to simultaneously perform a cognitively demanding 2-back working memory task to tax attentional systems. Following the initial baseline scan, participants returned for three separate counterbalanced sessions that combined transcranial magnetic stimulation (TMS) in the form of theta burst stimulation (TBS) with fMRI. Just prior to task performance, participants received either excitatory (intermittent TBS) or inhibitory (continuous TBS) stimulation protocols over right DLPFC. In the third session, participants received stimulation to a control site outside the cognitive and motor areas implicated in our task. Our within-subjects experimental design allowed us to examine the effects of stimulation on motor behavior, the influence of cognitive load on motor behavior, and the neural systems supporting cognitive control and motor execution. Consistent with our hypothesis, excitatory stimulation of DLPFC improved motor performance in a precision force-tracking task as indexed by reduced tracking error and smoother movement execution. These effects emerged preferentially under dual-task conditions when cognitive demands were high. Our results show that this improved motor performance coincides with reductions in functional connectivity not only between the stimulation site and primary motor cortex, but also within the recently described somato-cognitive action network (SCAN) thought to support action planning and whole-body movement coordination. We conclude that frontal cognitive control systems play a causal role in modulating movement in Parkinson's disease and suggest that targeting these systems with non-invasive interventions may enhance motor function.

neuroscience↗

bioRxiv2026

The Phantom of the PCR: detection and consequences of spurious UMIs in mainstream RNA sequencing

Unique molecular identifiers (UMIs) support digital molecular counting by tagging molecules before amplification, but assume that UMIs are incorporated only during reverse transcription. Residual UMI-bearing oligonucleotides can instead reprime during preamplification PCR, creating "phantom" UMIs on genuine cDNA that inflate counts and evade standard deduplication. We model phantom generation as a two-state branching process and show that it produces a heavy-tailed reads-per-UMI distribution distinct from that of true UMIs. Using this signature, PhantomUMI detects and estimates contamination from clone-size distributions, subject to a coverage-dependent identifiability limit. Across 23 datasets spanning published studies and companion experiments, we find signatures consistent with phantom-UMI generation, including in current 10x GEM-X chemistry. Simulations show that phantoms inflate molecule counts and distort fold-changes. Model-based correction removes average count inflation but does not recover the distorted fold-changes, indicating that phantom UMIs are best prevented experimentally, as implemented in the companion Omega-seq method.

bioinformatics↗

bioRxiv2026

Cryptic disease-prone states in human mesocortical assembloids revealed by multimodal profiling

Neurodegenerative diseases are characterized by synaptic failure, aberrant protein accumulation, and neuroglial dysfunction that emerge long before clinical onset. Although brain assembloids, which recapitulate interregional circuit connectivity beyond the scope of single organoids, significantly advance the modeling of circuit pathophysiology, they are predominantly evaluated through single-modality approaches that cannot resolve the functional and molecular heterogeneity underlying differential disease susceptibility. Here we show that morphologically identical human iPSC-derived dorso forebrain-midbrain mesocortical assembloids (MCAs) spontaneously bifurcate into disease-prone and non-prone states under identical culture conditions, revealing that MCA heterogeneity reflects intrinsic neurodegeneration susceptibility rather than stochastic culture variability. Using integrated electrophysiological, molecular, and spatial profiling, we find that disease-prone MCAs exhibit a temporally ordered molecular cascade in which neurofilament light chain elevation precedes tau dysregulation, mirroring the sequential biomarker trajectories observed in pre-symptomatic human neurodegeneration. Disease-prone MCAs further display selective cortical hyperexcitability and aberrant brainwave-like oscillatory dynamics that remain undetectable by any single modality. Spatially, a discrete junction-like neuronal population at the midbrain-forebrain interface shows transcriptional priming for synaptic overactivation alongside impaired astrocytic glutamate clearance, defining a spatially confined neuron-glial uncoupling as a candidate early origin of the disease-prone state. These findings reframe MCA heterogeneity as a biological window into pre-symptomatic neurodegeneration, with broad implications for disease modeling, risk stratification, and therapeutic discovery.

neuroscience↗

bioRxiv2026

Pore-Resolved High-Throughput Quantification of Amyloid Aggregation and Amplification

