The purple sea urchin, Strongylocentrotus purpuratus, lives along the eastern edge of the Pacific Ocean extending from Ensenada, Mexico to British Columbia, Canada. This sea urchin species is deep purple in color, eggs are orange when secreted in water, and lives in lower inter-tidal and nearshore sub-tidal communities. January, February, and March function as the typical active reproductive months for the species. Sexual maturity is reached around two years.
It normally grows to a diameter of about 4 inches and may live as long as 70 years.
While embryonic development is still a major part of the utilization of the sea urchin, studies on urchin's position as an evolutionary marvel have become increasingly frequent. Orthologs to human diseases have led scientists to investigate potential therapeutic uses for the sequences found in Strongylocentrotus purpuratus. For instance, in 2012, scientists at the University of St Andrews began investigating the "2A" viral region in the S. purpuratus genome which may be useful for Alzheimer's disease and cancer research. The study identified a sequence that can return cells to a 'stem-cell' like state, allowing for better treatment options. The species has also been a candidate in longevity studies, particularly because of its ability to regenerate damaged or aging tissue. Another study comparing 'young' vs. 'old' suggested that even in species with varying lifespans, the 'regenerative potential' was upheld in older specimens as they suffered no significant disadvantages compared to younger ones.
The genome of the purple sea urchin was completely sequenced and annotated in 2006 by teams of scientists from over 70 institutions including the Kerckhoff Marine Laboratory at the California Institute of Technology as well as the Human Genome Sequencing Center at the Baylor College of Medicine. Strongylocentrotus purpuratus is one of several biomedical research models in cell and developmental biology. The sea urchin is the first animal with a sequenced genome that (1) is a free-living, motile marine invertebrate; (2) has a bilaterally organized embryo but a radial adult body plan; (3) has the endoskeleton and water vascular system found only in echinoderms; and (4) has a nonadaptive immune system that is unique in the enormous complexity of its receptor repertoire.
The sea urchin genome is estimated to encode about 23,500 genes. The S. purpuratus has 353 protein kinases, containing members of 97% of human kinase subfamilies. Many of these genes were previously thought to be vertebrate innovations or were only known from groups outside the deuterostomes. The team sequencing the species concluded that some genes are not vertebrate specific as thought previously, while other genes still were found in the urchin but not the chordate.
The genome is largely non-redundant, making it very comparable to vertebrates, but without the complexity. For example, 200 to 700 chemosensory genes were found that lacked introns, a feature typical of vertebrates. Thus the sea urchin genome provides a comparison to our own and those of other deuterostomes, the larger group to which both echinoderms and humans belong. Sea urchins are also the closest living relative to chordates. Using the strictest measure, the purple sea urchin and humans share 7,700 genes. Many of these genes are involved in sensing the environment, a fact surprising for an animal lacking a head structure.
The sea urchin also has a chemical 'defensome' that reacts when stress is sensed to eliminate potentially toxic chemicals. S. purpuratuses' immune systems contains innate pathogen receptors like Toll-like receptors and genes that encode for LRR . There were genes identified for Biomineralization that were not counterparts of the typical human vertebrate variety SCCPs, and encode for transmembrane proteins like P16. Many orthologs exist for genes associated with human diseases, such as Reelin (from Norman-Roberts lissencephaly syndrome) and many cytoskeletal proteins of the Usher syndrome network like usherin and VLGR1.
The purple sea urchin, along with sea otters and abalones, is a prominent member of the kelp forest community. Sea urchins have been used for food by the indigenous peoples of California, who ate the yellow egg mass raw. The purple sea urchin also plays a key role in the disappearance of kelp forests that is currently occurring due to climate change.
Armour or armor in animals is external or superficial protection against attack by predators, formed as part of the body (rather than the behavioural use of protective external objects), usually through the hardening of body tissues, outgrowths or secretions. It has therefore mostly developed in 'prey' species.Bald sea urchin disease
Bald sea urchin disease is a bacterial disease known to affect several species of sea urchins in the Mediterranean Sea, North Atlantic and along the California coastline. Research suggests two pathogens are responsible for the disease, Listonella anguillarum and Aeromonas salmonicida.
