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Cell Nov 2021Jellyfish are radially symmetric organisms without a brain that arose more than 500 million years ago. They achieve organismal behaviors through coordinated interactions...
Jellyfish are radially symmetric organisms without a brain that arose more than 500 million years ago. They achieve organismal behaviors through coordinated interactions between autonomously functioning body parts. Jellyfish neurons have been studied electrophysiologically, but not at the systems level. We introduce Clytia hemisphaerica as a transparent, genetically tractable jellyfish model for systems and evolutionary neuroscience. We generate stable F transgenic lines for cell-type-specific conditional ablation and whole-organism GCaMP imaging. Using these tools and computational analyses, we find that an apparently diffuse network of RFamide-expressing umbrellar neurons is functionally subdivided into a series of spatially localized subassemblies whose synchronous activation controls directional food transfer from the tentacles to the mouth. These data reveal an unanticipated degree of structured neural organization in this species. Clytia affords a platform for systems-level studies of neural function, behavior, and evolution within a clade of marine organisms with growing ecological and economic importance.
Topics: Animals; Animals, Genetically Modified; Behavior, Animal; Biological Evolution; Feeding Behavior; Gene Targeting; Hydrozoa; Models, Animal; Models, Biological; Nerve Net; Neurons; Neuropeptides; Neurosciences
PubMed: 34822783
DOI: 10.1016/j.cell.2021.10.021 -
Molecular Cell Jul 2023RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts...
RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression and, when dysfunctional, underlie human diseases. Proteome-wide discovery efforts predict thousands of RBP candidates, many of which lack canonical RNA-binding domains (RBDs). Here, we present a hybrid ensemble RBP classifier (HydRA), which leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. Occlusion mapping by HydRA robustly detects known RBDs and predicts hundreds of uncharacterized RNA-binding associated domains. Enhanced CLIP (eCLIP) for HydRA-predicted RBP candidates reveals transcriptome-wide RNA targets and confirms RNA-binding activity for HydRA-predicted RNA-binding associated domains. HydRA accelerates construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.
Topics: Animals; Humans; RNA; Protein Binding; Binding Sites; Hydra; Deep Learning
PubMed: 37421941
DOI: 10.1016/j.molcel.2023.06.019 -
EvoDevo 2020, a genus of colonial marine cnidarians, has been used as a model organism for developmental biology and comparative immunology for over a century. It was this animal... (Review)
Review
, a genus of colonial marine cnidarians, has been used as a model organism for developmental biology and comparative immunology for over a century. It was this animal where stem cells and germ cells were first studied. However, protocols for efficient genetic engineering have only recently been established by a small but interactive community of researchers. The animal grows well in the lab, spawns daily, and its relatively short life cycle allows genetic studies. The availability of genomic tools and resources opens further opportunities for research using this animal. Its accessibility to experimental manipulation, growth- and cellular-plasticity, regenerative ability, and resistance to aging and cancer place as an emerging model for research in many biological and environmental disciplines.
PubMed: 32226598
DOI: 10.1186/s13227-020-00151-0 -
Marine Drugs Oct 2020Cnidarians have been known since ancient times for the painful stings they induce to humans. The effects of the stings range from skin irritation to cardiotoxicity and... (Review)
Review
Cnidarians have been known since ancient times for the painful stings they induce to humans. The effects of the stings range from skin irritation to cardiotoxicity and can result in death of human beings. The noxious effects of cnidarian venoms have stimulated the definition of their composition and their activity. Despite this interest, only a limited number of compounds extracted from cnidarian venoms have been identified and defined in detail. Venoms extracted from Anthozoa are likely the most studied, while venoms from Cubozoa attract research interests due to their lethal effects on humans. The investigation of cnidarian venoms has benefited in very recent times by the application of omics approaches. In this review, we propose an updated synopsis of the toxins identified in the venoms of the main classes of Cnidaria (Hydrozoa, Scyphozoa, Cubozoa, Staurozoa and Anthozoa). We have attempted to consider most of the available information, including a summary of the most recent results from omics and biotechnological studies, with the aim to define the state of the art in the field and provide a background for future research.
