Biology subjects

Rigosi, E.

Publications and source records attributed to Rigosi, E..

6 recordsLinked to original sources

bioRxiv2025

MetaBeeAI: an AI pipeline for full-text systematic reviews in biology

The volume and complexity of scientific literature are expanding rapidly, making it increasingly difficult to extract and synthesise information across studies. This challenge is particularly acute in the biological sciences, where evidence spans multiple levels of organisation and heterogeneous experimental designs. Large Language Model (LLM) pipelines offer a scalable route to evidence synthesis, but many existing approaches lack transparency, modularity, and effective mechanisms for human oversight. We present MetaBeeAI, an open-source, modular pipeline that integrates established LLM techniques into a coherent, auditable workflow for structured data extraction in biology. MetaBeeAI combines modular prompting, multi-pass extraction, and expert-in-the-loop validation within an interface that presents model outputs alongside source text, enabling inspection, correction, and iterative refinement. The pipeline produces machine-readable records of prompts, configurations, and expert annotations, supporting reproducibility and continuous improvement. We apply MetaBeeAI to 924 research papers on bees and pesticides, extracting structured information on species, compounds, exposure designs, and experimental context. Evaluation demonstrates improved consistency, convergence with expert judgement, and robustness across heterogeneous biological studies, highlighting the value of expert-guided refinement. MetaBeeAI provides a transparent and extensible framework for scalable evidence synthesis, supporting reliable integration of LLMs into biological research workflows.

ecology↗

bioRxiv2022

Acute and chronic toxicity of imidacloprid in the pollinator fly, Eristalis tenax

Imidacloprid is a neonicotinoid neurotoxin that remains the most used insecticide worldwide. It persists in the environment long after the initial application resulting in chronic exposure to non-target insects. To accurately map the dose-dependent effects of these exposures across taxa, toxicological assays need to assess various modes of exposure across relevant indicator species. However, due to the difficulty of these experiments, contact bioassays are frequently used to quantify dose, and dipterans remain underrepresented. Here, we developed a novel naturalistic feeding bioassay to precisely measure imidacloprid ingestion and its toxicity for acute and chronic exposures in a dipteran pollinator, Eristalis tenax. Flies which ingested imidacloprid dosages lower than 12.1 ng/mg all showed consistent intake volumes and learned improved feeding efficiency over successive feeding sessions. In contrast, at doses of 12.1 ng/mg and higher flies had a rapid onset of severe locomotive impairment which prevented them from completing the feeding task. Neither probability of survival nor severe locomotive impairment were significantly higher than the control group until doses of 1.43 ng/mg or higher were reached. We were unable to measure a median lethal dose for acute exposure (72 hours) due to flies possessing a relatively high tolerance for imidacloprid. However, with chronic exposure (18 days), mortality went up and an LD50 of 0.41 ng/mg was estimated. Severe locomotive impairment tended to occur earlier and at lower dosages than lethality, with ED50s of 0.17 ng/mg and 7.82 ng/mg for acute and chronic exposure, respectively. Although the adult Eristalis is a honeybee mimic, it possesses a much higher tolerance to this toxin than its model. The similarity in the LD50 to other dipterans such as the fruitfly and the housefly suggests that there may be a phylogenetic component to pesticide tolerance that needs to be further investigated. The absence of obvious adverse effects at sublethal dosages also underscores a need to develop better tools for quantifying animal behaviour to evaluate the impact of insecticides on foraging efficiency in economically important species.

pharmacology and toxicology↗

bioRxiv2021

Parallel processing of olfactory and mechanosensory information in the honeybee antennal lobe.

We report that airflow produces a complex activation pattern in the antennal lobes of the honeybee Apis mellifera. Glomerular response maps provide a stereotypical code for the intensity and the dynamics of mechanical stimuli that is superimposed on the olfactory code. We show responses to modulated stimuli suggesting that this combinatorial code could provide information about the intensity, direction, and dynamics of the airflow during flight and waggle dance communication.

neuroscience↗

bioRxiv2021

Modelling nonlinear dendritic processing of facilitation in a dragonfly target-tracking neuron