Infection generally occurs at the site of an existing physical injury. The affected area turns green and spines and other appendages are lost. If the lesion remains shallow and covers less than 30% of the animal's surface area, the animal tends to survive and eventually regenerates any lost tissue. However if the damage is more extensive or so deep that the hard inner test is perforated, the disease is fatal.BioTapestry
BioTapestry is an open source software application for modeling and visualizing gene regulatory networks (GRNs).Codon usage bias
Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
There are 64 different codons (61 codons encoding for amino acids plus 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others—that is, a greater frequency of one will be found than expected by chance. How such biases arise is a much debated area of molecular evolution. Codon usage tables detailing genomic codon usage bias for most organisms in GenBank and RefSeq can be found in the HIVE-Codon Usage Table database.It is generally acknowledged that codon biases reflect a balance between mutational biases and natural selection for translational optimization. Optimal codons in fast-growing microorganisms, like Escherichia coli or Saccharomyces cerevisiae (baker's yeast), reflect the composition of their respective genomic tRNA pool. It is thought that optimal codons help to achieve faster translation rates and high accuracy. As a result of these factors, translational selection is expected to be stronger in highly expressed genes, as is indeed the case for the above-mentioned organisms. In other organisms that do not show high growing rates or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. Examples of this are Homo sapiens (human) and Helicobacter pylori. Organisms that show an intermediate level of codon usage optimization include Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode worm), Strongylocentrotus purpuratus (sea urchin) or Arabidopsis thaliana (thale cress). Several viral families (herpesvirus, lentivirus, papillomavirus, polyomavirus, adenovirus, and parvovirus) are known to encode structural proteins that display heavily skewed codon usage compared to the host cell. The suggestion has been made that these codon biases play a role in the temporal regulation of their late proteins.The nature of the codon usage-tRNA optimization has been fiercely debated. It is not clear whether codon usage drives tRNA evolution or vice versa. At least one mathematical model has been developed where both codon usage and tRNA expression co-evolve in feedback fashion (i.e., codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons). However, this model does not seem to yet have experimental confirmation. Another problem is that the evolution of tRNA genes has been a very inactive area of research.Echinobase
Echinobase is a web information system that catalogs diverse genomic and biological data for the echinoderm clade. The system provides a gene search engine, genomics browser and other bioinformatics tools to explore genomic and transcriptomic data. The Echinobase information system focuses on information from eight echinoderm research models: Strongylocentrotus purpuratus, Strongylocentrotus fransciscanus, Allocentrotus fragilis, Lytechinus variegatus, Patiria miniata, Parastichopus parvimensis and Ophiothrix spiculata, Eucidaris tribuloides. The goal of Echinobase is to support molecular biological science including developmental processes and gene regulatory networks.Envelysin
Envelysin (EC 18.104.22.168, sea-urchin-hatching proteinase, hatching enzyme, chorionase, chorion-digesting proteinase, chymostrypsin, sea urchin embryo hatching enzyme) is an enzyme. This enzyme catalyses the following chemical reaction
Hydrolysis of proteins of the fertilization envelope and dimethylcaseinThis enzyme is a glycoprotein from various members of the class Echinoidea.Eric H. Davidson
Eric Harris Davidson (April 13, 1937 – September 1, 2015) was an American developmental biologist at the California Institute of Technology. Davidson was best known for his pioneering work on the role of gene regulation in evolution, on embryonic specification and for spearheading the effort to sequence the genome of the purple sea urchin, Strongylocentrotus purpuratus. He devoted a large part of his professional career to developing an understanding of embryogenesis at the genetic level. He wrote many academic works describing his work, including a textbook on early animal development.Fred Huffman Wilt
Fred Huffman Wilt is an American biologist who was elected a Fellow of the American Association for the Advancement of Science. His research currently includes the endoskeletal spicule of sea urchin embryos, and its biomineralization relative to its cellular and molecular foundation.Gnathichnus
Gnathichnus is a trace fossil on a hard substrate (typically a shell, rock or hardground made of calcium carbonate) formed by regular echinoids as they scraped the surface with their five-toothed Aristotle's Lantern feeding structures (Bromley, 1975).List of echinoderm orders
This List of echinoderm orders concerns the various classes and orders into which taxonomists categorize the roughly 7000 extant species as well as the extinct species of the exclusively marine phylum Echinodermata.MirGeneDB
MirGeneDB is a database of microRNA genes that have been validated and annotated as described in Fromm et al. 2015. The initial version contained 1'434 microRNA genes for human, mouse, chicken and zebrafish. Version 2.0 will contain more than 7'500 genes from 32 organisms representing nearly every metazoan group, and these microRNAs can be browsed, searched and downloaded. Planned release data for 2.0 is December 2017.
