Biology subjects

Chapman, K.

Publications and source records attributed to Chapman, K..

10 recordsLinked to original sources

bioRxiv2026

Contraction type dependence of serial sarcomere addition following resistance training

Longitudinal muscle growth occurs through the addition of sarcomeres in series, a process termed serial sarcomerogenesis. To investigate contraction mode dependence of sarcomerogenesis in Sprague-Dawley rats (n=36, 14 to18 weeks, ~468g), we compared the effects of isometric, eccentric, and concentric training (4 to 6 weeks; 3 times/week) on morphological and mechanical adaptations of the plantar flexors. Isometric training was performed at a joint angle corresponding to the plateau nearing the descending limb of the force length relationship, eccentric contractions began at a shorter muscle length and lengthened to this same joint position, and concentric contractions started at this lengthened position but then actively shortened. Owing to the rapid regulation of serial sarcomere number the 4-and 6-week timepoints were collapsed. While force output increased across all training modes (+16%; p<0.05), longitudinal muscle growth was regulated by contraction type. Both isometric and eccentric training were highly effective at increasing serial sarcomere number when optimal loading conditions (high forces at longer lengths) are provided (+7-9%; p<0.05). Concentric training, even when initiated at long lengths with high forces was not an effective stimulus for longitudinal remodelling (+2%; p>0.05). Therefore, these findings identify the mechanical loading environment associated with isometric and eccentric training as a key driver of serial sarcomerogenesis.

physiology↗

bioRxiv2026

Trade-offs between photosynthetic capacity, mesophyll conductance stability and leaf anatomy shape heat and water deficit resilience in Gossypium.

O_LIMesophyll conductance (gm) governs CO2 diffusion to Rubisco and is a key determinant of photosynthetic performance, yet the mechanisms underlying its sensitivity to heat and water stress remain unresolved. C_LIO_LIWe quantified gm temperature responses across diverse Gossypium species and examined anatomical drivers of gm plasticity in cultivated cotton (G. hirsutum) and the wild Australian species G. bickii under elevated temperature and soil water deficit. C_LIO_LISpecies exhibited contrasting gm strategies: G. hirsutum exhibited high gm and carbon assimilation near thermal optima but showed greater sensitivity under combined heat and water deficit, whereas G. bickii maintained comparatively stable gm and photosynthesis across stress conditions. C_LIO_LIUnder water deficit, structural adjustments in G. hirsutum (increased leaf porosity, cell wall thickness and mesophyll surface exposure to intercellular airspaces) were insufficient to sustain gm, suggesting that liquid-phase resistances impose dominant constraints on CO2 diffusion under extreme climatic stress. C_LIO_LIThese results identify gm as a dynamic, multi-component trait and a key physiological vulnerability in cotton, shaped by coordinated anatomical characteristics and potentially cell wall properties and membrane-associated processes, with major implications for mechanistic photosynthesis modelling and improving climate resilience in cotton and other C3 species. C_LI

plant biology↗

bioRxiv2026

Origin-1: a generative AI platform for de novo antibody design against novel epitopes

0Generative artificial intelligence has advanced antibody discovery, yet de novo design of therapeutic antibodies against targets with "zero-prior" epitopes remains a fundamental challenge. We define "zero-prior" epitopes as target sites lacking structural data from any reported antibody-antigen or protein-protein complex involving the target. Here we present Origin-1, a generative AI platform that overcomes this by integrating epitope-conditioned all-atom structure generation, paired complementarity determining region sequence design, and a specialized co-folding-based scoring protocol to select antibody designs predicted to be high-confidence, specific binders with favorable developability. We evaluated Origin-1 on a panel of ten targets selected to have no available protein-protein complex structures and minimal homology ([≤]60% sequence identity) to proteins with known complexes, creating stringent design conditions. In fewer than one hundred design attempts per target, we identified developable, specific antibodies, validated across multiple biophysical and developability assays, for four targets: COL6A3, AZGP1, CHI3L2, and IL36RA, with functional inhibition demonstrated for IL36RA. Cryogenic electron microscopy confirmed the atomic accuracy of our designs, revealing complexes that closely matched the computational models with high structural fidelity (3.0-3.3 [A] resolution; 0.83-0.91 DockQ). Furthermore, we employed AI-guided affinity maturation to optimize a de novo antibody binder against IL36RA, producing functional antagonists with sub-nanomolar affinities and a top EC50 of 12.3 nM. These results demonstrate a framework for targeting epitopes without structural precedent, expanding the programmable therapeutic antibody landscape.

