Biology subjects

Holmes, N.

Publications and source records attributed to Holmes, N..

34 records · Page 2Linked to original sources

bioRxiv2021

The Epiallelic Nature of Mouse rDNA

BackgroundRibosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed. ResultsUsing a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during ageing only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are <5%. ConclusionsOur work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases.

genomics↗

bioRxiv2021

Magnetic Field Mapping and Correction for Moving OP-MEG

BackgroundOptically pumped magnetometers (OPMs) have made moving, wearable magnetoencephalography (MEG) possible. The OPMs typically used for MEG require a low background magnetic field to operate, which is achieved using both passive and active magnetic shielding. However, the background magnetic field is never truly zero Tesla, and so the field at each of the OPMs changes as the participant moves. This leads to position and orientation dependent changes in the measurements, which manifest as low frequency artefacts in MEG data. ObjectiveWe modelled the spatial variation in the magnetic field and used the model to predict the movement artefact found in a dataset. MethodsWe demonstrate a method for modelling this field with a triaxial magnetometer, then showed that we can use the same technique to predict the movement artefact in a real OPM-based MEG (OP-MEG) dataset. ResultsUsing an 86-channel OP-MEG system, we found that this modelling method maximally reduced the power spectral density of the data by 26.2 {+/-} 0.6 dB at 0 Hz, when applied over 5 s non-overlapping windows. ConclusionThe magnetic field inside our state-of-the art magnetically shielded room can be well described by low-order spherical harmonic functions. We achieved a large reduction in movement noise when we applied this model to OP-MEG data. SignificanceReal-time implementation of this method could reduce passive shielding requirements for OP-MEG recording and allow the measurement of low-frequency brain activity during natural participant movement.

neuroscience↗

bioRxiv2020

Modelling optically pumped magnetometerinterference as a mean (magnetic) field

Here we propose that much of the magnetic interference observed when using optically pumped magnetometers can be modeled spatially as a mean (magnetic) field. We show that this approximation reduces sensor level variability and substantially improves statistical power. This model does not require knowledge of the underlying neuroanatomy nor the sensor positions. It only needs information about the sensor orientation. Due to the models low rank there is little risk of removing substantial neural signal. However, we provide a framework to assess this risk for any sensor number, design or subject neuroanatomy. We find that the risk of unintentionally removing neural signal is reduced when multi-axis recordings are performed. We validated the method using a binaural auditory evoked response paradigm and demonstrated that the mean field correction increases reconstructed SNR in relevant brain regions in both the spatial and temporal domain. Considering the models simplicity and efficacy, we suggest that this mean field correction can be a powerful preprocessing step for arrays of optically pumped magnetometers.

neuroscience↗

bioRxiv2020

Measuring functional connectivity with wearable MEG

Optically-pumped magnetometers (OPMs) offer the potential for a step change in magnetoencephalography (MEG) enabling wearable systems that: provide improved data quality; accommodate any subject group; allow data capture during movement and offer a reduction in costs. However, OPM-MEG is still a nascent technology and, to realise its potential, it must be shown to facilitate key neuroscientific measurements, such as the characterisation of human brain networks. Networks, and the connectivities that underlie them, have become a core area of neuroscientific investigation, and their importance is underscored by many demonstrations of their perturbation in brain disorders. Consequently, a demonstration of network measurements via OPM-MEG would be a significant step forward. Here, we aimed to show that a wearable 50-channel OPM-MEG system enables characterisation of the electrophysiological connectome. To this end, we characterise connectivity in the resting state and during a simple visuo-motor task, using both OPM-MEG and a state-of-the-art 275-channel cryogenic MEG device. Our results show that connectome matrices from OPM and cryogenic systems exhibit an extremely high degree of similarity, with correlation values >70 %. This value is not measurably different to the correlation observed between connectomes measured in different subject groups, on a single scanner. In addition, similar differences in connectivity between individuals (scanned multiple times) were observed in cryogenic and OPM-MEG data, again demonstrating the fidelity of OPM-MEG data. This demonstration shows that a nascent OPM-MEG system offers results similar to a cryogenic device, even despite having [~]5 times fewer sensors. This adds weight to the argument that OPMs will ultimately supersede cryogenic sensors for MEG measurement.

