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Biology subjects

Combe, M.

Publications and source records attributed to Combe, M..

5 recordsLinked to original sources

Decoding social integration in schooling fish using closed-loop real-virtual interactions

Collective motion in animal groups emerges from local interactions, yet how individuals select and integrate social information remains poorly understood. In schooling fish, inferring which neighbors drive an individuals behavior at any given moment is extremely challenging because the analysis of trajectories alone does not unambiguously reveal the underlying causal interactions that generate the observed motion. Here, we used a closed-loop virtual-reality system in which a single real rummy-nose tetra Hemigrammus rhodostomus interacted in real time with four model-driven virtual conspecifics whose interaction rules were precisely controlled. By systematically varying the number of influential neighbors of the virtual fish and combining experiments with simulations, we quantified how social information filtering shapes individual and collective dynamics. Collective coordination increased with stronger social coupling, but analyses of kinematics, spatial organization, correlations, and turning dynamics consistently showed that the real fish behaved as if it were responding primarily to the single most influential neighbor, whose identity could change over time. These results demonstrate that selective interaction with the most influential neighbor is sufficient to sustain coordinated group motion and highlight the power of bio-hybrid closed-loop experiments to reveal causal mechanisms of collective behavior.

animal behavior and cognition↗

Discovering search behaviour in black garden ant trajectories

Exploration of space plays an important role in many animals, in particular for social insects who have to feed and protect a whole colony. In a laboratory study, Khuong et al (2013) studied how the workers of the black garden ant Lasius niger move around in an unknown environment. They assumed that, in a homogeneous arena with no visual cues, ants had no information about their position in space. Based on this hypothesis, they modelled their ants in a Boltzmann Walker framework which describes an ants random walk as a series of straight segments separated by reorientation events. They assumed that on plain horizontal surfaces the ants direction of movement would not influence their average speed, segment lengths and reorientation decisions, thus leading to diffusive trajectories. However, published experiments indicate that L. niger ants are not completely devoid of directional information even in standard laboratory setups with no obvious landmarks. Moreover, many ant species are known to develop specific search strategies when they want to find a particular place in space, a situation that may apply to the analysed data. We re-analyze Khuong et al s data on non-inclined surfaces, this time taking into account the ants orientation in relation to its starting point in the arena. We discovered that, with this information taken into account, the ants trajectory is biased towards its starting point (biased random walk), revealing an advecto-diffusive process. In fact, the distributions of segment lengths and reorientation angles turned out to be modulated by the ants orientation in relation to its starting point. By simulating these biased trajectories, we show that this modulation halves the time it takes for an ant to come back towards its starting point. We conclude that not taking into account the animals cognitive abilities in data analysis may lead to incomplete or biased conclusions. The discovered search behaviour in L. niger can play a significant role in the colonys exploration and foraging ecology.

animal behavior and cognition↗

A low-cost immersive Virtual Reality system to study social interactions and collective behavior in fish

1This study introduces a low-cost, open-source, immersive Virtual Reality (VR) system designed to investigate real-time social interactions and collective behaviors in fish. Understanding collective animal behaviors, such as schooling in fish, presents significant observational challenges due to rapid and complex interactions. To address these difficulties, we developed an innovative closed-loop VR environment allowing precise control and measurement of interactions between real and virtual fish. This setup incorporates high-speed 3D tracking, real-time visual feedback, and automated data processing, creating realistic and interactive scenarios. We present experimental results, obtained with rummy-nose tetras (Hemigrammus rhodostomus ), showing that freely moving real fish consistently adjusted their speed, depth, and spatial positioning to follow virtual fish effectively. Fish matched moderate virtual speeds comfortably, struggled slightly at higher speeds, and actively maintained vertical positioning to sustain group cohesion. The implementation of this VR system provides critical insights into sensory and cognitive processes underlying collective movement and decision-making in fish. By revealing both flexibility and constraints in fish behavior, our findings underscore the potential of VR technology to study social interactions in controlled yet realistic settings. Ultimately, this VR system advances our understanding of collective animal behavior, providing a foundation for cross-species studies linking neural processes, behavioral interactions, and group dynamics.

animal behavior and cognition↗

ONTdeCIPHER: An amplicon-based nanopore sequencing pipeline for tracking pathogen variants

MotivationAmplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. ZIKA, EBOLA) or pandemics (e.g. SARS-CoV-2). However, there is still a lack of versatile and easy-to-use tools that allow users with minimal bioinformatics skills to perform the main steps of downstream analysis, from quality testing to SNPs effect to phylogenetic analysis. ResultsHere, we present ONTdeCIPHER, an amplicon-based Oxford Nanopore Technology (ONT) sequencing pipeline to analyze the genetic diversity of SARS-CoV-2 and other pathogenes. Our pipeline integrates 13 bioinformatics tools. With a single command line and a simple configuration file, users can pre-process their data and obtain the sequencing statistics, reconstruct the consensus genome, identify variants and their effects for each viral isolate, infer lineage and, finally perform multi-sequence alignments and phylogenetic analyses. Availability and implementationONTdeCIPHER is available at https://github.com/emiracherif/ONTdeCIPHER Contactemira.cherif@ird.fr Supplementary informationSupplementary data are available at ...

bioinformatics↗

Recurrent genetic abnormalities in human pluripotent stem cells: definition and routine detection in culture supernatant by targeted droplet digital PCR

Genomic integrity of human pluripotent stem cells (hPSCs) is essential for research and clinical applications. However, genetic abnormalities can accumulate during hPSC generation and routine culture and following gene editing. Their occurrence should be routinely monitored, but the current assays to assess hPSC genomic integrity are not fully suitable for suchregular screening. To address this issue, we first carried out a large meta-analysis of all hPSC genetic abnormalities reported in more than 100 publications and identified 738 recurrent genetic abnormalities (i.e., overlapping abnormalities found in at least five distinct scientific publications). We then developed a test based on the droplet digital PCR technology that can potentially detect 94.3% of these hPSC recurrent genetic abnormalities in DNA extracted from culture supernatant samples. This test can be used to routinely screen genomic integrity in hPSCs.

cell biology↗