Biology subjects

Smith, P. A.

Publications and source records attributed to Smith, P. A..

8 recordsLinked to original sources

bioRxiv2025

Validating folding energy estimates as a method for variant interpretation

Interpretation of variants of uncertain significance remains a major problem in genomic analysis. Whilst statistical models can be used to predict pathogenicity, they offer no insights into the biophysical mechanism of variant action, and genomic data available for training is biased towards the subpopulations who have access. Protein misfolding has been found to act as a frequent mechanism for loss of gene or domain activity, where it is typically responsible for [~]2/3 of disease-causing variants and somatic mutations. The accuracy of energy predictions however has consistently been challenged by highly variable correlation coefficients reported from different proteins, and the unknown impact of alternative structures where available. Here we address this directly through a systematic analysis of mega-scale folding experimental results, enabled by a fully automated predictive pipeline based on FoldX. We find that whilst absolute correlation coefficients are mediocre for three highly studied proteins (0.30-0.31), the correlation coefficient alone does not capture the full predictive power of the estimates. Specifically, we find a clear linear relationship between experimental and theoretical result, with a small number of outlier residues responsible for reducing the correlation. We show that the quantitative accuracy of predictions can be improved by aggregating estimates taken from different structures, and that the problematic outlier residues can be both empirically and theoretically identified, allowing us to flag low-confidence values. Our findings not only provide a framework for identifying problematic mutations in advance but also offers new insights into potential improvements of the FoldX protocol for more accurate protein stability predictions. Our insights support the use of FoldX in computational saturation screens to support variant analysis.

biophysics↗

bioRxiv2025

Utility of alternate stable isotope calibration equations and informative priors when estimating the breeding origin of Arctic-breeding shorebirds

Understanding migratory connectivity is essential for monitoring and conserving Arctic-breeding shorebirds, particularly given divergent rates of decline across populations. Stable hydrogen isotope analysis of feathers offers a scalable, non-invasive method to assign breeding origin, but current applications are limited by the absence of shorebird-specific calibration equations, which associate feather isotope values with environmental isotope gradients ("isoscapes"), and by longitudinal isoscape bands in the Arctic that result in diffuse origin estimates across broad, heterogeneous regions. We evaluated the utility of alternate calibration equations and the incorporation of occupancy-based informative priors for improving breeding origin assignments. Specifically, we analyzed feather isotope data from hatch-year semipalmated sandpipers (Calidris pusilla) captured at staging sites in the Canadian Maritimes, as well as known-origin Arctic samples, to compare calibration equations from different reference datasets and test priors derived from eBird habitat occupancy predictions. We demonstrate that Arctic samples of known origin largely align with calibration equations based on broad passerine datasets, although incorporating Arctic samples into the calibration may correct for a marginal westward bias in origin estimates. Using occupancy-based priors that reflect habitat preferences increased precision by 18.8%, identifying hotspots within otherwise expansive isotopic bands. We highlight the validity of existing reference datasets with broad geographic coverage and demonstrate the value of informative priors to refine origin estimates. We recommend expanding Arctic sample collections across a wider longitudinal gradient to define a shorebird-specific calibration equation and further exploring potential biases in prior data sources to improve accuracy of Arctic-breeding shorebird origin assignments.

ecology↗

bioRxiv2024

Source amplitude increases with body mass across avian genera

Amplitude, or intensity, of sound is a fundamental characteristic of inter acoustic communication, with relevance in many scientific fields. The amplitude of an animals acoustic signal at its source ("source amplitude") may be particularly relevant in the field of acoustic allometry, where relationships between species physical and acoustic features (e.g., dominant frequency) have been well-established across taxa. However, despite their potential scientific value, records and studies of source amplitudes remain remarkably scarce for avian species. Here we present novel estimates of source amplitude (range, mean, and median) for 17 species of Arctic-breeding birds, derived from measurements made in Utqia[g]vik, Alaska during June 2024. We found a strong positive correlation between body mass and source amplitude in this data via a Markov Chain Monte Carlo multivariate generalized linear mixed model (MCMCglmm). Both phylogeny and individual identity were important random effects in this model. In contrast, random effects from environmental factors and measurement characteristics were minimal. Our work represents the first model describing the relationship between source amplitude and allometry across avian genera. We hope that this study will spur other investigations into avian source amplitude and its relationship to morphological and life history features for species in the Arctic and elsewhere.

ecology↗

bioRxiv2020

Chronic BDNF simultaneously inhibits and unmasks superficial dorsal horn neuronal activity

