Biology subjects

Chapman, D.

Publications and source records attributed to Chapman, D..

13 recordsLinked to original sources

bioRxiv2026

Diminished Stimulus-Evoked Activity During Sustained Attention Without Behavioural Cost in ADHD

Attention-Deficit/Hyperactivity Disorder (ADHD) is often accompanied by attentional challenges, sleep difficulties and increased reports of daytime sleepiness, indicating potential links between attention and arousal mechanisms. Electroencephalographic (EEG) studies have shown that sleep-like wake slow wave (SW) activity during wakefulness, characterised by reduced cortical activity, corresponds with periods of inattention in both ADHD and neurotypical populations. However, it remains unclear whether group differences in waking SWs are consistent across different types of sustained attention tasks or may be context-dependent. The present study compared sustained attention performance and wake SW activity between adults with and without ADHD during a continuous visual target detection task. EEG data were collected while adults with (n = 52) and without ADHD (n = 49) completed a sustained attention paradigm. The task presented a continuous stream of rotating (anti-clockwise or clockwise) black-and-white checkerboard stimuli, and participants were required to detect infrequent targets that were marginally longer in duration than non-targets. Behavioural and neural measures (power spectra, steady-state visually evoked potentials (SSVEP), event-related potentials and SW density during wake) were analysed. No significant group differences were observed for task performance and wake SW activity. However, electrophysiological analyses revealed the ADHD group showed reduced P300, elevated beta-band power, and lower SSVEPs to target stimuli compared with the neurotypical group. These neural differences in the context of comparable performance suggest compensatory cortical recruitment in ADHD. The absence of SW differences further supports this, suggesting comparable performance and maintained arousal may reflect successful neural compensation in ADHD in this cognitive task. Significance StatementIndividuals with ADHD commonly experience attention differences, but emerging evidence suggests these difficulties may depend on task context. Using clinical diagnostic interviews, medication washout, and Bayesian statistics, we found strong evidence for comparable performance between ADHD and neurotypical adults on a sustained attention task. Notably, slow wave activity during wakefulness did not differ between groups, consistent with maintained arousal. Nevertheless, differences in brain activity, including altered target processing, increased cortical activation and reduced visual entrainment, suggested compensatory neural recruitment in ADHD. This context-dependent pattern has important theoretical and clinical implications: identifying task features that challenge or support performance in ADHD can reveal how individuals compensate neurally, and guide interventions that leverage task features to support attention in ADHD.

neuroscience↗

bioRxiv2025

Sleep-like Slow Waves During Wakefulness Mediate Attention and Vigilance Difficulties in Adult Attention-Deficit/Hyperactivity Disorder

BackgroundAttention-Deficit/Hyperactivity Disorder (ADHD) is characterised by behavioural variability and heightened inattention associated with increased mind wandering (MW) and mind blanking (MB). Individuals with ADHD frequently experience sleep disorders and excessive daytime sleepiness, suggesting interactions between attention and arousal systems. Research examining brain activity using electroencephalography (EEG) has demonstrated that sleep-like slow waves (SW) during wakefulness are linked to inattention in neurotypical individuals, particularly following sleep deprivation, yet their role in ADHD remains unclear. This study investigated whether individuals with ADHD present with altered waking SW distribution compared to neurotypical controls and whether SW explain attentional difficulties in ADHD. MethodsAdults with (n = 32) and without ADHD (n = 31) completed a sustained attention task while EEG recorded brain activity. Mental state probes (on-task, MW, MB) were embedded within the task. Sleep-like SW reflect a slowing of cortical activity and was detected from EEG activity. Omission/commission errors, reaction time (RT), RT variability, mental state reports and subjective sleepiness were analysed. Mediation analysis examined whether SW density explained ADHD-related performance differences. ResultsIndividuals with ADHD exhibited more commission errors, MW and MB, and higher SW density (SW/min), particularly over parieto-temporal electrodes. Increased SW density correlated with higher omission errors, slower RTs, greater RT variability, and elevated sleepiness ratings. On-task reports were negatively correlated with SW density. Mediation analysis revealed that SW density significantly accounted for ADHD-related attentional difficulties. ConclusionsWake SW may explain attentional difficulties in ADHD, providing a potential mechanistic link between sleep disturbances and attentional fluctuations.

neuroscience↗

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↗

bioRxiv2023

The mitophagy receptor Nix coordinates nuclear calcium signaling to modulate the muscle phenotype.