Dragonflies are highly skilled and successful aerial predators that are even capable of selectively attending to one target within a swarm. Detection and tracking prey is likely to be driven by small target motion detector (STMD) neurons identified from several insect groups. Prior work has shown that dragonfly STMD responses are facilitated by targets moving on a continuous path, enhancing the response gain at the present and predicted future location of targets. In this study, we combined detailed morphological data with computational modelling to test whether a combination of dendritic morphology combined with the nonlinear properties of NMDA receptors could explain these observations. We developed a hybrid neuronal model of neurons within the dragonfly optic lobe, which integrates numerical and morphological components. The model was able to generate potent facilitation for targets moving on continuous trajectories, including a localized spotlight of maximal sensitivity close to the last seen target location, as also measured during in vivo recordings. The model did not, however, include a mechanism capable of producing a traveling or spreading wave of facilitation. Our data support a strong role for the high dendritic density seen in the dragonfly neuron in enhancing non-linear facilitation. An alternative model based on morphology of an unrelated type of motion processing neuron from a dipteran fly required more than 3 times higher synaptic gain in order to elicit similar levels of facilitation, despite having only 20% fewer synapses. Our data supports a potential role for NMDA receptors in target tracking and also demonstrates the feasibility of combining biologically plausible dendritic computations with more abstract computational models for basic processing as used in earlier studies.

neuroscience↗

bioRxiv2020

Comparison of transparency and shrinkage of insect brains using novel and traditional clearing methods

Improvement of imaging quality has the potential to visualize previously unseen building blocks of the brain and is therefore one of the great challenges in neuroscience. Rapid development of new tissue clearing techniques in recent years have attempted to solve imaging compromises in thick brain samples, particularly for high resolution optical microscopy, where the clearing medium needs to match the refractive index of the objective immersion medium. These problems are exacerbated in insect tissue, where numerous (initially air-filled) tracheal tubes branching throughout the brain increase the scattering of light. To date, surprisingly few studies have systematically quantified the benefits of such clearing methods using objective transparency and tissue shrinkage measurements. In this study we compare a traditional and widely used insect clearing medium, methyl salicylate combined with permanent mounting in Permount ( MS/P) with several more recently applied clearing media that offer tunable refractive index (n): 2,2-thiodiethanol (TDE), SeeDB2 (in variants SeeDB2S & SeeDB2G matched to oil and glycerol immersion, n=1.52 & 1.47 respectively) and Rapiclear (also with n=1.52 & 1.47). We measured transparency and tissue shrinkage by comparing freshly dissected brains with cleared brains from dipteran flies, with or without addition of vacuum or ethanol pre-treatments (dehydration and rehydration) to evacuate air from the tracheal system. The results show that ethanol pre-treatment is very effective for improving transparency, regardless of the subsequent clearing medium, while vacuum treatment offers little measurable benefit. Ethanol pre-treated SeeDB2G and Rapiclear brains show much less shrinkage than using the traditional MS/P method. Furthermore, these newly developed media offer outstanding transparency compared to TDE and MS/P. Rapiclear protocols were less laborious compared to SeeDB2, but both offer sufficient transparency and refractive index tunability to permit super-resolution imaging of local volumes in whole mount brains from large insects, and even light-sheet microscopy. Although long-term permanency of Rapiclear stored samples remains to be established, our samples still showed good preservation of fluorescence after storage for more than a year at room temperature.

neuroscience↗

bioRxiv2018

The cholinergic pesticide imidacloprid impairs contrast and direction sensitivity in motion detecting neurons of an insect pollinator

Cholinergic pesticides such as the neonicotinoid imidacloprid are the most important insecticides used for plant protection worldwide. In recent decades concerns have been raised about side effects on non-target insect species, including altered foraging behaviour and navigation. Although pollinators rely on visual cues to forage and navigate their environment, the effect of neonicotinoids on visual processing have been largely overlooked. Here we describe a modified electrophysiological setup that allowed recordings of visually evoked responses while perfusing the brain in vivo. Long-lasting recordings from wide-field motion sensitive neurons of the hoverfly pollinator, Eristalis tenax, revealed that sub-lethal exposure to imidacloprid alters their physiological response to motion stimuli. We observed substantially increased spontaneous firing rate, reduced contrast sensitivity and weaker directional tuning to wide-field moving stimuli. This approach reveals sub-lethal effects of imidacloprid in the visual motion detecting system of an important pollinator with likely implications for flight control, hovering and routing.

neuroscience↗