Biology subjects

Smith, A.

Publications and source records attributed to Smith, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Temporal phosphoproteomic programmes set a redox-gated rheostat on neutrophil phagocytosis

Neutrophils are essential frontline immune cells in the defence against bacterial pathogens such as Staphylococcus aureus, but their killing machinery also causes host tissue damage. How neutrophils regulate these processes remains incompletely understood. Here, we profile the proteome and phosphoproteome of human neutrophils across a two-hour exposure to S. aureus, alongside five simultaneous functional readouts, before investigating how an initial encounter modulates the response to a second. The phosphoproteomic response resolves into qualitatively distinct early and late windows: the early landscape drives particle uptake, while by the late window this machinery is been deactivated, with a broadly supressed kinome, and cells geared towards inflammatory output. Correlating protein phosphorylation and functional kinetics - an approach we term KINETIC - implicates putative mediators of key neutrophil antimicrobial functions. A genome-wide CRISPR knockout screen in neutrophil-like PLB-985 cells, sorted on phagocytic load, recovers canonical engulfment machinery among the strongest facilitators of phagocytosis, additionally identifying the lysosomal Ragulator-mTORC1 nutrient sensing pathway and HOPS complex corresponding to the KINETIC-identified pathways. Conversely, the NRF2 repressor KEAP1 is revealed as the strongest phagocytic brake, positioning oxidative burden as a regulator of phagocytic appetite. Neutrophils in the late window exhibit impaired phagocytosis and phagosomal acidification on S.aureus re-challenge. Underlying these functional deficits, cells in the late window are refractory across multiomic layers: a second S. aureus meal alters no phosphoprotein, protein, or transcript, whereas the chemoattractants PAF and fMLP evoke a largely consistent phosphoproteomic programme, delineating the phenotype as receptor-specific rather than a global loss of signalling capacity. Consistent with de-repressing the antioxidant response via genetic loss of KEAP1 increasing phagocytosis, reducing ROS production via inhibition of the NADPH oxidase results in a partial rescue of phagocytosis of the re-exposed S. aureus. Together, these findings describe a ROS-gated phagocytic rheostat, enabling neutrophils to meter their phagocytic appetite according to their exposure history, likely limiting uptake of pathogens they lack the capacity to effectively digest. Inappropriate activation of this rheostat under conditions of physiological stress or severe illness may underpin the defects in phagocytosis identified in such patients.

immunology↗

bioRxiv2026

Discovery of frameshift-associated TCRs following personalized neoantigen vaccination in a patient with osteosarcoma

Personalized antigen-directed immunotherapies, including personalized cancer vaccines, are emerging as promising therapeutic modalities for a range of cancer types. Immune monitoring can be used to evaluate the efficacy of a vaccine in stimulating the immune response pre- and post-vaccination; however, such approaches typically stop short of identifying which T cell receptors (TCRs) are functionally driving therapeutic responses. Here, we present a case report of immune monitoring and subsequent TCR discovery experiments following administration of personalized cancer vaccines in a patient with locally recurrent osteosarcoma. Whole PBMCs were stimulated with vaccine peptides (>16 AA) in vitro for 11 days, after which IFN{gamma} ELISPOT identified total T cell responses for 12 of 15 tested peptides post-vaccination. In vitro expanded samples were submitted for 10x single-cell TCR sequencing, from which 26 TCRs were chosen for generation of TCR-T cells based on clonal expansion and culture specificity. Of the generated TCR-T cells, 25 produced functional TCRs, 4 of which were specific to vaccine peptides. However, downstream testing revealed each was MHC class-II restricted. To address this, we repeated the in vitro stimulations with co-cultures of isolated CD8+ T cells with autologous dendritic cells, and cultures of whole PBMCs with anti-MHC class-II blocking antibody. These cultures yielded 10 additional TCRs, 2 of which were responsive to a vaccine peptide containing a MAP2 frameshift mutation. These findings demonstrate an effective approach for leveraging post-vaccination expanded antigen-specific T cell populations for discovery of novel T cell receptors for downstream cellular therapies.

