Fetal alcohol spectrum disorders (FASD) encompass a broad range of effects caused by prenatal alcohol exposure. In the United States, conservative estimates place the incidence of FASD at a rate of 5 in 100 births. Children with FASD can have morphological afflictions including congenital defects of the brain, spinal cord, heart, eyes, and skeleton, as well as poor formation of facial structures such as the nose and mouth. Cognitive and behavioral abnormalities such as learning disabilities, socio-developmental delays and emotional disorders are also highly prevalent. There is no known cure for FASD and in utero detection methods are not available. In terms of urinary tract defects, kidney and renal related maladies may represent underreported aspects of FASD. To better understand the renal phenotypes associated with prenatal alcohol exposure, we employed the zebrafish, Danio rerio, a vertebrate species well suited for developmental nephrology and teratological work that has been used extensively to model FASD. We treated zebrafish embryos with ethanol then examined pattern formation and physiological activity of nephrons, which are the basic structural and functional unit of the kidney. Using whole mount in situ hybridization, we found that the formation of several cell types in the nephron blood filter and tubule, as well as renal progenitor populations, were perturbed by alcohol exposure. Interestingly, supplementation with all-trans retinoic acid, a vitamin A derivative associated with mitigating the effects of ethanol exposure in zebrafish and other animals, was sufficient to completely or partially rescue multiple ethanol induced kidney cell defects and restore nephron physiological activity. These studies have revealed several consequences of ethanol exposure that lead to the deregulation of renal ontogeny, and implicate a key role for reduced RA levels, thereby contributing useful insights relevant to the broader field of FASD research.

Pathogenic, presumed gain-of-function variants in the gene KCNT1, which encodes a sodium-activated potassium channel, cause a severe neurodevelopmental disorder with intractable epilepsy. In addition to seizures, affected individuals commonly present with severe respiratory issues and structural heart defects not commonly observed in other genetic pediatric epilepsies, suggesting additional developmental functions for KCNT1 in organs beyond the brain. Here we characterized the spectrum of clinical diagnoses present in a cohort of 46 individuals with genetic variants in KCNT1, ranging from 0 to 19 years of age, by medical record review. We documented the prevalence of diagnoses across organ systems, including dependence on assisted breathing, congenital structural heart defects, urinary dysfunction, and spine deformities, among others. Next, we explored the embryonic expression and function of KCNT1 in diploid frogs (Xenopus tropicalis) and observed expression in developing ciliated tissues such as the brain, heart, kidney, and epidermis. Embryonic perturbation of KCNT1 disrupted developmental signaling pathways and caused ciliogenesis defects in the mucociliary epidermis, a common model for the human airway. Loss of KCNT1 disrupted development of multiciliated cells, reminiscent of recent work on the ion channel Piezo1. Consistently, pharmacological inhibition of Piezo signaling enhanced the ciliogenesis phenotype observed following KCNT1 inhibition, while activation of Piezo1 activity partially rescued ciliogenesis in the context of KCNT1 inhibition. Finally, KCNT1 loss reduced expression of foxj1, a key transcriptional regulator of multiciliated cell specification, linking KCNT1 activity to the transcriptional programs underlying multiciliated cell formation and specification. Together, this work establishes that KCNT1 has embryonic functions in Xenopus beyond regulating neuronal activity, specifically in multiciliated cell development, and identifies an interaction with pharmacologically-tractable Piezo channels that may be productive for therapeutic efforts aimed at inhibiting KCNT1 activity.

