Biology subjects

Layden, M. J.

Publications and source records attributed to Layden, M. J..

9 recordsLinked to original sources

bioRxiv2026

Analysis of gene expression changes after Latrunculin B-induced actin depolymerization

Links between the cytoskeleton and gene expression are increasingly appreciated. The cytoskeleton dynamically regulates its own expression and organization through transcriptional feedback loops that sense cellular concentrations and mechanical forces. Disruption of cytoskeletal dynamics can also influence cell fate. However, the breadth, temporal dynamics, and mechanistic basis of the cytoskeleton-transcription coupling have yet to be fully resolved. To characterize this response more broadly, we re-analyzed time-resolved bulk RNA-seq data that were previously used to demonstrate that treatment with actin depolymerization drug Latrunculin B (LatB) drives differentiation of human pancreatic progenitor cells in culture. Beyond the previously identified induction of cell differentiation, we find that LatB produced extensive transcriptional changes within the actin cytoskeleton, including downregulation of actin, myosin II heavy chains, myosin I, tropomyosins, -actinins, filamins, talin, vinculin and plastin. The changes were not restricted to the actin system, but extended to microtubule and intermediate filament systems, with noticeable changes in the expression of KIF19, MAP1A, MAP1B, Type I and II keratins and Type IV neurofilaments. More broadly, the response extended to genes involved in transcription, vesicle trafficking, metabolism, translation, ion transport, protein homeostasis, and cell signaling. The breadth of this response suggested engagement of multiple transcriptional regulatory programs. Transcription factor activity inference using decoupleR identified MRTF/SRF as the most inactivated TF network, consistent with its known role in actin homeostasis, in addition to Hippo/YAP-TEAD, MYC, stress-response and other pathways. These results provide the broader landscape of cellular response to actin depolymerization, serving as a foundation for future studies to distinguish general mechanisms of cytoskeletal homeostasis from differentiation-associated responses, and to narrow the underlying regulatory mechanisms linking cytoskeletal state to gene expression.

cell biology↗

bioRxiv2025

NvashA function reveals temporal differences in neural subtype generation in cnidarians

Understanding how cnidarians pattern their nervous systems can provide insight into the ancestral mechanisms of neurogenesis that are shared with bilaterians, shedding light on the evolution of nervous systems. While previous studies have revealed deeply conserved mechanisms for neural induction and progenitor selection between cnidarians and bilaterians, less is known about how distinct neuronal subtypes are specified over time in cnidarians. We utilized single-cell mRNA sequencing to profile NvashA-expressing cells across embryonic and planula-larva stages of Nematostella neurogenesis, and functional experiments identified a dynamic role for NvashA over time. Our analysis revealed that unique neuronal subtypes emerge at different developmental stages, providing evidence for temporal patterning in developing cnidarian nerve nets. This can provide a foundation to better our understanding of neurogenic gene regulatory networks, and to compare neurogenesis across cnidarians, and with bilaterians, to improve our knowledge of nervous system evolution.

developmental biology↗

bioRxiv2025

Conserved and lineage-restricted gene regulatory programs modulate developmental cnidocyte specification in Nematostella vectensis.

Cnidocytes are a synapomorphy of cnidarians that have evolved a range of morphologies and functions within and across extant species, which makes them an excellent model to investigate how novel cell types emerge and radiate in evolution. One way to gain insight into how cell types evolve is to investigate the gene regulatory networks (GRNs) that pattern them, leading to the identification of shared and divergent programs that likely represent components of the ancestral and evolved phenotypes. Efforts to identify early acting transcription factors in the sea anemone Nematostella vectensis revealed that NvfoxE-like is a lineage-restricted cnidocyte transcription factor. Expression and functional studies confirmed that NvfoxE-like and its targets are found exclusively in cnidocytes. By investigating interactions with regulators of the known cnidogenesis GRN and comparing the targets of known cnidocyte regulators, we identified at least four regulatory programs contributing to the cnidogenic GRN in Nematostella. The previously identified cnidocyte regulators Nvznf845 and NvpaxA represent two core pan-cnidarian regulatory programs, while the NvfoxE-like dependent program appears to be restricted to Hexacorallia or Actinaria, where we hypothesize it functions to pattern the unique capsule features present in those lineages. Here, we confirm the hypothesized core conserved transcriptional program, as well as demonstrate how a novel transcription factor was co-opted into cnidogenesis in a subset of cnidarians, thus contributing to the diversification and continued evolution of cnidocytes.

