Biology subjects

Williams, N.

Publications and source records attributed to Williams, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Two Novel Rod-Like Circular RNAs from the Oroarctic Tundra Soil Display Candidate Ribozyme-Like Features: An In Silico Characterization

The recent discovery of obelisks, novel deltaviruses, and other viroid-like circular RNAs has greatly expanded the known diversity of autonomous RNA elements. However, cold terrestrial ecosystems remain comparatively undersampled for these molecules. Using a structure-based modification of the Tormentor pipeline, we assembled two putative non-coding rod-like circular RNAs from winter metatranscriptomes of oroarctic tundra soil collected near Kilpisjarvi, Finland. Sequence-based searches identified no meaningful homologs for either RNA. Structure-based analyses identified affinities to deltavirus-like ribozymes in Rod 1 and to hammerhead ribozymes in Rod 2, with structural compatibility confirmed by integration into an established covariation model. Rod 1 was additionally detected in independent alpine metatranscriptomic datasets, whereas Rod 2 was not identified beyond the original sample. Collectively, these results identify Rod 1 as a strong candidate viroid-like RNA bearing a putative ribozyme-like structure motif that warrants experimental validation, while Rod 1 remains a preliminary candidate requiring further confirmation.

microbiology↗

bioRxiv2026

Spatially defined axonal guidance in neural organoids with micropatterned microfluidic channels

Three-dimensional stem cell-derived neural organoids provide a promising platform for investigating early brain development and interregional circuit formation. Although co-culture of region-specific organoids into assembloids has enabled the study of cortical and subcortical interactions, these models lack directional specificity and spatial control, limiting their ability to recapitulate canonical circuit architecture. Here, we present a microfluidic platform for constructing directional and tunable interregional circuits while preserving anatomical distinction. This system, which we term "directoids" incorporates micropatterned polydimethylsiloxane (PDMS) microstructures to control uni- and bidirectional axonal growth between cortical and thalamic organoids. We observed a 70.4% success rate of axons traversing the full channel length in the permissive direction and reaching the opposing organoid, whereas no neurites successfully crossed the probative direction. These results demonstrate robust directionally bias in axon outgrowth and establish a scalable, reproducible strategy for controlling asymmetric connectivity between anatomically distinct neural organoids. Using high-density CMOS microelectrode arrays, we further validated directional tuning of extracellular action potential propagation within directoid microchannels, a feature not observed in straight-channel connectoid controls. Directoids also exhibited significant asymmetry in firing rates between channel entry and exit sites, consistent with engineered bias in signal flow. This provides an experimental paradigm for dissecting how anatomical connectivity and functional activity converge to shape neuronal networks. Together, these findings establish a microfluidic platform for investigating the mechanisms underlying hierarchical circuit formation, regional specification, and functional integration in developing human neural organoid models at cellular resolution not possible in vivo.

bioengineering↗

bioRxiv2026

Objective Quality Assessment for Precision Functional MRI Data

Precision functional mapping (PFM) enables individual-level characterization of brain network organization but requires substantially more and higher-quality fMRI data than is standard. Despite its growing use, objective criteria for data sufficiency and quality needed to ensure interpretable and replicable individual-level results remain unclear. Here, we introduce the Network Similarity Index (NSI), an objective measure of the extent to which functional connectivity (FC) patterns in an individual dataset express the large-scale network structure required for PFM. NSI captures the integrity of low-spatial-frequency, coherent network organization and denoising fidelity, and aligns closely with blinded expert assessments of PFM usability. NSI also accounts for variability in the rate at which FC becomes reliable across individuals. Here, we provide an open-source framework for NSI-based data quality evaluation and models for linking NSI values with expert-judged PFM suitability. This framework can also inform expected returns from additional data collection, enabling principled decisions about data sufficiency and replication in precision fMRI research.

neuroscience↗

bioRxiv2025

The non-kinase function of CDK6 is a key driver of acquired resistance to CDK4/6 inhibitors in Estrogen Receptor-positive breast cancer