immunology↗

bioRxiv2026

HIV-1 envelope glycan loss links receptor adaptation and innate immune escape in SHIVs

Simian-human immunodeficiency viruses (SHIVs) are widely used to model HIV-1 infection in macaques, yet most SHIVs encoding circulating HIV-1 envelope glycoproteins (Env) replicate poorly because of inefficient use of macaque CD4 and sensitivity to host antiviral responses. During adaptation to macaques, Env is therefore subject to multiple selective pressures to improve receptor utilization while maintaining function in the face of host immune restriction. Type I interferon (IFN) is a major component of the host antiviral response during acute infection, and IFN resistance increases during SHIV adaptation to macaques through serial passage. However, the viral determinants of this resistance have remained unclear. Here, we show that serial passage of a lineage of SHIVs in macaques selected Env variants with markedly increased resistance to IFN- and enhanced replication in macaque CD4+ T lymphocytes. IFN- resistance mapped principally to loss of two highly conserved N-linked glycans at N197 and N276 near the CD4-binding site. Glycan loss altered the conformational landscape of virus-associated Env, enhanced macaque CD4-dependent entry and membrane fusion without increasing human CD4-dependent entry, and reduced incorporation of the IFN-inducible restriction factors IFITM3 and IFITM3A into progeny virions. Depletion of IFITM3/3A rendered the parental SHIV highly resistant to IFN- and abolished differential IFN- sensitivity among parental, adapted, and glycan-loss viruses. These findings reveal that loss of receptor-proximal Env glycans can simultaneously improve utilization of a heterologous CD4 receptor and promote escape from IFN-mediated restriction, linking receptor adaptation and innate immune evasion during lentiviral adaptation to a new host.

microbiology↗

bioRxiv2026

Chromosome-scale genome assembly of the North American invasive Asteraceae, Tanacetum vulgare (common tansy)

Common tansy (Tanacetum vulgare), a significant agricultural invasive species, threatens forage productivity, livestock carrying capacity, and plant biodiversity across North American agroecosystems. Despite being a close relative to the ornamental Asteraceae Chrysanthemum, T. vulgare genomic studies are severely lacking, but remain critical to the development of novel weed management tools and the investigation of plant invasion evolution. In this study, we performed the assembly and annotation of the diploid genome (2n=2x=18) of an invasive North American T. vulgare genotype using long-read PacBio HiFi and Iso-Seq sequencing technology. The assembled haplotype genome comprised 9 pseudomolecules with a total size of ~4.8 Gb and a scaffold N50 of 546 Mb. In addition, both the plastid and mitochondrial genome sequences were assembled. BUSCO analysis revealed a high overall genome completeness with 69,343 predicted protein-coding genes (AED<0.6: 98%). A high-quality North American invasive reference T. vulgare genome, complementing a recent one assembled for a native European accession, is critical for the investigation of plant invasion biology, genome evolution, and the future development of novel genetic biocontrol weed management technologies.

genomics↗

bioRxiv2026

Epithelial to mesenchymal transition and M2 macrophages drive aggressiveness in murine and human sarcomatoid urothelial carcinoma.

