Biology subjects

Holmes, N.

Publications and source records attributed to Holmes, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Neural Fingerprinting based on Brain Network Dynamics: A Cross-Platform MEG Study

Neural fingerprinting seeks to identify individuals based on measurements of brain activity, exploiting the fact that aspects of brain function unique to an individual remain stable across repeated scans. Magnetoencephalography (MEG) is a powerful technique for fingerprinting. However, most MEG studies have used conventional (SQUID-based) MEG technology and typically rely on data aggregated over time, overlooking the rich temporal dynamics available in MEG. Here, using SQUID-MEG and the more recently introduced OPM-MEG, we showed fingerprinting was possible within and between modalities using static (time-aggregated) features; this is consistent with previous work. We further asked whether fingerprinting was possible based on network dynamics, estimated using a canonical hidden Markov model (CHMM). Results showed that the CHMM-derived networks provide a better fit to SQUID data than to OPM data; however, this effect was small and to be expected given the canonical networks were trained on SQUID data. We further showed that fingerprinting was possible within and between modalities using CHMM-derived state activation time courses and state power spectral densities. However, state summary statistics and transition probabilities only supported within modality fingerprinting. Our findings suggest that subject-specific information is preserved within CHMM states and across MEG technologies. This represents an important step towards advancing our understanding of brain dynamics, and particularly the brain networks delineated by the CHMM. The study also supports the future use of the CHMM for processing and interpretation of OPM-MEG data.

neuroscience↗

bioRxiv2026

Number, order and time influence how the brain integrates distinct experiences

How does the brain integrate experiences that are separated in time? The present study addressed this question using sensory preconditioning protocols in rats. In these protocols, rats integrate an A-B association (e.g., tone-light) formed in stage 1 with a B-shock association (e.g., light-shock) formed in stage 2 to generate fear responses (freezing) when tested with A alone in stage 3. Here we show that the mechanism of integration depends on the number, order and timing of events across the two stages of training. When the events are novel (low number of exposures) and the interval between stages 1 and 2 is short (24 hours), the A-B and B-shock associations are integrated through formation of a mediated A-shock association during stage 2. By contrast, when the events are more familiar (greater number of exposures), ordered in a particular way, and the interval between stages 1 and 2 is long (14-days), the A-B and B-shock associations are integrated through their chaining at the time of testing with A alone. Thus, number, order and time determine how distinct experiences are integrated in the brain. These findings are discussed with respect to theories of integration and information processing in the medial temporal lobe.

neuroscience↗

bioRxiv2026

Beta-band dynamics during a naturalistic motor task: an OPM-MEG study

Beta oscillations are a fundamental feature of brain activity, linked to long-range connectivity within canonical networks, inhibition of sensorimotor cortices and the maintenance of a stable sensorimotor state in situations where the external world is predictable. The importance of beta oscillations in brain function is underscored by observations of their perturbation in neurological and psychiatric disorders. However, the precise role played by beta activity, particularly in mediating complex or skilful movements, remains incompletely understood. Here, we used a newly developed wearable optically pumped magnetometer-based magnetoencephalography (OPM-MEG) system to measure beta dynamics as participants learned to play a musical instrument. Twenty-two novice players took part in a study in which OPM-MEG data were recorded during two scanning sessions, while participants attempted to play a tune on a violin. Between the two sessions, participants received a violin lesson from an expert teacher. Results showed that robust data could be acquired during this naturalistic task, with beta oscillations decreasing in amplitude during movement and increasing upon movement cessation, as expected. Moreover, beta power whilst playing, in the motor and pre-motor areas, was significantly elevated after the lesson compared to before, and the movement-related modulation of beta amplitude was more pronounced after the lesson. These findings align with predictive coding models which suggest that beta amplitude should increase when individuals have greater certainty over the movements they carry out. Our study adds to an expanding literature on the role of beta oscillations and provides further evidence for the utility of OPM-MEG in naturalistic neuroscience.

neuroscience↗

bioRxiv2025

Paternal over- and under-nutrition program fetal and placental development in a sex-specific manner in mice

