Generating molecular markers from zooxanthellate cnidarians

Genetic techniques are providing tools that are necessary to answer questions concerning the ecology and evolution of cnidarians that, until recently, could not be easily addressed. In developing molecular markers for cnidarians with algal symbionts (zooxanthellae), however, caution must be used to ensure the markers in question are derived from the cnidarian host and not zooxanthellae. Unless the DNA template is from asymbiotic tissue, both host and symbiont genomes are present in the DNA template and zooxanthella-specific markers are often inadvertently generated. Steps should be taken to minimize the contamination by zooxanthella DNA in the template, and the origin of the molecular marker (host or symbiont) must be verified. Including zooxanthella-specific markers in analyses for cnidarians will confound interpretations of the results as biogeographic and phylogeographic patterns of zooxanthellae do not necessarily reflect those of the host.     

Acoel flatworms are not platyhelminthes: evidence from phylogenomics

Acoel flatworms are small marine worms traditionally considered to belong to the phylum Platyhelminthes. However, molecular phylogenetic analyses suggest that acoels are not members of Platyhelminthes, but are rather extant members of the earliest diverging Bilateria. This result has been called into question, under suspicions of a long branch attraction (LBA) artefact. Here we re-examine this problem through a phylogenomic approach using 68 different protein-coding genes from the acoel Convoluta pulchra and 51 metazoan species belonging to 15 different phyla. We employ a mixture model, named CAT, previously found to overcome LBA artefacts where classical models fail. Our results unequivocally show that acoels are not part of the classically defined Platyhelminthes, making the latter polyphyletic. Moreover, they indicate a deuterostome affinity for acoels, potentially as a sister group to all deuterostomes, to Xenoturbellida, to Ambulacraria, or even to chordates. However, the weak support found for most deuterostome nodes, together with the very fast evolutionary rate of the acoel Convoluta pulchra, call for more data from slowly evolving acoels (or from its sister-group, the Nemertodermatida) to solve this challenging phylogenetic problem.     

Biological relationships derived from morphology of permanent teeth: recent evidence from prehistoric India

Morphological variation in permanent teeth of prehistoric populations yields clues to their relationships with other prehistoric and living people. This paper documents variation in fourteen variants of the permanent tooth crown for the late Chalcolithic skeletal series from Inamgaon (1600-700 BC), an early farming settlement in western India. In comparison of the dental morphology profile at Inamgaon with American Indians and American Whites, the people of Inamgaon were found to more closely resemble American Whites. However, specific traits deviated in the direction of Amerindian dental trait frequencies, suggesting gene flow from north and east Asian populations. The dental morphology of the Inamgaon sample is similar to dental patterns characteristic of prehistoric Pakistani samples from Sarai Khola and Timargarha. However, Inamgaon and Timargarha exhibit somewhat more complex crown morphology than the Sarai Khola sample, suggesting a closer relationship between them and greater antiquity of residence in the subcontinent, in contrast to Sarai Khola sample.     

When growth models are not universal: evidence from marine invertebrates

The accumulation of body mass, as growth, is fundamental to all organisms. Being able to understand which model(s) best describe this growth trajectory, both empirically and ultimately mechanistically, is an important challenge. A variety of equations have been proposed to describe growth during ontogeny. Recently, the West Brown Enquist (WBE) equation, formulated as part of the metabolic theory of ecology, has been proposed as a universal model of growth. This equation has the advantage of having a biological basis, but its ability to describe invertebrate growth patterns has not been well tested against other, more simple models. In this study, we collected data for 58 species of marine invertebrate from 15 different taxa. The data were fitted to three growth models (power, exponential and WBE), and their abilities were examined using an information theoretic approach. Using Akaike information criteria, we found changes in mass through time to fit an exponential equation form best (in approx. 73% of cases). The WBE model predominantly overestimates body size in early ontogeny and underestimates it in later ontogeny; it was the best fit in approximately 14% of cases. The exponential model described growth well in nine taxa, whereas the WBE described growth well in one of the 15 taxa, the Amphipoda. Although the WBE has the advantage of being developed with an underlying proximate mechanism, it provides a poor fit to the majority of marine invertebrates examined here, including species with determinate and indeterminate growth types. In the original formulation of the WBE model, it was tested almost exclusively against vertebrates, to which it fitted well; the model does not however appear to be universal given its poor ability to describe growth in benthic or pelagic marine invertebrates.     