Mitochondrial quality control is critical in muscle to ensure both contractile and metabolic function. Nix is a BCL-2 family member, mitophagy receptor, and has been implicated in muscle atrophy. Human GWAS suggests altered Nix expression could predispose to manifestations of mitochondrial disease. To interrogate Nix function, we generated a muscle-specific knockout model. Nix knockout mice displayed a ragged-red fibre phenotype, along with accumulation of mitochondria and endo/sarcoplasmic reticulum with altered morphology. Intriguingly, Nix knockout mice were more insulin sensitive with a corresponding increase in glycogen-rich muscle fibres. Kinome- and gene expression analyses revealed that Nix knockout impairs NFAT and canonical myostatin signaling, with alterations in muscle fibre-type composition and evidence of regeneration. Mechanistic experiments demonstrated that Nix modulates mitophagy, along with ER-phagy leading to altered nuclear calcium signaling. Collectively, these observations identify novel roles for Nix coordinating selective autophagy, oxidative gene expression, and signaling pathways that maintain the muscle phenotype.

cell biology↗

bioRxiv2023

Unlocking de novo antibody design with generative artificial intelligence

Generative AI has the potential to redefine the process of therapeutic antibody discovery. In this report, we describe and validate deep generative models for the de novo design of antibodies against human epidermal growth factor receptor (HER2) without additional optimization. The models enabled an efficient workflow that combined in silico design methods with high-throughput experimental techniques to rapidly identify binders from a library of [~]106 heavy chain complementarity-determining region (HCDR) variants. We demonstrated that the workflow achieves binding rates of 10.6% for HCDR3 and 1.8% for HCDR123 designs and is statistically superior to baselines. We further characterized 421 diverse binders using surface plasmon resonance (SPR), finding 71 with low nanomolar affinity similar to the therapeutic anti-HER2 antibody trastuzumab. A selected subset of 11 diverse high-affinity binders were functionally equivalent or superior to trastuzumab, with most demonstrating suitable developability features. We designed one binder with [~]3x higher cell-based potency compared to trastuzumab and another with improved cross-species reactivity1. Our generative AI approach unlocks an accelerated path to designing therapeutic antibodies against diverse targets.

synthetic biology↗

bioRxiv2022

Conserved basal lamina proteins, laminin and nidogen, are repurposed to organize mechanosensory complexes responsible for touch sensation.

The sense of touch is conferred by the conjoint function of somatosensory neurons and skin cells. These cells meet across a gap filled by a basal lamina, an ancient structure found in metazoans. Using Caenorhabditis elegans, we show that membrane-matrix complexes containing laminin, nidogen, and the MEC-4 mechano-electrical transduction channel reside at this interface and are instrumental for proper touch sensation. These complexes fail to coalesce in touch-insensitive extracellular matrix mutants and in dissociated neurons. MEC-4, but not laminin or nidogen, is destabilized by point mutations in the C-terminal Kunitz domain of the extracellular matrix component, MEC-1. Thus, neuron-epithelial cell interfaces are instrumental in mechanosensory complex assembly and function. Loss of nidogen reduces the density of mechanoreceptor complexes and the amplitude of the touch-evoked currents they carry. These findings imply that somatosensory neurons secrete proteins that actively repurpose the basal lamina to generate special-purpose mechanosensory complexes responsible for vibrotactile sensing.

cell biology↗

bioRxiv2022

Differential Impact of Doxorubicin Dose on Cell Death and Autophagy Pathways during Acute Cardiotoxicity.