Eutheria (Placental mammals)
• Human (Homo sapiens)
• Rhesus monkey (Macaca mulatta)
• House mouse (Mus musculus)
• Norway rat (Rattus norvegicus)
• Guinea pig (Cavia porcellus)
• Rabbit (Oryctolagus cuniculus)
• Dog (Canis familiaris)
• Cow (Bos taurus)
• Nine-banded armadillo (Dasypus novemcinctus)
• Lesser hedgehog tenrec (Echinops telfairi)Aves (Birds)
• Chicken (Gallus gallus)
• Rock pigeon (Columba livia)Crocodylia (Alligators and Crocodiles)
• American alligator (Alligator mississippiensis)Testudines (Turtles)
• Western painted turtle (Chrysemys picta bellii)Squamata (Lizards and snakes)
• Green anole lizard (Anolis carolinensis)Anura (Frogs and toads)
• Tropical clawed frog (Xenopus tropicalis)Teleostei (Teleost fish)
• Zebrafish (Danio rerio)Cephalochordata
• Florida lancelet (Branchiostoma floridae)Hemichordata
• Acorn worm (Saccoglossus kowalevskii)
• Acorn worm 2 (Ptychodera flava)Echinodermata
• Purple sea urchin (Strongylocentrotus purpuratus)
• Bat starfish (Patiria miniata)Hexapoda
• Fruit fly (Drosophila melanogaster)
• Red flour beetle (Tribolium castaneum)Crustacea
• Common water flea (Daphnia pulex)Chelicerata
• Black-legged tick (Ixodes scapularis)Nematoda
• Roundworm (Caenorhabditis elegans)
• Large roundworm (Ascaris suum)Mollusca
• Owl limpet (Lottia gigantea)
• Pacific oyster (Crassostrea gigas)Annelida
• Polychaete worm (Capitella teleta)
• Common brandling worm (Eisenia fetida)Proline-Rich Coiled Coil 1
Proline Rich Coiled Coil-1 (PRCC1) is the commonly identified protein name of CAD38605. The PRCC1 gene is found on the long arm of Chromosome 5. It encodes for 445 amino acids for a predicted total of 6 exons. The predicted molecular weight is 46.7 kDa, and the isoelectric point is 5.46. Orthologs have been determined in most eukaryotes, the most highly conserved being found in most mammalian species. Moderate conservation is maintained among other distant species such as: Gallus gallus, Xenopus, Strongylocentrotus purpuratus, Tetraodon, etc.
The PRCC1 gene has two distinct regions: a proline-rich region on the N-terminus, and the DUF84 region on the C-terminus.
The DUF84 region is found in the genome of a bacterium called Vibrio cholerae. The region consists of approximately 183 amino acid residues. V. cholorae causes cholera and stomach flu in humans. The DUF84 region alone is about 160 amino acid residues. It is the only other protein that consists of DUF84 other than PRCC1.
The subcellular localization prediction program pTarget, predicted PRCC1 to be localized in the nucleus with a confidence of 95%. However, a research paper by Kamakari et al. determined the protein to localize in the Golgi Apparatus. PRCC1 is ubiquitously expressed, with high-density expression in the brain, hypothalamus and hippocampus in particular. No evidence of protein-protein interactions were found. No evidence of RNA alternate splicing was determined.Sea urchin
Sea urchins or urchins () are typically spiny, globular animals, echinoderms in the class Echinoidea. About 950 species live on the seabed, inhabiting all oceans and depth zones from the intertidal to 5,000 metres (16,000 ft; 2,700 fathoms). Their tests (hard shells) are round and spiny, typically from 3 to 10 cm (1 to 4 in) across. Sea urchins move slowly, crawling with their tube feet, and sometimes pushing themselves with their spines. They feed primarily on algae but also eat slow-moving or sessile animals. Their predators include sea otters, starfish, wolf eels, and triggerfish.
Like other echinoderms, urchins have fivefold symmetry as adults, but their pluteus larvae have bilateral (mirror) symmetry, indicating that they belong to the Bilateria, the large group of animal phyla that includes chordates, arthropods, annelids and molluscs. They are widely distributed across all the oceans, all climates from tropical to polar, and inhabit marine benthic (sea bed) habitats from rocky shores to hadal zone depths. Echinoids have a rich fossil record dating back to the Ordovician, some 450 million years ago. Their closest relatives among the echinoderms are the sea cucumbers (Holothuroidea); both are deuterostomes, a clade which includes the chordates.