evolutionary biology↗

bioRxiv2025

Ectopic head regeneration after nervous system ablation in a sea anemone

Some animals are able to regenerate all missing cell types and large body parts after bisection, a phenomenon called whole-body regeneration. Many of these animals regenerate the correct tissues and structures with remarkable fidelity according to the original polarity of the body, reflecting positional information present in the remaining tissue. Understanding the cellular and molecular basis of this positional information is a central question in regeneration biology. In planarians and acoels, muscle cells have been shown to carry such positional information, but where this information originates and whether this function is conserved in other highly regenerative animals, is not well understood. Here we use the cnidarian Nematostella vectensis to address the role of the nervous system in whole-body regeneration. We generated a transgenic line for conditional ablation of neurons and first showed that Nematostella can repeatedly regenerate its nervous system. Bisection experiments following nervous system ablation showed that all head fragments regenerate a second head instead of a foot, whereas foot fragments correctly regenerate the missing head. We further found that regenerating head fragments of nervous system-ablated animals increase the expression of Wnt signaling genes that in wildtype animals are only upregulated in regenerating foot fragments. These molecular changes and the initiation of ectopic head regeneration precede the re-appearance of neurons, suggesting that the nervous system does not directly control whether a head or foot will be regenerated. Instead, we propose a model in which the nervous system provides positional information to the tissue of the body column, and that this information allows foot regeneration by suppressing a default program for head regeneration.

developmental biology↗

bioRxiv2023

Environmental and molecular regulation of asexual reproduction in the sea anemone Nematostella vectensis

Cnidarians exhibit incredible reproductive diversity, with most capable of sexual and asexual reproduction. Here we investigate factors that influence asexual reproduction in the burrowing sea anemone Nematostella vectensis, which can propagate asexually by transverse fission of the body column. By altering culture conditions, we demonstrate that the presence of a burrowing substrate strongly promotes transverse fission. In addition, we show that animal size does not affect fission rates, and that the plane of fission is fixed along the oral-aboral axis of the polyp. Homeobox transcription factors and components of the TGF{beta}, Notch, and FGF signaling pathways are differentially expressed in polyps undergoing physal pinching suggesting they are important regulators of transverse fission. Gene ontology analyses further suggest that during transverse fission the cell cycle is suppressed and that cell adhesion and patterning mechanisms are downregulated to promote separation of the body column. Finally, we demonstrate that the rate of asexual reproduction is sensitive to population density. Collectively, these experiments provide a foundation for mechanistic studies of asexual reproduction in Nematostella, with implications for understanding the reproductive and regenerative biology of other cnidarian species.

animal behavior and cognition↗

bioRxiv2021

Brain regulatory program predates central nervous system evolution

Understanding if bilaterian centralized nervous systems (CNS) evolved once or multiple times has been debated for over a century. Recent efforts determined that the nerve chords found in bilaterian CNSs likely evolved independently, but the origin(s) of brains remains debatable. Developing brains are regionalized by stripes of gene expression along the anteroposterior axis. Gene homologs are expressed in the same relative order in disparate species, which has been interpreted as evidence for homology. However, regionalization programs resemble anteroposterior axial patterning programs, which supports an alternative model by which conserved expression in brains arose convergently through the independent co-option of deeply conserved axial patterning programs. To begin resolving these hypotheses, we sought to determine when the neurogenic role for axial programs evolved. Here we show that the nerve net in the cnidarian Nematostella vectensis and bilaterian brain are regionalized by the same molecular programs, which indicates nervous system regionalization predates the emergence of bilaterians and CNSs altogether. This argues that shared regionalization mechanisms are insufficient to support the homology of brains and supports the notion that axial programs were able to be co-opted multiple times during evolution of brains.

evolutionary biology↗

bioRxiv2019

Dynamics and variability in regenerative potential of neuronal subtypes in the Nematostella nerve net

