Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators.
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Members of the SOX family of transcription factors are found throughout the animal kingdom, are characterized by the presence of a DNA-binding HMG domain, and are involved in a diverse range of developmental processes. Previous attempts to group SOX genes and deduce their structural, functional, and evolutionary relationships have relied largely on complete or partial HMG box sequence of a limited number of genes. In this study, we have used complete HMG domain sequence, full-length protein structure, and gene organization data to study the pattern of evolution within the family. For the first time, a substantial number of invertebrate SOX sequences have been included in the analysis. We find support for subdivision of the family into groups A-H, as has been suggested in some previous studies, and for the assignment of two new groups, I and J. For vertebrate genes, it appears that relatedness as suggested by HMG domain sequence is congruent with relatedness as indicated by overall structure of the full-length protein and intron-exon structure of the genes. Most of the SOX groups identified in vertebrates were represented by a single SOX sequence in each invertebrate species studied. We have named anonymous sequences and, where appropriate, have suggested systematic names for some previously identified sequences. In addition, we identify an HMG domain signature motif which may be considered representative of the SOX family. Based on our data, we propose a robust phylogeny of SOX genes that reflects their evolutionary history in metazoans. (+info)
Regulation and regeneration in the ctenophore Mnemiopsis leidyi.
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Lobate ctenophores (tentaculates) generally exhibit a remarkable ability to regenerate missing structures as adults. On the other hand, their embryos exhibit a highly mosaic behavior when cut into halves or when specific cells are ablated. These deficient embryos do not exhibit embryonic regulation, and generate incomplete adult body plans. Under certain conditions, however, these deficient animals are subsequently able to replace the missing structures during the adult phase in a process referred to as "post-regeneration." We have determined that successful post-regeneration can be predicted on the basis of a modified polar coordinate model, and the rules of intercalary regeneration, as defined by French et al. (V. French, P. J. Bryant, and S. V. Bryant, 1976, Science 193, 969-981.) The model makes certain assumptions about the organization of the ctenophore body plan that fit well with what we have determined on the basis of cell lineage fates maps, and their twofold rotational ("biradial") symmetry. The results suggest that cells composing the ctenophore adult body plan possess positional information, which is utilized to reconstruct the adult body plan. More specifically, we have found that the progeny of three specific cell lineages are required to support post-regeneration of the comb rows (the e(1), e(2), and m(1) micromeres). Furthermore, post-regeneration of the comb rows involves a suite of cell-cell inductive interactions, which are similar to those that take place during their embryonic formation. The significance of these findings is discussed in terms of the organization of the ctenophore body plan, and the mechanisms involved in cell fate specification. This situation is also contrasted with that of the atentaculate ctenophores, which are unable to undergo post-regeneration. (+info)
Regional specification during embryogenesis in the craniiform brachiopod Crania anomala.
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A fate map has been constructed for the embryo of Crania. The animal half of the egg forms the ectodermal epithelium of the larva's apical lobe. The vegetal half of the egg forms endoderm, mesoderm, and the ectoderm of the mantle lobe. The vegetal pole is the site of gastrulation; this site becomes the posterior ventral region of the mantle lobe of the larva. The plane of the first cleavage goes through the animal-vegetal axis of the egg; it bears no relationship to the future plane of bilateral symmetry of the larva. The timing of regional specification was examined by isolating animal, vegetal, or meridional halves from oocytes, eggs, or embryos from prior to germinal vesicle breakdown through gastrulation. Animal halves isolated from oocytes formed either the epithelium of the apical lobe or a larva with all three germ layers. Animal halves isolated from unfertilized eggs and eight-cell embryos formed only apical lobe epithelium. Beginning at the blastula stage, animal halves formed mantle in addition to apical lobe epithelium. In animal halves isolated after gastrulation, the mantle lobe was always truncated. Vegetal halves isolated at all stages prior to gastrulation gastrulated and formed apical and mantle lobes with endoderm and mesoderm; however, the relative size of the apical lobe that formed decreased substantially when vegetal halves were isolated at later developmental stages. When meridional halves were isolated from unfertilized eggs and two- to four-cell embryos, both halves frequently formed normally proportioned larvae. Beginning at the blastula stage, a number of pairs frequently had a member that lacked dorsal setae on its mantle lobe while the other member of the pair formed setae, indicating that the dorsoventral axis had been set up. The process of regional specification in Crania is compared to those of Discinisca and Glottidia in the brachiopod subphylum Linguliformea and Phoronis in the phylum Phoronida. (+info)
The parkinsonian models: invertebrates to mammals.