Topics: Animals; Cnidaria; Cnidarian Venoms; Genomics; Metabolomics
PubMed: 33036158
DOI: 10.3390/md18100507 -
Annals of Oncology : Official Journal... Jan 2023Modern medicine continues to evolve, and the treatment armamentarium for various diseases grows more individualized across a breadth of medical disciplines. Cure rates... (Review)
Review
Modern medicine continues to evolve, and the treatment armamentarium for various diseases grows more individualized across a breadth of medical disciplines. Cure rates for infectious diseases that were previously pan-fatal approach 100% because of the identification of the specific pathogen(s) involved and the use of appropriate combinations of drugs, where needed, to completely extinguish infection and hence prevent emergence of resistant strains. Similarly, with the assistance of technologies such as next-generation sequencing and immunomic analysis as part of the contemporary oncology armory, therapies can be tailored to each tumor. Importantly, molecular interrogation has revealed that metastatic cancers are distinct from each other and complex. Therefore, it is conceivable that rational personalized drug combinations will be needed to eradicate cancers, and eradication will be necessary to mitigate clonal evolution and resistance.
Topics: Animals; Humans; Hydra; Neoplasms; Medical Oncology
PubMed: 35931318
DOI: 10.1016/j.annonc.2022.07.010 -
PLoS Biology Nov 2020Using mRNA sequencing and de novo transcriptome assembly, we identified, cloned, and characterized 9 previously undiscovered fluorescent protein (FP) homologs from...
Using mRNA sequencing and de novo transcriptome assembly, we identified, cloned, and characterized 9 previously undiscovered fluorescent protein (FP) homologs from Aequorea victoria and a related Aequorea species, with most sequences highly divergent from A. victoria green fluorescent protein (avGFP). Among these FPs are the brightest green fluorescent protein (GFP) homolog yet characterized and a reversibly photochromic FP that responds to UV and blue light. Beyond green emitters, Aequorea species express purple- and blue-pigmented chromoproteins (CPs) with absorbances ranging from green to far-red, including 2 that are photoconvertible. X-ray crystallography revealed that Aequorea CPs contain a chemically novel chromophore with an unexpected crosslink to the main polypeptide chain. Because of the unique attributes of several of these newly discovered FPs, we expect that Aequorea will, once again, give rise to an entirely new generation of useful probes for bioimaging and biosensing.
Topics: Animals; Biosensing Techniques; Color; Crystallography, X-Ray; Green Fluorescent Proteins; Hydrozoa; Luminescent Proteins; Models, Molecular; Optical Imaging; Phylogeny; Static Electricity
PubMed: 33137097
DOI: 10.1371/journal.pbio.3000936 -
Frontiers in Endocrinology 2020Cnidarians are early-branching animals in the eukaryotic tree of life. The phylum Cnidaria are divided into five classes: Scyphozoa (true jellyfish), Cubozoa (box... (Review)
Review
Cnidarians are early-branching animals in the eukaryotic tree of life. The phylum Cnidaria are divided into five classes: Scyphozoa (true jellyfish), Cubozoa (box jellyfish), Hydrozoa (species, and ), Anthozoa (sea anemone, corals, and sea pen), and Staurozoa (stalked jellyfish). Peptides play important roles as signaling molecules in development and differentiation in cnidaria. For example, cnidaria use peptides for cell-to cell communication. Recent discoveries show that neuropeptides control several biological processes including muscle contraction, neuron differentiation, and metamorphosis. Here, I describe the structure and functions of neuropeptides in and other cnidarian species. I also discuss that so-called primitive nervous system of is in more complex than generally believed. I also discuss how cnidaria use peptides for communication among cells rather than in higher animals.