neuroscience↗

bioRxiv2020

Mouth magnetoencephalography: A unique perspective on the human hippocampus

Traditional magnetoencephalographic (MEG) brain imaging scanners consist of a rigid sensor array surrounding the head; this means that they are maximally sensitive to superficial brain structures. New technology based on optical pumping means that we can now consider more flexible and creative sensor placement. Here we explored the magnetic fields generated by a model of the human hippocampus not only across scalp but also at the roof of the mouth. We found that simulated hippocampal sources gave rise to dipolar field patterns with one scalp surface field extremum at the temporal lobe and a corresponding maximum or minimum at the roof of the mouth. We then constructed a fitted dental mould to accommodate an Optically Pumped Magnetometer (OPM). We collected data using a previously validated hippocampal-dependent task to test the empirical utility of a mouth-based sensor, with an accompanying array of left and right temporal lobe OPMs. We found that the mouth sensor showed the greatest task-related theta power change. We also found that, as predicted by the simulations, the mouth sensor was anti-correlated with those on over the temporal lobes. We found that this sensor had a mild effect on the reconstructed power in the hippocampus (~10% change) but that coherence images between the mouth sensor and reconstructed source images showed a global maximum in the right hippocampus. We conclude that augmenting a scalp-based MEG array with sensors in the mouth shows unique promise for both basic scientists and clinicians interested in interrogating the hippocampus.

neuroscience↗

bioRxiv2020

Multi-Channel Whole-Head OPM-MEG: Helmet Design and a Comparison with a Conventional System

Magnetoencephalography (MEG) is a powerful technique for functional neuroimaging, offering a non-invasive window on brain electrophysiology. MEG systems have traditionally been based on cryogenic sensors which detect the small extracranial magnetic fields generated by synchronised current in neuronal assemblies, however such systems have fundamental limitations. In recent years quantum-enabled devices, called optically-pumped magnetometers (OPMs), have promised to lift those restrictions, offering an adaptable, motion-robust MEG device, with improved data quality, at reduced cost. However, OPM-MEG remains a nascent technology, and whilst viable systems exist, most employ small numbers of sensors sited above targeted brain regions. Here, building on previous work, we construct a wearable OPM-MEG system with whole-head coverage based upon commercially available OPMs, and test its capabilities to measure alpha, beta and gamma oscillations. We design two methods for OPM mounting; a flexible (EEG-like) cap and rigid (additively-manufactured) helmet. Whilst both designs allow for high quality data to be collected, we argue that the rigid helmet offers a more robust option with significant advantages for reconstruction of field data into 3D images of changes in neuronal current. Using repeat measurements in two participants, we show signal detection for our device to be highly robust. Moreover, via application of source-space modelling, we show that, despite having 5 times fewer sensors, our system exhibits comparable performance to an established cryogenic MEG device. While significant challenges still remain, these developments provide further evidence that OPM-MEG is likely to facilitate a step change for functional neuroimaging. HIGHLIGHTSO_LIA 49-channel whole-head OPM-MEG system is constructed C_LIO_LISystem evaluated via repeat measurements of alpha, beta and gamma oscillations C_LIO_LITwo OPM-helmet designs are contrasted, a flexible (EEG-like) cap and a rigid helmet C_LIO_LIThe rigid helmet offers significant advantages for a viable OPM-MEG device C_LIO_LI49-channel OPM-MEG offers performance comparable to established cryogenic devices C_LI

neuroscience↗

bioRxiv2020

Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels.

Nanopore sequencers enable selective sequencing of single molecules in real time by individually reversing the voltage across specific nanopores. Thus DNA molecules can be rejected and replaced with new molecules enabling targeted sequencing to enrich, deplete or achieve specific coverage in a set of reads to address a biological question. We previously demonstrated this method worked using dynamic time warping mapping signal to reference, but required significant compute and did not scale to gigabase references. Using direct base calling with GPU we can now scale to gigabase references. We enrich for specific chromosomes mapping against the human genome and we develop pipelines enriching low abundance organisms from mixed populations without prior knowledge of sample composition. Finally, we enrich panels including 25,600 exon targets from 10,000 human genes and 717 genes implicated in cancer. Using this approach we identify PML-RARA fusions in the NB4 cell line in under 15 hours sequencing. These methods can be used to efficiently screen any target panel of genes without specialised sample preparation using a single computer and suitably powerful GPU.

genomics↗

bioRxiv2019

Pragmatic spatial sampling for wearable MEG arrays

Several new technologies have recently emerged promising new MEG systems in which the sensors can be placed close to the scalp. One such technology, Optically Pumped Magnetometry MEG (OP-MEG) allows for a scalp mounted flexible system that provides field measurements within mm of the scalp surface. A question that arises in developing on-scalp systems, such as OP-MEG scanners, is: how many sensors are necessary to achieve adequate performance/spatial discrimination? There are many factors to consider in answering this question such as the signal to noise ratio (SNR), the locations and depths of the sources of interest, the density of spatial sampling, sensor gain errors (due to interference, subject movement, cross-talk, etc.) and, of course, the desired spatial discrimination. In this paper, we provide simulations which show the impact these factors have on designing sensor arrays for wearable MEG. While OP-MEG has the potential to provide high information content at dense spatial samplings, we find that adequate spatial discrimination of sources (<1cm) can be achieved with relatively few sensors (<100) at coarse spatial samplings (~30mm) at high SNR. Comparable discrimination for traditional cryogenic systems require far more channels by these same metrics. Finally we show that sensor gain errors have the greatest impact on discrimination between deep sources at high SNR.