BackgroundWe are interested in nervous system dynamics in adult and regenerating animals. Preliminary studies suggest that some species alter neuronal number to scale with changes in body size. Similarly, in some species regenerates resulting from wholebody axis regeneration are smaller than their pre-amputated parent, but they maintain the correct proportionality, suggesting that tissue and neuronal scaling also occurs in regenerates. The cell dynamics and responses of neuronal subtypes during nervous system regeneration, scaling, and whole-body axis regeneration are not well understood in any system. The cnidarian sea anemone Nematostella vectensis is capable of wholebody axis regeneration, and its transparent, "simple" body plan and the availability of fluorescent reporter transgenic lines allow neuronal subtypes to be tracked in vivo in adult and regenerating animals. A number of observations suggest this anemone is able to alter its size in responses to changes in feeding. We utilized the NvLWamide-like::mCherry neuronal subtype transgenic reporter line to determine the in vivo response of neuronal subtypes during growth, degrowth, and regeneration. ResultsNematostella alters its size in response to caloric intake, and the nervous system responds by altering neuronal number to scale as the animal changes in size. Neuronal numbers in both the endodermal and ectodermal nerve nets decreased as animals shrunk, increased as they grew, and the changes were reversible. Whole-body axis regeneration resulted in regenerates that were smaller than their pre-amputated size, and the regenerated nerve nets were reduced in neuronal number. Different neuronal subtypes had several distinct responses during regeneration that included consistent, no, and conditional increases in number. Conditional responses were regulated, in part, by the size of the remnant fragment and the position of the amputation site. Regenerates and adults with reduced nerve nets displayed normal behaviors, indicating that the nerve net retains functionality as it scales. ConclusionThese data suggest that the Nematostella nerve net is dynamic, capable of scaling with changes in body size, and that neuronal subtypes display differential regenerative responses, which we propose may be linked to the scale state of the regenerating animals.

neuroscience↗

bioRxiv2018

The origin and evolution of acetylcholine signaling through AchRs in metazoans

BackgroundAcetylcholine is a cell signaling molecule that has been identified in plants, bacteria, and metazoans to play multiple roles in cells and as a neurotransmitter capable of exciting both neurons and muscle. While cell-cell communication activity has been reported in all phyla that have been investigated, its role as a neurotransmitter is less clear. Work within cnidarians implies that neurotransmitter activity emerged within or prior to the emergence of the cnidarian-bilaterian ancestor, but whether or not it is able to excite both muscles and neurons has not been addressed.\n\nResultsTo investigate the evolution of acetylcholine signaling we characterized the expression pattern of acetylcholine receptors (AchRs) and the neurotransmitter activity of acetylcholine in Nematostella vectensis. Expression patterns for 13 of the 21 known NvAchRs are consistent with acetylcholine acting as a cell signaling molecule and a neurotransmitter in neurons, muscles, or both. To dissect neurotransmitter activity we investigated the mechanism by which acetylcholine activates tentacular contractions in Nematostella. Tentacular contractions induced by application of acetylcholine are suppressed by inactivating voltage gated sodium channels with lidocaine indicating that acetylcholine specifically activates neurons in the tentacular contractile circuit.\n\nConclusionOur results verify that acetylcholines neurotransmitter activity emerged prior to cnidarian-bilaterian divergence and that non-neuronal roles were likely retained in Nematostella. Additionally, we found no evidence to support a muscle activating role for acetylcholine indicating that its role in muscle excitability evolved during bilaterian evolution.

developmental biology↗

bioRxiv2017

Characterization Of NvLWamide-Like Neurons Reveals Stereotypy In Nematostella Nerve Net Development

Cnidarian nervous systems are traditionally described as diffuse nerve nets lacking true organization. However, there are examples of stereotypical structure in the nerve nets of multiple cnidarian species that suggest nerve nets are organized. We previously demonstrated that the NvashA target gene NvLWamide-like is expressed in a small subset of the Nematostella nerve net and speculated that observing a few neurons within the developing nerve net would provide a better indication of potential stereotypy. Here we document NvLWamide-like expression more systematically. NvLWamide-like is initially expressed in the typical neurogenic salt and pepper pattern within the ectoderm at the gastrula stage, and expression expands to include endodermal salt and pepper expression at the planula larval stage. Expression persists in both ectoderm and endoderm in adults. We generated an NvLWamide-like::mCherry transgenic reporter line to visualize the neural architecture. NvLWamide-like is expressed in six neural subtypes identifiable by neural morphology and location. Upon completing development the numbers of neurons in each neural subtype are minimally variable between animals and the projection patterns of each subtype are consistent. Between the juvenile polyp and adult stages the number of neurons for each subtype increases. We conclude that cnidarian nerve nets are organized, develop in a stereotyped fashion, and that one aspect of generating the adult nervous system is to modify the juvenile nervous system by increasing neural number proportionally with size.

developmental biology↗