Biology subjects

Holmes, N.

Publications and source records attributed to Holmes, N..

4 recordsLinked to original sources

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↗