Biology subjects

Atkinson, N. S.

Publications and source records attributed to Atkinson, N. S..

3 recordsLinked to original sources

bioRxiv2025

PPI-ID: Streamlining Protein-Protein Interaction Prediction through Domain and SLiM Mapping

AlphaFold-Multimer models protein complexes and facilitates protein-protein interaction (PPI) prediction. Mapping of protein interaction domains and motifs onto the 3D structure can lend credence to the model and provide insight into the function of a given interaction. Furthermore, limiting structure prediction to only the domains and motifs that are likely to interact can reduce the computational demand and produce a higher quality model. To satisfy these needs, we built the Protein-Protein Interaction Identifier (PPI-ID). PPI-ID maps interaction domains and motifs onto molecular structures and filters for those that are sufficiently close to interact. Once an interface is found, PPI-ID labels interacting amino acids. Given only sequences, PPI-ID predicts regions for AlphaFold-Multimer modeling, reporting potential interactions only when each protein has one-half of a paired sequence. Testing with known dimers confirms high accuracy of the tool.

bioinformatics↗

bioRxiv2019

Alcohol increases aggression in flies

Alcohol-induced aggression is a destructive and widespread phenomenon, but we understand very little about the mechanisms that produce this behavior. We found that two different alcohol exposures potentiate aggression in male flies. (1) A pharmacologically relevant dose of alcohol increases aggression and decreases a goal-directed behavior in male flies. (2) In addition, the odor of alcohol itself enhances intermale aggression by potentiating olfactory signaling by cis-vaccenyl acetate (cVa), a volatile male pheromone. Characterizing these behaviors in the genetically tractable fruit fly can lead to a better understanding of the molecular correlates that regulate alcohol-induced aggression in humans and provide insights into an ethologically relevant behavior.\n\nOne Sentence SummaryWe identified two pathways through which alcohol stimulates intermale aggression in flies; one acts by potentiating a male olfactory pheromone while the other is mediated by the systemic effects of alcohol.

ecology↗

bioRxiv2018

Microbiota-dependent elevation of Alcohol Dehydrogenase in Drosophila is associated with changes in alcohol-induced hyperactivity and alcohol preference

The gut microbiota impacts diverse aspects of host biology including metabolism, immunity, and behavior, but the scope of those effects and their underlying molecular mechanisms are poorly understood. To address these gaps, we used Two-dimensional Difference Gel Electrophoresis (2D-DIGE) to identify proteomic differences in male and female Drosophila heads raised with a conventional microbiota and those raised in a sterile environment (axenic). We discovered 22 microbiota-dependent protein differences, and identified a specific elevation in Alcohol Dehydrogenase (ADH) in axenic male flies. Because ADH is a key enzyme in alcohol metabolism, we asked whether physiological and behavioral responses to alcohol were altered in axenic males. Here we show that alcohol induced hyperactivity, the first response to alcohol exposure, is significantly increased in axenic males, requires ADH activity, and is modified by genetic background. While ADH activity is required, we did not detect significant microbe-dependent differences in systemic ADH activity or ethanol level. Like other animals, Drosophila exhibit a preference for ethanol consumption, and here we show significant microbiota-dependent differences in ethanol preference specifically in males. This work demonstrates that male Drosophilas association with their microbiota affects their physiological and behavioral responses to ethanol.

microbiology↗