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International Journal of Molecular... May 2018This review presents a detailed analysis of published research data focused on the pharmacological activity exerted by biologically active compounds isolated from sea... (Review)
Review
This review presents a detailed analysis of published research data focused on the pharmacological activity exerted by biologically active compounds isolated from sea cucumbers belonging to the class of Holothuroidea, phylum Echinodermata. The review contains descriptions of the structure, physico-chemical properties and pharmacological effects of these active substances. Particular attention is given to compounds with anticoagulant, antithrombotic, antioxidant, anticancer, anti-infectious, immune-stimulating and anti-ACE (angiotensin converting enzyme) activities as well as to the substances exerting a regulating influence on lipid and carbohydrate metabolism. All these compounds may be considered as prototypes for development of new pharmaceutical substances and medicines.
Topics: Animals; Ceramides; Drug Discovery; Humans; Mice; Molecular Structure; Molecular Weight; Phytochemicals; Polysaccharides; Saponins; Sea Cucumbers
PubMed: 29724051
DOI: 10.3390/ijms19051342 -
Proceedings. Biological Sciences Nov 2014Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the... (Review)
Review
Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics.
Topics: Animals; Biological Evolution; Body Patterning; Chordata; Echinodermata; Embryonic Development; Larva; Phylogeny
PubMed: 25232138
DOI: 10.1098/rspb.2014.1729 -
Nucleic Acids Research Apr 1999Animal mitochondrial DNA is a small, extrachromosomal genome, typically approximately 16 kb in size. With few exceptions, all animal mitochondrial genomes contain the... (Review)
Review
Animal mitochondrial DNA is a small, extrachromosomal genome, typically approximately 16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems-'mitochondrial genomics'-serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.
Topics: Animals; Arthropods; Chordata, Nonvertebrate; DNA, Mitochondrial; Echinodermata; Humans; Mitochondria
PubMed: 10101183
DOI: 10.1093/nar/27.8.1767 -
Marine Drugs Jun 2021Sphingolipids are complex lipids widespread in nature as structural components of biomembranes. Commonly, the sphingolipids of marine organisms differ from those of... (Review)
Review
Sphingolipids are complex lipids widespread in nature as structural components of biomembranes. Commonly, the sphingolipids of marine organisms differ from those of terrestrial animals and plants. The gangliosides are the most complex sphingolipids characteristic of vertebrates that have been found in only the Echinodermata (echinoderms) phylum of invertebrates. Sphingolipids of the representatives of the Asteroidea and Holothuroidea classes are the most studied among all echinoderms. In this review, we have summarized the data on sphingolipids of these two classes of marine invertebrates over the past two decades. Recently established structures, properties, and peculiarities of biogenesis of ceramides, cerebrosides, and gangliosides from starfishes and holothurians are discussed. The purpose of this review is to provide the most complete information on the chemical structures, structural features, and biological activities of sphingolipids of the Asteroidea and Holothuroidea classes.
Topics: Animals; Aquatic Organisms; Ceramides; Cerebrosides; Echinodermata; Gangliosides; Molecular Structure; Sea Cucumbers; Sphingolipids; Starfish
PubMed: 34200995
DOI: 10.3390/md19060330 -
ELife Jun 2017Unexpected findings from the immune system of sea urchin larvae potentially provide insights into immune signaling in ancestral animals.
Unexpected findings from the immune system of sea urchin larvae potentially provide insights into immune signaling in ancestral animals.
Topics: Animals; Epithelium; Larva; Sea Urchins; Strongylocentrotus purpuratus; Vibrio
PubMed: 28574337
DOI: 10.7554/eLife.28152 -
Marine Drugs Dec 2022The phylum Echinodermata comprising the classes Asteroidea, Ophiuroidea, Echinoidea, Holothuroidea, and Crinodeia, is one of the important invertebrate groups. Members... (Review)
Review
The phylum Echinodermata comprising the classes Asteroidea, Ophiuroidea, Echinoidea, Holothuroidea, and Crinodeia, is one of the important invertebrate groups. Members of this phylum live exclusively in marine habitats and are distributed in almost all depths and latitudes. Some of them, such as sea urchins and sea cucumbers, are commercially valuable and constitute a major fishery resource. Echinoderms are increasingly recognized as a unique source of various metabolites with a wide range of biological activities. The importance of dietary polyunsaturated fatty acids, such as eicosapentaenoic acid, in human health has drawn attention to echinoderms as a promising source of essential fatty acids (FAs). Extensive information on the FAs of the phylum has been accumulated to date. The biosynthetic capabilities and feeding habits of echinoderms explain the findings of the unusual FAs in them. Certain common and unusual FAs may serve as chemotaxonomic markers of the classes. The main goal of the review was to gather the relevant information on the distribution of FAs among the echinoderm classes, describe the structures, distribution, biosynthetic pathways, and bioactivity, with an emphasis on the FAs specific for echinoderms. A large part of the review is devoted to the FAs derived from echinoderms that exhibit various biological activities promising for potential therapeutic applications.
Topics: Animals; Humans; Fatty Acids; Echinodermata; Sea Cucumbers; Sea Urchins; Starfish
PubMed: 36662194
DOI: 10.3390/md21010021 -
Database : the Journal of Biological... Aug 2021Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now...
Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guidelines that both communicates meaningful orthology information in protein-coding gene symbols and names and establishes continuity with nomenclatures developed for major vertebrate model organisms, including humans. Differences between the echinoderm gene nomenclature guidelines and vertebrate guidelines are examined and explained. This nomenclature incorporates novel solutions to allow for several types of orthologous relationships, including the single echinoderm genes with multiple vertebrate co-orthologs that result from whole-genome-duplication events. The current version of the Echinoderm Gene Nomenclature Guidelines can be found at https://www.echinobase.org/gene/static/geneNomenclature.jsp Database URL https://www.echinobase.org/.
Topics: Animals; Databases, Factual; Echinodermata; Genome; Humans; Vertebrates
PubMed: 34386815
DOI: 10.1093/database/baab052 -
Developmental Biology Jul 2017The highly recognizable animals within the phylum Echinodermata encompass an enormous disparity of adult and larval body plans. The extensive knowledge of sea urchin... (Review)
Review
The highly recognizable animals within the phylum Echinodermata encompass an enormous disparity of adult and larval body plans. The extensive knowledge of sea urchin development has culminated in the description of the exquisitely detailed gene regulatory network (GRN) that governs the specification of various embryonic territories. This information provides a unique opportunity for comparative studies in other echinoderm taxa to understand the evolution and developmental mechanisms underlying body plan change. This review focuses on recent work that has utilized new genomic resources and systems-level experiments to address questions of evolutionary developmental biology. In particular, we synthesize the results of several recent studies from various echinoderm classes that have explored the development and evolution of the larval skeleton, which is a major feature that distinguishes the two predominant larval subtypes within the Phylum. We specifically examine the ways in which GRNs can evolve, either through cis regulatory and/or protein-level changes in transcription factors. We also examine recent work comparing evolution across shorter time scales that occur within and between species of sea urchin, and highlight the kinds of questions that can be addressed by these comparisons. The advent of new genomic and transcriptomic datasets in additional species from all classes of echinoderm will continue to empower the use of these taxa for evolutionary developmental studies.
Topics: Animals; Echinodermata; Evolution, Molecular; Gene Regulatory Networks; Genomics
PubMed: 28185788
DOI: 10.1016/j.ydbio.2017.02.003 -
Methods in Cell Biology 2019Gene regulatory networks reveal how transcription factors contribute to a dynamic cascade of cellular information processing. Recent advances in technologies have... (Review)
Review
Gene regulatory networks reveal how transcription factors contribute to a dynamic cascade of cellular information processing. Recent advances in technologies have enhanced the toolkit for testing GRN mechanisms and connections. Here we emphasize three approaches that we have found important for interrogating transcriptional mechanisms in echinoderms: single cell mRNA sequencing (drop-seq), nascent RNA detection and identification, and chromatin immunoprecipitation (ChIP). We present these applications in order since it is a logical experimental protocol. With preliminary information from bulk mRNA transcriptome analysis and differential gene expression studies (DE-seq), one may need to test in what specific cells important genes may be expressed and to use single cell sequencing to define such links. Nascent RNA analysis with the Click-iT chemistry allows the investigator to deduce when the RNA was transcribed, not just identify its presence, and ChIP allows the investigator to study direct interactions of putative transcriptional regulators with the gene promoter of interest. This flow of thinking, and the technologies to support it, is presented here for echinoderms. While many of the procedures are general and applicable to many organisms and cell types, we emphasize unique aspects of the protocols for consideration in using echinoderm embryos, larvae, and adult tissues.
Topics: Animals; Chromatin Immunoprecipitation; Echinodermata; Gene Expression Profiling; Gene Expression Regulation; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; Single-Cell Analysis; Transcription Factors; Transcriptome
PubMed: 30948004
DOI: 10.1016/bs.mcb.2018.11.018 -
Developmental Biology Dec 2006Although the development of sea urchin embryos has been studied extensively and clearly involves both cell adhesion and cell migration, rather little is known about the...
Although the development of sea urchin embryos has been studied extensively and clearly involves both cell adhesion and cell migration, rather little is known about the adhesion receptors and extracellular matrix molecules involved. The completion of the genome of Strongylocentrotus purpuratus allows a comprehensive survey of the complement of cell-cell and cell-matrix adhesion molecules in this organism. Furthermore, the phylogenetic position of echinoderms offers the opportunity to compare the complement of adhesion proteins between protostome and deuterostome invertebrates and between invertebrate and vertebrate deuterostomes. Many aspects of development and cell interactions differ among these different taxa and it is likely that analysis of the spectrum of adhesion receptors and extracellular matrix proteins can open up new insights into which molecules have evolved to suit particular developmental processes. In this paper, we report the results of an initial analysis along these lines. The echinoderm adhesome (complement of adhesion-related genes/proteins) is similar overall to that of other invertebrates although there are significant deuterostome-specific innovations and some interesting features previously thought to be chordate or vertebrate specific.
Topics: Animals; Cell Adhesion; Collagen; Echinodermata; Laminin; Models, Molecular; Phylogeny; Porifera; Protein Conformation; Protein Subunits; Sea Urchins
PubMed: 16950242
DOI: 10.1016/j.ydbio.2006.07.044