At head levels, neural crest (NC) multipotent stem cells are specified in the ectoderm territory located between the anterior neural plate ectoderm and the future pre-placodal and lateral non-neural ectoderm. While the fine-tuning of NC specification is increasingly being elucidated, many questions remain, including how microRNAs may govern expression of gene programs during these processes. We have identified miR-219 as a candidate regulator of craniofacial development in the vertebrate Xenopus laevis. Here, we characterize this phenotype and explore miR-219-dependent molecular pathways by morpholino knock-down. The development of the NC and adjacent ectoderm was evaluated using whole mount in situ hybridization (WISH) of key markers (pax3, zic1, xhe2, sox10, snai2, sox2), alcian blue cartilage staining, phenotype analysis, RNA sequencing of microdissected dorsal ectoderm and microRNA rescue experiments. These complementary approaches show that while neural induction is mainly unaffected, miR-219 depletion alters gene expression programs associated with neural border development, explaining the phenotype. WISH and RNA sequencing of the miR-219 morphant tissue highlights that NC progenitor programs (pax3, zic1, pou5f3, sall3) are maintained or increased at the expense of the progression of NC development (twist1, rpe65), resulting in defective NC specification. While increased pax3 expression seems an important part of this program, reducing pax3 in miR-219 morphant embryos is not sufficient to rescue the phenotype, highlighting that other key partners remain to be identified. This study supports an important and complex role of miR-219 in the early steps of neural crest formation.

Unlike the adult mammalian heart, the adult zebrafish heart can robustly regenerate via processes that include cardiomyocyte (CM) dedifferentiation, proliferation, and repopulation of the damaged tissue. Although CM dedifferentiation is considered indispensable for cardiac regeneration, the factors driving it remain elusive. Here, we examine the role of Mustn1b in CM dedifferentiation during zebrafish cardiac regeneration. Mustn1b is a small protein highly expressed in skeletal, smooth, and cardiac muscle tissues. Using a mustn1b:EGFP reporter line, we first find that its expression is specific to CMs during heart development, and that it peaks at early larval stages. In the regenerating adult heart, mustn1b reporter expression is re-induced in dedifferentiating CMs, establishing it as a novel marker for this subset of CMs. By evaluating two newly generated mustn1b loss-of-function mutant alleles, including a large deletion allele, we find that Mustn1b deficiency leads to decreased CM dedifferentiation and proliferation, and ultimately results in impaired cardiac regeneration. Furthermore, CM-specific overexpression of mustn1b can enhance CM dedifferentiation and proliferation after cardiac cryoinjury. Mechanistically, mass spectrometry data suggest that upon cryoinjury, Mustn1b interacts with sarcomeric and cytoskeletal proteins, pointing towards a role in structural remodeling that could facilitate CM dedifferentiation during heart regeneration. Altogether, our findings identify Mustn1b as a regulator of CM dedifferentiation during zebrafish cardiac regeneration.

Mechanosensing and mechanotransduction are essential for all living cells. In mammals, Piezo1 and Piezo2 are two mechanically activated cation channels that serve as mechanosensors for a variety of physiological and pathological processes, ranging from touch sensing to sickle cell disease. These two channels are well evolutionarily conserved, and orthologous genes can be traced back to the origin of vertebrates, which underwent whole-genome duplications (WGDs). The number of paralogous genes originating from the vertebrate WGD varies across gene families. Thus, whether there are more PIEZO paralogous genes in vertebrates remains understudied. Here, we identified piezo3, a new paralog of the piezo gene family, and analyzed its evolutionary history using phylogenetic and synteny analyses. The piezo3 gene is present in most vertebrate lineages but absent in birds and most mammals, likely due to nonfunctionalization after WGDs. In addition, we demonstrated that this channel could mediate calcium flux in response to mechanical stimuli in HEK293T cells, suggesting that Piezo3 exhibits PIEZO1/2-like activation and conduction channel functions. Our CRISPR mutation analysis revealed that the zebrafish piezo3 gene is not developmentally essential for skeletons and survival, possibly because its expression overlaps with other PIEZO channels. Mutant zebrafish showed elevated sensitivity to mechanical force and increased locomotor activity under (photopic) light illumination. Our results suggest that this new mechanical-sensing Piezo channel is widespread in vertebrates and may be critical for vertebrate adaptation by modulating mechanical sensing and light responses during evolution.

