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Court, R.

Publications and source records attributed to Court, R..

4 recordsLinked to original sources
bioRxiv2026

VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase

Biological databases store curated knowledge that researchers traditionally access through web interfaces or APIs. To move beyond casual browsing requires domain-specific knowledge and expertise to frame the queries necessary to explore this data. This generates barriers to both experienced users trying to integrate wide-ranging sources of information and for new users entering scientific fields undergoing paradigm shifts such as connectomics. A potentially powerful method to lower these barriers is to facilitate natural-language access to these databases by exposing them to large language models (LLMs) via the Model Context Protocol (MCP). Here we implement this for Virtual Fly Brain (VFB), an expert-curated and ontology-backed knowledgebase of Drosophila neuroscience, providing the precision needed to make recently integrated connectome and molecular data accessible. Benchmarked on 30 neuroscience tasks against a bare LLM and a web-search-assisted LLM, the VFB-MCP-equipped LLM produces precise, verifiable and appropriately quantified answers on 25/30 tasks vs 14/30 for web and 2/30 for bare. The MCP advantage is largest for tasks where data quantification is required (89% vs 11% web). This work establishes MCP layered over ontology-backed knowledge graphs as an effective method to improve LLM response quality for neuroscience and connectomics data, promoting accessibility and accelerating the reliable analysis of complex integrated datasets.

neuroscience↗
bioRxiv2024

Rapid Caspian sea level decline requires dynamic spatio-temporal conservation planning to keep biodiversity protection measures relevant

The Caspian Sea is the worlds largest landlocked waterbody, providing habitat for hundreds of endemic and migratory species, along with ecosystem services that sustain millions of people. Global warming is projected to drive declines in water levels of up to 21 m by 2100. Using geospatial analyses, we assessed the impact of sea level decline on habitats, protected areas, and human infrastructure. We show that a water level decline of just 5-10 m will critically disrupt key ecosystems, reduce existing marine protected area coverage by up to 94%, and render billions of dollars of civil and industrial infrastructure obsolete. Urgent action is needed to replace traditional static conservation planning with a pre-emptive, dynamic approach that allows protected areas to track shifting ecosystems. This will be essential to help the Caspian Seas endemic biodiversity adapt to these changes, and avoid conflicts with mitigation efforts directed at protecting human activity. 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ecology↗
bioRxiv2024

Variable prevalence of protective Spiroplasma infection over time in two natural populations of Drosophila hydei

The temporal dynamics of protective symbionts have rarely been characterized outside of aphid hosts. Here, we determine the prevalence of Spiroplasma in two populations of D. hydei where Spiroplasma infection had been previously recorded (UK and Japan). We observe that infection in both populations is variable over time and confirm the persistence of Spiroplasma in the UK population for 9 years. Thus, variable prevalence over time appears to be a common feature of these symbioses.

ecology↗
bioRxiv2022

Culture and genomic analysis of Arsenophonus apicola sp. nov. isolated from the honeybee Apis mellifera

The genus Arsenophonus has been traditionally considered to be comprised of heritable bacterial symbionts of arthropods. Recent work has reported a microbe related to the type species A. nasoniae as infecting the honey bee, Apis mellifera. The association was unusual for members of the genus in that the microbe-host interaction arose through environmental and social exposure rather than vertical transmission. In this study, we describe the in vitro culture of ArsBeeUS, a strain of this microbe isolated from A. mellifera in the USA. The 16S rRNA sequence of the isolated strain clearly indicates it falls within the genus Arsenophonus. Biolog analysis indicates the bacterium has a restricted range of nutrients that support growth. In vivo experiments demonstrate the strain proliferates rapidly on injection into A. mellifera hosts. We further report the closed genome sequence for the strain. The genome is 3.3 MB and 37.6% GC, which is smaller than A. nasoniae but larger than the genomes reported for non-culturable Arsenophonus symbionts. The genome is complex, with 6 plasmids and 11 predicted intact phage elements, but notably less complex than A. nasoniae. With 92% average nucleotide identity (ANI) to the type strain A. nasoniae, the ArsBeeUS strain isolated is clearly distinct from the type species, and we propose the name Arsenophonus apicola sp. nov. (CECT 30499; LMG 32504).

microbiology↗