Patients with majority variant subtype histology including sarcomatoid urothelial carcinoma (SUC) have poor outcomes and limited treatment options, and there are few preclinical resources to investigate rare histologic subtypes. We developed three novel variant subtype histology bladder cancer (BC) cell lines by finding that basal BC tumor cells derived from mice treated with N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) were initially not competent to grow in immune competent mice, but then acquired tumorigenicity following passaging (recycling) in mice lacking mature B and T cells. Three genitourinary oncology pathologists identified BBN966 as SUC, BBN964 as a hybrid between SUC and squamous, and BBN975 as squamous, and each had unique growth characteristics. Using a publicly available dataset and our spatial transcriptomics analysis of a cohort of human tumors with mixed SUC and UC as comparators, we found that consistent with human SUC, BBN966 lack expression of basal and luminal genes. Consistent with human SUC and spatial transcriptomics analysis of canine SUC, BBN966 had the highest epithelial to mesenchymal transition (EMT) upregulation, and all three recycled tumor cells had increased EMT pathway expression in recycled tumor cells. Moreover, increased expression of genes upregulated in all three recycled tumor cells associated with worse overall survival in patients with muscle invasive UC. Similar to human SUC, BBN966 tumors had higher proportion of M2 macrophage gene expression. Finally, we found in the largest cohort of PD-L1 IHC to date that 20 of 38 (52.6%) human SUC had CPS > 50, which was driven mostly by tumor proportion score. Consistent with this, we found anti-PD1 immune checkpoint inhibitor (ICI) significantly inhibited BBN966 tumor growth, while the hybrid BBN964 tumors had mixed response to ICI. Thus, the murine BBN966 tumors exhibited similarities to human SUC, and can be used to examine novel therapies for translation into future SUC clinical studies.

cancer biology↗

bioRxiv2026

Early dynamics of a neutrophil interferon program drive immunotherapy resistance and limit durable anti-tumor immunity

Despite the remarkable success of immune checkpoint blockade (ICB), durable clinical benefit remains limited to a subset of patients, highlighting the need for predictive biomarkers and new therapeutic targets. Here, we investigated the early immune dynamics associated with anti-PD1 responsiveness using longitudinal single-cell transcriptomics, spatial transcriptomics, and neutrophil-specific genetic perturbations in preclinical models of triple-negative breast cancer. We identified a conserved neutrophil interferon-stimulated gene (ISG) program that emerges before overt tumor divergence and predicts resistance to anti-PD1 therapy. Successful treatment was associated with an early reduction of IFN-responsive neutrophils in both blood and tumor tissues, whereas persistent neutrophil IFN signaling correlated with therapeutic resistance. Mechanistically, genetic disruption of either type I or type II interferon signaling in neutrophils enhanced anti-PD1 efficacy and promoted durable anti-tumor immune memory. Spatial analyses further revealed an inverse association between IFN-responsive neutrophils and tertiary lymphoid structure-enriched regions during effective therapy. Together, these findings identify IFN-responsive neutrophils as early determinants of immunotherapy outcome and establish dynamic neutrophil interferon programs as candidate blood-based biomarkers and therapeutic targets for cancer immunotherapy.

cancer biology↗

bioRxiv2026

Predicting VHH-Fc Developability from Large-Scale IgG Data

The VHH-Fc antibody scaffold is an emerging therapeutic modality. No public large-scale, standardized developability VHH-Fc dataset exists. Filling that gap, we introduce GDPa5, a 160-member VHH-Fc library profiled across 10 biophysical assays on the PROPHET-Ab platform. Cross format models trained on the developability properties of 559 IgGs outperformed intra-format models trained on GDPa5 alone, which is an advantage driven by the larger scale of standardized IgG data rather than by format. The most accurately predicted properties were heparin binding (HAC, Spearman {rho}=0.82), hydrophobicity (HIC, {rho}=0.63), and self-association (AC-SINS, {rho}=0.62), all of which are largely governed by antibody surface properties. Tabular neural networks (TabICLv2, TabPFN v2.5), applied here for the first time to antibody developability prediction, outperformed conventional modeling approaches. Adding experimental HIC and HAC measurements as model inputs improved prediction of the more complex polyreactivity liability (PR-CHO, {Delta}{rho} = +0.10), supporting a tiered assay strategy that extends predictive performance while limiting experimental burden. We demonstrate through this work that IgG-trained models are a practical, data-efficient starting point for VHH-Fc developability prediction.

biophysics↗

bioRxiv2026

Aquatic bacterial metabolic rates from RNA quantitative stable isotope probing (RNA-qSIP) depend on experimental design