In canonical developmental patterning, the embryo is exposed to gradients of signaling activators that elicit different cellular responses depending on the activator's concentration. It remains largely unknown how very low doses of an inductive signal are read out to produce potent developmental responses. Recent optogenetic studies in early Drosophila embryos show that a brief, 5-minute ERK stimulus is sufficient to rescue the development of larval tail structures. Here, we reveal components of the molecular network that produces this sensitive developmental fate response. We find that low ERK doses produce sustained Abdominal-B (Abd-B) expression. We then show that Abd-B expression is adjacent to, but non-overlapping with, two transcriptional repressors, the ERK effector Tailless (Tll) and the gap gene Giant (Gt), under a broad range of genetic and optogenetic perturbations. We detect sensitive changes to tll, Abd-B, and gt expression in response to optogenetic ERK activation and propose that ERK-to-tailless signaling mediates the effect on Abd-B and gt. The spectrum of phenotypes produced through optogenetic manipulation is thus a powerful tool for defining how robust patterning can arise from low doses of inductive signals.

Cell motility is essential for processes such as immune responses, wound healing, and fertilization. Caenorhabditis elegans is an excellent model for studying sperm motility, due to the worm's transparency and high sperm production. C. elegans amoeboid sperm move by extending and retracting pseudopods, which are powered internally by the dynamic polymerization and depolymerization of the nematode Major Sperm Protein (MSP). Previous biochemical studies in the parasitic nematode Ascaris suum identified MSP polymerization-activating kinase (MPAK) as a key regulator of MSP assembly within the pseudopod. Here we investigate two C. elegans homologs, Tau Tubulin Kinase 8.1 (ttbk-8.1) and Tau Tubulin Kinase 8.2 (ttbk-8.2), that arose from a C. elegans-specific gene duplication. We generated both single and double knockout mutants; single knockout animals have fertility comparable to wildtype. Self-fertilizing double knockout (ttbk-8.1/2) hermaphrodites are severely sub-fertile, and males are completely infertile. ttbk-8.1/2 males successfully transfer sperm to females; however, their sperm cannot crawl to the site of fertilization. During sperm activation, ttbk-8.1/2 sperm undergo the two key events of sperm activation (membranous organelle fusion and pseudopod extension), however the process is abnormally slow. Furthermore, the resulting pseudopods are non-motile and abnormally smooth. Localization of key proteins to the pseudopods remains unaffected. TTBK-8.1/2 colocalizes with MSP to the fibrous bodies in mature spermatocytes, distributes throughout the cytoplasm in spermatids, and is confined to pseudopods of spermatozoa. These findings suggest an essential role for TTBK-8.1/2 in timely sperm activation and pseudopod motility.

Some major discoveries come as the culmination of a long progression of incremental findings and evolving ideas. The discovery of maternal mRNA was different, its instancy noteworthy as a matter of epistemology. But it had a second impact, one that was far greater than the fast kinetics of the discovery per se. This was because it was the moment when embryology became molecular biology. This key event then soon aligned with genetics, deployed particularly in Drosophila and C. elegans, there proving this approach to be the emperor of all disciplines for the study of development. But the 1960's discovery of maternal mRNA, in the sea urchin, was the milestone in catalyzing this later heuristic vector.

