Biology subjects

Fry, B.

Publications and source records attributed to Fry, B..

4 recordsLinked to original sources

bioRxiv2026

Molecular basis of mitochondrial leucine transport by human Sideroflexin 1

Leucine is a central nutrient signal and a ketogenic amino acid that fuels metabolism, yet how it is imported into mitochondria remains incompletely defined. Sideroflexins are conserved inner mitochondrial membrane proteins implicated in amino acid transport, but their mechanism and substrate specificity remain unclear. Using cryogenic electron microscopy, we determined the structure of SFXN1 in its matrix-open conformation. AlphaFold and Boltz co-folding of SFXN1 with a library of human metabolites identified leucine as a candidate substrate, findings supported by thermal stability measurements and mitochondrial transport assays. Comparison with a cytoplasmic-open-model reveals an alternating-access "toggle-switch" mechanism of transport. Together, these findings uncover the molecular basis of leucine transport by SFXN1 and provide a framework for understanding its role in metabolism and disease.

Molecular Biology↗

bioRxiv2025

Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks

Pathogen genomic analysis is central to tracking, understanding, and containing outbreaks, but complexity and high costs of state-of-the-art (SOTA) phylogenetic tools limit global access and impact. We introduce Delphy, an exact reformulation of Bayesian phylogenetics designed to transform its speed, scalability and accessibility while retaining SOTA accuracy. Delphys central data structure, an Explicit Mutation Annotated Tree, exploits the high sequence similarity in large-scale epidemic datasets for efficient tree exploration and convergence. By reproducing key analyses from recent major epidemics (Ebola, Zika, SARS-CoV-2, mpox, and H5N1), we demonstrate SOTA accuracy with up to 1,000x speedups. Assessing Delphys scalability, we show that a simulated dataset of 100,000 sequences can be analyzed in under a day-the largest such computation to date. We distribute Delphy as a client-side web application, enabling users worldwide to turn raw data into interactive results within minutes, without the data ever leaving the users machine. Delphy automatically identifies key viral lineages and mutations, as well as their emergence and prevalence through time, all with quantified uncertainties derived from a solid theoretical foundation. Delphy shows the power of Bayesian phylogenetics as a fast, accessible frontline tool for tackling future outbreaks.

genomics↗

bioRxiv2024

Devaluing memories of reward: A case for dopamine

We describe a novel role for dopamine in devaluing sensory memories of reward. Mesencephalic dopamine cells activated during a mediated devaluation phase were later chemogenetically reactivated. This retrieval of the devalued reward memory elicited a reduction in the hedonic evaluation of sucrose reward. Through optogenetic and chemogenetic manipulations, we confirm dopamine cells are both sufficient and necessary for mediated devaluation, and retrieval of these memories reflected dopamine release in the nucleus accumbens. Consistent with our computational modelling data, our findings indicate a critical role for dopamine in encoding predictive representations of the sensory features of reinforcement. Overall, we illuminate the elaborate nature of reinforcement signals encoded by dopamine and suggest novel approaches to treating a host of psychobiological disorders.

neuroscience↗

bioRxiv2020

Disruptions in effort-based decision-making following acute optogenetic stimulation of ventral tegmental area dopamine cells

The dopamine system has been implicated in decision-making particularly when associated with effortful behavior. We examined acute optogenetic stimulation of dopamine cells in the ventral tegmental area (VTA) as mice engaged in an effort-based decision-making task. Tyrosine hydroxylase-Cre mice were injected with Cre-dependent ChR2 or eYFP control in VTA. While eYFP control mice showed effortful discounting, stimulation of dopamine cells in ChR2 mice disrupted effort-based decision-making by reducing choice towards the lever associated with a preferred outcome and greater effort. Surprisingly, disruptions in effortful discounting were observed in subsequent test sessions conducted in the absence of optogenetic stimulation, however during these sessions ChR2 mice displayed enhanced high choice responding across trial blocks. These findings suggest increases in VTA dopamine cell activity can disrupt effort-based decision-making in distinct ways dependent on the timing of optogenetic stimulation.

neuroscience↗