Brain-derived neurotrophic factor (BDNF) is critically involved in the pathophysiology of chronic pain. However, the mechanisms of BDNF action on specific neuronal populations in the spinal superficial dorsal horn (SDH) requires further study. We used chronic BDNF treatment (200 ng/ml, 5-6 days) of defined-medium, serum-free spinal organotypic cultures to study intracellular calcium ([Ca2+]i) fluctuations. A detailed quantitative analysis of these fluctuations using the Frequency-independent biological signal identification (FIBSI) program revealed that BDNF simultaneously depressed activity in some SDH neurons while it unmasked a particular subpopulation of silent neurons causing them to become spontaneously active. Blockade of gap junctions disinhibited a subpopulation of SDH neurons and reduced BDNF-induced synchrony in BDNF-treated cultures. BDNF reduced neuronal excitability by measuring spontaneous excitatory postsynaptic currents. This was similar to the depressive effect of BDNF on the [Ca2+]i fluctuations. This study reveals novel regulatory mechanisms of SDH neuronal excitability in response to BDNF.

neuroscience↗

bioRxiv2020

Voltage-gated Ca2+ influx in murine white fat adipocytes: stimulation by growth hormone but not membrane depolarization

In white fat adipocytes voltage-gated Ca2+ channels are constitutively active. Since the adipocyte membrane potential (Vm) is controlled by Cl- we investigated if changes in [Cl-]o can affect the activity of voltage-gated Ca2+ channels and intracellular calcium, [Ca2+]i. Adipocytes were isolated from epididymal fat of CD-1 mice. [Ca2+]i was imaged with epifluorescent microscopy at 28{degrees}C. Constitutive voltage-gated channel activity was confirmed by the ability of verapamil to decrease [Ca2+]i. Substitution of [Cl-]o to 113, 53 and 18 mM with the membrane impermeant gluconate anion decreased [Ca2+]i from 114{+/-}8.7 to 106{+/-}7.5, 101{+/-}7.1 and 97{+/-}6 nM respectively. Substitution of [Cl-]o with glutamate mimicked the ability of gluconate to decrease [Ca2+]i. To explore if anions affected [Ca2+]i via chelation of external Ca2+, [Ca2+]o was analyzed by potentiometry. Gluconate, glutamate, aspartate and methylsulphonate had Ca2+ association constants of 17{+/-}1.8, 12{+/-}1, 8.2{+/-}4.1 and 3.3{+/-}0.5 L-1 M respectively. Substitution of 134 mM [Cl-]o with gluconate decreased [Ca2+]o from 2.6 mM to 200 M; the effect of this anion on [Ca2+]i was mimicked by a decrease of [Ca2+]o to 200 M in standard [Cl-]o solution. Conversely, titration of [Ca2+]o from 200 M back to 2.6 mM in 134 mM gluconate solutions abolished the effect of this anion on [Ca2+]i. Substitution of [Cl-]o with methylsulphonate to affect Vm did not affect [Ca2+]i. Whereas, growth hormone at 10-20 nM increased [Ca2+]i, an effect blocked by verapamil or absence of [Ca2+]o. In conclusion, growth hormone, but not changes in Vm, can increase voltage-gated Ca2+ channel activity and [Ca2+]i in white fat adipocytes. Key pointsO_LI[Ca2+]i plays a key role in the metabolic and endocrine functions of white fat adipocytes. C_LIO_LIIn adipocytes basal [Ca2+]i is maintained by voltage-gated Ca2+ channels constitutively active at their resting membrane potential, Vm, which is predominantly controlled by Cl- permeability. C_LIO_LISubstitution of [Cl-]o to depolarize Vm with gluconate or glutamate, did not increase but decreased [Ca2+]i. an action due to chelation of extracellular Ca2+. This effect was not seen with methylsulphonate, which did no chelate Ca2+ but did not affect [Ca2+]i. C_LIO_LIGrowth hormone elevated, [Ca2+]i an effect blocked by inhibitors of voltage-gated Ca2+ channels C_LIO_LIIn adipocytes, voltage-gated Ca2+ channel activity appear recalcitrant to changes in Vm, but are however gated by growth hormone. C_LI

physiology↗

bioRxiv2019

Migrant semipalmated sandpipers (Calidris pusilla) have over four decades steadily shifted towards safer stopover locations