The therapeutic efficacy of CDK4/6 inhibitors in ER+ breast cancer (BC) patients is presumed to arise from inhibition of the kinase function of CDK4 and 6 proteins. Despite their initial efficacy, development of acquired resistance to CDK4/6 inhibitors in metastatic ER+ BC patients is nearly universal, commonly through compensatory overexpression of CDK6. Here, we show that primary ER+ tumors show high CDK4 but very low to undetectable expression of CDK6, which suggests that the therapeutic efficacy of CDK4/6 inhibitors in ER+ BC patients is largely driven by inhibition of CDK4, rather than CDK6. Furthermore, we show that overexpression of CDK6 confers acquired resistance to CDK4/6 inhibitors, largely, through a kinase-independent function. Our findings challenge the dogma that CDK4/6-mediated phosphorylation of retinoblastoma protein (pRB) is necessary to ER+ BC cells to progress from G1 to S phase of cell cycle. Consequently, by taking advantage of the non-kinase function of CDK6, ER+ BC cells acquire independence from the kinase function of CDK4 and 6 for cell cycle progression. These findings highlight the limitations of the current standard-of-care treatments, which focus on merely inhibiting the kinase function of CDK4 and 6, and uncover the non-kinase function of CDK6 as a new targetable vulnerability to overcome acquired resistance to CDK4/6 inhibitors in ER+ BC.

cancer biology↗

bioRxiv2025

DNMT3A-R882 mutations intrinsically drive dysfunctional neutropoiesis from human haematopoietic stem cells

Clonal haematopoiesis (CH) arises from the expansion of hematopoietic stem cells (HSCs) carrying leukaemia-associated somatic mutations. CH is linked to pathological immune dysregulation and a greater risk of age-related inflammatory diseases. Yet, how CH mutations impact HSC differentiation into immune effector cells remains understudied. Here, we report a single-cell resolution functional and multi-omic investigation of HSC clonal and differentiation dynamics in individuals with DNMT3A-R882 CH. DNMT3A-R882 reshapes the clonal architecture of haematopoiesis towards an aged phylogenetic structure. Functionally, DNMT3A-R882 HSCs produce decreased monocytic output but more abundant and mature neutrophil progeny compared to WT HSCs in the same individual. Whereas DNMT3A-R882 myeloid progenitors display attenuated inflammatory transcriptional programmes, DNMT3A- R882 mature neutrophils acquire proinflammatory and immunomodulatory features typical of maladaptive immunity and CH co-morbidities. Our findings, validated in humanised mice, identify aberrant DNMT3A-R882 HSC-driven neutropoiesis as a key link between CH, immune dysregulation and risk of inflammatory disease.

cell biology↗

bioRxiv2025

Invasive plants affect native plant pollination through pollinator-mediated cross-boundary effects

Invasive plants may facilitate or compete with native plants by changing the foraging behavior and/or abundance of shared pollinators. Such effects have been explored within single habitats; however, many pollinators are highly mobile and can cross ecological boundaries. Whether via shared pollinators, invasive plants affect native plants in neighboring habitats remains an open question. Here, we ask this question in a mosaic of 22 native-plant-dominated meadows on serpentine soil, embedded in a matrix of non-serpentine meadows. The non-serpentine meadows contain dense stands of two insect-pollinated invasive species: Vicia villosa, and Centaurea solstitialis. The serpentine meadows contain two common native species that co-flower and share pollinators with these invasives: Trifolium fucatum and Helianthus exilis, respectively. Across three years, we determined that the abundance ratio of each invasive species in the surrounding landscape to its co-flowering native species within focal patches was associated with decreased visitation rates, seed set, and functional importance in the plant-pollinator network for the native species. We conclude that invasive plants can have indirect, negative effects on native plants in neighboring habitats, via competition for shared pollinators. Open research statementAll data and code are accessible to the public via: https://figshare.com/projects/Data_for_Invasive_plants_affect_native_plant_pollination_through_pollinator-mediated_cross-boundary_effects/243587

ecology↗

bioRxiv2025

Excitation-Inhibition Balance and Fronto-Limbic Connectivity Drive TMS Treatment Outcomes in Refractory Depression