The association between sub-optimal paternal diet and offspring well-being is becoming established. However, the underlying mechanisms are yet to be fully defined. The aim of this study was to establish the impact of over- and under-nutrition, with or without macronutrient supplementation, on male reproductive fitness and post-fertilisation development. Male C57/BL6J mice were fed either control diet (CD), isocaloric low protein diet (LPD), high fat/sugar Western diet (WD) or LPD or WD supplemented with methyl-donors and carriers (MD-LPD or MD-WD respectively) for 8 weeks before mating with virgin C57/BL6J females. Placental tissue was collected at embryonic day (E)8.5, to assess early placental (ectoplacental cone) morphology and metabolism and E17.5 for sex-specific transcriptomic profiling. Post-mating, stud male tissues were harvested for assessment of testicular morphology and gene expression, gut microbiota composition and metabolic status. WD and MD-WD males displayed increased adiposity, hepatic cholesterol and free fatty acids and gut microbiota dysbiosis when compared to CD fed males. In the testes, WD and MD-WD perturbed the expression of genes associated with metabolism and transcription regulation. Additionally, we observed differential expression of multiple genes within the Wnt signalling pathway, central in the regulation of cellular proliferation, migration, survival, and cell fate determination during development. Despite no impact on fundamental male fertility, significant changes in ectoplacental cone metabolism, fetal growth, and placental gene expression were observed in response to specific dietary regimens. Interestingly, while CD male and female placentas displayed 301 genome-wide, sexually-dimorphic genes, LPD, MD-LPD, WD and MD-WD male and female placentas possessed only 13, 0, 14 and 15 sexually-dimorphic genes respectively. Our data show that while sub-optimal paternal diet has minimal impact on male fertility, fetal and placental development are perturbed in a sex-specific manner.

developmental biology↗

bioRxiv2024

Measuring the neurodevelopmental trajectory of excitatory-inhibitory balance via visual gamma oscillations

Disruption of the balance between excitatory and inhibitory neurotransmission (E-I balance) underlies theories of many neurodevelopmental disorders, however, its study is typically restricted to adults, animal models and the lab-bench. Neurophysiological oscillations in the gamma frequency band relate closely to E-I balance, and a new technology - OPM-MEG - offers the possibility to measure such signals across the lifespan. We used OPM-MEG to measure gamma oscillations induced by visual stimulation in >100 participants, aged 2-34 years. We demonstrate a significantly changing spectrum with age, with low amplitude broadband gamma oscillations in children and high amplitude band limited oscillations dominating in adults. We used a canonical cortical microcircuit to model these gamma signals, revealing significant age-related shifts in E-I balance in superficial pyramidal neurons in visual cortex. Our findings detail the first MEG metrics of gamma oscillations and their underlying generators from toddlerhood, providing a benchmark against which future studies can contextualise.

neuroscience↗

bioRxiv2024

FindingNemo: A Toolkit for DNA Extraction, Library Preparation and Purification for Ultra Long Nanopore Sequencing

Since the advent of long read sequencing, achieving longer read lengths has been a key goal for many users. Ultra-long read sets (N50 [≥] 100 kb) produced from Oxford Nanopore sequencers have improved genome assemblies in recent years. However, despite progress in extraction protocols and library preparation methods, ultra-long sequencing remains challenging for many sample types. Here we compare various methods and introduce the FindingNemo protocol that: (1) optimises ultra-high molecular weight (UHMW) DNA extraction and library clean-up by using glass beads and Hexamminecobalt(III) chloride (CoHex), (2) can deliver high ultra-long sequencing yield of >20 Gb of reads from a single MinION flow cell or >100 Gb from PromethION devices (R9.4 to R10.4 pore variants), and (3) is scalable to using fewer input cells or lower DNA amounts, with extraction to sequencing possible in a single working day. By comparison, we show this protocol is superior to previous ones due to precise determination of input DNA quantity and quality by cell count, sample dilution and homogenization approaches.

genomics↗

bioRxiv2024

Noise Reduction and Localization Accuracy in a Mobile Magnetoencephalography System

Magnetoencephalography (MEG) non-invasively provides important information about human brain electrophysiology. The growing use of optically pumped magnetometers (OPM) for MEG, as opposed to fixed arrays of cryogenic sensors, has opened the door for innovation in system design and use cases. For example, cryogenic MEG systems are housed in large shielded rooms to provide sufficient space for the system dewar. Here, we investigate the performance of OPM recordings inside of a cylindrical shield with a 1x2 m2 footprint. The efficacy of shielding was measured in terms of field attenuation and isotropy, and the value of post hoc noise reduction algorithms was also investigated. Localization accuracy was quantified for 104 OPM sensors mounted on a fixed helmet array based on simulations and recordings from a bespoke current dipole phantom. Passive shielding attenuated direct current (DC) and power line (60 Hz) fields by approximately 60 dB, and all other frequencies by 80-90 dB. Post hoc noise reduction provided an additional 5-15 dB attenuation. Substantial field anisotropy remained in the volume encompassing the sensor array. The consistency of the anisotropy over months suggests that a field nulling solution could be readily applied. A current dipole phantom generating source activity at an appropriate magnitude for the human brain generated field fluctuations on the order of 0.5-1 pT. Phantom signals were localized with 3 mm localization accuracy and no significant bias in localization was observed, which is in line with performance for cryogenic and OPM MEG systems. This validation of the performance of a small footprint MEG system opens the door for lower cost MEG installations in terms of raw materials and facility space, as well as mobile imaging systems (e.g., truck-based). Such implementations are relevant for global adoption of MEG outside of highly resourced research and clinical institutions.