Quantitative stable isotope probing (qSIP) allows researchers to calculate taxon-specific carbon incorporation from sequencing of natural microbial communities, which can be used as a proxy for metabolic activity rates and subsequently as an input for biogeochemical modeling. While qSIP is widely utilized in soils to investigate the identity and metabolic activity of largely unculturable microbes, the application of qSIP in marine and aquatic ecosystems is more recent. Here, we investigated how bioreactor type (batch vs. chemostat) and carbon substrate complexity (single vs. multiple substrates) affect the incorporation of {superscript 1}3C-labeled glucose into rRNA after 24 hours using excess atomic fraction (EAF) as a proxy for metabolic activity rate. We found that the growth dynamics and community composition of the {superscript 1}3C-incorporating bacteria differed significantly for each treatment. EAF was positively correlated with both 16S gene copy number and a genomic index of copiotrophy in both batch treatments, but not in the chemostat, suggesting that chemostats dampen the competitive advantage of fast-growing copiotrophic taxa. Our results demonstrate that both substrate complexity and experimental regime influence qSIP-derived metabolic activity estimates and provide guidance for future applications of qSIP in aquatic environments.

molecular biology↗

bioRxiv2026

Cerclage Wire as an Affordable Alternative for Internal Fixation in Murine Critical Sized Defect Models

Critical sized defects (CSDs) are a serious challenge in orthopedics that require the development of more robust and effective treatments to improve quality of life for patients. Current CSD research is limited by the applicable and affordable animal models available. Mice would be the preferred species as they are cheaply housed and have many transgenic variations readily available; however, their small size makes CSD surgeries difficult and expensive. We propose the use of cerclage wires to achieve internal plate fixation. PEEK plates were secured to the right femur of 26 C57BL/6 mice using four cerclage wires to achieve modified double-loop fixation implemented through bicortical holes and defects were created. 10 received 3mm defects and 6 received 4mm defects that were left empty and were taken out to 20 weeks (Group E3, E4). Another 10 received 3mm defects that were filled with a morselized bone graft and were taken out to 8 weeks (Group G3). Blinded longitudinal x-ray grading by orthopedic surgeons was conducted on the empty defects for plate stability and wire fixation. All samples received microCT analysis at their endpoints. There were no significant differences in plate or wire stability between the empty groups and wire scores worsened negligibly over time. MicroCT analysis further supported wire integration as bone growth directly upon the wires was observed in all samples. The efficacy of this model in achieving non-union when left untreated was also confirmed via microCT. Further, only three mice in group G3 achieved union and two of these unions were not optimal. Our study is the first to successfully show that cerclage wire can be used in a murine CSD model to achieve affordability and clinical relevancy.

bioengineering↗

bioRxiv2026

SFPQ dysregulation promotes TDP-43 pathology through a pathogenic feedback loop

TDP-43 proteinopathies comprise a group of clinically distinct neurodegenerative disorders unified by common pathological changes in the RNA-binding protein TDP-43, including nuclear loss of function (LOF), cytoplasmic mislocalisation and aggregation. The presence of these hallmarks across diverse diseases, such as frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), alzheimers disease (AD) and Limbic-predominant Age-related TDP-43 Encephalopathy (LATE), suggests the involvement of convergent upstream regulatory mechanisms. This study identified SFPQ (Splicing Factor Proline and Glutamine Rich) as one such factor. The depletion of nuclear SFPQ, in addition to its cytoplasmic accumulation and aggregation has been described across ALS, AD and FTD patient studies and in multiple genetic models of these diseases. Evidence to date places SFPQ pathology downstream of TDP-43 dysfunction. This study provided further evidence that TDP-43 drives SFPQ pathology while revealing a reciprocal role for SFPQ in regulating TDP-43 homeostasis. Our data shoed that SFPQ LOF was associated with a shift in TDP-43 RNA isoform usage away from the canonical protein-coding transcript towards isoforms predicted to undergo nonsense-mediated decay (NMD). Consistent with this, TDP-43 protein expression was reduced across multiple model systems in which SFPQ expression was suppressed. Furthermore, cytoplasmic accumulation of SFPQ was found to promote the mislocalisation of TDP-43 and its sequestration within SFPQ-containing cytoplasmic condensates that exhibited progressively reduced molecular mobility over time. Collectively, these findings identify SFPQ as an active contributor to multiple facets of TDP-43 pathology, support a bidirectional relationship between the two proteins, and suggest the existence of a feed-forward, self-amplifying mechanism that may contribute to disease progression in TDP-43 proteinopathies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/740184v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@12855eorg.highwire.dtl.DTLVardef@1f1e068org.highwire.dtl.DTLVardef@c3fb00org.highwire.dtl.DTLVardef@93f0ae_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Bacterial histone-like proteins released during antibiotic treatment mediate vascular injury in meningococcal sepsis.