Depression affects over 350 million people worldwide, with treatment resistance occurring in up to 30% of cases. Intermittent theta burst stimulation (iTBS) targeting the left dorsolateral prefrontal cortex (DLPFC) has emerged as a promising intervention, yet the neurophysiological mechanisms determining which patients will respond remain poorly understood. Here, we combined transcranial magnetic stimulation with electroencephalography and whole-brain computational modeling to uncover the mechanistic basis of treatment efficacy in 90 patients with treatment-resistant depression. We identified two distinct neurophysiological signatures that differentiate responders from non-responders: (1) post-treatment shifts in excitation-inhibition balance toward greater inhibitory control, and (2) a pre-treatment brain state characterized by anticorrelated dynamics between subgenual anterior cingulate cortex and DLPFC. These features were significantly correlated with clinical improvement and could not be explained by non-specific factors. Our findings provide a neurophysiologically-informed framework for developing personalized and optimized neuromodulation approaches in treatment-resistant depression.

neuroscience↗

bioRxiv2025

Pollen diet, more than geographic distance, shapes provision microbiome composition in two species of cavity-nesting bees

The microbial composition of stored food can influence its stability and determine the microbial species consumed by the organism feeding on it. Many bee species store nectar and pollen in provisions constructed to feed developing offspring. Previous work has shown variation in provision microbiome among bee populations, yet whether this variation is determined by the pollen types within provisions, variation between bee species at the same nesting sites, or geographic distance was unclear. Here, we sampled two species of co-occurring cavity nesting bees in the genus Osmia at 13 sites across the Sierra foothills in California and examined the composition of pollen, fungi and bacteria found in their provisions across sites. As expected, pollen, bacterial and fungal composition exhibited significant turnover between bees and sites, with bee species characterized by particular pollen and microbial species. Pollen composition explained 15% of variation in bacterial composition and [~]30% of variation in fungal composition, whereas spatial distance among sites explained minimal additional variation. Symbiotic or bee-specialized microbe genera Ascosphaera, Sodalis and Wolbachia showed contrasting patterns of association with pollen composition, suggesting distinct acquisition and transmission routes for each. Comparing provisions from both bee species comprised of the same pollens points to environmental acquisition rather than bee species as a key factor shaping the early stages of the bee microbiome in Osmia. The patterns we observed also contrast with Apilactobacillus-dominated provision microbiome in other solitary bee species, suggesting variable mechanisms of microbial assembly in stored food among bee species.

ecology↗

bioRxiv2024

Tryptophan metabolite atlas uncovers organ, age, and sex-specific variations

Although tryptophan (Trp) is the largest and most structurally complex amino acid, it is the least abundant in the proteome. Its distinct indole ring and high carbon content enable it to generate various biologically active metabolites such as serotonin, kynurenine (Kyn), and indole-3-pyruvate (I3P). Dysregulation of Trp metabolism has been implicated in diseases ranging from depression to cancer. Investigating Trp and its metabolites in healthy tissues offers pathways to target disease-associated disruptions selectively, while preserving essential functions. In this study, we comprehensively mapped Trp metabolites across the Kyn, serotonin, and I3P pathways, as well as the microbiome-derived metabolite tryptamine, in C57BL/6 mice. Our comprehensive analysis covered 12 peripheral organs, the central nervous system, and serum in both male and female mice at three life stages: young (3 weeks), adult (54 weeks), and aged (74 weeks). We found significant tissue-, sex-, and age-specific variations in Trp metabolism, with notably higher levels of the oncometabolites I3P and Kyn in aging males. These findings emphasize the value of organ-specific analysis of Trp metabolism for understanding its role in disease progression and identifying targeted therapeutic opportunities. AUTHOR SUMMARYTrp metabolism has primarily been studied in cell lines, often leading to generalized assumptions about its role in health and disease. However, how Trp and its metabolites are allocated across tissues, sexes, and life stages has remained poorly understood. This gap is critical, as Trp is the largest amino acid, minimally used for protein synthesis, and largely metabolized in the liver, yet its distribution and metabolism in other tissues are unknown. Misconceptions, such as the idea that all cancers universally increase Kyn production, have contributed to therapeutic failures, highlighting the need for rigorous, tissue-specific studies. Our study systematically quantifies Trp metabolites across organs and tissues in vivo, revealing significant organ-, sex-, and age-specific variations. These findings provide a foundational resource for understanding Trp metabolism in normal physiology and disease, with potential applications in cancer, neurodegeneration, and other metabolic disorders.

