Biology subjects

Gompel, N.

Publications and source records attributed to Gompel, N..

8 recordsLinked to original sources

bioRxiv2026

Trends in the representation of research on model organisms in scientific literature

Research using model organisms to tackle questions in life sciences and biomedical sciences has been in the spotlight of scientific literature for the better part of the twentieth century. This attention has perceptibly faded over the last twenty years, at least. We set to document this process by examining the publication trends of 48 journals encompassing a broad range of topics and impact factors for eight classic model organisms. We found that the representation of model-organism research has been in continuous decline in the last three decades, with a significant acceleration since 2010. We investigated the origin of the change, from the size of research communities to the shifts in topics and in use of model organisms. While model organism communities appear stable, model organism papers are outpaced by the rest of scientific literature. Also, among papers using model organisms, we note a progressive shift toward applied research, with differences between different model organism species. The mouse, in particular, logically remains the preferred system to study diseases, while non-mouse model organisms continue to be used predominantly to dissect mechanisms of life. We reflect on the consequences of the fading representation that we measured for the future of life sciences. Fundamentally, model organisms afford a direct access to causality in life sciences and their fading from the picture may impact life sciences as a whole. More pragmatically, it will also affect funding, and thereby jeopardizes the maintenance of model organism resources such as repositories built over decades.

scientific communication and education↗

bioRxiv2025

The TRP-channel painless mediates substrate stiffness sensing in the legs during Drosophila oviposition

The distinct textural properties of fruits in varying stages of ripening present unique ecological opportunities for several species of fruit flies, resulting, over evolutionary times, in specialized egg-laying behaviors. In this study we identified a TrpA channel-dependent mechanosensory pathway in the legs, through the gene painless, that modulates the discernment of softer patches for oviposition in gravid D. melanogaster females. We report that the stiffness-sensing role of tarsi is mediated through external sensory organs housed, namely ventral mechanosensory bristles and subsets of campaniform sensilla present primarily at the joints between tarsomeres. Our findings provide new evidence that campaniform sensilla function as indirect stiffness sensors of oviposition substrates, owing to their placement at joints that experience maximal cuticular distortion. We show that Painless is expressed in mechanosensory neurons innervating peripheral organs where it likely participates in the transduction of stiffness-evoked stimuli. Furthermore, we observed that overexpression of painless in both campaniform sensilla and mechanosensory bristles partially rescues preference for the softer substrates in painless mutants, indicating that painless activity in these organs is necessary to mediate the preference. We propose that different interactions with a soft vs. a hard substrate (compression of the cuticle, distribution of contacts) results in differential mechanotransduction in painless-expressing neurons, determining oviposition preferences.

neuroscience↗

bioRxiv2024

Entangled and non-modular enhancer sequences producing independent spatial activities

The modularity of transcriptional enhancers (1, 2) is central to our understanding of morphological evolution, as it allows specific changes to a gene expression pattern component, without affecting others (3). Enhancer modularity refers to physically separated stretches of regulatory sequence producing discrete spatiotemporal transcriptional activity. This concept stems mainly from assays that test the sufficiency of a DNA segment (4) to drive spatial reporter expression resembling that of the corresponding gene. Focusing on sufficiency to produce spatial patterns, it overlooks quantitative aspects of gene expression, underestimating the regulatory sequence actually required to reach full endogenous expression levels. Here we show that five regulatory activities of the pigmentation gene yellow in Drosophila, classically described as modular (5-7), result from extensively overlapping sequences, with broadly distributed regulatory information. Nevertheless, the independent regulatory activities of these entangled enhancers appear to be nucleated by specific segments that we called enhancer cores. Our work calls for a reappraisal of enhancer definition and properties, as well as of the consequences on regulatory evolution.

developmental biology↗

bioRxiv2022

Odor-gated oviposition behavior in an ecological specialist

Colonization of a novel ecological niche can require, or be driven by, evolution of an animals behaviors promoting their reproductive success in the new environment. Little is known about the underlying mechanisms. We have exploited an emerging genetic model for behavioral neuroecology, Drosophila sechellia - a close relative of Drosophila melanogaster that exhibits extreme specialism for Morinda citrifolia noni fruit - to study the evolution and sensory basis of oviposition. D. sechellia produces fewer eggs compared to other drosophilids, but lays these almost exclusively on noni substrates, contrasting with avoidance or indifference of noni by generalist species. Visual, textural and social cues do not explain the species-specificity of this preference. By contrast, loss of olfactory input in D. sechellia, but not D. melanogaster, essentially abolishes egg-laying, suggesting that this sensory modality gates gustatory-driven noni preference. We find the noni bouquet is detected by redundant olfactory pathways. By parsing the fruits volatile chemicals and genetic perturbation of individual olfactory pathways in D. sechellia, we discover a key role for hexanoic acid and its cognate receptor, the Ionotropic receptor Ir75b, in odor-evoked oviposition. Through receptor exchange in D. melanogaster, we provide evidence for a causal contribution of odor-tuning changes in Ir75b to the evolution of oviposition behavior during D. sechellias host specialization.