molecular biology↗

bioRxiv2025

Streamlining Spatial Transcriptomics for Human Kidney Tissue

Single-cell spatial technologies have emerged in recent years, enabling tissue architecture and organization characterization at unprecedented resolution. However, computational analysis of spatial transcriptomics data is often a bottleneck for scientific discoveries in the absence of a dedicated bioinformatician. Here, we describes a workflow to annotate cell types from a dataset generated using NanoStrings CosMx single-cell resolution spatial transcriptomic technology, enabling a comparison between healthy kidney biopsies and diseased tissue. We validated our pipelines accuracy with both gene expression analysis and pathological changes associated with biopsy-proven diabetic kidney disease (DKD). Through precise cell type annotation, we observed significant changes in the proportions of podocytes and immune cells in DKD, with DKD tissue showing regional enrichment of immune cells and differential gene expression. Notably, injured proximal tubules had the expected increased expression of HAVCR1 and VCAM1 and genes associated with diabetes, including IL18, ITGA3 and ITGB1. The entire workflow, now fully integrated into the BioTuring SpatialX (Lens V2.0), is available as a platform designed for users with no formal bioinformatics training.

bioinformatics↗

bioRxiv2023

In vitro validated antibody design against multiple therapeutic antigens using generative inverse folding

Deep learning approaches have demonstrated the ability to design protein sequences given backbone structures [1, 2, 3, 4, 5]. While these approaches have been applied in silico to designing antibody complementarity-determining regions (CDRs), they have yet to be validated in vitro for designing antibody binders, which is the true measure of success for antibody design. Here we describe IgDesign, a deep learning method for antibody CDR design, and demonstrate its robustness with successful binder design for 8 therapeutic antigens. The model is tasked with designing heavy chain CDR3 (HCDR3) or all three heavy chain CDRs (HCDR123) using native backbone structures of antibody-antigen complexes, along with the antigen and antibody framework (FWR) sequences as context. For each of the 8 antigens, we design 100 HCDR3s and 100 HCDR123s, scaffold them into the native antibodys variable region, and screen them for binding against the antigen using surface plasmon resonance (SPR). As a baseline, we screen 100 HCDR3s taken from the models training set and paired with the native HCDR1 and HCDR2. We observe that both HCDR3 design and HCDR123 design outperform this HCDR3-only baseline. IgDesign is the first experimentally validated antibody inverse folding model. It can design antibody binders to multiple therapeutic antigens with high success rates and, in some cases, improved affinities over clinically validated reference antibodies. Antibody inverse folding has applications to both de novo antibody design and lead optimization, making IgDesign a valuable tool for accelerating drug development and enabling therapeutic design. The data generated in this study serve as a useful benchmark of diverse antibody-antigen interactions. We use this data to benchmark self-consistency RMSD (scRMSD), using ABodyBuilder2 [6], ABodyBuilder3 [7], and ESMFold [8], as a metric for assessing binding. We open source the code for IgDesign and the SPR datasets. Code and datasets can be found at https://github.com/AbSciBio/igdesign.

synthetic biology↗

bioRxiv2022

Differential Effects of Mutations of Popeye Domain Containing Proteins on Heteromeric Interaction and Membrane Trafficking