One-carbon (1C) metabolism is a central metabolic network that integrates nutrient availability with biosynthetic and epigenetic processes essential for embryonic and placental development. By transferring carbon units derived from amino acids and folate metabolism, this pathway generates nucleotides, methyl donors, and other intermediates required for cell proliferation and differentiation. The pathway is compartmentalized between mitochondria and cytosol, with mitochondrial reactions frequently supplying formate and other 1C units to sustain cytosolic biosynthesis in rapidly dividing cells. Pluripotent stem cells illustrate the strong dependence of cell identity on 1C metabolism. Mouse embryonic stem cells rely on threonine catabolism to produce glycine, acetyl-CoA, and S-adenosylmethionine (SAM), which supports chromatin methylation and self-renewal. In contrast, human ESCs lack a functional threonine catabolic pathway and instead depend on high methionine metabolism and glycine cleavage to maintain SAM levels and pluripotency. Genetic and metabolomic studies in diverse animal models have revealed stage-specific roles for 1C metabolism in processes including zygotic genome activation, DNA replication, epigenetic reprogramming, cell-cycle progression, organogenesis, cell migration, and longevity. Importantly, disruption of individual enzymes often produces defined developmental defects rather than general metabolic failure. Beyond early development, 1C metabolism also contributes to transgenerational epigenetic inheritance through its effects on germline DNA and histone methylation which are sensitive to perturbations in the folate and methionine pathways. Together, these findings show that 1C-metabolism links cellular metabolism with epigenetic regulation and developmental processes.

Receptor tyrosine kinase (RTK) signaling is a central mechanism by which local tissue interactions are translated into coordinated morphogenesis during eye development. The vertebrate eye provides a uniquely tractable system for studying this logic because it is assembled from neural epithelium, surface ectoderm, neural crest-derived mesenchyme, vascular endothelium, and specialized epithelial and endothelial derivatives across a prolonged developmental timeline. In this review, we synthesize how major RTK families, including FGF-FGFR, EGF-ErbB, PDGF-PDGFR, VEGF-VEGFR, Eph-ephrin, ANGPT-TEK/Tie2, IGF-INS receptors, and collagen-sensing DDRs, control optic cup formation, optic fissure closure, lens differentiation and architecture, corneal and anterior segment morphogenesis, retinal vascularization, Schlemm's canal development, and lacrimal gland branching. Rather than acting through pathway-specific outputs, these receptors repeatedly converge on shared MAPK/ERK, PI3K-AKT, PLCγ-PKC, SRC/FAK, and Rho-family cytoskeletal modules. Developmental specificity emerges from ligand geography, receptor dosage, co-receptor and extracellular matrix context, signal duration, receptor trafficking, mechanical state, and cross-talk with other signaling pathways. We also highlight how emerging single-cell, spatial, and multiomic atlases are shifting the field from static expression maps toward ligand-receptor source mapping and quantitative pathway-state inference. Finally, we connect developmental RTK mechanisms to congenital and pediatric eye disease. Together, these studies position the eye as a powerful model for understanding how reiterative RTK signaling builds complex organ form and informs therapeutic modulation, regenerative medicine, and disease mechanism.

Traditionally redox regulation has been interpreted through the lens of intracellular signaling, metabolic adaptation, or oxidative damage. In the vascular system, this view has been particularly influential: endothelial reactive oxygen species, nitric oxide, lipid peroxidation, and antioxidant pathways are commonly discussed as cell-autonomous regulators of vascular tone, permeability, inflammation, angiogenesis, dysfunction or aging. Here, we propose a broader perspective. We argue that the vasculature does not merely experience redox stress; it generates, edits, buffers, packages, and exports redox-active information beyond the traditionally recognized signaling molecules. This exported information-the secreted redoxome-may include oxidatively modified proteins, thiol/disulfide states, extracellular vesicle cargo, and additional circulating redox buffers. We first summarize what is known about vascular oxidative post-translational modifications and circulating redox systems. We then develop the opinion that secreted redox proteins may function as an angiocrine communication layer that instructs tissue homeostasis and disease transition. This view shifts the field from asking how vessels suffer oxidative stress to asking how vessels communicate regulated redox instructions.