neuroscience↗

bioRxiv2019

GLP-1R is downregulated in beta cells of NOD mice and T1D patients

Glucagon-like peptide 1 (GLP-1) is produced by L cells in the small intestine in response to ingested glucose and increases insulin release from pancreatic beta cells by activation of its cognate receptor (GLP-1R). Stimulation of this receptor also contributes to increased beta cell survival and regeneration. We have found that pancreatic beta cells from Non Obese Diabetic (NOD) mice express significantly lower levels of GLP-1R than C57BL/6 mice, leaving the NOD beta cells with an impaired response to GLP-1 stimulation. The lower expression appears to be caused by accelerated degradation of GLP-1R in the beta cells, a process that can be reversed by inhibiting trafficking to the lysosome. Importantly, our results appear to translate to the human disease since we also observed significantly lower expression of the GLP-1R in pancreatic islets from donors with type 1 diabetes. These results suggest that beta cell physiology may play a role in susceptibility to autoimmune inflammation.

physiology↗

bioRxiv2019

Telomere-to-telomere assembly of a complete human X chromosome

After nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist 1,2. The remaining gaps include ribosomal rDNA arrays, large near-identical segmental duplications, and satellite DNA arrays. These regions harbor largely unexplored variation of unknown consequence, and their absence from the current reference genome can lead to experimental artifacts and hide true variants when re-sequencing additional human genomes. Here we present a de novo human genome assembly that surpasses the continuity of GRCh38 2, along with the first gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome 3, we reconstructed the [~]2.8 megabase centromeric satellite DNA array and closed all 29 remaining gaps in the current reference, including new sequence from the human pseudoautosomal regions and cancer-testis ampliconic gene families (CT-X and GAGE). This complete chromosome X, combined with the ultra-long nanopore data, also allowed us to map methylation patterns across complex tandem repeats and satellite arrays for the first time. These results demonstrate that finishing the human genome is now within reach and will enable ongoing efforts to complete the remaining human chromosomes.

bioinformatics↗

bioRxiv2019

VariCarta: a comprehensive database of harmonized genomic variants found in ASD sequencing studies

BackgroundRecent years has seen a boom in the application of the next-generation sequencing technology to the study of human diseases, including Autism Spectrum Disorder (ASD), where the focus has been on identifying rare, possibly causative genomic variants in ASD individuals. Because of the high genetic heterogeneity of ASD, a large number of subjects is needed to establish evidence for a variant or gene ASD-association, thus aggregating data across cohorts and studies is necessary. However, methodological inconsistencies and subject overlap across studies complicate data aggregation.\n\nDescriptionHere we present VariCarta, a web-based database developed to address these challenges by collecting, reconciling and consistently cataloguing literature-derived genomic variants found in ASD subjects using ongoing semi-manual curation. The careful manual curation combined with a robust data import pipeline rectifies errors, converts variants into a standardized format, identifies and harmonizes cohort overlaps and documents data provenance. The harmonization aspect is especially important since it prevents the potential double-counting of variants which can lead to inflation of gene-based evidence for ASD-association.\n\nConclusionVariCarta is the largest collection of systematically curated, harmonized and comprehensively annotated literature-derived ASD-associated variants. The database currently contains 35,615 variant events from 8,044 subjects, collected across 50 publications, and reconciles 6,057 variants that have been reported in literature multiple times. VariCarta is freely accessible at http://varicarta.msl.ubc.ca.

genomics↗

bioRxiv2018

Nanopore native RNA sequencing of a human poly(A) transcriptome

High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not carried forward in cDNA. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads. These native RNA reads had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. We describe strategies for assessing 3' poly(A) tail length, base modifications and transcript haplotypes from nanopore RNA data. Together, these nanopore-based techniques are poised to deliver new insights into RNA biology.\n\nDISCLOSURESMA holds shares in Oxford Nanopore Technologies (ONT). MA is a paid consultant to ONT. REW, WT, TG, JRT, JQ, NJL, JTS, NS, AB, MA, HEO, MJ, and ML received reimbursement for travel, accommodation and conference fees to speak at events organised by ONT. NL has received an honorarium to speak at an ONT company meeting. WT has two patents (8,748,091 and 8,394,584) licensed to Oxford Nanopore. JTS, ML and MA received research funding from ONT.

genomics↗

bioRxiv2018

Using optically-pumped magnetometers to measure magnetoencephalographic signals in the human cerebellum

