Biology subjects

Jones, D. N.

Publications and source records attributed to Jones, D. N..

5 recordsLinked to original sources

bioRxiv2024

Rapid GIT transit time in volant vertebrates, with implications for convergence in microbiome composition

Flying birds and bats have simplified gastrointestinal tracts (GITs) and low intestinal mass to support flight. While previous work showed reduced GIT passage times in birds relative to other vertebrates, GIT passage times have never been collectively quantified for bats. We conducted a meta-analysis of published digesta passage times across vertebrates, comparing volant and non-volant vertebrates, while considering the effects of body mass and diet. We hypothesized that, like flying birds, bats have significantly faster digesta passage times relative to nonvolant vertebrates, likely due to their adaptations for flight. Our study supports this, revealing significant differences in passage times among flying and non-flying groups, with bats exhibiting faster transit times compared to non-volant vertebrates. Using a phylogenetic comparative analysis, we show that flight and diet have a strong effect on GIT transit times across diverse taxa, while body mass plays a more limited role. Accelerated transit times in bats likely promote the rapid turnover of gut contents, which may contribute to their distinct GIT microbe compositions. Unique among mammals, bat GIT microbiomes are dominated by Pseudomonadota bacteria, a pattern also observed in flying birds. We hypothesize this convergence may result from rapid GIT transit times quantified here for volant taxa.

ecology↗

bioRxiv2024

A Hierarchical Model for eDNA Fate and Transport Dynamics Accommodating Low Concentration Samples

Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of ecological inference from eDNA sampling. Two particular challenges are 1) determining species source location(s) and 2) accurately and precisely measuring low concentration eDNA samples in the presence of multiple sources of ecological and measurement variability. The recently introduced eDNA Integrating Transport and Hydrology (eDITH) model provides a framework for relating eDNA measurements to source locations in riverine networks, but little empirical work has been done to test and refine model assumptions or accommodate low concentration samples, that can be systematically undermeasured. To better understand eDNA fate and transport dynamics and our ability to reliably quantify low concentration samples, we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as a latent variable with a count distribution and conditioning detection and quantification on replicate copy number. We provide evidence that the eDNA removal rate declined through time, estimating that over 80% of eDNA was removed over the first 10 meters, traversed in 41 seconds. After this initial period of rapid decay, eDNA decayed slowly with consistent detection through our farthest site 1km from the release location, traversed in 250 seconds. Our model further allowed us to detect extra-Poisson variation in the allocation of copies to replicates. We extended our hierarchical model to accommodate a continuous effect of inhibitors and used our model to provide evidence for the inhibitor hypothesis and explore the potential implications. While our model is not a panacea for all challenges faced when quantifying low-concentration eDNA samples, it provides a framework for a more complete accounting of uncertainty.

ecology↗

bioRxiv2023

Impacts of mate quality on female intrasexual aggression in two sister Malurus fairywren species

In a large and ever-growing number of animal species, it is now appreciated that females use colors as a visual signal in a range of social interactions, including both courtship and territorial aggression. Yet, it remains unclear whether female color phenotypes and/or aggressive behaviors are correlated with any attributes of their mates phenotype. For example, we might expect species in which males contribute more to parental care or territorial defense to have more colorful or aggressive females. On the other hand, within species, we might expect those females mated to higher quality males to be more colorful or aggressive than those mated to lower quality males. To begin to address these possibilities, we conducted a preliminary study in two sister taxa of fairywren (Maluridae) with distinct life-history strategies and plumage dichromatism: white-shouldered fairywrens (Malurus alboscapulatus moretoni) in tropical Papua New Guinea, a species in which both males and females have ornamented plumage and jointly defend territories year-round, and red-backed fairywrens (M. melanocephalus melanocephalus) in temperate Australia, a sexually dichromatic species with ornamented males and unornamented females. At the between species level, we predicted white-shouldered fairywren females would be more aggressive in same-sex interactions than red-backed fairywrens, as both white-shouldered males contribute to year-round territorial defense, whereas territories break-down during non-breeding in red-backed fairywrens. Further, we predicted that, within species, females mated to males of higher quality would be more aggressive in simulated same-sex encounters. Between species, female white-shouldered fairywrens were more aggressive on average than female red-backed fairywrens as predicted. Within both species, indices of male quality were not related to female aggression (although there was a non-significant tendency for more aggressive female white-shouldered fairywren to have heavier mates with longer tails). These results point to a need for additional research exploring relationships between life history, female plumage, and female aggressive behaviors in a wider range of species.

ecology↗

bioRxiv2023

Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2

Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix F segments surrounding the activation loop, as well as helix L16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix C, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

biochemistry↗

bioRxiv2023

Periodic shifts in viral load increase risk of spillover from bats

Prediction and management of zoonotic pathogen spillover requires an understanding of infection dynamics within reservoir host populations. Transmission risk is often assessed using prevalence of infected hosts, with infection status based on the presence of genomic material. However, detection of viral genomic material alone does not necessarily indicate the presence of infectious virus, which could decouple prevalence from transmission risk. We undertook a multi-faceted investigation of Hendra virus shedding in Pteropus bats, combining insights from virus isolation, viral load proxies, viral prevalence, and longitudinal patterns of shedding, from 6,151 samples. In addition to seasonal and interannual fluctuation in prevalence, we found evidence for periodic shifts in the distribution of viral loads. The proportion of bats shedding high viral loads was higher during peak prevalence periods during which spillover events were observed, and lower during non-peak periods when there were no spillovers. We suggest that prolonged periods of low viral load and low prevalence reflect prolonged shedding of non-infectious RNA, or viral loads that are insufficient or unlikely to overcome dose barriers to spillover infection. These findings show that incorporating viral load (or proxies of viral load) into longitudinal studies of virus excretion will better inform predictions of spillover risk than prevalence alone. Significance statementWe present a comprehensive analysis of a high-profile bat-virus system (Hendra virus in Australian flying-foxes) to demonstrate that both prevalence and viral loads can shift systematically over time, resulting in concentrated periods of increased spillover risk when prevalence and viral loads are high. We further suggest that prolonged periods of low-prevalence, low-load shedding may not reflect excretion of infectious virus, resolving the outstanding puzzle of why spillovers have not been observed during periods of low off-season prevalence in subtropical Australia, or more frequently in tropical Australia despite consistent low-prevalence shedding. The consideration of viral loads (or proxies of viral load) along with prevalence may improve risk inference from longitudinal surveys of zoonotic viruses across wildlife reservoir hosts.

ecology↗