biochemistry↗

bioRxiv2024

Clonal dynamics and somatic evolution of haematopoiesis in mouse

Haematopoietic stem cells maintain blood production throughout life. While extensively characterised using the laboratory mouse, little is known about how the population is sustained and evolves with age. We isolated stem cells and progenitors from young and old mice, identifying 221,890 somatic mutations genome-wide in 1845 single cell-derived colonies, and used phylogenetic analysis to infer the ontogeny and population dynamics of the stem cell pool. Mouse stem cells and progenitors accrue [~]45 somatic mutations per year, a rate only about 2-fold greater than human progenitors despite the vastly different organismal sizes and lifespans. Phylogenetic patterns reveal that stem and multipotent progenitor cell pools are both established during embryogenesis, after which they independently self-renew in parallel over life. The stem cell pool grows steadily over the mouse lifespan to approximately 70,000 cells, self-renewing about every six weeks. Aged mice did not display the profound loss of stem cell clonal diversity characteristic of human haematopoietic ageing. However, targeted sequencing revealed small, expanded clones in the context of murine ageing, which were larger and more numerous following haematological perturbations and exhibited a selection landscape similar to humans. Our data illustrate both conserved features of population dynamics of blood and distinct patterns of age-associated somatic evolution in the short-lived mouse.

genomics↗

bioRxiv2024

Analogues of the anti-malaria drug mefloquine have broad spectrum antifungal activity and are efficacious in a model of disseminated Candida auris infection.

Only three classes of antifungal drugs are currently in clinical use. Here, we report that derivatives of the malarial drug mefloquine have broad spectrum antifungal activity including difficult to treat molds and endemic fungi. Pharmacokinetic and efficacy studies of NSC-4377 indicate it penetrates the central nervous system and is active against Candida auris in vivo. These data strongly support the further development of mefloquine analogs as a potentially new class of antifungal molecules.

microbiology↗

bioRxiv2024

The long-term effects of chemotherapy on normal blood cells

In developed countries, [~]10% of individuals are exposed to systemic chemotherapy for cancer and other diseases. Many chemotherapeutic agents act by increasing DNA damage in cancer cells, triggering cell death. However, there is limited understanding of the extent and long-term consequences of collateral DNA damage to normal tissues. To investigate the impact of chemotherapy on mutation burdens and cell population structure of a normal tissue we sequenced blood cell genomes from 23 individuals, aged 3-80 years, treated with a range of chemotherapy regimens. Substantial additional mutation loads with characteristic mutational signatures were imposed by some chemotherapeutic agents, but there were differences in burden between different classes of agent, different agents of the same class and different blood cell types. Chemotherapy also induced premature changes in the cell population structure of normal blood, similar to those of normal ageing. The results constitute an initial survey of the long-term biological consequences of cytotoxic agents to which a substantial fraction of the population is exposed during the course of their disease management, raising mechanistic questions and highlighting opportunities for mitigation of adverse effects.

cell biology↗

bioRxiv2023

Expansion of a frontostriatal salience network in individuals with depression

Hundreds of neuroimaging studies spanning two decades have revealed differences in brain structure and functional connectivity in depression, but with modest effect sizes, complicating efforts to derive mechanistic pathophysiologic insights or develop biomarkers.1 Furthermore, although depression is a fundamentally episodic condition, few neuroimaging studies have taken a longitudinal approach, which is critical for understanding cause and effect and delineating mechanisms that drive mood state transitions over time. The emerging field of precision functional mapping using densely-sampled longitudinal neuroimaging data has revealed unexpected, functionally meaningful individual differences in brain network topology in healthy individuals,2-5 but these approaches have never been applied to individuals with depression. Here, using precision functional mapping techniques and 11 datasets comprising n=187 repeatedly sampled individuals and >21,000 minutes of fMRI data, we show that the frontostriatal salience network is expanded two-fold in most individuals with depression. This effect was replicable in multiple samples, including large-scale, group-average data (N=1,231 subjects), and caused primarily by network border shifts affecting specific functional systems, with three distinct modes of encroachment occurring in different individuals. Salience network expansion was unexpectedly stable over time, unaffected by changes in mood state, and detectable in children before the subsequent onset of depressive symptoms in adolescence. Longitudinal analyses of individuals scanned up to 62 times over 1.5 years identified connectivity changes in specific frontostriatal circuits that tracked fluctuations in specific symptom domains and predicted future anhedonia symptoms before they emerged. Together, these findings identify a stable trait-like brain network topology that may confer risk for depression and mood-state dependent connectivity changes in frontostriatal circuits that predict the emergence and remission of depressive symptoms over time.