Vascular injury and coagulopathy are key drivers of mortality in bacterial sepsis. In Neisseria meningitidis infection, endothelial adhesion and thrombosis cause the characteristic petechial rash and, in the most severe cases, purpura fulminans. Although antibiotics rapidly kill bacteria, inflammation and vascular injury often persist or worsen after bacterial clearance, suggesting ongoing toxicity from released bacterial components. Here we identify bacterial histone-like proteins (HLPs), small positively charged DNA-binding proteins conserved across bacterial species, as previously unrecognized mediators of vascular damage. In vitro HLPs are released following antibiotic exposure, disrupting endothelial integrity. In patients with severe sepsis, they are detectable in plasma and tissue, colocalising with areas of vascular leak and coagulopathy. Non-anticoagulant heparins and anti-HLP antibodies neutralize HLP-induced endothelial disruption and toxicity in vitro and in vivo. These findings reveal HLPs as antibiotic-released bacterial toxins and suggest new therapeutic strategies to prevent vascular injury in sepsis. One sentence summaryAntibiotic treatment of meningococcal and other sepsis causative bacteria triggers the release of histone-like proteins (HLPs) that damage the endothelium and drive coagulopathy, but these effects can be neutralized by non-anticoagulant heparins or anti-HLP antibodies.

microbiology↗

bioRxiv2026

Decoding Bispecific Antibody Developability: Design Rules and Predictive Models from a 160-Member Library

Bispecific antibodies deliver functional outcomes that monospecific antibodies cannot, yet emergent self-association, polyreactivity, and aggregation often degrade their developability relative to their parental arms. Whether bispecific developability inherits from the parents or is driven by the format has not been tested at scale. We characterized 160 bispecific antibodies and their 65 parental arms on a uniform knobs-into-holes CrossMab IgG1 scaffold across 10 assays on the PROPHET-Ab high-throughput platform. Bispecific developability separates into three classes of inheritance. Hydrophobicity and surface charge inherit cleanly from the parents (Spearman {rho} {approx} 0.85 to 0.95), so parental-level screening predicts bispecific fate. Self-association and polyreactivity inherit partially ({rho} {approx} 0.60 to 0.88), with mechanistically interpretable emergent outliers driven in part by Fv-Fv charge complementarity and a parental biophysical ceiling on the hydrophobicity (HIC) by surface-charge (HAC) plane. Thermostability is poorly predicted from parental antibodies ({rho} < 0.4), so it requires bispecific-level testing. The class framework yields actionable selection rules: triage hydrophobicity and charge at the parental level, avoid pairing two high-HIC x high-HAC arms, pair opposite-sign Fv charges to suppress self-association but re-validate at the formulation buffer, and measure thermostability on the bispecific itself. This work charts a tractable path from monospecific sequence to bispecific developability prediction. SignificanceBispecific antibodies are a fast-growing therapeutic class, yet the rational design of well-behaving bispecific antibodies from validated monospecific antibody building blocks remains challenging. A key bottleneck is the lack of comprehensive, high-quality public datasets linking parental antibody developability properties to corresponding bispecific antibody developability properties. We address this gap by releasing a dataset comprising 160 bispecific antibodies and the 65 parental monospecific antibodies profiled in 10 developability assays. The data show that bispecific antibody developability is complex. Some properties are easily predictable from the parents, whereas others emerge in the bispecific format or from the bispecific format itself. The factors that govern each property can be identified empirically and used to make practical selection decisions. The mechanistic explanations and predictive models reported here establish a compact set of actionable rules. Together, they define a framework for using computational pipelines to convert monospecific antibodies into bispecific antibodies with drug-like developability properties, enabling faster and more effective generation of high-quality bispecific antibodies for diverse therapeutic applications.

