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An analysis of behavioural, eco-morphological and genomic data in 60 species of Lake Tanganyika cichlids reveals a remarkable diversity of temporal activity patterns across species, suggesting that temporal niche partitioning may have played a role in the adaptive diversification of this group.

Planar cell polarity (PCP) regulates hair cell orientation in the zebrafish lateral line. Here, the authors show that mutating Wnt pathway genes (wnt11f1, fzd7a/b, and gpc4) causes concentric hair cell patterns not regulated by PCP, thus showing PCP/Wnt pathway genes have different consequences on hair cell orientation.

scGESTALT enables large-scale characterization of cell types and lineage relationships during vertebrate brain development.

This protocol describes how to generate transgenic zebrafish expressing a barcode array that can be edited by CRISPR–Cas9 at multiple developmental stages. Single-cell RNA sequencing of edited barcodes and cellular transcriptomes allows reconstruction of lineage relationships.

Single-cell transcriptomics of hypothalamic cells from zebrafish and surface and cave morphs of Mexican tetra shows conservation of cell types and that cellular novelty is associated with genetic novelty and the species-specific expression of paralogous genes.

Upstream open reading frames (uORFs) can repress gene expression. Here, Guo-Liang Chew and colleagues use bioinformatics approaches to show that conservation of uORF-mediated translational repression is mediated by sequence features in human, mouse and zebrafish genomes.

Almuedo-Castillo et al. show that extirpated embryos are reduced in size but exhibit normal proportions. Following a computational screen, the authors identify an increased concentration of the Nodal inhibitor Lefty to be responsible for the size scaling.

Single-cell transcriptome profiling of mouse embryos and newborn pups is combined with previously published data to construct a tree of cell-type relationships tracing development from zygote to birth.

Food intake is determined by learned appetitive responses and physiological “appetition” signals after eating begins. Here, authors show melanin-concentrating hormone (MCH)-producing neurons integrate these processes to promote caloric intake.

Structure-guided protein engineering of Cas12a yields variants that have increased activity and that can edit sites with previously inaccessible PAMs.

Detecting and responding to noxious stimuli is essential for survival. Wee et al. show that noxious stimuli elicit intense and widespread activity in zebrafish oxytocin neurons, which promote defensive behavior by activating hindbrain premotor neurons.

Neural activity is recorded at the cellular level, throughout the brain of larval zebrafish, while the animals interact with a virtual environment and adapt their motor output to changes in visual feedback; this is used to derive candidates of functional elements driving motor learning.

While the CRISPR-Cas9 system has revolutionised molecular biology, it is still a mystery why not every guide RNA elicits target DNA cleavage. Here the authors show that genomic context and internal gRNA interactions can inhibit cleavage.

Gradients of signalling molecules dictate where specific cell types form in developing tissues, but how these gradients are set up is much debated. A model proposed 40 years ago by Francis Crick may provide an answer.

Directed gene knockout in a vertebrate has been achieved using zinc-finger nucleases.

The reported sequence of the zebrafish genome, together with the production of mutant strains representing more than one-third of all its protein-coding regions, will accelerate the characterization of human genes. See Letters p.494 & p.498

Impulsive behaviour is common in various neuropsychiatric disorders. Here, the authors identify a pathway from the lateral hypothalamus to the ventral hippocampus and the role of melanin-concentrating hormone signaling in these neurons in specifically regulating impulsivity.

MicroRNAs and long non-coding RNAs regulate diverse aspects of animal embryogenesis. Recent evidence from several species shows their importance in driving and maintaining cell fate decisions, from early patterning through to tissue specification and morphogenesis.

To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency during the maternal–zygotic transition (MZT), the genomic locations of histone H3 modifications and RNA polymerase II have been mapped during this transition in zebrafish embryos. H3 lysine 27 trimethylation and H3 lysine 4 trimethylation are only detected after MZT; evidence is provided that the bivalent chromatin domains found in cultured embryonic stem cells also exist in embryos.

RNA-seq data from single cells are mapped to their location in complex tissues using gene expression atlases based on in situ hybridization.

Quantum electrodynamics predicts a rare process in which light is scattered by light. The ATLAS Collaboration reports signs of this elusive effect in the collisions of ultra-relativistic lead ions.

A complete larval zebrafish brain is examined and its myelinated axons reconstructed using serial-section electron microscopy, revealing remarkable symmetry and providing a valuable resource.

Z-Brain is an atlas of the larval zebrafish brain. It can be combined with pERK-based neural-activity measurements from freely behaving zebrafish to identify brain regions involved in generating behavior.

Humans and other vertebrates develop in a head-to-tail sequence. A mechanism that is based on a gradual decay of RNA appears to contribute to this process.

The field of single-cell RNA sequencing (scRNA-seq) has been paired with genomics, epigenomics, spatial omics, proteomics and imaging to achieve multimodal measurements of individual cellular phenotypes and genotypes. In its purest form, single-cell multimodal omics involves the simultaneous detection of multiple traits in the same cell. More broadly, multimodal omics also encompasses comparative pairing and computational integration of measurements made across multiple distinct cells to reconstruct phenotypes. Here I highlight some of the biological insights gained from multimodal studies and discuss the challenges and opportunities in this emerging field.

The authors devised a method for detecting the bioluminescent Ca²⁺ sensor GFP-Aequorin in freely behaving zebrafish larvae. To demonstrate the efficacy of the technique, they targeted the sensor to a genetically specified population of hypothalamic neurons. The resulting neuroluminescence reveals patterns of neuronal activity that are associated with distinct swimming behaviors.

Recent advances in genome engineering are enabling the recording of cellular histories into genomes, with single-cell and spatial omics technologies enabling their reconstruction into cellular lineages, states and exposures. This Perspective explores the rationale and technical basis of DNA recording, what aspects of cellular biology can be recorded and how, and the types of discovery that DNA recording will enable when studying development and disease.

Iain Drummond, Heymut Omran, Stephen King and colleagues show that CCDC103 mutations cause primary ciliary dyskinesia. Their studies suggest that CCDC103 is a core axonemal factor that helps anchor dynein motor complexes to ciliary microtubules.

This Technical Report describes light-activatable metabotropic glutamate receptors based on synthetic photoswitchable tethered ligands, and demonstrates optogenetic control of G protein–coupled receptor activity in neurons in vivo and ex vivo.

Experimental evidence that global Kctd13 reduction leads to increased RhoA levels that reduce synaptic transmission, implicating RhoA as a potential therapeutic target for neuropsychiatric disorders associated with copy-number variants that include KCTD13.