Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs)—generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data—for visualizing population genetic variation. VAEs incorporate nonlinear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.

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In the last two decades, the zebrafish has emerged as an important model species for heart regeneration studies. Various approaches to model loss of cardiac myocytes and myocardial infarction in the zebrafish have been devised, and have included resection, genetic ablation, and cryoinjury. However, to date, the response of the zebrafish ventricle to cautery injury has not been reported. Here, we describe a simple and reproducible method using cautery injury via a modified nichrome inoculating needle as a probe to model myocardial infarction in the zebrafish ventricle. Using light and electron microscopy, we show that cardiac cautery injury is attended by significant inflammatory cell infiltration, accumulation of collagen in the injured area, and the reconstitution of the ventricular myocardium. Additionally, we document the ablation of cardiac nerve fibers, and report that the re-innervation of the injured zebrafish ventricle is protracted, compared to other repair processes that accompany the regeneration of the cauterized ventricle. Taken together, our study demonstrates that cautery injury is a simple and effective means for generating necrotic tissue and eliciting a remodeling and regenerative response in the zebrafish heart. This approach may serve as an important tool in the methods toolbox for regeneration studies in the zebrafish.

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs) – generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data – for visualizing population genetic variation. VAEs incorporate non-linear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.

Background Aquatic species in several clades possess cement glands producing adhesive secretions of various strengths. In vertebrates, transient adhesive organs have been extensively studied in Xenopus laevis, other anurans, and in several fish species. However, the development of these structures is not fully understood. Results Here, we report on the development and functional morphology of the adhesive gland of a giant danio species, Devario malabaricus. We found that the gland is localized on the larval head, is composed of goblet‐like secretory cells framed by basal, bordering, and intercalated apical epithelial cells, and is innervated by the trigeminal ganglion. The gland allows nonswimming larvae to adhere to various substrates. Its secretory cells differentiate by 12 hours postfertilization and begin to disappear in the second week of life. Exogenous retinoic acid disrupts the gland's patterning. More importantly, the single mature gland emerges from fusion of two differentiated secretory cells fields; this fusion is dependent on nonmuscle myosin II function. Conclusions Taken together, our studies provide the first documentation of the embryonic development, structure, and function of the adhesive apparatus of a danioninae. To our knowledge, this is also the first report of a cement gland arising from convergence of two bilateral fields.