Evolution of eumetazoan nervous systems: insights from cnidarians

Cnidarians, the sister group to bilaterians, have a simple diffuse nervous system. This morphological simplicity and their phylogenetic position make them a crucial group in the study of the evolution of the nervous system. The development of their nervous systems is of particular interest, as by uncovering the genetic programme that underlies it, and comparing it with the bilaterian developmental programme, it is possible to make assumptions about the genes and processes involved in the development of ancestral nervous systems. Recent advances in sequencing methods, genetic interference techniques and transgenic technology have enabled us to get a first glimpse into the molecular network underlying the development of a cnidarian nervous system—in particular the nervous system of the anthozoan Nematostella vectensis. It appears that much of the genetic network of the nervous system development is partly conserved between cnidarians and bilaterians, with Wnt and bone morphogenetic protein (BMP) signalling, and Sox genes playing a crucial part in the differentiation of neurons. However, cnidarians possess some specific characteristics, and further studies are necessary to elucidate the full regulatory network. The work on cnidarian neurogenesis further accentuates the need to study non-model organisms in order to gain insights into processes that shaped present-day lineages during the course of evolution.     

Sea urchin embryo fertilization envelope: immunological evidence that soluble envelope proteins are derived from cortical granule secretions

Although structural studies support the hypothesis that the sea urchin embryo fertilization envelope is derived from the preexisting vitelline envelope template and structural proteins secreted during the cortical reaction, biochemical evidence is minimal. We used an immunological approach to determine the subcellular origin of proteins which were extracted from the fertilization envelope. Fertilization envelopes were isolated from Stronglyocentrotus purpuratus embryos 30 min postinsemination and extracted with 6.0 M urea-0.15 M 2-mercaptoethanol, pH 10.5, for 10 min at 80°C. Extracted proteins were exhaustively dialyzed against 0.015 M 2-mercaptoethanol-0.100 M Tris-HCl at pH 8.6 and mixed with Fruend's complete adjuvant prior to injection into female New Zealand white rabbits. The antiserum which was prepared contained antibodies to six major and two minor polypeptides in the soluble fertilization envelope fraction based on two-dimensional sodium dodecyl sulfate immunoelectrophoresis. Extracts of vitelline envelopes and extracts of unfertilized egg surfaces which are known to contain viteline envelope proteins did not form immunoprecipitates with antiserum against soluble fertilization envelope polypeptides. Extracts of isolated cortical granules and the secreted paracystalline protein fraction formed four and three immunoprecipitates, respectively, which showed complete identity with the soluble fertilization envelope polypeptides based on rocket-line immunoelectrophoresis. Two-dimensional sodium dodecyl sulfate immunoelectrophoresis of cortical granule extract and the secreted paracrystalline protein fraction showed a complex pattern of immunoprecipitates, but a major finding was that cortical granules contain a 193,000-dalton polypeptide which was not found in the paracrystalline protein fraction. These results suggest that proteolytic processing of a cortical granule precursor of the paracrystalline protein fraction occurs during fertilization and that not all of the cortical granule polypeptides are incorporated into the fertilization envelope by means of di- and trityrosine crosslinks with the vitelline envelope proteins.     

