Trilobite compound eyes with crystalline cones and rhabdoms show mandibulate affinities.
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ABSTRACT:
SUBMITTER: Scholtz G
PROVIDER: S-EPMC6555793 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundUnderstanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography (micro-CT) is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models.ResultsWe developed a computing method named InSegtCone to automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60-80% of the crystalline cones and is about as accurate and 250 times faster than manual labelling of the individual cones.ConclusionsWe believe that InSegtCone can be an important tool for peer scientists to measure the orientation, size and dynamics of crystalline cones, leading to the accurate optical modelling of the diversity of arthropod eyes with micro-CT.
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Project description:The trilobite head served multiple functions and was composed of several fused segments. Yet, the underlying organization of the trilobite head, and whether patterns are conserved across trilobites, remains unclear. Modeling the head as being composed of modules, or subunits that vary and thus have the potential to evolve semi-independently can reveal underlying patterns of organization. Hypotheses of modular organization based on the comparative developmental biology of arthropods were evaluated using geometric morphometrics. Two-dimensional (semi)landmark datasets collected from the cranidia of two Ordovician trilobite species, Calyptaulax annulata (Phacopida) and Cloacaspis senilis (Olenida sensu Adrain, 2011) were analyzed. The degree and pattern of modularity were assessed using the covariance ratio (CR), which compares the covariation within putative modules to the covariation between them, and the fit of different models was compared using an effect size measure derived from the CR. When treating the eyes as a distinct module, the best modular hypothesis identified for C. annulata shows the eyes and anteriormost region of the head integrated as a single module. The best modular hypotheses for C. senilis are more complex but the eyes still covary mostly strongly with the anterior part of the head. The latter is also the case for all other well-supported models for both species. These results can be interpreted as a developmental signal corresponding to the anteriormost ocular segment of early arthropods that is retained throughout development, despite any likely selective pressures related to functional needs.
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Project description:In most animal species, vision is mediated by compound eyes, which offer lower resolution than vertebrate single-lens eyes, but significantly larger fields of view with negligible distortion and spherical aberration, as well as high temporal resolution in a tiny package. Compound eyes are ideally suited for fast panoramic motion perception. Engineering a miniature artificial compound eye is challenging because it requires accurate alignment of photoreceptive and optical components on a curved surface. Here, we describe a unique design method for biomimetic compound eyes featuring a panoramic, undistorted field of view in a very thin package. The design consists of three planar layers of separately produced arrays, namely, a microlens array, a neuromorphic photodetector array, and a flexible printed circuit board that are stacked, cut, and curved to produce a mechanically flexible imager. Following this method, we have prototyped and characterized an artificial compound eye bearing a hemispherical field of view with embedded and programmable low-power signal processing, high temporal resolution, and local adaptation to illumination. The prototyped artificial compound eye possesses several characteristics similar to the eye of the fruit fly Drosophila and other arthropod species. This design method opens up additional vistas for a broad range of applications in which wide field motion detection is at a premium, such as collision-free navigation of terrestrial and aerospace vehicles, and for the experimental testing of insect vision theories.
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Project description:Custom Spectral Domain Optical Coherence Tomography (SD-OCT) provided with automatic quantification and distortion correction algorithms was used to measure anterior and posterior crystalline lens surface elevation in accommodating eyes and to evaluate relationships between anterior segment surfaces. Nine young eyes were measured at different accommodative demands. Anterior and posterior lens radii of curvature decreased at a rate of 0.78 ± 0.18 and 0.13 ± 0.07 mm/D, anterior chamber depth decreased at 0.04 ± 0.01 mm/D and lens thickness increased at 0.04 ± 0.01 mm/D with accommodation. Three-dimensional surface elevations were estimated by subtracting best fitting spheres. In the relaxed state, the spherical term accounted for most of the surface irregularity in the anterior lens (47%) and astigmatism (70%) in the posterior lens. However, in accommodated lenses astigmatism was the predominant surface irregularity (90%) in the anterior lens. The RMS of high-order irregularities of the posterior lens surface was statistically significantly higher than that of the anterior lens surface (x2.02, p<0.0001). There was significant negative correlation in vertical coma (Z3 (-1)) and oblique trefoil (Z3 (-3)) between lens surfaces. The astigmatic angle showed high degree of alignment between corneal surfaces, moderate between corneal and anterior lens surface (~27 deg), but differed by ~80 deg between the anterior and posterior lens surfaces (including relative anterior/posterior lens astigmatic angle shifts (10-20 deg).
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Project description:Predicting compound-protein affinity is beneficial for accelerating drug discovery. Doing so without the often-unavailable structure data is gaining interest. However, recent progress in structure-free affinity prediction, made by machine learning, focuses on accuracy but leaves much to be desired for interpretability. Defining intermolecular contacts underlying affinities as a vehicle for interpretability; our large-scale interpretability assessment finds previously used attention mechanisms inadequate. We thus formulate a hierarchical multiobjective learning problem, where predicted contacts form the basis for predicted affinities. We solve the problem by embedding protein sequences (by hierarchical recurrent neural networks) and compound graphs (by graph neural networks) with joint attentions between protein residues and compound atoms. We further introduce three methodological advances to enhance interpretability: (1) structure-aware regularization of attentions using protein sequence-predicted solvent exposure and residue-residue contact maps; (2) supervision of attentions using known intermolecular contacts in training data; and (3) an intrinsically explainable architecture where atomic-level contacts or "relations" lead to molecular-level affinity prediction. The first two and all three advances result in DeepAffinity+ and DeepRelations, respectively. Our methods show generalizability in affinity prediction for molecules that are new and dissimilar to training examples. Moreover, they show superior interpretability compared to state-of-the-art interpretable methods: with similar or better affinity prediction, they boost the AUPRC of contact prediction by around 33-, 35-, 10-, and 9-fold for the default test, new-compound, new-protein, and both-new sets, respectively. We further demonstrate their potential utilities in contact-assisted docking, structure-free binding site prediction, and structure-activity relationship studies without docking. Our study represents the first model development and systematic model assessment dedicated to interpretable machine learning for structure-free compound-protein affinity prediction.
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Project description:Complex traits like limbs, brains, or eyes form through coordinated integration of diverse cell fates across developmental space and time, yet understanding how complexity and integration emerge from uniform, undifferentiated precursor tissues remains limited. Here, we use ectopic eye formation as a paradigm to investigate the emergence and integration of novel complex structures following massive ontogenetic perturbation. We show that down-regulation via RNAi of a single head patterning gene-orthodenticle-induces ectopic structures externally resembling compound eyes at the middorsal adult head of both basal and derived scarabaeid beetle species (Onthophagini and Oniticellini). Scanning electron microscopy documents ommatidial organization of these induced structures, while immunohistochemistry reveals the presence of rudimentary ommatidial lenses, crystalline cones, and associated neural-like tissue within them. Further, RNA-sequencing experiments show that after orthodenticle down-regulation, the transcriptional signature of the middorsal head-the location of ectopic eye induction-converges onto that of regular compound eyes, including up-regulation of several retina-specific genes. Finally, a light-aversion behavioral assay to assess functionality reveals that ectopic compound eyes can rescue the ability to respond to visual stimuli when wild-type eyes are surgically removed. Combined, our results show that knockdown of a single gene is sufficient for the middorsal head to acquire the competence to ectopically generate a functional compound eye-like structure. These findings highlight the buffering capacity of developmental systems, allowing massive genetic perturbations to be channeled toward orderly and functional developmental outcomes, and render ectopic eye formation a widely accessible paradigm to study the evolution of complex systems.
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