The animals have been studied since the 19th century as model organisms in developmental biology, as their embryos were easy to observe; this has continued with studies of their genomes because of their unusual fivefold symmetry and relationship to chordates. Species such as the slate pencil urchin are popular in aquariums, where they are useful for controlling algae. Fossil urchins have been used as protective amulets.Sea urchin skeletogenesis
Skeletogenesis is a key morphogenetic event in the embryonic development of vertebrates and is of equal, although transient, importance in the development of the sea urchin, a marine invertebrate. The larval sea urchin does not resemble its adult form, because the sea urchin is an indirect developer, meaning its larva form must undergo metamorphosis to form the juvenile adult. Here, the focus is on skeletogenesis in the sea urchin species Strongylocentrotus purpuratus, as this species has been most thoroughly studied and characterized.Sea urchins of the Gulf of California
The sea urchins of the Gulf of California live between the coasts of the Baja California Peninsula to the west and mainland state of Sonora, Mexico to the east. The northern boundary is the lateral band of land with the remains of the Colorado River Delta, and the southern is the Pacific Ocean.
The Gulf of California is known for its high diversity and endemism of biota. One type of marine animal that can be found in this region is the sea urchin (class echinoidea, in the phylum echinodermata). One echinoid, Mellita granti, is a sea urchin endemic to the Gulf of California.Strongylocentrotidae
The Strongylocentrotidae are a family of sea urchins in the order Echinoida.Strongylocentrotus
Strongylocentrotus is a genus of sea urchins in the family Strongylocentrotidae containing several species.Tonicella lineata
Tonicella lineata, commonly known as the lined chiton, is a species of chiton from the North Pacific.Trophic cascade
Trophic cascades are powerful indirect interactions that can control entire ecosystems, occurring when a trophic level in a food web is suppressed. For example, a top-down cascade will occur if predators are effective enough in predation to reduce the abundance, or alter the behavior, of their prey, thereby releasing the next lower trophic level from predation (or herbivory if the intermediate trophic level is a herbivore).
The trophic cascade is an ecological concept which has stimulated new research in many areas of ecology. For example, it can be important for understanding the knock-on effects of removing top predators from food webs, as humans have done in many places through hunting and fishing.
A top-down cascade is a trophic cascade where the top consumer/predator controls the primary consumer population. In turn, the primary producer population thrives. The removal of the top predator can alter the food web dynamics. In this case, the primary consumers would overpopulate and exploit the primary producers. Eventually there would not be enough primary producers to sustain the consumer population. Top-down food web stability depends on competition and predation in the higher trophic levels. Invasive species can also alter this cascade by removing or becoming a top predator. This interaction may not always be negative. Studies have shown that certain invasive species have begun to shift cascades; and as a consequence, ecosystem degradation has been repaired.For example, if the abundance of large piscivorous fish is increased in a lake, the abundance of their prey, smaller fish that eat zooplankton, should decrease. The resulting increase in zooplankton should, in turn, cause the biomass of its prey, phytoplankton, to decrease.
In a bottom-up cascade, the population of primary producers will always control the increase/decrease of the energy in the higher trophic levels. Primary producers are plants, phytoplankton and zooplankton that require photosynthesis. Although light is important, primary producer populations are altered by the amount of nutrients in the system. This food web relies on the availability and limitation of resources. All populations will experience growth if there is initially a large amount of nutrients.In a subsidy cascade, species populations at one trophic level can be supplemented by external food. For example, native animals can forage on resources that don't originate in their same habitat, such a native predators eating livestock. This may increase their local abundances thereby affecting other species in the ecosystem and causing an ecological cascade. For example, Luskin et al (2017) found that native animals living in protected primary rainforest in Malaysia found food subsidies in neighboring oil palm plantations. This subsidy allowed native animal populations to increase, which then triggered powerful secondary ‘cascading’ effects on forest tree community. Specifically, crop-raiding wild boar (Sus scofa) built thousands of nests from the forest understory vegetation and this caused a 62% decline in forest tree sapling density over a 24-year study period. Such cross-boundary subsidy cascades may be widespread in both terrestrial and marine ecosystems and present significant conservation challenges.
These trophic interactions shape patterns of biodiversity globally. Humans and climate change have affected these cascades drastically. One example can be seen with sea otters (Enhydra lutris) on the Pacific coast of the United States of America. Over time, human interactions caused a removal of sea otters. One of their main prey, the pacific purple sea urchin (Strongylocentrotus purpuratus) eventually began to overpopulate. The overpopulation caused increased predation of giant kelp (Macrocystis pyrifera). As a result, there was extreme deterioration of the kelp forests along the California coast. This is why it is important for countries to regulate marine and terrestrial ecosystems.Predator-induced interactions could heavily influence the flux of atmospheric carbon if managed on a global scale. For example, a study was conducted to determine the cost of potential stored carbon in living kelp biomass in Sea Otter enhanced ecosystems. The study valued the potential storage between $205 million and $408 million dollars (US) on the European Carbon Exchange (2012).