biophysics↗

bioRxiv2024

A Novel, Robust, and Portable Platform for Magnetoencephalography using Optically Pumped Magnetometers

Magnetoencephalography (MEG) measures brain function via assessment of magnetic fields generated by neural currents. Conventional MEG uses superconducting sensors, which place significant limitations on performance, practicality, and deployment; however, the field has been revolutionised in recent years by the introduction of optically-pumped-magnetometers (OPMs). OPMs enable measurement of the MEG signal without cryogenics, and consequently the conception of OPM-MEG systems which ostensibly allow increased sensitivity and resolution, lifespan compliance, free subject movement, and lower cost. However, OPM-MEG remains in its infancy with limitations on both sensor and system design. Here, we report a new OPM-MEG design with miniaturised and integrated electronic control, a high level of portability, and improved sensor dynamic range (arguably the biggest limitation of existing instrumentation). We show that this system produces equivalent measures when compared to an established instrument; specifically, when measuring task-induced beta-band, gamma-band and evoked neuro-electrical responses, source localisations from the two systems were highly comparable and temporal correlation was >0.7 at the individual level and >0.9 for groups. Using an electromagnetic phantom, we demonstrate improved dynamic range by running the system in background fields up to 8 nT. We show that the system is effective in gathering data during free movement (including a sitting-to-standing paradigm) and that it is compatible with simultaneous electroencephalography (EEG - the clinical standard). Finally, we demonstrate portability by moving the system between two laboratories. Overall, our new system is shown to be a significant step forward for OPM-MEG technology and offers an attractive platform for next generation functional medical imaging.

neuroscience↗

bioRxiv2024

The neurodevelopmental trajectory of beta band oscillations: an OPM-MEG study

Neural oscillations mediate the coordination of activity within and between brain networks, supporting cognition and behaviour. How these processes develop throughout childhood is not only an important neuroscientific question but could also shed light on the mechanisms underlying neurological and psychiatric disorders. However, measuring the neurodevelopmental trajectory of oscillations has been hampered by confounds from instrumentation. In this paper, we investigate the suitability of a disruptive new imaging platform - Optically Pumped Magnetometer-based magnetoencephalography (OPM-MEG) - to study oscillations during brain development. We show how a unique 192-channel OPM-MEG device, which is adaptable to head size and robust to participant movement, can be used to collect high-fidelity electrophysiological data in individuals aged between 2 and 34 years. Data were collected during a somatosensory task, and we measured both stimulus-induced modulation of beta oscillations in sensory cortex, and whole-brain connectivity, showing that both modulate significantly with age. Moreover, we show that pan-spectral bursts of electrophysiological activity drive task-induced beta modulation, and that their probability of occurrence and spectral content change with age. Our results offer new insights into the developmental trajectory of beta oscillations and provide clear evidence that OPM-MEG is an ideal platform for studying electrophysiology in neurodevelopment.

neuroscience↗

bioRxiv2023

A rapid method for generating transplantable and biologically responsive colonic tissue from human induced pluripotent stem cells.

BackgroundThe colonic mucosa consists of cell populations derived from multiple lineages. Induced pluripotent stem cells (iPSCs) are capable of generating large numbers of differentiated cells from any lineage. Thus, iPSCs are highly versatile for derivation of intestinal cells for generation of colonic mucosal tissue for clinical and biological applications. ObjectiveWe set out to create a human iPSC (hiPSC) multi-lineage co-differentiation platform capable of generating colonic mucosal tissue in vitro. DesignWe used hiPSCs and designed a differentiation protocol consisting of small molecules and recombinant growth factors to generate multiple cell lineages. Cells were seeded onto collagen hydrogels (forming colonic patches - CoPs) and modulated with multiple growth factors important in intestinal biology. CoPs were transplanted into immunosuppressed mice. Generated cells and tissues were profiled with transcriptomic analysis. ResultshiPSC co-differentiation led to multiple intestinal epithelial, mesenchymal and endothelial cell populations. Seeded onto collagen scaffolds these cells created CoPs, which were transplanted into mouse subcutis. Engrafted CoPs developed into normal-looking colonic mucosa containing epithelial crypts (with enterocytes, goblet cells and neuroendocrine cells), multiple lamina propria-resident stromal populations and muscularis mucosae smooth muscle. They anastomosed to murine vasculature and maintained in-vitro for several weeks. We demonstrated that CoPs respond to known signalling pathways important in colonic mucosal biology and fibrogenesis, showing potential to provide a complex model of colonic pathobiology. ConclusionThis platform could offer an accurate model of intestinal pathobiology, supply cells for regenerative cell therapies to treat intestinal disease, and provide therapeutic autologous grafts to repair damaged colon.