biophysics↗

bioRxiv2026

Behavioural plasticity in Caenorhabditis elegans navigating dynamic granular environments

The mechanisms that steer behavioural plasticity in complex environments remain poorly understood. Here, we introduce Peb2les, a quasi-two-dimensional granular arena, for the behavioural assessment of Caenorhabditis elegans nematodes, as they interact with deformable, dynamic terrains. Using customized deep-learning-based methods, we track both nematodes and particles to characterize coupled animal-environment dynamics. We find that nematodes locomotor performance depends on particle density and surface properties, and is largely independent of mechanosensation, whereas functional touch sense is required for the initial decision to enter rough-textured arenas. In addition, we identify a previously undescribed touch-seeking behaviour that partially depends on mechanosensation, in which C. elegans actively return to the granular arena after exiting. In parallel, locomoting nematodes rearrange and stack surrounding particles, continuously modifying the granular terrain. Together, these findings establish Peb2les as a versatile platform for probing the mechanism and limits of behavioural plasticity and locomotory adaptability of nematodes in sensory-enriched, soil-like environments, while also providing insight into the potential evolutionary origins of adaptive touch-seeking behaviours in animals.

animal behavior and cognition↗

bioRxiv2026

Phosphorylated ubiquitin is a secondary messenger and an epigenetic mark mediating mitochondria to nucleus signaling

AbstractParkinsons disease (PD) is commonly associated with dysfunctional mitochondrial homeostasis. PINK1, a S/T kinase mutated in early-onset PD, generates phosphoserine 65 ubiquitin (pS65Ub) on damaged mitochondria facilitating their removal. Here, we show that pS65Ub translocates into the nucleus after generation at damaged mitochondria and is directly attached to substrates by resident E3 ligases. Histone H2A is a major substrate and is modified at lysine 119 (H2AK119) by the polycomb silencer, E3 ligase RING1B. At nucleosomes, pS65Ub simultaneously suppresses RING1B and potentiates H2A deubiquitinases USP16 and USP21. Epigenetic profiling and RNA sequencing reveal that pS65Ub is enriched at the promoters of poorly expressed yet dynamically regulated genes and is associated with H2AK119ub depletion. Functionally, we show that pS65Ub enrichment drives polycomb target gene expression, which accelerates the maturation of dopaminergic neurons. Importantly, post-mortem PD brains exhibit elevated nuclear pS65Ub, potentially linking nuclear pS65Ub accumulation with disease pathogenesis. Together, these data indicate that pS65Ub generated at damaged mitochondria regulates fundamental cellular processes at distant sites.

cell biology↗

bioRxiv2026

Springtail-inspired compliant hinge enables terrain-adaptable takeoff in insect-scale robots

Springtails execute millisecond-scale escape jumps with a single appendage, the furca, on soil, snow, leaf litter, and water. Across 15 taxonomic families (n=552 individuals), relative furca length is bimodal. High-speed video and confocal imaging show that in some long-furca springtails, the resilin-rich manubrium-dens joint behaves as a compliant hinge. It bends during push-off to prolong contact, suppress pitch, and bias takeoff forward, whereas rigid joints drive backward launches with rapid body rotation. We translate this mechanism to a 20-mm, 84-mg jumping robot with an elastic robo-furca hinge. This flexible hinge reduces body rotation by [~] 90% on flat ground compared to rigid-hinge designs, while maintaining takeoff speed on gravel, springboards, leaves, and pine needles, enabling passive, terrain-adaptable launches for power-limited insect-scale robots without onboard sensing or active control.

