Biology subjects

Bishop, D.

Publications and source records attributed to Bishop, D..

6 recordsLinked to original sources

bioRxiv2026

On Breathing Variability in the Tree Shrew

Tree shrews (Tupaia belangeri) are increasingly used in comparative neuroscience, yet their respiratory physiology remains poorly characterized. We quantified spontaneous breathing and respiratory rhythm variability in awake adult tree shrews (n = 10; 5 males, 5 females) using whole-body plethysmography. Respiratory frequency decreased by approximately 16% with acclimatization to the recording chamber, while respiratory timing, body-mass-normalized respiratory amplitude, inspiratory flow, and minute ventilation remained relatively stable. After acclimatization, mean respiratory parameters were similar between sexes, but short-term breath-to-breath variability (SD1) was greater in males than females, whereas SD2 was comparable. These findings establish baseline respiratory characteristics in awake tree shrews and identify sex-dependent differences in short-term respiratory rhythm stability.

neuroscience↗

bioRxiv2025

A stuttering-associated Gnptab variant alters fine-motor kinematics

Precise reach-to-grasp movements rely on complex cortico-basal ganglia and cerebellar circuits, and can be affected by cellular pathway defects. We investigated whether mild Gnptab deficiency, affecting mannose-6-phosphate-dependent lysosomal enzyme targeting, impairs fine motor behaviors in mice. Using the staircase test, high-frame-rate video, and markerless tracking, we assessed reaching and grasping in Gnptab-mutant and control littermates. Our data suggest that Gnptab-mutant mice retrieved about 75% fewer pellets than controls and exhibited abnormal grasping, characterized by increased wrist extension and larger digit angles, decreased digital velocity, and shorter reach distances, while elbow angles remained largely unchanged. These findings suggest a specific deficit in grasp shaping and trajectory control, rather than overall limb positioning. Our data establishes a quantitative link between GNPTAB-related lysosomal pathway disruption and fine-motor impairments, providing a valuable model for understanding how cellular dysfunction impacts motor circuit function.

neuroscience↗

bioRxiv2025

Iron dysregulation in mice engineered with a mutation associated with stuttering

Stuttering is a neurodevelopmental disorder characterized by involuntary disruptions in the normal fluency and timing of speech. Recently, stuttering has been related to specific point mutations in GNPTAB, a gene involved in lysosomal enzyme-targeting pathways, though it remains unclear how such a mutation might cause the stuttering phenotype. Herein, we studied mice engineered with the mutation in the Gnptab gene found in humans who stutter and found increased iron deposition in the basal ganglia of these mice. Further, we found these iron deposits localized predominantly with regional astrocytes when Perls stain was combined with an astrocyte-specific marker. Reducing iron deposition in the brain with iron chelation therapy improved vocalization symptoms in Gnptab-mutant mice. Our data suggest a relationship between the Gnptab mutation, iron homeostasis in astrocytes, and the stuttering phenotype, for which the underlying mechanisms remain to be elucidated.

cell biology↗

bioRxiv2023

Approaches to measuring language lateralisation: an exploratory study comparing two fMRI methods and functional transcranial Doppler ultrasound

In this exploratory study we compare and contrast two methods for deriving a laterality index (LI) from functional magnetic resonance imaging (fMRI) data: the weighted bootstrapped mean from the widely-used Laterality Toolbox (toolbox method), and a novel method that uses subtraction of activations from homologous regions in left and right hemisphere to give an array of difference scores (mirror method). Data came from 31 individuals who had been selected to include a high proportion of people with atypical laterality when tested with functional transcranial Doppler ultrasound (fTCD), and who had fMRI data for two tasks, word generation and semantic matching, which were selected as likely to activate different brain regions. In general, the mirror method gave better agreement with fTCD laterality than the toolbox method, both for individual regions of interest, and for a large region corresponding to the middle cerebral artery. LI estimates from this method had much smaller CIs than those from the toolbox method; with the mirror method, most participants were reliably lateralised to left or right, whereas with the toolbox method, a higher proportion were categorised as bilateral (i.e. the CI for the LI spanned zero). Reasons for discrepancies between fMRI methods are discussed: one issue is that the toolbox method averages the LI across a wide range of thresholds. Furthermore, examination of task-related t-statistic maps from the two hemispheres showed that language lateralisation is evident in regions characterised by deactivation, and so key information may be lost by ignoring voxel activations below zero, as is done with conventional estimates of the LI.

neuroscience↗

bioRxiv2021

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a "first pass" angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the worlds natural history collections.

evolutionary biology↗

bioRxiv2021

'Nepotistic journals: a survey of biomedical journals.

ContextConvergent analyses in different disciplines support the use of the Percentage of Papers by the Most Prolific author (PPMP) as a red flag to identify journals that can be suspected of questionable editorial practices. We examined whether this index, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using a large sample of biomedical journals. MethodsWe extracted metadata for all biomedical journals referenced in the National Library of Medicine, with any attributed Broad Subject Terms, and at least 50 authored (i.e. by at least one author) articles between 2015 and 2019, identifying the most prolific author (i.e. the person who signed the most papers in each particular journal). We calculated the PPMP and the 2015-2019 Gini index for the distribution of articles across authors. When the relevant information was reported, we also computed the median publication lag (time between submission and acceptance) for articles authored by any of the most prolific authors and that for articles not authored by prolific authors. For outlier journals, defined as a PPMP or Gini index above the 95th percentile of their respective distributions, a random sample of 100 journals was selected and described in relation to status on the editorial board for the most prolific author. Results5 468 journals that published 4 986 335 papers between 2015 and 2019 were analysed. The PPMP 95th percentile was 10.6% (median 2.9%). The Gini index 95th percentile was 0.355 (median 0.183). Correlation between the two indices was 0.35 (95CI 0.33 to 0.37). Information on publication lag was available for 2 743 journals. We found that 277 journals (10.2%) had a median time lag to publication for articles by the most prolific author(s) that was shorter than 3 weeks, versus 51 (1.9%) journals with articles not authored by prolific author(s). Among the random sample of outlier journals, 98 provided information about their editorial board. Among these 98, the most prolific author was part of the editorial board in 60 cases (61%), among whom 25 (26% of the 98) were editors-in-chief. DiscussionIn most journals publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. The papers by these authors were more likely to be accepted for publication within 3 weeks of their submission. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

scientific communication and education↗