cell biology↗

bioRxiv2023

A single-cell atlas of pig gastrulation as a resource for comparative embryology

Early mammalian gastrulations cell-fate decisions are poorly understood due to difficulties obtaining non-rodent embryos. The bilaminar disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-type development, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm (DE). We find early FOXA2+/TBXT-embryonic disc cells directly from DE, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. DE/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon DE differentiation. These findings emphasise the interplay between temporal and topological signalling in early fate decisions during gastrulation.

developmental biology↗

bioRxiv2022

Test-Retest Reliability of the Human Connectome: An OPM-MEG study

Magnetoencephalography with optically pumped magnetometers (OPM-MEG) offers a new way to record electrophysiological brain function, with significant advantages over conventional MEG including adaptability to head shape/size, free movement during scanning, better spatial resolution, increased signal, and no reliance on cryogenics. However, OPM-MEG remains in its infancy, with significant questions to be answered regarding optimal system design and robustness. Here, we present an open-source dataset acquired using a newly constructed OPM-MEG system with a triaxial sensor design averaging 168 channels. Using OPM-optimised magnetic shielding and active background-field control, we measure the test-retest reliability of the human connectome. We employ amplitude envelope correlation to measure whole-brain functional connectivity in 10 individuals whilst they watch a 600 s move clip. Our results show high repeatability between experimental runs at the group level, with a correlation coefficient of 0.81 in the theta, 0.93 in alpha and 0.94 in beta frequency ranges. At the individual subject level, we found marked differences between individuals, but high within-subject robustness (correlations of 0.56 {+/-} 0.25, 0.72 {+/-} 0.15 and 0.78 {+/-} 0.13 in theta, alpha and beta respectively). These results compare well to previously reported findings using conventional MEG; they show that OPM-MEG is a viable way to characterise whole brain connectivity and add significant weight to a growing argument that OPMs can overtake cryogenic sensors as the fundamental building block of MEG systems.

neuroscience↗

bioRxiv2022

The Nanog epigenetic remodeling complex was essential to vertebrate mesoderm evolution

Pluripotency defines the unlimited potential of cells in the primitive ectoderm of vertebrate embryos, from which all adult somatic cells and germ cells are derived. Understanding how the programing of pluripotency evolved has been obscured by the study of early development in models from lower vertebrates in which pluripotency is not conserved. Here we investigated how the axolotl ortholog of the mammalian core pluripotency factor NANOG, programs pluripotency during axolotl development to model the tetrapod ancestor from which terrestrial vertebrates evolved. We show that in axolotl primitive ectoderm (animal caps; AC) NANOG synergizes with NODAL activity and the epigenetic modifying enzyme DPY30 to direct the deposition of H3K4me3 in chromatin prior to the waves of transcription required for lineage commitment and developmental progression. We show that the interaction of NANOG and NODAL with DPY30 is required to direct development downstream of pluripotency and this is conserved in axolotls and human. These data demonstrate that the interaction of NANOG and NODAL signaling represents the basal state of vertebrate pluripotency.

developmental biology↗

bioRxiv2021

Barcode aware adaptive sampling for Oxford Nanopore sequencers.

Adaptive sampling enables selection of individual DNA molecules from sequencing libraries, a unique property of nanopore sequencing. Here we develop our adaptive sampling tool readfish to become "barcode-aware" enabling selection of different targets within barcoded samples or filtering out individual barcodes. We show that multiple human genomes can be assessed for copy number and structural variation on a single sequencing flow cell using sample specific customised target panels on both GridION and PromethION devices.

