Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms.

Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named "derivedness index" to quantify the degree of derivedness.

The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms.

Background: Proteomic studies of skeletal proteins have revealed large, complex mixtures of proteins occluded within the mineral. Many skeletal proteomes contain rapidly evolving proteins with repetitive domains, further complicating our understanding. In echinoderms, proteomic analysis of the skeletal proteomes of mineralized tissues of the sea urchin Strongylocentrotus purpuratus prominently featured spicule matrix proteins with repetitive sequences linked to a C-type lectin domain.

Examination of the skeletal proteome of the brittle star Ophiocoma wendtii reveals overall conservation of proteins but variation in spicule matrix proteins.

Background: While formation of mineralized tissue is characteristic of many animal taxa, the proteins that interact with mineral are diverse and appear in many cases to be of independent origin. Extracellular matrix proteins involved in mineralization do share some common features. They tend to be disordered, secreted proteins with repetitive, low complexity.

Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii.

Background: The gastrula stage represents the point in development at which the three primary germ layers diverge. At this point the gene regulatory networks that specify the germ layers are established and the genes that define the differentiated states of the tissues have begun to be activated. These networks have been well-characterized in sea urchins, but not in other echinoderms.

Tracing misalignment and unequal crossing over during evolution of the repetitive region of the SM50 gene in sea urchins.

The location of misalignment and unequal crossover involved in concerted evolution of tandemly repetitive sequences is difficult to document owing to the homogeneity of sequences that are subject to this process. However, the repetitive domain of the SM50 gene in sea urchins contains variation, within the gene itself, between alleles, and between species that has allowed us to determine where misalignment and unequal crossing over occurred during evolution of this gene. We have therefore analyzed the SM50 repeat regions in a variety of species to determine where recent changes in repeat numbers have occurred, and from this have deduced the mechanisms that lead to these changes.

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome.

Sea urchin metalloproteases: a genomic survey of the BMP-1/tolloid-like, MMP and ADAM families.

Analysis of the Strongylocentrotus purpuratus genome has revealed approximately 240 metalloprotease genes, and they represent all 23 families expressed in vertebrates. EST/cDNA sequencing and microarray analysis show that nearly 70% are represented in embryo RNA. Among them are many metalloproteases with demonstrated developmental roles in other systems-BMP-1/TLD (tolloid) (astacins), MMPs (matrix metalloproteases) and the ADAMs (disintegrin/metalloproteases).

Overexpression and mechanistic characterization of blastula protease 10, a metalloprotease involved in sea urchin embryogenesis and development.

Blastula protease 10 (BP10) is a metalloenzyme involved in sea urchin embryogenesis, which has been assigned to the astacin family of zinc-dependent endopeptidases. It shows greatest homology with the mammalian tolloid-like genes and contains conserved structural motifs consistent with astacin, tolloid, and bone morphogenetic protein 1. Astacin, a crustacean digestive enzyme, has been proposed to carry out hydrolysis via a metal-centered mechanism that involves a metal-coordinated "tyrosine switch.

Identification of cis-regulatory elements involved in transcriptional regulation of the sea urchin SpFoxB gene.

The SpFoxB gene is transiently expressed first in the mesoderm, then in the endoderm and oral ectoderm during sea urchin gastrulation. Perturbations of a number of proteins involved in endomesoderm specification have been shown to alter the mRNA levels of SpFoxB, but the cis-regulatory elements required for expression of SpFoxB have not been examined. In order to investigate this, we have screened the SpFoxB gene for sequences that can drive its expression.

Development of calcareous skeletal elements in invertebrates.

Most metazoans require skeletal support systems. While the formation of bones and teeth in vertebrates has been well studied, endo- and exoskeleton development of non-vertebrates, especially calcification during terminal differentiation, has been neglected. Biomineralization of skeletons in invertebrates presents interesting research opportunities.

Injection of myo-inositol reverses the effects of lithium on sea urchin blastomeres.

Lithium is known to cause sea urchin blastomeres destined to give rise to epithelium rather than to differentiate into gut or skeleton. While it has been proposed that lithium alters development by interfering with the inositol-tris phosphate-protein kinase C (IP -PKC) signaling pathway, the mechanism of action of lithium in sea urchins has remained elusive. Here we describe experiments that examine the hypothesis that lithium exerts its effect on sea urchin embryos via the IP -PKC pathway.