Doxorubicin (DOX) is an effective anthracycline used in chemotherapeutic regimens for a variety of haematological and solid tumors. However, its utility remains limited by its well-described, but poorly understood cardiotoxicity. Despite numerous studies describing various forms of regulated cell death and their involvement in DOX-mediated cardiotoxicity, the predominate form of cell death remains unclear. Part of this inconsistency lies in a lack of standardization of in vivo and in vitro model design. To this end, the objective of this study was to characterize acute low- and high-dose DOX exposure on cardiac structure and function in C57BL/6N mice, and evaluate regulated cell death pathways and autophagy both in vivo and in cardiomyocyte culture models. Acute low-dose DOX had little impact on cardiac structure or function; however, acute high-dose DOX elicited substantial cardiac necrosis resulting in diminished cardiac mass and volume, with a corresponding reduced cardiac output, and without impacting ejection fraction or fibrosis. Low-dose DOX consistently activated caspase-signaling with evidence of mitochondrial permeability transition. However, acute high-dose DOX had only modest impact on common necrotic signaling pathways, but instead led to an inhibition in autophagic flux. Intriguingly, when autophagy was inhibited in cultured cardiomyoblasts, DOX-induced necrosis was enhanced. Collectively, these observations implicate inhibition of autophagy flux as an important component of the acute necrotic response to DOX, but also suggest that acute high-dose DOX exposure does not recapitulate the disease phenotype observed in human cardiotoxicity.

physiology↗

bioRxiv2020

Misoprostol Treatment Prevents Hypoxia-Induced Cardiac Dysfunction, Aberrant Cardiomyocyte Mitochondrial Dynamics and Permeability Transition Through Bnip3 Phosphorylation

Systemic hypoxia is a common element in most perinatal emergencies and is a known driver of Bnip3 expression in the neonatal heart. Bnip3 plays a prominent role in the evolution of necrotic cell death, disrupting ER calcium homeostasis and initiating mitochondrial permeability transition (MPT). Emerging evidence suggests a cardioprotective role for the prostaglandin E1 analogue misoprostol during periods of hypoxia, but the mechanisms for this protection are not completely understood. Using a combination of mouse and cell models, we tested if misoprostol is cardioprotective during neonatal hypoxic injury by altering Bnip3 function. Here we report that hypoxia elicits mitochondrial-fragmentation, MPT, reduced ejection fraction, and evidence of necroinflammation, which were abrogated with misoprostol treatment or Bnip3 knockout. Through molecular studies we show that misoprostol leads to PKA-dependent Bnip3 phosphorylation at threonine-181, and subsequent redistribution of Bnip3 from mitochondrial Opa1 and the ER through an interaction with 14-3-3 proteins. Taken together, our results demonstrate a role for Bnip3 phosphorylation in the regulation of cardiomyocyte contractile/metabolic dysfunction, and necroinflammation. Furthermore, we identify a potential pharmacological mechanism to prevent neonatal hypoxic injury.

cell biology↗

bioRxiv2019

A Multiple-trait Bayesian Variable Selection Regression Method for Integrating Phenotypic Causal Networks in Genome-Wide Association Studies

Bayesian regression methods that incorporate different mixture priors for marker effects are used in multi-trait genomic prediction. These methods can also be extended to genome-wide association studies (GWAS). In multiple-trait GWAS, incorporating the underlying causal structures among traits is essential for comprehensively understanding the relationship between genotypes and traits of interest. Therefore, we develop a GWAS methodology, SEM-BayesC{Pi}, which, by applying the structural equation model (SEM), can be used to incorporate causal structures into a multi-trait Bayesian regression method using mixture priors. The performance of SEM-BayesC{Pi} was demonstrated by comparing its GWAS results with those from multi-trait BayesC{Pi}. Through the inductive causation (IC) algorithm, three potential causal structures were inferred of 0.9 highest posterior density (HPD) interval. SEM-BayesC{Pi} provides a more comprehensive understanding of the genotype-phenotype mapping than multi-trait BayesC{Pi} by performing GWAS based on indirect, direct and overall marker effects. The software tool JWAS offers open-source routines to perform these analyses.

genomics↗

bioRxiv2019

Nix induced mitochondrial fission, mitophagy, and myocyte insulin resistance are abrogated by PKA phosphorylation.

Lipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor Nix is responsive to lipotoxicity and accumulates in response to diacylglycerols induced by high-fat (HF) feeding. In addition, previous studies have implicated autophagy and mitophagy in muscle insulin sensitivity. To provide a better understanding of these observations, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes including Beclin-1, ATG3, and -5. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the previously reported roles of these phospholipids and Nix in mitochondrial dynamics, we investigated aberrant mitochondrial fission and turn-over as a mechanism of myocyte insulin resistance. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that Nix accumulation triggers mitochondrial depolarization, fragmentation, calcium-dependent activation of DRP1, and mitophagy. In addition, Nix-induced mitochondrial fission leads to myotube insulin resistance through activation of mTOR-p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and Rheb. Finally, we demonstrate that Nix-induced mitophagy and insulin resistance can be reversed by direct phosphorylation of Nix by PKA, leading to the translocation of Nix from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of Nix-induced mitophagy and myocyte insulin resistance during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggests a mechanism by which exercise or pharmacological activation of PKA may overcome myocyte insulin resistance. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/825828v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@15d0a4org.highwire.dtl.DTLVardef@34f358org.highwire.dtl.DTLVardef@5427f3org.highwire.dtl.DTLVardef@10ae48a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Misoprostol Attenuates Cardiomyocyte Proliferation in the Neonatal Heart Through Bnip3 and Perinuclear Calcium Signaling

Systemic hypoxia resulting from preterm birth, altered lung development, and cyanotic congenital heart disease is known to impede the regulatory and developmental pathways in the neonatal heart. While the molecular mechanisms are still unknown, hypoxia induces aberrant cardiomyocyte proliferation, which may be initially adaptive, but can ultimately program the heart to fail in early life. Recent evidence suggests that the prostaglandin E1 analogue, misoprostol, is cytoprotective in the hypoxia-exposed neonatal heart by impacting alternative splicing of the Bcl-2 family member Bnip3, resulting in the generation of a variant lacking the third exon (Bnip3{Delta}Exon3 or small Nip; sNip). Using a rodent model of neonatal hypoxia, in combination with rat primary neonatal cardiomyocytes (PVNCs) and H9c2 cells, we sought to determine if misoprostol can prevent cardiomyocyte proliferation and what the key molecular mechanisms might be in this pathway. In PVNCs, exposure to 10% oxygen induced myocyte proliferation concurrent with molecular markers of cell-cycle progression, such as Cyclin-D1, which were prevented by misoprostol treatment. Furthermore, we describe a critical role for sNip in opposing cardiomyocyte proliferation through several mechanisms, including reduced expression of the proliferative MEF2C-myocardin-BMP10 pathway, accumulation of nuclear calcium leading to NFATc3 activation, and increased expression of the cardiac maturation factor BMP2. Intriguingly, misoprostol and sNip inhibited hypoxia-induced glycolytic flux, which directly influenced myocyte proliferation. These observations were further supported by knockdown studies, where hypoxia-induced cardiomyocyte proliferation is restored in misoprostol-treated cells by an siRNA targeting sNip. Finally, in postnatal day (PND)-10 rat pups exposed to hypoxia, we observed histological evidence of increased nuclei number and increased PPH3 staining, which were completely attenuated by misoprostol treatment. Collectively, this data demonstrates how neonatal cardiomyocyte proliferation can be pharmacologically modulated by misoprostol treatment, which may have important implications for both neonatal and regenerative medicine.