animal behavior and cognition↗

bioRxiv2021

Resolving Between Novelty and Homology in the Rapidly Evolving Phallus of Drosophila

The genitalia present some of the most rapidly evolving anatomical structures in the animal kingdom, possessing a variety of parts that can distinguish recently diverged species. In the Drosophila melanogaster group, the phallus is adorned with several processes, pointed outgrowths, that are similar in size and shape between species. However, the complex three-dimensional nature of the phallus can obscure the exact connection points of each process. Previous descriptions based upon adult morphology have primarily assigned phallic processes by their approximate positions in the phallus and have remained largely agnostic regarding their homology relationships. In the absence of clearly identified homology, it can be challenging to model when each structure first evolved. Here, we employ a comparative developmental analysis of these processes in eight members of the melanogaster species group to precisely identify the tissue from which each process forms. Our results indicate that adult phallic processes arise from three pupal primordia in all species. We found that in some cases the same primordia generate homologous structures whereas in other cases, different primordia produce phenotypically similar but remarkably non-homologous structures. This suggests that the same gene regulatory network may have been redeployed to different primordia to induce phenotypically similar traits. Our results highlight how traits diversify and can be redeployed, even at short evolutionary scales. Research HighlightBy incorporating developmental analysis, we find that genital structures previously identified as homologs are novel structures. This highlights how developmental analysis can help resolve contentious claims of homology.

evolutionary biology↗

bioRxiv2020

Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysis

Transcriptional enhancers are short DNA sequences controlling the spatial activity, timing and levels of eukaryotic gene transcription. Their quantitative transcriptional output is thought to result from the number and organization of transcription factor binding sites (TFBSs). Yet, how the various aspects of regulatory information are encoded in enhancer sequences remains elusive. We addressed this question by quantifying the spatial activity of the yellow spot enhancer active in developing Drosophila wings. To identify which enhancer DNA sequence contributes to enhancer activity, we introduced systematic mutations along the enhancer. We developed an analytic framework that uses comprehensive descriptors to quantify reporter assay in transgenic flies and measure spatial variations in activity levels across the wing. Our analysis highlights an unexpected density of regulatory information in the spot enhancer sequence. Furthermore, it reveals an unanticipated regulatory logic underlying the activity of this enhancer, and how it reads the wing trans-regulatory landscape to encode a spatial pattern.

genetics↗

bioRxiv2020

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies based on short-read sequencing were released in 2013 for this species. Although valuable, these resources contain pervasive assembly errors and are highly fragmented, two features limiting their values. Our purpose here was to improve the assembly of the D. suzukii genome. For this, we generated PacBio long-read sequencing data at 160X sequence coverage and assembled a novel, contiguous D. suzukii genome. We obtained a high-quality assembly of 270 Mb (with 546 contigs, a N50 of 2.6Mb, a L50 of 15, and a BUSCO score of 95%) that we called WT3-2.0. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome (ca. 19Mb). As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our WT3-2.0 assembly provides a higher quality genomic resource compared to the previous one in terms of general assembly statistics, sequence quality and gene annotation. This new D. suzukii genome assembly is therefore an improved resource for high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.

ecology↗

bioRxiv2018

Evolution of ovipositor length in Drosophila suzukii is driven by enhanced cell size expansion and anisotropic tissue reorganization

Morphological diversity is dominated by variation in body proportion. Yet the cellular processes underlying differential growth of morphological traits between species remain largely unknown. Here we compare the ovipositors of two closely related species, Drosophila melanogaster and D. suzukii. D. suzukii has switched its egg-laying niche from rotting to ripe fruit. Along with this shift, the D. suzukii ovipositor has undergone a significant change in size and shape. Using an allometric approach we find that, while adult ovipositor width has hardly changed between the species, D. suzukii ovipositor length is almost double that of D. melanogaster. We show that this size difference mostly arises during a 6-hour time window in the middle of pupal development. We observe that the developing ovipositors of the two species comprise an almost identical number of cells, with a very similar profile of cell shapes and orientations. After cell division stops, we find that the ovipositor area continues to grow through the isotropic expansion of cell apical area. Remarkably, at one point, the rate of cell apical area expansion is more than 4 times faster in D. suzukii than in D. melanogaster. In addition, we find that an anisotropic cellular reorganization of the developing ovipositor results in a net elongation of the tissue, despite the isotropic expansion of cell size, and is enhanced in D. suzukii. Therefore, the quantitative fine-tuning of shared, morphogenetic processes -the rate of cell size expansion and the cellular rearrangements-can drive macroscopic evolutionary changes in organ size and shape.

evolutionary biology↗