animal behavior and cognition↗

bioRxiv2025

A window trial in metastatic pancreatic ductal adenocarcinoma reveals resistance mechanisms to targeting the KRAS-MEK pathway

Copy number alterations of KRAS, mutated in over 90% of pancreatic ductal adenocarcinomas (PDAC), and MYC occur in 30-40% of PDAC. Here we demonstrate that KRAS and MYC are frequently co-gained and accompanied with worse prognosis in PDAC. In a Window-of-Opportunity clinical trial for metastatic PDAC, serial biopsies and deep multi-omics analyses were utilized to explore resistance mechanisms to MEK inhibition, as a surrogate for KRAS inhibition. Tumors from four of 14 patients showed Ki-67/CA19-9-based biomarker response (BR). Non-BR tumors were enriched for KRAS/MYC co-gain and KRASG12D variant. A transcriptomic signature of BR tumors was inversely correlated with KRASG12D/MYC co-gain in a large PDAC dataset and predictive for KRAS inhibitor response in multiple models. Finally, co-targeting KRAS and MYC was synergistic in KRASG12D/MYC co-gain PDAC. Together, this study provides insight into KRAS inhibitor resistance and supports MYC as an important target to improve patient outcomes in this deadly disease.

cancer biology↗

bioRxiv2025

SAMPLE-BASED TRAINING DATA FOR EFFECTIVE 3D CELL SEGMENTATION

Deep learning remains the leading choice for cell segmentation, a critical step in bioimaging analysis. Whilst deep learning models provide excellent segmentation accuracy, a large number of hand-annotated samples are required which are scarce in 3D. We propose a method for generating synthetic data for training deep learning models to augment or replace such datasets. By preserving key features in real data, we show that a standard UNet trained on synthetic data can segment single motile cells with branching filopodia with high accuracy. We also demonstrate how low-effort slice annotations can sufficiently replace volume annotations in our data generation pipeline. Overall, we provide a simple alternative to annotating large 3D datasets for training neural networks to segment cell imaging data.

bioinformatics↗

bioRxiv2025

Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity

The radiations of cichlid fishes in East African Lakes Victoria, Malawi, and Tanganyika showcase a remarkable example of rapid adaptive speciation, with over 2000 species evolving diverse morphological and ecological adaptations within the last few million years. Understanding the molecular basis of this phenotypic diversity remains a key challenge. Building on prior evidence of gene regulatory network (GRN) rewiring underpinning adaptive traits, we profiled chromatin accessibility (ATAC-seq) and matched transcriptomes across forebrain, retina, liver, and testis tissues in five representative cichlid species using optimised protocols. We show extensive divergence in chromatin accessibility corresponding to phylogenetic lineages and tissue identity, with many regulatory regions exhibiting accelerated nucleotide evolution. Transcription factor binding site (TFBS) variation correlates with both chromatin accessibility and differential gene expression, particularly in genes linked to sensory systems. Building on this, we reconstructed tissue- and species-specific GRNs and show that motif-supported network inference reveals pervasive but tissue-dependent rewiring, with the strongest candidate edges concentrated among accessible, highly expressed genes linked to adaptive traits. By integrating TF footprinting with regulatory motif turnover analyses, we demonstrate that dynamic nucleotide changes are associated with GRN rewiring, concordant with ecological niche and lineage-specific adaptations. Our findings highlight that regulatory variation at conserved and novel TFBSs associates with genes linked to phenotypic innovation across radiating and non-radiating East African cichlids. This study provides foundational epigenomic evidence linking GRN divergence to key mechanisms facilitating rapid adaptive diversification in this iconic vertebrate radiation.

evolutionary biology↗