Amyloid fibrils are implicated in a wide spectrum of neurodegenerative and systemic disorders, yet their biological consequences are governed not only by total fibril content but also by how fibrillar species are organized, clustered, and amplified within heterogeneous populations. Conventional thioflavin T (ThT)-based assays provide sensitive sample-level readouts of {beta}-sheet-rich material but offer limited access to the local population structure underlying amyloid aggregation and amplification. Here, we introduce the Amyloid Pore Quantification (APQ) chip, a pore-resolved geometric partitioning platform that converts heterogeneous amyloid assembly states into fluorescence intensity distributions across thousands of defined pore-level units. Using hen egg-white lysozyme as a model amyloid-forming protein, we combine length-controlled truncated amyloid nanofibrils with vacuum-assisted ThT infiltration to establish a reproducible pore fluorescence intensity reference. APQ provided quantitative concentration-dependent calibration across a 50-fold concentration range, enabling bulk-comparable quantification while preserving pore-level distribution information. Deviations from this reference resolved pH-dependent fibril clustering near the isoelectric point as pore-signal suppression and accessibility loss, captured pepsin-associated fibrillar amplification as a population-wide increase in pore intensity, and distinguished monomer- and oligomer-driven fibril processing through coupled amplification-aggregation fingerprints. When benchmarked against ensemble fluorescence measurements and AFM morphological analysis, APQ revealed assembly-state changes that were not fully represented by sample-level ThT intensity alone. These results establish APQ as a high-throughput, distribution-aware analytical framework for translating amyloid aggregation and amplification into quantitative pore-resolved fingerprints.

bioengineering↗

bioRxiv2026

Conserved TIR-only proteins drive transcriptional defense and basal immunity in dicot and monocot plants

Toll/interleukin-1/resistance (TIR) domain NADase enzymes signal in plant immunity by producing ribosylated nucleotide second messengers which activate EDS1 dimer-helper NLR pathways to restrict pathogen growth. Members of a small, distinctive group of TIR-only proteins are conserved between dicots and monocots, yet their functions remain poorly understood. Here, we show that conserved TIR-only proteins in Arabidopsis and barley share a fundamental enzymatic role in promoting basal defense against virulent filamentous pathogens, independently of NLR mediated effector-triggered immunity. Metabolite analysis of transiently expressed Arabidopsis and barley TIR-only proteins revealed their capacity to produce ribosylated cyclic nucleotides in vivo. By comparing phenotypes of tir-only and eds1 pad4 CRISPR mutants in the two species, as well as adr1 mutants in barley, we established that the TIR-only proteins promote PAMP-triggered transcriptional defenses associated with pathogen restriction. Barley possesses just one essential TIR-only enzyme and mutations of the two conserved TIR-only members in Arabidopsis were not compensated for by numerous other TIR-domain genes in the basal immune response. These findings suggest that conserved TIR-only proteins make a crucial contribution to TIR basal defense signaling networks of Arabidopsis and barley. We propose that a shared function in transcriptional defense regulation could explain the evolutionary retention of this discrete TIR-only group across monocot and dicot lineages.

plant biology↗

bioRxiv2026

Mechanochemically Programmed, Oligomer-Selective Amyloid Assembly via Axial Rotation

Amyloid oligomers have been widely implicated as primary cytotoxic intermediates; however, their selective and scalable production remains challenging due to rapid fibril amplification. Here, we demonstrated that sustained axial rotation enables programmable mechanochemical control over amyloid pathway selection without the use of chemical additives. Using a thermal axial rotator, native monomeric hen egg-white lysozyme was incubated at 60 {degrees}C under quantitatively tunable rotational speeds, imposing defined centrifugal forces and wall-associated shear that restructured the hydrodynamic boundary conditions. A discrete transition emerged near 600 RPM, separating the two distinct assembly regimes. Below this threshold, aggregation followed a fibril-amplifying pathway characterized by elevated {beta}-sheet content and elongated fibrillar morphologies. Above this threshold, fibrillar growth was strongly attenuated and oligomer-dominant assemblies predominated. Spectroscopic analyses and atomic force microscopy revealed that axial rotation redistributes the amyloid assembly states rather than simply suppressing aggregation. Functionally, the RPM-defined assemblies exhibited kinetically distinct seeding behaviors and induced divergent cytotoxic phenotypes in SH-SY5Y neuroblastoma cells. These findings establish axial rotation-mediated hydrodynamic boundary control as a scalable, chemical-free strategy for reprogramming amyloid assembly pathways and producing oligomer-rich assemblies with well-defined structural and functional properties.

bioengineering↗

bioRxiv2026

Cerebellar perturbation impairs human working memory and degrades spatial tuning throughout cortex