neuroscience↗

bioRxiv2023

Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson's disease: A DNA co-methylation network analysis

Parkinsons disease is a highly heterogeneous disorder, encompassing a complex spectrum of clinical presentation including motor, sleep, cognitive and neuropsychiatric symptoms. We aimed to investigate genome-wide DNA methylation networks in post-mortem Parkinsons disease brain samples and test for region-specific association with common neuropsychiatric and cognitive symptoms. Of traits tested, we identify a co-methylation module in the substantia nigra with significant correlation to depressive symptoms and with ontological enrichment for terms relevant to neuronal and synaptic processes. Notably, expression of the genes annotated to the methylation loci present within this module are found to be significantly enriched in neuronal subtypes within the substantia nigra. These findings highlight the potential involvement of neuronal-specific changes within the substantia nigra with regard to depressive symptoms in Parkinsons disease.

neuroscience↗

bioRxiv2023

56Fe ion exposure increases the incidence of lung and brain tumors at a similar rate in male and female mice

The main deterrent to long-term space travel is the risk of Radiation Exposure Induced Death (REID). The National Aeronautics and Space Administration (NASA) has adopted Permissible Exposure Levels (PELs) to limit the probability of REID to 3% for the risk of death due to radiation-induced carcinogenesis. The most significant contributor to current REID estimates for astronauts is the risk of lung cancer. Recently updated lung cancer estimates from Japans atomic bomb survivors showed that the excess relative risk of lung cancer by age 70 is roughly four-fold higher in females compared to males. However, whether sex differences may impact the risk of lung cancer due to exposure to high charge and energy (HZE) radiation is not well studied. Thus, to evaluate the impact of sex differences on the risk of solid cancer development post-HZE radiation exposure, we irradiated Rbfl/fl; Trp53fl/+ male and female mice infected with Adeno-Cre with various doses of 320 kVp X-rays or 600 MeV/n 56Fe ions and monitored them for any radiation-induced malignancies. We observed that lung adenomas/carcinomas and esthesioneuroblastomas (ENBs) were the most common primary malignancies in X-ray and 56Fe ion-exposed mice, respectively. In addition, 1 Gy 56Fe ion exposure compared to X-rays led to a significantly higher incidence of lung adenomas/carcinomas (p=0.02) and ENBs (p<0.0001). However, we did not find a significantly higher incidence of any solid malignancies in female mice as compared to male mice, regardless of radiation quality. Furthermore, gene expression analysis of ENBs suggested a distinct gene expression pattern with similar hallmark pathways altered, such as MYC targets and MTORC1 signaling, in X-ray and 56Fe ion-induced ENBs. Thus, our data revealed that 56Fe ion exposure significantly accelerated the development of lung adenomas/carcinomas and ENBs compared to X-rays, but the rate of solid malignancies was similar between male and female mice, regardless of radiation quality.

cancer biology↗

bioRxiv2023

Both CD8 and CD4 T cells contribute to immunosurveillance preventing the development of neoantigen-expressing autochthonous sarcomas

The adaptive immune system plays an essential anti-tumor role through immunosurveillance and response to immunotherapies. Characterizing phenotypic features and mechanisms of dysfunction of tumor-specific T cell populations may uncover novel immunotherapeutic targets and biomarkers of response. To study tumor-specific T cell responses in vivo, a tumor model must express a known neoantigen. While transplant models with known neoantigen expression are widely available, autochthonous tumor models in which the tumor coevolves with the immune system are limited. In this study, we combined CRISPR/Cas9 and sleeping beauty transposase technology to develop an autochthonous orthotopic murine sarcoma model with oncogenic KrasG12D, functionally impaired p53, and expression of known MHCI and MHCII sarcoma neoantigens. Using MHC tetramer flow cytometry, we identified a tumor-specific immune response in the peripheral blood as early as 10 days after tumor induction leading to tumor clearance. Tumors developed at high penetrance after co-depletion of CD8 and CD4 T cells, but depletion of either CD8 or CD4 T cells alone was insufficient to permit tumor growth. These results suggest that CD8 and CD4 T cells can independently contribute to immunosurveillance leading to clearance of sarcomas expressing MHCI and MHCII neoantigens.