cell biology↗

bioRxiv2019

Renewal theory provides a universal quantitative framework to characterise the continuous regeneration of rotational events in cardiac fibrillation

BackgroundCardiac fibrillation is thought to be maintained by rotational activity, with pivoting regions called phase singularities (PSs). Despite a century of research, no clear quantitative framework exists to model the fundamental processes responsible for the continuous formation and destruction of rotors in fibrillation.\n\nObjectiveWe conducted a multi-modality, multi-species study of AF/VF under the hypothesis that PS formation/destruction in fibrillation can be modelled as self-regenerating renewal processes, producing exponential distributions of inter-event times governed by constant rate-parameters defined by the prevailing properties of the system.\n\nMethodsPS formation/destruction was studied and cross-validated in 5 models, using basket recordings and optical mapping from: i) human persistent AF (n = 20), ii) tachypaced sheep AF (n = 5), iii) rat AF (n = 4), iv) rat VF (n = 11) and v) computer simulated AF (SIM). Hilbert phase maps were constructed. PS lifetime data were fitted by exponential probability distribution functions (PDFs) computed using maximum entropy theory, and the rate parameter ({lambda}) determined. A systematic review was conducted to cross-validate with source data from literature.\n\nResultsPS destruction/formation distributions showed good fits to an exponential in all systems (R2 [≥] 0.90). In humans,{lambda} = 4.6%/ms (95%CI,4.3,4.9)), sheep 4.4%/ms (95%CI,4.1,4.7)), rat AF 38%/ms (95%CI,22,55), rat VF 46%/ms (95%CI,31.2,60.2) and SIM 5.4%/ms (95%CI,4.1,6.7). All PS distributions identified through systematic review were exponential with {lambda} comparable to experimental data.\n\nConclusionThese results provide a universal quantitative framework to explain rotor formation and destruction in AF/VF, and a platform for therapeutic advances in cardiac fibrillation.

physiology↗

bioRxiv2018

Misoprostol regulates Bnip3 repression and alternative splicing to control cellular calcium homeostasis during hypoxic stress.

The cellular response to hypoxia involves the activation of a conserved pathway for gene expression regulated by the transcription factor complex called hypoxia-inducible factor (HIF). This pathway has been implicated in both the adaptive response to hypoxia and in several hypoxic-ischemic related pathologies. Perinatal hypoxic injury, often associated with prematurity, leads to multi-organ dysfunction resulting in significant morbidity and mortality. Using a rodent model of neonatal hypoxia and several representative cell lines, we observed HIF1 activation and down-stream induction of the cell death gene Bnip3 in brain, large intestine, and heart which was mitigated by administration of the prostaglandin E1 analog misoprostol. Mechanistically, we determined that misoprostol inhibits full-length Bnip3 (Bnip3-FL) expression through PKA-mediated NF-{kappa}B (P65) nuclear retention, and the induction of pro-survival splice variants. We observed that the dominant small pro-survival variant of Bnip3 in mouse cells lacks the third exon (Bnip3{Delta}Exon3), whereas human cells produce a pro-survival BNIP3 variant lacking exon 2 (BNIP3{Delta}Exon2). In addition, these small Bnip3 splice variants prevent mitochondrial dysfunction, permeability transition, and necrosis triggered by Bnip3-FL by blocking calcium transfer from the sarco/endoplasmic reticulum to the mitochondria. Furthermore, misoprostol and Bnip3{Delta}Exon3 promote nuclear calcium accumulation, resulting in HDAC5 nuclear export, NFAT activation, and adaptive changes in cell morphology and gene expression. Collectively, our data suggests that misoprostol can mitigate the potential damaging effects of hypoxia on multiple cell types by activating adaptive cell survival pathways through Bnip3 repression and alternative splicing.

cell biology↗