Working memory, the transient maintenance and manipulation of information, is fundamental to human cognition. While working memory is typically thought to rely on frontoparietal cortex, the cerebellum communicates with association cortex through closed-loop cerebro-cerebellar pathways and is well positioned to influence cortical dynamics supporting cognition. It is currently unknown whether cerebellar processing is causally necessary for the maintenance of visual information and whether cortical population coding is dependent on cerebellum. We combined functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) of frontal, parietal, and cerebellar cortex in humans. Using a generative model of population receptive fields, we show that cerebellar perturbation impairs spatial working memory recall and broadly degrades cortical spatial tuning. Direct comparisons revealed dissociable effects on population coding: cerebellar perturbation preferentially reduced stimulus-specific gain in early visual cortex, parietal perturbation preferentially suppressed stimulus-independent visual responses, and frontal perturbation preferentially increased response variability across higher-order visual, parietal, and frontal regions. These findings demonstrate that intact cerebellar function is necessary for maintaining cortical working memory representations and that cerebellar, parietal, and frontal nodes support working memory fidelity via distinct mechanisms.

neuroscience↗

bioRxiv2026

Spatially Resolved Banff Tubulitis and Glomerulitis Scoring in Kidney Allograft Biopsies via Artificial Intelligent-Based Structure Segmentation and Spatial Transcriptomics

BackgroundTubulitis is a defining histologic feature of T cell-mediated rejection (TCMR), while glomerulitis is often characteristic of antibody mediated rejection (AMR). Histologic quantification of tubulitis and glomerulitis using Banff criteria is subject to interobserver variability. Bulk transcriptomic assays (e.g., MMDx) have introduced molecular correlations of tubulitis with TCMR and glomerulitis with AMR, but lack spatial resolution. MethodsWe applied a web-based platform, FUSION (Functional Unit State Identification in Whole Slide Images), to a cohort of 8 cases (n=2 per condition) with kidney allograft biopsy samples acute TCMR, active AMR, chronic active AMR, and no rejection (control). The machine-learning (ML) platform enabled integrated visualization and analysis of spatial transcriptomics (10x Genomics Visium v2) together with high-resolution whole-slide histology. ResultsTranscriptomics-derived immune cell proportions within AI-segmented tubular and glomerular regions were used to generate spatial Banff t- and g-scores. Derived t-scores showed full concordance with pathologist scores in both acute TCMR cases; g-scores showed concordance in 2 of 4 AMR cases, with discordant cases characterized by low absolute immune signal near the classification boundary. ConclusionsWe demonstrate the feasibility of using AI-based FTU segmentation integrated with spatial transcriptomics-derived immune cell proportions to generate spatially informed t- and g-scores aligned with Banff criteria, with full concordance in severe rejection and partial concordance in mild rejection. This approach lays the foundation for validated, spatial transcriptomics-augmented t-scores and g-scores that enhance diagnostic precision, reduces inter-observer variability among renal pathologists, and support potential clinical adoption.

pathology↗

bioRxiv2026

Manganese Accumulation for Genetically Induced Contrast (MAGIC) MRI in the brain across species

Mapping the mesoscale architecture of neural circuits is essential for understanding brain function, yet high-resolution anatomical tracing remains largely dependent on fluorescent reporters that require terminal histology. Here, we present Manganese Accumulation for Genetically Inducible Contrast (MAGIC) MRI, a gene expression reporter system based on the metal ion transporter Zip14 (Slc39a14) which enables noninvasive, in vivo neural tracing. In rodents, viral delivery of Zip14 enables both anterograde and retrograde tracing of cortico-thalamic and basal ganglia circuits. Mechanistic validation via laser ablation-inductively coupled plasma-time-of-flight-mass spectrometry (LA-ICP-TOF-MS) confirmed that MRI contrast changes are driven by specific Mn2+ accumulation. This permitted high-resolution visualization of neural populations and projections using clinical standard MRI sequences without supplementary contrast agents. However, addition of systemic Mn2+ further increased the signal by a factor of 2-5 fold. To facilitate objective, high-throughput analysis, we developed a fully automated pipeline for voxel-wise anomaly detection that accurately identifies and quantifies MAGIC enhanced regions in individual subjects. Finally, it is demonstrated that MAGIC is translatable to the large mammalian brain, providing the first functional demonstration of an MRI-visible reporter in the rhesus macaque. By enabling the non-invasive monitoring of neural connectivity across species, MAGIC provides a versatile, longitudinal tool for studying structural plasticity and circuit organization in the living brain.

neuroscience↗

bioRxiv2026

RfxCas13d Mediates Broad-Spectrum Suppression of Highly Pathogenic Avian Influenza

