Advanced optical imaging in living embryos

Developmental biology investigations have evolved from static studies of embryo anatomy and into dynamic studies of the genetic and cellular mechanisms responsible for shaping the embryo anatomy. With the advancement of fluorescent protein fusions, the ability to visualize and comprehend how thousands to millions of cells interact with one another to form tissues and organs in three dimensions (xyz) over time (t) is just beginning to be realized and exploited. In this review, we explore recent advances utilizing confocal and multi-photon time-lapse microscopy to capture gene expression, cell behavior, and embryo development. From choosing the appropriate fluorophore, to labeling strategy, to experimental set-up, and data pipeline handling, this review covers the various aspects related to acquiring and analyzing multi-dimensional data sets. These innovative techniques in multi-dimensional imaging and analysis can be applied across a number of fields in time and space including protein dynamics to cell biology to morphogenesis

Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions

Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions

Dynamic Coupling of Pattern Formation and Morphogenesis in the Developing Vertebrate Retina

In this Research Article, Picker et al. show how cells in the retina get their spatial coordinates

Collective cell migration: general themes and new paradigms

Collective cell migration plays essential roles in embryogenesis and also contributes to disease states. Recent years have seen immense progress in understanding mechanisms and overarching concepts of collective cell migration. Self-organization of moving groups emerges as an important common feature. This includes self-generating gradients, internal chemotaxis or mechanotaxis and contact-dependent polarization within migrating cell groups. Here, we will discuss these concepts and their applications to classical models of collective cell migration. Further, we discuss new models and paradigms of collective cell migration and elaborate on open questions and future challenges. Answering these questions will help to expand our appreciation of this exciting theme in developmental cell biology and contribute to the understanding of disease states

Dynamic Fgf signaling couples morphogenesis and migration in the zebrafish lateral line primordium

The collective migration of cells in the form of cohesive tissues is a hallmark of both morphogenesis and repair. The extrinsic cues that direct these complex migrations usually act by regulating the dynamics of a specific subset of cells, those at the leading edge. Given that normally the function of tissue migration is to lay down multicellular structures, such as branched epithelial networks or sensory organs, it is surprising how little is known about the mechanisms that organize cells behind the leading edge. Cells of the zebrafish lateral line primordium switch from mesenchyme-like leader cells to epithelial rosettes that develop into mechanosensory organs. Here, we show that this transition is regulated by an Fgf signaling circuit that is active within the migrating primordium. Point sources of Fgf ligand drive surrounding cells towards a ;non-leader' fate by increasing their epithelial character, a prerequisite for rosette formation. We demonstrate that the dynamic expression of Fgf ligands determines the spatiotemporal pattern of epithelialization underlying sensory organ formation in the lateral line. Furthermore, this work uncovers a surprising link between internal tissue organization and collective migration

Control of convergent yolk syncytial layer nuclear movement in zebrafish

Nuclear movements play an essential role in metazoan development. Although the intracellular transport mechanisms underlying nuclear movements have been studied in detail, relatively little is known about signals from surrounding cells and tissues controlling these movements. Here, we show that, in gastrulating zebrafish embryos, convergence movements of nuclei within the yolk syncytial layer (YSL) are guided by mesoderm and endoderm progenitors migrating along the surface of the yolk towards the dorsal side of the developing gastrula. Progenitor cells direct the convergence movements of internal yolk syncytial nuclei (iYSN) by modulating cortical flow within the YSL in which the iYSN are entrained. The effect of mesoderm and endoderm progenitors on the convergence movement of iYSN depends on the expression of E-cadherin, indicating that adhesive contact between the cells and the YSL is required for the mesendoderm-modulated YSL cortical flow mediating nuclear convergence. In summary, our data reveal a crucial function for cortical flow in the coordination of syncytial nuclear movements with surrounding cells and tissues during zebrafish gastrulation

Fish diversity assessment in the headwaters of the Volga River using environmental DNA metabarcoding

The headwaters of the Volga River exhibit large reaches with near‐pristine conditions, and therefore long‐term biodiversity monitoring of this catchment can provide rare and valuable information on a European lowland river. More specifically, freshwater fish species assemblages are a good indicator of ecosystem status, as they are particularly sensitive to environmental changes and hydromorphological alterations. Historical records show that the fish fauna of the Upper Volga has changed over time, both in species composition and in abundance. The construction of the Volga–Kama cascade (a series of large dams) has specifically affected the migration of diadromous species. Environmental DNA metabarcoding offers a non‐invasive approach to determine the number of species in an aquatic ecosystem, as well as their identity and distribution. This approach is especially useful for fish fauna surveys along large rivers and long‐term biomonitoring, with the advantage of having no impact on the species and their habitats. To infer the current fish species diversity and the spatial distribution of each species in the free‐flowing section of the Upper Volga River, as well as in selected tributaries, an environmental DNA metabarcoding approach was applied, using three mitochondrial DNA markers. This method allowed the positive identification of 23 fish species and their respective distributions in the headwaters of the Volga. This assessment provides a valuable example of the application of environmental DNA metabarcoding in a large river system, and constitutes a starting point for future investigations and long‐term biomonitoring in the Upper Volga system. In addition, the results can also serve as a reference for fish diversity assessments of other large European lowland rivers, and can guide future conservation and management measures in the headwaters of the Volga