Vision depends on the function of retinal circuits, supported by the retinal pigment epithelium (RPE) that lines the back of the eye. This single-cell layer thick epithelium provides growth factors and nutrients for the underlying photoreceptors, phagocytoses shed photoreceptor outer segment debris, and contributes to the blood-retinal barrier. Whether the cells of the RPE represent a single homogeneous population or represent distinct functional entities or states is poorly understood. Here, we use single cell RNA sequencing (scRNAseq) data from our mature 5-day post-fertilization zebrafish retina dataset and a publicly available adult zebrafish eye dataset, alongside in situ hybridization, to explore the transcriptomic diversity of RPE cells, its emergence over development, and its persistence into the adult. We identify 6 transcriptomically distinct RPE populations in the 5 day larval eye, representing either RPE subtypes or states, that exhibit different localization within the eye. Specifically, we find potential proliferative, iris-associated, dorso-ventral differentiating, and mature RPE subpopulations. These populations appear to emerge via separate developmental trajectories and may be distinct from the transcriptomic RPE subpopulations of the adult eye.

Mammalian limb development is a complex system involving several signaling centers and coordinated cell behaviors to sculpt a functioning limb capable of the diverse locomotory strategies that mammals exhibit. To investigate the changes in development that facilitate the generation of the wide array of limb phenotypes across mammals, we take a correlation network approach to investigate the developing limbs of mice, bats, and opossums, which represent typical limb development, a novel limb phenotype, and a shift in developmental timing, respectively. Using transcriptomic data of early limb development across these taxa, we build module correlation networks and identify a difference in network connectivity and the distribution of limb development genes across bat limb development. We identify a unique signature of increased modularity in the bat forelimb that is not detected in mouse or opossum. This modularity is not associated with increased specialization of limb development modules, but rather is marked by target limb development genes being spread evenly across several modules. The opossum, with its standard phenotype but altered developmental timing, does not show a difference in modularity relative to mouse. This work points toward the benefit of a network-minded approach to transcriptomic networks, which reveals developmental modularity and potential gene targets for exploration of developmental system evolution.

The cochlea resolves sound frequencies through molecular, structural, and functional specializations established along its tonotopic axis. Although transient morphogen gradients establish positional information during embryogenesis, the mechanisms that maintain and refine this information as cochlear function matures remain poorly understood. Here, we identify the chromatin modifier HMGA2 as a candidate molecular link between opposing hedgehog (HH) and retinoic acid (RA) signals and long-term auditory function. In vivo manipulation of RA and HH signaling demonstrated that RA suppresses, whereas HH activation promotes, Hmga2 expression, establishing its apex-to-base decreasing gradient. Conditional deletion of Hmga2 did not affect cochlear length, hair cell numbers, mechanotransduction, or Prestin localization but caused a delayed and persistent low-frequency hearing deficit. Longitudinal auditory measurements revealed two distinct functional phenotypes that may contribute to this deficit: non-tonotopic DPOAE abnormalities consistent with altered cochlear micromechanics and a late, low-frequency reduction in ABR P1 amplitude consistent with impaired inner hair cell-afferent signaling. Together, these findings identify HMGA2 as a molecular link between embryonic morphogen signaling and long-term low-frequency auditory function and suggest that persistent HMGA2-dependent regulation contributes to the maintenance of low-frequency auditory function.

Within the neuronal classes of the retina, amacrine cells (ACs) exhibit the greatest neuronal diversity in morphology and function. We show that the selective expression of the transcription factor Gbx2 is required for dendritic stratification of an individual AC subtype in the mouse retina. We identify Robo1 and Robo2 as downstream effectors that when deleted, phenocopy the dendritic misprojections seen in Gbx2 mutants. Slit1 and Slit2, the ligands of Robo receptors, are localized to the upper layers of the inner plexiform layer where we observe the dendritic misprojections in both Gbx2 and Robo1/2 mutants. We show that Robo receptors also are required for the proper dendritic stratification of additional AC subtypes, such as Vglut3+ ACs. These results show both that Gbx2 regulates the terminal differentiation of a single AC subtype and identify Slit-Robo signaling as a developmental mechanism for dendrite stratification in the retina.