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In contrast to Alzheimer's disease, effective therapeutic options are available for Parkinson's disease. Therapy of dopamine replacement such as levodopa improves the symptoms of this disease, but does not inhibit neurodegeneration in the substantia nigra. Numerous studies have suggested that endogenous and environmental neurotoxins, and oxidative stress may participate in this disease, but the detailed mechanisms are still unclear. Recent genetic studies in familial Parkinson's disease and parkinsonism show several gene mutations. This new information regarding pathogenesis offers novel prospects for therapy. To develop novel neuroprotective drugs, it is necessary to have a model for each type of parkinsonism. This review summarizes current findings regarding parkinsonian models in vertebrates and invertebrates and discusses their value. (+info)
Evolution of hematopoiesis: Three members of the PU.1 transcription factor family in a cartilaginous fish, Raja eglanteria.
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T lymphocytes and B lymphocytes are present in jawed vertebrates, including cartilaginous fishes, but not in jawless vertebrates or invertebrates. The origins of these lineages may be understood in terms of evolutionary changes in the structure and regulation of transcription factors that control lymphocyte development, such as PU.1. The identification and characterization of three members of the PU.1 family of transcription factors in a cartilaginous fish, Raja eglanteria, are described here. Two of these genes are orthologs of mammalian PU.1 and Spi-C, respectively, whereas the third gene, Spi-D, is a different family member. In addition, a PU.1-like gene has been identified in a jawless vertebrate, Petromyzon marinus (sea lamprey). Both DNA-binding and transactivation domains are highly conserved between mammalian and skate PU.1, in marked contrast to lamprey Spi, in which similarity is evident only in the DNA-binding domain. Phylogenetic analysis of sequence data suggests that the appearance of Spi-C may predate the divergence of the jawed and jawless vertebrates and that Spi-D arose before the divergence of the cartilaginous fish from the lineage leading to the mammals. The tissue-specific expression patterns of skate PU.1 and Spi-C suggest that these genes share regulatory as well as structural properties with their mammalian orthologs. (+info)
Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology.
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The statistical testing of alternative phylogenetic trees is central to evaluating competing evolutionary hypotheses. Fleming proposed that the New Zealand cicada species Maoricicada iolanthe is the sister species to the major radiation of both low-altitude and montane Maoricicada species. However, using 1,520 bp of mitochondrial DNA sequence data from the cytochrome oxidase subunit I, tRNA aspartic acid, and the ATPase subunit 6 and 8 genes, we inferred that both M. iolanthe and another low-altitude species, Maoricicada campbelli, are nested within the montane Maoricicada radiation. Therefore, we examined the stability of the inferred phylogenetic placement of these two species using the newly developed Shimodaira-Hasegawa test (SH test) implemented in a maximum-likelihood framework. The SH test has two advantages over the more commonly used Kishino-Hasegawa (KH) and Templeton tests. First, the SH test simultaneously compares multiple topologies and corrects the corresponding P: values to accommodate the multiplicity of testing. Second, the SH test is correct when applied to a posteriori hypotheses, unlike the KH test, because it readjusts the expectation of the null hypothesis (that two trees are not different) accordingly. The comparison of P: values estimated under the assumptions of both the KH test and the SH test clearly demonstrate that the KH test has the potential to be misleading when the issue of comparing of a posteriori hypotheses is ignored and when multiple comparisons are not taken into account. The SH test, in combination with a variety of character-weighting schemes applied to our data, reveals a surprising amount of ambiguity in the phylogenetic placement of M. iolanthe and M. campbelli. (+info)
The function and regulation of vasa-like genes in germ-cell development.
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The vasa gene, essential for germ-cell development, was originally identified in Drosophila, and has since been found in other invertebrates and vertebrates. Analysis of these vasa homologs has revealed a highly conserved role for Vasa protein among different organisms, as well as some important differences in its regulation. (+info)
Flexural and torsional stiffness in multi-jointed biological beams.
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Flexibility, the ability to deform in response to loads, is a common property of biological beams. This paper investigates the mechanical behavior of multi-jointed beams, which are characterized by a linear series of morphologically similar joints. Flexural stiffness and torsional stiffness were measured in two structurally distinct beams, crinoid arms (Echinodermata, Comatulida) and crustacean antennae (Arthropoda, Decapoda). Morphological data from these beams were used to determine the relative contributions of beam diameter and joint density (number of joints per millimeter of beam length) to the flexural and torsional stiffness of these two structures. As predicted by beam theory, beam diameter influenced stiffness in both crinoid arms and crustacean antennae. In crinoid arms, increases in joint density were associated with decreases in stiffness, but joint density had no significant influence on stiffness in crustacean antennae. In both crinoid arms and crustacean antennae, the magnitudes of flexural and torsional stiffness, as well as the ratio of these two variables, were similar to previously reported values for non-jointed biological beams. These results suggest that the structural design of a biological beam is not a limiting factor determining its mechanical properties. (+info)