BackgroundThe Popeye domain containing (POPDC) genes encode sarcolemma-localised cAMP effector proteins. Mutations in BVES (POPDC1) and POPDC2 have been associated with limb-girdle muscular dystrophy and cardiac arrhythmia. Muscle biopsies of affected patients display impaired membrane trafficking of both POPDC isoforms. MethodsBiopsy material of patients carrying mutations in BVES were immunostained with POPDC antibodies. The interaction of POPDC proteins was investigated by co-precipitation, proximity ligation, bioluminescence resonance energy transfer and bimolecular fluorescence complementation. Site-directed mutagenesis was utilised to map the domains involved in protein interaction. FindingsPatients carrying a novel homozygous variant, BVES (c.547G>T, p.V183F) displayed only a skeletal muscle pathology and a mild impairment of membrane trafficking of both POPDC isoforms. This is in contrast to variants such as BVES p.Q153X or POPDC2 p.W188X, which were associated with a greater impairment of membrane trafficking. Co-transfection analysis in HEK293 cells revealed that POPDC proteins interact with each other through a helix-helix interface located at the C-terminus of the Popeye domain. Site-directed mutagenesis of an array of ultra-conserved hydrophobic residues demonstrated that some of them are required for membrane trafficking of the POPDC1-POPDC2 complex. InterpretationMutations in POPDC proteins that cause an impairment in membrane localisation affect POPDC complex formation while mutations which leave the protein interaction intact likely affect some other essential function of POPDC proteins. FundingThis study was funded by an EPSRC/British Heart Foundation co-funded Imperial Institute of Chemical Biology (ICB) Centre for Doctoral Training (CDT) PhD studentship (EP/S023518/1), a project grant of the British Heart Foundation (PG19/13/34247) and the Deutsche Forschungsgemeinschaft (DE1482/9-1). Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSSeveral biallelic missense and nonsense variants in BVES (POPDC1) have been described and are associated with heart and skeletal muscle disease. Skeletal muscle biopsies of homozygous carriers of these variants display a loss of sarcolemmal localisation of POPDC1 and POPDC2. Added value of this studyWe demonstrate that POPDC1 and POPDC2 form a heteromeric complex and that complex formation is required for plasma membrane trafficking of POPDC proteins. Transfection of different disease variants in HEK293 cells replicates their defective membrane targeting observed in biopsy material. Structural modelling and site-directed mutagenesis identifies an interface of strongly conserved hydrophobic residues in POPDC proteins, which likely mediate the interaction of POPDC proteins. Implications of all the available evidenceThese data provide novel insight into the membrane targeting requirements of POPDC proteins. We recommend testing the membrane targeting properties of any novel variant in POPDC isoforms using a newly developed co-transfection assay in HEK293 cells to characterise its pathogenicity. Our novel insight into the requirement of heterodimerization for proper membrane targeting may also offer novel opportunities to treat patients carrying mutations in POPDC proteins.

genetics↗

bioRxiv2022

CEP peptide and cytokinin pathways converge on CEPD glutaredoxins to inhibit root growth

C-TERMINALLY ENCODED PEPTIDE (CEP) and cytokinin hormones act over short and long distances to control plant responses to environmental cues. CEP and cytokinin pathway mutants share phenotypes, however, it is not known if these pathways intersect. We show that CEP and cytokinin signalling converge on CEP DOWNSTREAM (CEPD) glutaredoxins to inhibit primary root growth. CEP inhibition of root growth was impaired in mutants defective in trans-zeatin (tZ)-type cytokinin biosynthesis, transport, perception, and output. Concordantly, mutants affected in CEP RECEPTOR 1 showed reduced root growth inhibition in response to tZ, and altered levels of tZ-type cytokinins. Grafting and organ-specific hormone treatments showed that tZ-mediated root growth inhibition required CEPD activity in roots. By contrast, root growth inhibition by CEP depended on shoot CEPD function. The results demonstrate that CEP and cytokinin pathways intersect, and utilise signalling circuits in separate organs involving common glutaredoxin genes to coordinate root growth.