Topics: Animals; Cnidaria; Metamorphosis, Biological; Muscle Contraction; Neurogenesis; Neuropeptides
PubMed: 32528418
DOI: 10.3389/fendo.2020.00339 -
Proceedings of the National Academy of... Sep 2022is the only metazoan able to rejuvenate repeatedly after its medusae reproduce, hinting at biological immortality and challenging our understanding of aging. We present...
is the only metazoan able to rejuvenate repeatedly after its medusae reproduce, hinting at biological immortality and challenging our understanding of aging. We present and compare whole-genome assemblies of and the nonimmortal using automatic and manual annotations, together with the transcriptome of life cycle reversal (LCR) process of We have identified variants and expansions of genes associated with replication, DNA repair, telomere maintenance, redox environment, stem cell population, and intercellular communication. Moreover, we have found silencing of polycomb repressive complex 2 targets and activation of pluripotency targets during LCR, which points to these transcription factors as pluripotency inducers in . Accordingly, we propose these factors as key elements in the ability of to undergo rejuvenation.
Topics: Animals; Genomics; Hydrozoa; Life Cycle Stages; Rejuvenation; Transcriptome
PubMed: 36037356
DOI: 10.1073/pnas.2118763119 -
Cellular and Molecular Life Sciences :... Feb 2021Research on the evolutionary and mechanistic aspects of aging and longevity has a reductionist nature, as the majority of knowledge originates from experiments on a... (Review)
Review
Research on the evolutionary and mechanistic aspects of aging and longevity has a reductionist nature, as the majority of knowledge originates from experiments on a relatively small number of systems and species. Good examples are the studies on the cellular, molecular, and genetic attributes of aging (senescence) that are primarily based on a narrow group of somatic cells, especially fibroblasts. Research on aging and/or longevity at the organismal level is dominated, in turn, by experiments on Drosophila melanogaster, worms (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and higher organisms such as mice and humans. Other systems of aging, though numerous, constitute the minority. In this review, we collected and discussed a plethora of up-to-date findings about studies of aging, longevity, and sometimes even immortality in several valuable but less frequently used systems, including bacteria (Caulobacter crescentus, Escherichia coli), invertebrates (Turritopsis dohrnii, Hydra sp., Arctica islandica), fishes (Nothobranchius sp., Greenland shark), reptiles (giant tortoise), mammals (blind mole rats, naked mole rats, bats, elephants, killer whale), and even 3D organoids, to prove that they offer biogerontologists as much as the more conventional tools. At the same time, the diversified knowledge gained owing to research on those species may help to reconsider aging from a broader perspective, which should translate into a better understanding of this tremendously complex and clearly system-specific phenomenon.
Topics: Aging; Animals; Biological Evolution; Caulobacter crescentus; Elephants; Escherichia coli; Fibroblasts; Humans; Hydra; Longevity; Mammals; Mice; Mole Rats; Turtles
PubMed: 33034696
DOI: 10.1007/s00018-020-03658-w -
Cells & Development Jun 2023Cnidarians are >600 million years old and are considered the sister group of Bilateria based on numerous molecular phylogenetic studies. Apart from Hydra, the genomes of... (Review)
Review
Cnidarians are >600 million years old and are considered the sister group of Bilateria based on numerous molecular phylogenetic studies. Apart from Hydra, the genomes of all major clades of Cnidaria have been uncovered (e.g. Aurelia, Clytia, Nematostella and Acropora) and they reveal a remarkable completeness of the metazoan genomic toolbox. Of particular interest is Hydra, a model system of aging research, regenerative biology, and stem cell biology. With the knowledge gained from scRNA research, it is now possible to characterize the expression profiles of all cell types with great precision. In functional studies, our picture of the Hydra stem cell biology has changed, and we are in the process of obtaining a clear picture of the homeostasis and properties of the different stem cell populations. Even though Hydra is often compared to plant systems, the new data on germline and regeneration, but also on the dynamics and plasticity of the nervous system, show that Hydra with its simple body plan represents in a nutshell the prototype of an animal with stem cell lineages, whose properties correspond in many ways to Bilateria. This review provides an overview of the four stem cell lineages, the two epithelial lineages that constitute the ectoderm and the endoderm, as well as the multipotent somatic interstitial lineage (MPSC) and the germline stem cell lineage (GSC), also known as the interstitial cells of Hydra.
Topics: Animals; Hydra; Phylogeny; Stem Cells; Cell Lineage; Anthozoa
PubMed: 37121433
DOI: 10.1016/j.cdev.2023.203846