Biology subjects

Johnson, O.

Publications and source records attributed to Johnson, O..

5 recordsLinked to original sources

bioRxiv2025

Song complexity in suboscine birds: evolutionary drivers and ecological constraints

Acoustic signal complexity varies widely in the animal kingdom for reasons that remain unclear. In birds, it is widely proposed that vocal complexity evolves as an honest signal of individual quality driven by sexual selection. Other hypotheses related to social interactions include competition for ecological resources (social selection) and intra-group communication in group- living animals, both of which may favour signal complexity. However, these hypotheses are rarely explored at macroevolutionary scales, particularly in the context of constraints on sound production, transmission and detection, leading to ongoing uncertainty about the evolutionary origins of complex vocal signals. Using Bayesian phylogenetic models, we test whether different forms of social communication and ecological constraints predict the temporal and spectral complexity of songs in 1,288 species of suboscine passerine birds. We found that song complexity was reduced by sexual selection, along with other limiting factors including large body size and dense vegetation. Conversely, territoriality boosted the temporal complexity of songs. These findings challenge the common assumption that sexual selection is the main driver of increased signal complexity, and instead highlight the role of social selection as a key component of multiple inter-related drivers and constraints.

evolutionary biology↗

bioRxiv2020

Transarterial embolization modulates the immune response within target and non-target hepatocellular carcinomas.

Recent successes in the field of immuno-oncology have generated considerable interest in the investigation of approaches that combine standard of care treatments with immunotherapies. Transarterial embolization (TAE) represents an attractive candidate for this approach given the potential for immune system stimulation, however little is known about the influence of TAE on the tumor immunoenvironment. The purpose of this study was to perform a cellular analysis of tumor infiltrating lymphocytes (TILs) and PD-L1 expression following TAE in a translational rat model of hepatocellular carcinoma (HCC) and to identify factors that influence this response. We show that TAE causes dynamic changes in immune cell populations, with variable increases in CD3, CD4, and CD8 cells within embolized tumors over time. We also show that TAE alters the immunobiology of distant, non-target tumors as demonstrated by an increased number of CD4, CD8, and Foxp3+ cells within the intratumoral compartment of non-target tumors. We demonstrate that, in response to TAE, tumor cells up-regulate expression of PD-L1. Finally, we demonstrate marked differences in terms of the foreign body reactions induced by two commonly used embolic particles, and show changes in lymphocyte and macrophage recruitment that depend on the type of embolic particles and their propensity to extravasate beyond the vasculature and into the tumor parenchyma. These findings hold important implications for the on-going development of novel therapeutic strategies combining locoregional therapy with immunomodulators, as well as for the development of techniques and materials that can further leverage the unique modulation of the tumor immune microenvironment.

immunology↗

bioRxiv2020

Systematics of a radiation of Neotropical suboscines (Aves: Thamnophilidae: Epinecrophylla)

The stipple-throated antwrens of the genus Epinecrophylla (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of Epinecrophylla antwrens and the first population-level genetic analyses for most species in the genus. Most of our analyses are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to confidently place the western Amazonian taxon pyrrhonota. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the ornata group currently regarded as species, and in the haematonota and leucophthalma groups we found paraphyly at the species and subspecies levels, respectively. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group, discuss the biogeographic patterns that we uncover, and suggest areas for further study.

evolutionary biology↗

bioRxiv2019

A highly contiguous reference genome for Northern Bobwhite (Colinus virginianus)

Northern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. Using Dovetail Chicago and HiC libraries with the HiRise assembly pipeline, we produced an 866.8 Mbp assembly including 1,512 scaffolds with a contig N50 of 66.8 Mbp, a scaffold L50 of four, and a BUSCO completeness score of 90.8%. This new assembly greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.

genomics↗

bioRxiv2019

MRGPRX4 is a novel bile acid receptor in cholestatic itch

Patients with liver diseases often suffer from chronic itch or pruritus, yet the itch-causing pruritogen(s) and their cognate receptor(s) remain largely elusive. Using transcriptomics and GPCR activation assays, we found that an orphan, primate specific MRGPRX4 is expressed in human dorsal root ganglia (hDRG) and selectively activated by bile acids. In situ hybridization and immunohistochemistry revealed that MRGPRX4 is expressed in [~]7% of hDRG neurons and co-localizes with HRH1, a known itch-inducing GPCR. Bile acids elicited a robust Ca2+ response in a subset of cultured hDRG neurons, and intradermal injection of bile acids and an MRGPRX4 specific agonist induced significant itch in healthy human subjects. Surprisingly, application of agonist for TGR5, a known sequence conserved bile acid receptor previously implicated in cholestatic itch, failed to elicit Ca2+ response in cultured hDRG neurons, nor did it induce pruritus in human subjects. In situ hybridization and immunostaining results revealed that hTGR5 is selectively expressed in satellite glial cells, unlike mTGR5 (in mouse DRG neurons), likely accounting for the inter-species difference functionally. Finally, we found that patients with cholestatic itch have significantly higher plasma bile acid levels compared to non-itchy patients and the bile acid levels significantly decreased after itch relief. This elevated bile acid level in itchy patients is sufficient to activate MRGPRX4. Taken together, our data strongly suggest that MRGPRX4 is a novel bile acid receptor that likely underlies cholestatic itch, providing a promising new drug target for anti-itch therapies.

neuroscience↗