plant biology↗

bioRxiv2021

GLUCOCORTICOIDS REGULATE MITOCHONDRIAL FATTY ACID OXIDATION IN FETAL CARDIOMYOCYTES

The late gestational rise in glucocorticoids contributes to the structural and functional maturation of the perinatal heart. Here, we hypothesised that glucocorticoid action contributes to the metabolic switch in perinatal cardiomyocytes from carbohydrate to fatty acid oxidation. In primary mouse fetal cardiomyocytes, dexamethasone treatment induced expression of genes involved in fatty acid oxidation and increased mitochondrial oxidation of palmitate, dependent upon glucocorticoid receptor (GR). Dexamethasone did not, however, induce mitophagy or alter the morphology of the mitochondrial network. In neonatal mice, dexamethasone treatment induced cardiac expression of fatty acid oxidation genes in vivo. However, dexamethasone treatment of pregnant C57Bl/6 mice at embryonic day (E)13.5 or E16.5 failed to induce fatty acid oxidation genes in fetal hearts assessed 24 hours later. Instead, at E17.5, fatty acid oxidation genes were down-regulated by dexamethasone, as was GR itself. PGC-1, required for glucocorticoid-induced maturation of primary mouse fetal cardiomyocytes in vitro, was down-regulated in vivo in fetal hearts at E17.5, 24 hours after dexamethasone administration. Similarly, following a course of antenatal corticosteroids in a sheep model of preterm birth, both GR and PGC-1 were down-regulated in fetal heart. These data suggest endogenous glucocorticoids support the perinatal switch to fatty acid oxidation in cardiomyocytes through changes in gene expression rather than gross changes in mitochondrial volume or mitochondrial turnover. Moreover, our data suggest that treatment with exogenous glucocorticoids may interfere with normal fetal heart maturation, possibly by down-regulating GR. This has implications for clinical use of antenatal corticosteroids when preterm birth is considered a possibility.

physiology↗

bioRxiv2020

Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies

The global outbreak of SARS-CoV-2 necessitates the rapid development of new therapies against COVID-19 infection. Here, we present the identification of 200 approved drugs, appropriate for repurposing against COVID-19. We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. This analysis identified 200 drugs predicted to target SARS-CoV-2-induced pathways, 40 of which are already in COVID-19 clinical trials(Clinicaltrials.gov, 2020) testifying to the validity of the approach. Using artificial neural network analysis we classified these 200 drugs into 9 distinct pathways, within two overarching mechanisms of action (MoAs): viral replication (130) and immune response (70). A subset of drugs implicated in viral replication were tested in cellular assays and two (proguanil and sulfasalazine) were shown to inhibit replication. This unbiased and validated analysis opens new avenues for the rapid repurposing of approved drugs into clinical trials.

pharmacology and toxicology↗

bioRxiv2017

Light-Activated Cell Identification and Sorting (LACIS): A New Method to Identify and Select Edited Clones on a Microfluidic Device

CRISPR-Cas9 gene editing has revolutionized cell engineering and promises to open new doors in gene and cell therapies. Despite improvements in the CRISPR-editing molecular toolbox in cell lines and primary cells, identifying and purifying properly edited clones remains slow, laborious and low-yield. Here, we establish a new method that uses cell manipulation on a chip with Opto-Electronic Positioning (OEP) technology to enable clonal isolation and selection of edited cells. We focused on editing CXCR4 in primary human T cells, a gene that encodes a co-receptor for HIV entry. T cells hold significant potential for cell-based therapy, but the gene-editing efficiency and expansion potential of these cells is limited. We describe here a method to obviate these limitations. Briefly, after electroporation of cells with CXCR4-targeting Cas9 ribonucleoproteins (RNPs), single T cells were isolated on a chip, where they proliferated over time into well-resolved colonies. Phenotypic consequences of genome editing could be rapidly assessed on-chip with cell-surface staining for CXCR4. Furthermore, independent of phenotype, individual colonies could be identified based on their specific genotype at the 5-10 cell stage. Each colony was split and sequentially exported for immediate on-target sequencing and validation, and further off-chip clonal expansion of the validated clones. We were able to assess single-clone editing efficiencies, including the rate of monoallelic and biallelic indels or precise nucleotide replacements. This new method will enable identification and selection of perfectly edited clones within 10 days from Cas9-RNP introduction in cells based on the phenotype and/or genotype.

bioengineering↗