Highly pathogenic avian influenza viruses (HPAIVs) continue to cause substantial disease in birds and mammals, with repeated H5N1 spillovers highlighting the need for broadly protective antiviral strategies. Here we develop a programmable RNA-targeting antiviral platform based on RfxCas13d and evaluate its activity in avian cells. Screening of five Cas13 orthologs in chicken DF1 fibroblasts revealed RfxCas13d as the most potent and well tolerated effector. Virus-specific CRISPR RNAs (crRNAs) targeting conserved regions of positive- and negative-sense influenza RNA were tested against A/WSN/033[H1N1] and multiple HPAIV isolates, including a member of clade 2.3.4.4b H5N1. Targeting positive-sense RNA conferred superior influenza inhibitory activity and further enhanced by multiplexed crRNA expression. These findings establish RfxCas13d as a versatile RNA-guided antiviral platform and provide a route for broad-spectrum influenza control through conserved RNA targeting.

microbiology↗

bioRxiv2026

ESPeR-seq: Extremely Sensitive and Pure, End-to-end, RNA-seq library preparation

PCR-based RNA sequencing methods generate phantom unique molecular identifiers (UMIs) when residual UMI-bearing oligonucleotides reprime during amplification, inflating molecule counts and corrupting relative abundances. They also incur non-specific amplification that limits sensitivity, while synthetic poly-T tracts disrupt sequencing and obscure transcript 3' ends. Here we present Omega-seq, which restricts UMI incorporation to reverse transcription using uracil-containing, USER-excisable template-switching oligonucleotides and a uracil-intolerant polymerase. Omega-seq produces near-background-free libraries, distinguishes 10 fg of input RNA from negative controls, and eliminates bead cleanup. An Omega-shaped dT primer prevents poly-T-induced dephasing, enabling stranded, nucleotide-resolution mapping of transcript ends. Dilution series, ERCC spike-ins, and a rarefaction metric show that Omega-seq has the lowest UMI inflation among methods tested. In individual Drosophila neuroblasts, phantom-UMI inflation remains minimal; pooled neuroblast and neuron coverage enables de novo discovery of novel multi-exon genes, 3' UTR extensions, and candidate enhancer RNAs.

genomics↗

bioRxiv2025

Distributed fMRI patterns coupled to low-frequency cardiorespiratory dynamics provide markers of aging

How aging affects brain-body connections can be investigated through changes in the coupling between functional magnetic resonance imaging (fMRI) signals and bodily autonomic processes across the adult lifespan. Recent studies using univariate approaches have identified age-related changes in the association between fMRI signals from multiple individual brain regions and low-frequency respiratory and cardiac activity. Here, we investigate if whole-brain spatial fMRI patterns associated with low-frequency physiological processes (heart rate and respiratory volume fluctuations) present generalizable changes with age. Data from human participants of both sexes are included in the analysis. We find that chronological age can be predicted statistically beyond chance from patterns of low-frequency fMRI-physiology coupling, even after accounting for individual differences in physiological signal characteristics and brain anatomy. Notably, brain areas implicated in central autonomic regulation, including nodes within salience and ventral attention networks (e.g., insula and middle cingulate cortex), are amongst the strongest contributors to age prediction. Further, we observe that after removing physiological effects from fMRI data, the residual blood oxygen level-dependent (BOLD) signal variability is still a reliable indicator of age. Together, these findings underscore the close integration between brain and body physiology, and highlight this interaction as a potential biomarker of the aging process. Significance StatementThe association between brain activity and respiratory or cardiac activity is often dismissed as "noise" in functional magnetic resonance imaging (fMRI) studies. However, emerging evidence suggests that coupling between fMRI and peripheral physiological signals can provide valuable insight into the brain-body connection. In this study, we show that whole brain patterns of coupling between fMRI signals and low-frequency respiratory and cardiac processes can reliably predict age across the adult lifespan. Brain regions involved in autonomic regulation, such as insula and cingulate cortex, were among the most informative predictors of age. These findings suggest that fMRI-physiology coupling may capture aging-related changes in brain vascular health and autonomic function and may have broader relevance for tracking disease-related disruptions in brain-body interaction.

neuroscience↗

bioRxiv2025

Agonism of mosquito and human transient receptor potential ankyrin 1 (TRPA1) channels by the natural drimane sesquiterpene cinnamodial

