Biology subjects

Atkins, S.

Publications and source records attributed to Atkins, S..

3 recordsLinked to original sources

bioRxiv2026

Using a GPT-5-driven autonomous lab to optimize the cost and titer of cell-free protein synthesis

We used an autonomous lab, comprising a large language model (LLM) and a fully automated cloud laboratory, to optimize the cost efficiency of cell-free protein synthesis (CFPS). By conducting iterative optimization, the LLM-driven autonomous lab was able to achieve a 40% reduction in the specific cost ($/g protein) of CFPS relative to the state of the art (SOTA). This cost reduction was accompanied by a 27% increase in protein production titer (g/L). Iterative experimental design, experiment execution, data capture and analysis, data interpretation, and new hypothesis generation were all handled by the LLM-driven autonomous lab. The interface between OpenAIs GPT-5 LLM and Ginkgo Bioworks cloud laboratory incorporated built-in validation checks via a Pydantic schema to ensure that AI-designed experiments were properly specified. Experimental designs were translated into programmatic specification of multi-instrument biological workflows by Ginkgos Catalyst software and executed on Ginkgos Reconfigurable Automation Cart (RAC) laboratory automation platform, with human intervention largely limited to reagent and consumables preparation, loading and unloading. By integrating LLMs with programmatic control of a cloud lab, we demonstrate that an LLM-driven autonomous lab can successfully perform a real-world scientific task, highlighting the potential of AI-driven autonomous labs for scientific advancement.

synthetic biology↗

bioRxiv2024

Investigation of cellular and molecular changes linked with neuropathic pain in healthy and injured human trigeminal nerves

Injuries to the trigeminal nerve, responsible for sensory innervation to the face, may occur during routine dental procedures, resulting in the formation of a neuroma accompanied by loss of sensation and/or symptoms of pain. In order to gain insight into the molecular mechanisms underpinning the sensory changes, single nuclei RNA sequencing and spatial transcriptomics were employed to profile the transcriptional landscape at single cell resolution of human trigeminal nerves and neuromas. Cellular and transcriptional changes were identified that correlated with the presence of pain, including an expansion of endothelial cells with a pro-inflammatory phenotype and over-expression of HLA-A, CXCL2 and CXCL8. Interactome analysis highlighted signalling changes linked with the presence of pain. HLA-A protein expression was confirmed in neuromas and positively correlated with symptoms of pain. The atlas generated represents a valuable resource for pain research, highlighting the role of inflammation, endothelial cell dysfunction and chemokine signalling in neuropathic pain.

neuroscience↗

bioRxiv2023

An Immuno-Epidemiological Model of Foot-and-Mouth Disease (FMD) in the African Buffalo Population with Carrier Transmission

Foot-and-mouth disease (FMD) is a highly contagious disease that spreads among cloven-hoofed animals. Although not deadly, FMD can cause major delays in meat and dairy production. One major concern is that the foot-and-mouth disease virus (FMDV) can persist in African buffalo hosts as natural reservoirs for long periods of time, causing the pathogens to reemerge in susceptible populations. In this paper, we present a novel immuno-epidemiological model of FMD in the African buffalo host populations. Upon infection, the hosts can undergo two phases, namely the acute and the carrier stages. In our model, we divide the infectious population based upon these two stages so that we can dynamically capture the immunological characteristics of both phases of the disease to better understand the carriers role in disease transmission. We first define the within-host viral-immune kinetics dependent epidemiological basic reproduction number[R] 0 and show that it is a threshold condition for the local stability of the disease-free equilibrium and existence of the endemic equilibrium. We also analytically show that the system always displays forward bifurcation with respect to between-host epidemic parameters. Later, by using a sensitivity analysis (SA) approach developed for multi-scale models, we assess the impact of the acute infection and carrier phase immunological parameters on[R] 0. Interestingly, our numerical results show that the within-carrier infected host immune kinetics parameters and the susceptible individual recruitment rates play significant roles in disease persistence, which are consistent with experimental and field studies.

systems biology↗