Space colonization by branching trachea explains the morphospace of a simple respiratory organ

Ruiz-Sobrino, A.; Martín-Blanco, Carlos; Navarro, Tomás Mancha; Almudí, Isabel; Masiero, Giulio; Jiménez-Caballero, M.; Buchwalter, David B.; Funk, David H.; Gattolliat, Jean‐Luc; Lemos, María Carmen; Jiménez, Fernando; Casares, Fernando

doi:10.1016/j.ydbio.2020.02.005

Cited by 3 publications

(5 citation statements)

References 30 publications

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“…For nuclei counting nymphs were taken from different timepoints (1,2,4,5,7,14,21,23,26,29,32 dph and last nymphal instar (LNI)). The gut was removed and then nymphs were fixed in 4% formaldehyde in PBS overnight at 4ºC with shaking.…”

Section: Dapi Staining Image Collection and Image Data Analysis (Trac...mentioning

confidence: 99%

“…Then, DESeq2 library in R and Rstudio was used to perform differential expression analysis of the samples. Functional annotation was retrieved from available data at NCBI [21] and Uniprot (https://www.uniprot.org/). To retrieve GO annotations for Drosophila melanogaster ortholog genes BioMart was used.…”

Section: Rnaseq Experimental Design Rna Extraction Library Preparatio...mentioning

confidence: 99%

“…These gills are flat, paddle-like organs joined to the abdomen through a thin hinge (Figure 1A). The gills on A1-6 have two lamellae each and are motile, while the gills on A7 are mono-lamellated and non-motile (21). Gills are tracheated and thought to be involved in gas exchange/respiration (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Gill regeneration in the mayflyCloeonuncovers new molecular pathways in insect regeneration

Martin-Blanco,

Navarro,

Esteban-Collado

et al. 2024

Preprint

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The capacity to regenerate lost or damaged organs is widespread among animals, and yet, the species in which regeneration has been experimentally probed using molecular and functional assays is very small. This is also the case for insects, for which we still lack a complete picture of their regeneration mechanisms and the extent of conservation of these mechanisms. Here we contribute to filling this gap by investigating regeneration in the mayfly Cloeon dipterum. Mayflies, or Ephemeroptera, appeared early in the evolution of insects. We focus on the abdominal gills of Cloeon nymphs, which are critical for osmoregulation and gas exchange. After amputation, gills re-grow faster than they do during normal development. Direct cell count and EdU proliferation assays indicate that growth acceleration involves an uniform increase in cell proliferation throughout the gill, rather than a localized growth zone. Transcriptomic analysis reveals an early enrichment in cell cycle-related genes, in agreement with fast proliferation. Several other gene classes are also enriched in regenerating gills, including protein neddylation and other proteostatic processes. We then showed that protein neddylation, the activin signaling pathway or the mRNA-binding protein Lin28, among other genes and processes, are required for Drosophila larval/pupal wing regeneration, and that some of these genes may have a regeneration-specific function in the wing. Globally, our results contribute to elucidating regeneration mechanisms in mayflies and suggest a conservation of regeneration mechanisms across insects, as evidenced by the regenerative role of candidate genes identified in Cloeon in the distant Drosophila.

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Section: Dapi Staining Image Collection and Image Data Analysis (Trac...mentioning

confidence: 99%

Section: Rnaseq Experimental Design Rna Extraction Library Preparatio...mentioning

confidence: 99%

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Gill regeneration in the mayflyCloeonuncovers new molecular pathways in insect regeneration

Martin-Blanco,

Navarro,

Esteban-Collado

et al. 2024

Preprint

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“…Pattern generation formed by the foraging of some multicellular organisms (i.e. Physarum polycephalum) [118,119] Constrained constructive optimisation [120] Computational modeling Intravascular volume and branching angles (cost function) Complex arterial trees [121,122], human cerebrovasculature [123] Active shape model [124] Computational modeling Reference points of real images Retinal vascular network [125] Diffusion-limited aggregation [126] Computational modeling Density correlations in terms of the distance separating the two sites Branching structures (arteries/veins) [127], river networks [128], simulation of natural texture [129] Particle system [130] Computational modeling Particle distribution and motion Leaf structures [130] and topology optimization of heat conduction systems [131] Lindenmayer system (Lsystem) [132] Computational modeling Branching angles, elongation rates and vigor of branches Virtual plants [132], retinal vasculature [26] and blood vessel [133] Space colonization algorithm [30] Computational modeling Attraction points, radius of influence and kill distance Branching structure of trees [30], leaf venation [29], finger vein images [4] and tracheal gills of mayfly larvae [134] Hybrid models [135,136] Computational modeling…”

Section: Concentration and Nutrient Gradientsmentioning

confidence: 99%

“…The spatial colonization algorithm has also allowed the generation of other types of structures. In [4], they use the algorithm for the generation of synthetic images of finger veins, and in [134] simulate the branching patterns of mayfly gills to investigate the global mechanism driving their generation and morphological evolution.…”

Section: Concentration and Nutrient Gradientsmentioning

confidence: 99%

Towards the Generation of Synthetic Images of Palm Vein Patterns: A Review

Salazar-Jurado,

Hernández-García,

Vilches-Ponce

et al. 2022

Preprint

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With the recent success of computer vision and deep learning, remarkable progress has been achieved on automatic personal recognition using vein biometrics. However, collecting large-scale real-world training data for palm vein recognition has turned out to be challenging, mainly due to the noise and irregular variations included at the time of acquisition. Meanwhile, existing palm vein recognition datasets are usually collected under near-infrared light, lacking detailed annotations on attributes (e.g., pose), so the influences of different attributes on vein recognition have been poorly investigated. Therefore, this paper examines the suitability of synthetic vein images generated to compensate for the urgent lack of publicly available large-scale datasets. Firstly, we present an overview of recent research progress of palm vein recognition, from the basic background knowledge to vein anatomical structure, data acquisition, public database, and quality assessment procedures. Then, we focus on the state-of-the-art methods that have allowed the generation of vascular structures for biometric purposes and the modeling of biological networks with their respective application domains. In addition, we review the existing research on the generation of style transfer and biological nature-based synthetic palm vein images algorithms. Afterward, we formalize a general flowchart for the creation of a synthetic database comparing real palm vein images and generated synthetic samples to obtain some understanding into the development of the realistic vein imaging system. Ultimately, we conclude by

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