cancer biology↗

bioRxiv2023

The influence of inter-regional delays in generating large-scale brain networks of phase synchronization

Large-scale networks of phase synchronization are considered to regulate the communication between brain regions fundamental to cognitive function, but the mapping to their structural substrates, i.e., the structure-function relationship, remains poorly understood. Biophysical Network Models (BNMs) have demonstrated the influences of local oscillatory activity and inter-regional anatomical connections in generating alpha-band (8-12 Hz) networks of phase synchronization observed with Electroencephalography (EEG) and Magnetoencephalography (MEG). Yet, the influence of inter-regional conduction delays remains unknown. In this study, we compared a BNM with standard "distance-dependent delays", which assumes constant conduction velocity, to BNMs with delays specified by two alternative methods accounting for spatially varying conduction velocities, "isochronous delays" and "mixed delays". We followed the Approximate Bayesian Computation (ABC) workflow, i) specifying neurophysiologically informed prior distributions of BNM parameters, ii) verifying the suitability of the prior distributions with Prior Predictive Checks, iii) fitting each of the three BNMs to alpha-band MEG resting-state data (N = 75) with Bayesian Optimisation for Likelihood-Free Inference (BOLFI), and iv) choosing between the fitted BNMs with ABC model comparison on a separate MEG dataset (N = 30). Prior Predictive Checks revealed the range of dynamics generated by each of the BNMs to encompass those seen in the MEG data, suggesting the suitability of the prior distributions. Fitting the models to MEG data yielded reliable posterior distributions of the parameters of each of the BNMs. Finally, model comparison revealed the BNM with "distance-dependent delays", as the most probable to describe the generation of alpha-band networks of phase synchronization seen in MEG. These findings suggest that distance-dependent delays contribute significantly to the neocortical architecture of human alpha-band networks of phase synchronization. Hence, our study illuminates the role of inter-regional delays in generating the large-scale networks of phase synchronization that might subserve the communication between regions vital to cognition. HighlightsO_LICompared methods to specify delays in Biophysical Network Models (BNMs) C_LIO_LIBNM with "distance-dependent" conduction delays more probable than alternatives C_LIO_LIBNMs with biologically informed prior distributions generate dynamics seen in MEG C_LIO_LIFitting BNMs yields reliable posterior distributions informed by MEG data (N = 75) C_LI

neuroscience↗

bioRxiv2023

Susceptible bacteria survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

In vitro systems have provided great insight into the mechanisms of antibiotic resistance. Yet, in vitro approaches cannot reflect the full complexity of what transpires within a host. As the mammalian gut is host to trillions of resident bacteria and thus a potential breeding ground for antibiotic resistance, we sought to better understand how gut bacteria respond to antibiotic treatment in vivo. Here, we colonized germ-free mice with a genetically barcoded antibiotic pan-susceptible Escherichia coli clinical isolate and then administered the antibiotic cefepime via programmable subcutaneous pumps which allowed for closer emulation of human parenteral antibiotic pharmacokinetics/dynamics. After seven days of antibiotics, we were unable to culture E. coli from feces. We were, however, able to recover barcoded E. coli from harvested gastrointestinal (GI) tissue, despite high GI tract and plasma cefepime concentrations. Strikingly, these E. coli isolates were not resistant to cefepime but had acquired mutations - most notably in the wbaP gene, which encodes an enzyme required for the initiation of the synthesis of the polysaccharide capsule and lipopolysaccharide O antigen - that increased their ability to invade and survive within intestinal cells, including cultured human colonocytes. Further, these E. coli mutants exhibited a persister phenotype when exposed to cefepime, allowing for greater survival to pulses of cefepime treatment when compared to the wildtype strain. Our findings highlight a mechanism by which bacteria in the gastrointestinal tract can adapt to antibiotic treatment by increasing their ability to persist during antibiotic treatment and invade intestinal epithelial cells where antibiotic concentrations are substantially reduced.

microbiology↗