genomics↗

bioRxiv2021

Using OPM-MEG in contrasting magnetic environments

Magnetoencephalography (MEG) has been revolutionised in recent years by optically pumped magnetometers (OPMs). "OPM-MEG" offers higher sensitivity, better spatial resolution and lower cost than conventional instrumentation based on superconducting quantum interference devices (SQUIDS). Moreover, OPMs offer the possibility of motion robustness and lifespan compliance, dramatically expanding the range of MEG applications. However, OPM-MEG remains nascent technology; it places stringent requirements on magnetic shielding, and whilst a number of viable systems exist, most are custom made and there have been no cross-site investigations showing the reliability of data. In this paper, we undertake the first cross-site OPM-MEG comparison, using near identical commercial systems scanning the same participant. The two sites are deliberately contrasting, with different magnetic environments: a "green field" campus university site with an OPM-optimised shielded room (low interference) and a city centre hospital site with a "standard" (non-optimised) MSR (high interference). We show that despite a 25-fold difference in background field, and a 30-fold difference in low frequency interference, using dynamic field control and software-based suppression of interference we can generate comparable noise floors at both sites. In human data recorded during a visuo-motor task and a face processing paradigm, we were able to generate similar data, with source localisation showing that brain regions could be pinpointed with just ~10 mm spatial discrepancy and temporal correlations of > 80%. Overall, our study demonstrates that "plug- and-play" OPM-MEG systems exist and can be sited even in challenging magnetic environments.

neuroscience↗

bioRxiv2021

Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour.

MotivationThe ongoing SARS-CoV-2 pandemic has demonstrated the utility of real-time analysis of sequencing data, with a wide range of databases and resources for analysis now available. Here we show how the real-time nature of Oxford Nanopore Technologies sequencers can accelerate consensus generation, lineage and variant status assignment. We exploit the fact that multiplexed viral sequencing libraries quickly generate sufficient data for the majority of samples, with diminishing returns on remaining samples as the sequencing run progresses. We demonstrate methods to determine when a sequencing run has passed this point in order to reduce the time required and cost of sequencing. ResultsWe extended MinoTour, our real-time analysis and monitoring platform for nanopore sequencers, to provide SARS-CoV2 analysis using ARTIC network pipelines. We additionally developed an algorithm to predict which samples will achieve sufficient coverage, automatically running the ARTIC medaka informatics pipeline once specific coverage thresholds have been reached on these samples. After testing on run data, we find significant run time savings are possible, enabling flow cells to be used more efficiently and enabling higher throughput data analysis. The resultant consensus genomes are assigned both PANGO lineage and variant status as defined by Public Health England. Samples from within individual runs are used to generate phylogenetic trees incorporating optional background samples as well as summaries of individual SNPs. As minoTour uses ARTIC pipelines, new primer schemes and pathogens can be added to allow minoTour to aid in real-time analysis of pathogens in the future. Availability and ImplementationSource code and documentation is available at https://github.com/LooseLab/minotourapp. Supplementary informationSupplementary data are available from https://github.com/LooseLab/artic_minotour_analyses.

bioinformatics↗

bioRxiv2021

MinoTour, real-time monitoring and analysis for Nanopore Sequencers.

SummaryMinoTour offers a LIMS system for Oxford Nanopore Technology (ONT) sequencers, with real-time metrics and analysis available permanently for review. Integration of unique real-time automated analysis can reduce the time required to answer biological questions, including mapping and classification of sequence whilst a run is in progress. Real-time sequence data requires new methods of analysis which do not wait for the completion of a run and MinoTour provides a framework to allow users to exploit these features. Availability and ImplementationSource code and documentation are available at https://github.com/LooseLab/minotourcli and https://github.com/LooseLab/minotourapp. Docker images are available from https://hub.docker.com/r/adoni5/, and can be installed using a preconfigured docker-compose script at https://github.com/LooseLab/minotour-docker. An example server is available at http://137.44.59.170.

bioinformatics↗

bioRxiv2021

Naturalistic hyperscanning with wearable magnetoencephalography

The evolution of human cognitive function is reliant on complex social interactions which form the behavioural foundation of who we are. These social capacities are subject to dramatic change in disease and injury; yet their supporting neural substrates remain poorly understood. Hyperscanning employs functional neuroimaging to simultaneously assess brain activity in two individuals and offers the best means to understand the neural basis of social interaction. However, present technologies are limited, either by poor performance (low spatial/temporal precision) or unnatural scanning environment (claustrophobic scanners, with interactions via video). Here, we solve this problem by developing a new form of hyperscanning using wearable magnetoencephalography (MEG). This approach exploits quantum sensors for MEG signal detection, in combination with high-fidelity magnetic field control - afforded by a novel "matrix coil" system - to enable simultaneous scanning of two freely moving participants. We demonstrate our approach in a somatosensory task and an interactive ball game. Despite large and unpredictable subject motion, sensorimotor brain activity was delineated clearly in space and time, and correlation of the envelope of neuronal oscillations between people was demonstrated. In sum, unlike existing modalities, wearable-MEG combines high fidelity data acquisition and a naturalistic setting, which will facilitate a new generation of hyperscanning.

neuroscience↗