Peregrine falcons (Falco peregrinus) have undergone a steady hemisphere-wide recovery since the ban on DDT in 1973, resulting in an ongoing increase in the level of danger posed for migrant birds, such as Arctic-breeding sandpipers. We anticipate that in response migrant semipalmated sandpipers (Calidris pusilla) have adjusted migratory behaviour, including a shift in stopover site usage towards locations offering greater safety from falcon predation. We assessed semipalmated sandpiper stopover usage within the Atlantic Canada Shorebird Survey dataset. Based on 3,030 surveys (totalling [~]32M birds) made during southward migration, 1974 - 2017, at 198 stopover locations, we assessed the spatial distribution of site usage in each year (with a priority matching distribution index, PMD) in relation to the size (intertidal area) and safety (proportion of a sites intertidal area further than 150m of the shoreline) of each location. The PMD index value is > 1 when usage is concentrated at dangerous locations, 1.0 when usage matches location size, and < 1 when usage is concentrated at safer locations. A large majority of migrants were found at the safest sites in all years, however our analysis of the PMD demonstrated that the fraction using safer sites increased over time. In 1974, 80% of birds were found at the safest 20% of the sites, while in 2017, this had increased to 97%. A sensitivity analysis shows that the shift was made specifically towards safer (and not just larger) sites. The shift as measured by a PMD index decline cannot be accounted for by possible biases inherent in the data set. We conclude that the data support the prediction that increasing predator danger has induced a shift by southbound migrant semipalmated sandpipers to safer sites.

animal behavior and cognition↗

bioRxiv2018

Mobility in Osteogenesis Imperfecta: A Multicenter North American Study

BackgroundOsteogenesis imperfecta (OI) is a genetic connective tissue disorder characterized by increased bone fragility and recurrent fractures. The phenotypic severity of OI has a significant influence on the ability to walk but little is known about the ambulatory characteristics, strength, or functional abilities in individuals with OI, especially in the more severe forms. To advance clinical research in OI, the Linked Clinical Research Centers, network of clinical centers in North America with significant experience in treating patients with OI, was established in 2009. The purpose of this work was to characterize mobility in OI using standard clinical assessment tools. and determine if any patient characteristics could be used to predict mobility outcomes.\n\nMethodsData were collected at five clinical sites and included age, gender, ethnicity, height, weight, use of assistive device, and bisphosphonate use and mobility metrics (age at first walk, Gillette Functional Assessment Questionnaire, Functional Mobility Scale, and distance walked in the 6 minute walk test). Linear mixed models were developed to explore the relationships between subject demographics and mobility metrics.\n\nResultsThe study identified 491 individuals age 3 and older. In general, the results showed minor limitations in the type I group while the more severe types showed more significant limitations in all mobility metrics analyzed. Height and weight were shown to be the most significant predictors of mobility metrics. Relationships with mobility and bisphosphonates varied with OI type and whether oral or IV was used.\n\nConclusionThis paper is the most comprehensive report of mobility in individuals with OI to date. These results are vital to understanding the mobility limitations of specific types of OI and beneficial when developing rehabilitation protocols for this population. It is important for physicians, patients, and caregivers to gain insight into severity and classification of the disease and the influence of disease-related characteristics on the prognosis for mobility.

bioengineering↗

bioRxiv2017

Females recruit faster alpha motor neurons than males during the patellar stretch reflex: evidence for neurophysiological sexual dimorphism

ObjectiveHuman neurophysiology is sexually dimorphic where the pre-motor latency of the patella stretch reflex (PR) in females occurs earlier than males; an effect unaccounted for by stature difference. Using surface electromyography we investigated whether this difference is due to dimorphism in the conduction velocity (MNCV) of the associated alpha-motor neurons.\n\nMethodsExtracellular linear electrode arrays measured vastus lateralis (VL) motor unit action potential activity (MUAP). MNCV was determined from the relationship between the latency of MUAP initiation and VL distance during a PR.\n\nResultsIn females, the PR premotor latency occurred 2.1{+/-}0.3 ms earlier than in males and recruited alpha-motor neurons with a MNCV 5 ms-1 faster (p<0.02) than males: 52.4{+/-}1.5 5 m s-1 (n=40) compared to 47.6{+/-}1.3 5 m s-1 (n=41) respectively.\n\nConclusionsIn males the longer PR premotor latency was accounted for by their slower MNCV. Our finding is contrary to the observations of larger diameter alpha-motor axons and somas seen in males. Since the PR yields MNCVs values at the lower end of published values supports the \"size-principle\" of motor unit recruitment with a physiological stimulus.\n\nSignificanceOur findings evidence gender dimorphism in a routine neurophysiologic test which suggest androgen modulation of skeletal muscle innervation.

physiology↗