TRPA1 channels are multi-modal receptors in animals for sensing noxious physical and chemical factors. They are considered promising biochemical targets for developing repellents of arthropod disease vectors and drugs to treat a variety of medical conditions including pain, inflammation, and itch. Recently, we discovered that cinnamodial (CDIAL), a natural drimane sesquiterpene produced by the medicinal plant Cinnamosma fragrans, agonizes mosquito TRPA1 channels and is antifeedant and repellent to Aedes aegypti. However, the selectivity of CDIAL for mosquito vs. human TRPA1 and how CDIAL binds to TRPA1 channels are unknown. Here we characterize the agonism by CDIAL of Aedes aegypti (Aa) and Homo sapiens (Hs) TRPA1 channels and compare it to that induced by two other known TRPA1 agonists, nepetalactone and JT010. Heterologous expression of AaTRPA1 and HsTRPA1 in Xenopus laevis oocytes revealed that CDIAL agonized both channels with similar potency. Nepetalactone was less potent of an agonist than CDIAL for both AaTRPA1 and HsTRPA1, but was a more specific agonist for AaTRPA1 over HsTRPA1 compared to CDIAL. JT010 did not detectably activate AaTRPA1, but was a more potent agonist of HsTRPA1 than CDIAL. To generate insights into a putative binding site of CDIAL on AaTRPA1 we mutated six Lys residues (656, 678, 681, 728, 738, 744) and/or a Cys residue (684) in the coupling domain previously hypothesized to be involved. Simultaneous mutation of the six Lys residues to Ala dampened agonistic responses of AaTRPA1 to CDIAL, whereas changing Cys684 to Ser had no detectable impact. Protein modeling and molecular docking simulations for both AaTRPA1 and HsTRPA1 suggest species-specific CDIAL-binding mechanisms to the coupling domain, which involve Lys681 in AaTRPA1 and Cys621 in HsTRPA1.

pharmacology and toxicology↗

bioRxiv2025

Genetic factors driving multi-host infection in a core member of the root mycobiota

Core members of the fungal root microbiota include pathogens capable of colonizing multiple hosts, yet the underlying genetic determinants remain unknown. We report that Plectosphaerella cucumerina is a core member of the Arabidopsis thaliana root microbiota displaying high pathogenic potential and multi-host colonization capabilities. Establishment of a Plectosphaerella reference culture collection, followed by whole-genome sequencing of 72 strains reveals subtle phenotypic and genotypic variation that associate with fungal phylogeny, but not host plant identity. Transcriptome profiling of a model P. cucumerina isolate in roots of multiple hosts identifies core and host-specific fungal processes linked to carbon catabolism and root cell wall deconstruction of the hosts. A fungal gene encoding a candidate {beta}-1,3-glucanase (GH64) was identified as a key genetic factor driving infection and disease in plants that diverged 110 million years ago. The gene is enriched in plant-colonizing fungi and consistently functions as a disease determinant in the root pathogen Colletotrichum incanum. We conclude that diverse and tunable fungal repertoires of carbohydrate-active enzymes act as disease determinants and drive multi-host compatibility belowground.

microbiology↗

bioRxiv2025

Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis

Cortical neurogenesis proceeds through a precise temporal program in which radial glia sequentially generate distinct neuronal subtypes and later glia, yet how post-transcriptional regulators coordinate these transitions remain poorly understood. We previously identified that a decreasing temporal gradient of the RNA-binding protein Imp encodes neural stem cell age in Drosophila. In this work, we extend our investigation to Imp1, a mammalian homologue of Imp, and its role in murine neocortical development. Using TEMPO to track birth-order dynamics, we demonstrate that sustained Imp1 overexpression during early neurogenesis arrests temporal fate progression, shifting neuronal populations toward deeper cortical layers V-VI. Immunostaining with layer-specific transcription factors Cux1 and Ctip2 confirmed that laminar repositioning results from genuine changes in neuronal identity rather than migratory defects, with neurons adopting molecular identities matching their final positions. Temporal window-specific manipulations reveal distinct stage-specific effects where early-stage Imp1 induction produces cascading effects on fate specification and moderately delays the neuronal-to-gliogenic transition, while mid-stage induction induces neuronal accumulation in the subplate region. Live imaging of organotypic cultures reveals continuous neuronal recruitment within intermediate and ventricular zones, with mid-stage-born neurons accumulating at significantly faster rates than earlier cohorts. Strikingly, mid-stage Imp1 overexpression also induces ectopic glial-like foci distributed throughout the cortical plate, featuring dramatic cellular expansion and morphological heterogeneity. These findings establish Imp1 as a dosage- and stage-dependent temporal rheostat orchestrating developmental transitions in radial glial progenitors, controlling neuronal fate decisions and spatial organization. This work advances our understanding of molecular timing mechanisms governing neuronal diversity in the mammalian cortex.

developmental biology↗