Biology subjects

Dobson, K.

Publications and source records attributed to Dobson, K..

4 recordsLinked to original sources

bioRxiv2024

Nanopore sequencing of intact aminoacylated tRNAs

Transfer RNAs (tRNA) are decorated during biogenesis with a variety of modifications that modulate their stability, aminoacylation, and decoding potential during translation. The complex landscape of tRNA modification presents significant analysis challenges and to date no single approach enables the simultaneous measurement of important but disparate chemical properties of individual, mature tRNA molecules. We developed a new, integrated approach to analyze the sequence, modification, and aminoacylation state of tRNA molecules in a high throughput nanopore sequencing experiment, leveraging a chemical ligation that embeds the charged amino acid in an adapted tRNA molecule. During nanopore sequencing, the embedded amino acid generates unique distortions in ionic current and translocation speed, enabling application of machine learning approaches to classify charging status and amino acid identity. Specific applications of the method indicate it will be broadly useful for examining relationships and dependencies between tRNA sequence, modification, and aminoacylation.

molecular biology↗

bioRxiv2024

Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing

Transfer RNAs are the fundamental adapter molecules of protein synthesis and the most abundant and heterogeneous class of noncoding RNA molecules in cells. The study of tRNA repertoires remains challenging, complicated by the presence of dozens of post transcriptional modifications. Nanopore sequencing is an emerging technology with promise for both tRNA sequencing and the detection of RNA modifications; however, such studies have been limited by the throughput and accuracy of direct RNA sequencing methods. Moreover, detection of the complete set of tRNA modifications by nanopore sequencing remains challenging. Here we show that recent updates to nanopore direct RNA sequencing chemistry (RNA004) combined with our own optimizations to tRNA sequencing protocols and analysis workflows enable high throughput coverage of tRNA molecules and characterization of nanopore signals produced by 43 distinct RNA modifications. We share best practices and protocols for nanopore sequencing of tRNA and further report successful detection of low abundance mitochondrial and viral tRNAs, providing proof of concept for use of nanopore sequencing to study tRNA populations in the context of infection and organelle biology. This work provides a roadmap to guide future efforts towards de novo detection of RNA modifications across multiple organisms using nanopore sequencing.

molecular biology↗

bioRxiv2024

Behavioural Investigations of Psilocybin in Animals 1962-2021: A Scoping Review

Background and AimsPsilocybin is a psychedelic drug that may hold promise for a wide range of human health conditions, yet the identification of therapeutic processes and mechanisms of action remains exploratory. We conducted a scoping review on pre-clinical behavioural investigations of psilocybin in non-human animals to help determine the behavioural effects of psilocybin in non-human animals, to identify studies completed, behavioural tests employed, and what dosing modalities had been studied. MethodsA librarian-conducted literature search was performed using predefined key terms and search criteria and additional searching was conducted by reviewers, using electronic databases, grey literature sources, and reference lists of relevant articles or reviews. The final search updated occurred in October, 2021. Studies were reviewed, screened and selected against an a priori protocol using Covidence software by multiple reviewers with results plotted across the Research Domains Criteria construct. ResultsFrom 4124 records identified by database searching, 260 publications were subjected to full-text review with 77 studies included in this scoping review, published between 1962-2021. The preponderance of studies (n=64) investigated behavioural outcomes in rodents. Only 43 studies (55.8%) reported on housing conditions, and seventeen studies (22.1%) failed to report sample size. All studies reported behavioural outcomes following drug administration, with fifty-one studies (66.2%) using psilocybin, thirty studies (42.9%) psilocin, four studies (5.2%) administering whole mushroom extracts (WME), and a further eight studies investigating both psilocybin and psilocin and one study reporting the effects of both psilocin and WME. One hundred and thirty distinct behavioural investigations using fifty different behavioral paradigms were identified. Few adverse events were reported, and even exceedingly high doses were apparently well tolerated. ConclusionWith seventy-seven publications spanning close to sixty years, there is huge variation in study design and quality. Overall psilocybin presents a unique and strong safety profile with no evidence of biological toxicity, is characterized by unique time and dose-dependent effects, and its pattern of drug action is significantly context and training-sensitive. Data suggest putative effects of psilocybin include acute arousal, dose-dependent sedation, reductions in fear conditioning at low doses, reduced aggression, improved valence, acute disruption of working memory, the rescuing of deficits from chronic stress, and improved learning when combined with repeated environmental exposure after resolution of drug effect.

animal behavior and cognition↗

bioRxiv2022

Savanna chimpanzees (Pan troglodytes verus) in Senegal react to deadly snakes and other reptiles: Testing the snake detection hypothesis

The hypothesis that dangerous snakes served as evolutionary selective pressures on traits characterizing the Order Primates (Snake Detection Hypothesis, SDH), specifically vision and aspects of the brain, has received recent attention. We provide data on 52 encounters between chimpanzees (Pan troglodytes verus) in a savanna landscape and snakes and other large reptiles at the Fongoli site in Senegal, over the course of eight years. These encounters yielded data on 178 interactions between identified individual chimpanzees and reptiles. The majority of encounters with identified reptiles (62%) involved potentially deadly snakes. Constrictors of the family Pythonidae were encountered more frequently than any other reptile. Chimpanzees exhibited a variety of reactions to reptiles, ranging from attacking with objects to ignoring them. Even reptiles other than snakes were met with some degree of alarm when they were in water or moving quickly. We assessed variables that may affect apes reactions, as well as the age-sex class of chimpanzees. As a test of Isbells snake detection hypothesis, we examined chimpanzees reaction intensity to venomous versus constricting snakes but found no difference. We did find significant age-sex differences in chimpanzees reactions to snakes, with adolescent males exhibiting higher-intensity reactions than adult males and females and adolescent female chimpanzees. Chimpanzees reacted at significantly higher intensities when snakes were arboreal in location, but reptile species, size, and activity did not significantly influence individuals reactions to snakes. We also report one inferred encounter between an adult female chimpanzee and a venomous snake, which led to her death. Our data suggest that snakes are significant threats to chimpanzees in savanna environments and support the hypothesis that danger from snakes could have exerted significant evolutionary pressure on the Order Primates.

animal behavior and cognition↗