We test the feasibility of an optically pumped magnetometer (OPM)-MEG system for the measurement of human cerebellar activity. We show that the OPM system allows for excellent coverage of this structure by decreasing the average sensor-to-cerebellum distance by around 33% (16mm), compared to a standard MEG helmet. This closer proximity to the cerebellum approximately doubles the signal-to-noise ratio (SNR). As a proof of principle, we used an air-puff stimulus to the eyeball in order to elicit cerebellar evoked and induced responses that are well characterized in non-human models. In three subjects, we observed an evoked component at 50ms post stimulus, which originates in the cerebellum (predominantly ipsilateral). This response was followed by a second component at 100ms post stimulus (predominantly contra-lateral). Sensory stimulation also elicited an event-related broadband spectral power change in the ipsilateral cerebellum at ~100ms in all subjects. We conclude that the OPM-MEG technology offers a promising way to advance the understanding of the information processing mechanisms in the human cerebellum.

neuroscience↗

bioRxiv2018

Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome

Many animals and plants recruit beneficial microbes from the environment, enhancing their defence against pathogens. However, we have only a limited understanding of the assembly mechanisms involved. A game-theoretical concept from economics, screening, potentially explains how a host selectively recruits mutualistic microbes from the environment by fomenting and biasing competition among potential symbionts in such a way that the more likely winners are antibiotic producers. The cuticular microbiomes of Acromyrmex leaf-cutting ants inspired one of the first applications of screening theory, and here we simulate this system in vitro to test screening. On agar infused with antibacterial metabolites from Acromyrmexs vertically transmitted Pseudonocardia bacteria, we show that antibiotic-producing Streptomyces bacteria exhibit higher growth rates than do non-antibiotic-producer strains and are more likely to win in direct competition. Our results demonstrate how game-theoretical concepts can provide powerful insight into host-microbiome coevolution.

evolutionary biology↗

bioRxiv2018

Whale watching with BulkVis: A graphical viewer for Oxford Nanopore bulk fast5 files.

MotivationThe Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output fast5 files containing signal data subsequently base called to fastq format. Optionally, ONT devices can collect data from all sequencing channels simultaneously in a bulk fast5 file enabling inspection of signal in any channel at any point. We sought to visualise this signal to inspect challenging or difficult to sequence samples, or where flow cell performance is modified by an external agent, such as Read Until.\n\nResultsThe BulkVis tool can load a bulk fast5 file and overlays MinKNOW classifications on the signal trace. Users can navigate to a channel and time or, given a fastq header from a read, jump to its specific position. BulkVis can export regions as Nanopore base caller compatible reads. Using BulkVis, we find long reads can be incorrectly divided by MinKNOW resulting in single DNA molecules being split into two or more reads. The longest seen to date is 2,272,580 bases in length and reported in eleven consecutive reads. We provide helper scripts that identify and reconstruct split reads given a sequencing summary file and alignment to a reference. We note that incorrect read splitting appears to vary according to input sample type and is more common in ultra long read preparations.\n\nAvailabilityThe software is available freely under an MIT license at https://github.com/LooseLab/bulkVis. The software requires python3 to run.

genomics↗

bioRxiv2017

TMS SMART - Scalp Mapping of Annoyance Ratings and Twitches caused by Transcranial Magnetic Stimulation

The magnetic pulse generated during Transcranial magnetic stimulation [TMS] also stimulates cutaneous nerves and muscle fibres, with the most commonly reported side effect being muscle twitches and sometimes painful sensations. These sensations affect behaviour during experimental tasks, presenting a potential confound for online single-pulse TMS studies. Our objective was to systematically map the degree of disturbance (ratings of annoyance, pain, and muscle twitches) caused by TMS at 43 locations across the scalp. Ten participants provided ratings whilst completing a choice reaction time task, and ten participants provided ratings whilst completing a flanker reaction time task. TMS over frontal and inferior regions resulted in the highest ratings of annoyance, pain, and muscle twitches caused by TMS. In separate analyses we predicted the difference in reaction times (RT) under TMS by scalp location and subjective ratings. Frontal and inferior scalp locations showed the greatest cost to RTs under TMS (i.e., slowing), with midline sites showing no or minimal slowing. Increases in subjective ratings of disturbance predicted longer RTs under TMS. Critically, ratings were a better predictor of the cost of TMS than scalp location or scalp-to-cortex distance, and the more difficult flanker task showed a greater effect of subjective disturbance. The peripheral sensations and discomfort caused by TMS pulses significantly and systematically influence RTs during single-pulse, online TMS experiments. We provide the data as an online resource (www.tms-smart.info) so that researchers can select control sites that account for the level of general interference in task performance caused by online single-pulse TMS.

neuroscience↗