Occurrence of nonlymphoid leukocytes that are not derived from blood islands in Xenopus laevis larvae

Previous immunohistochemical observations using the monoclonal antibody (XL-1) which recognizes all types of leukocytes in Xenopus laevis revealed the occurrence of XL-1+ cells in the mesenchyme throughout the early larval body, before the appearance of any lymphocytes. The present experiments were performed to determine whether these leukocytes originate, like lymphocytes and red blood cells (RBCs), in the ventral blood islands (VBI) or the dorsolateral plate (DLP). For tracing the derivation of cells, a specific staining by quinacrine to nuclei of X. laevis and Xenopus borealis hybrid (LB) cells was used to distinguish them from X. laevis (LL) cells. Orthotopic graftings of VBI tissue from st.22-23 LB embryos to the stage-matched LL embryos and examinations at st.44-45 before differentiation of the lymphocytes showed that the proportion of XL-1+ LB cells was always significantly lower than that of RBCs with the same marker in all experimental larvae. The head (LB)-body (LL) chimeras from st.22-23 embryos and culture of the head-portions as VBI- and DLP-free explants from st.14-23 embryos both demonstrated that a significant number of XL-1+ cells which had originated in the head portions had begun to differentiate by st.42-43. These results indicate that there is a significant population of larval nonlymphoid leukocytes (mostly macrophages) that do not originate from either the VBI or DLP region, and are distributed in the mesenchyme throughout the body.     

Molecular evidence that SJL reticulum cell sarcomas are derived from pre-B cell. Clonal rearrangement of heavy chain but not of light chain immunoglobulin genes

In order to investigate the clonal origin of SJL reticulum cell sarcoma (RCS), two-color cell membrane-staining and molecular biologic analyses were performed. Flow cytometric analysis revealed that the SJL RCS consists of about 50 to 60% Thy-1-positive and 20 to 30% B220-positive cells and that the majority of the Thy-1-positive cells are L3T4-positive, whereas a few are Lyt-2-positive. In spite of this pleomorphic nature of SJL RCS shown by cell membrane analysis, when the immunoglobulin heavy chain J segment (JH) was used to probe the DNA obtained from the tumor, we observed clonal rearrangements of the gene. Results of the cell-sorting experiment combined with Southern hybridization using the JH gene probe confirmed that those clonally expanding cells are Ia and B220 antigen-positive. Furthermore, all tumors derived from a given mouse showed the same rearrangement pattern. However, no clonal rearrangement was observed when the DNA was probed with the T cell receptor beta-chain gene or with immunoglobulin kappa- or lambda-light chain genes. From these data, we conclude that SJL RCS is a tumor of B cells and that the neoplastic event takes place at an immature B cell stage.     

"Ag-NORs" are not always true NORs: new evidence in mammals

In spite of uncertainty about the biochemical processes involved, silver staining is a widely used technique for assessing the locations of active NORs in eukaryotic genomes in general, and in mammalian genomes in particular. However, following a previous study of hedgehog chromosomes, we present here a second example from two gerbil species (Rodentia, Muridae), which have several clear Ag-positive signals that do not correspond to 28S rDNA clusters. Although this pattern may be characteristic of particular genomes displaying unusual heterochromatic features, our study casts doubt upon the reliability and universality of Ag-staining for detecting active NORs.     

These squatters are not innocent: the evidence of parasitism in sponge-inhabiting shrimps

Marine sponges are frequently inhabited by a wide range of associated invertebrates, including caridean shrimps. Symbiotic shrimps are often considered to be commensals; however, in most cases, the relationship with sponge hosts remains unclear. Here we demonstrate that sponge-inhabiting shrimps are often parasites adapted to consumption of sponge tissues. First, we provide detailed examination of morphology and stomach contents of Typton carneus (Decapoda: Palaemonidae: Pontoniinae), a West Atlantic tropical shrimp living in fire sponges of the genus Tedania. Remarkable shear-like claws of T. carneus show evidence of intensive shearing, likely the result of crushing siliceous sponge spicules. Examination of stomach contents revealed that the host sponge tissue is a major source of food for T. carneus. A parasitic mode of life is also reflected in adaptations of mouth appendages, in the reproduction strategy, and in apparent sequestration of host pigments by shrimp. Consistent results were obtained also for congeneric species T. distinctus (Western Atlantic) and T. spongicola (Mediterranean). The distribution of shrimps among sponge hosts (mostly solitary individuals or heterosexual pairs) suggests that Typton shrimps actively prevent colonisation of their sponge by additional conspecifics, thus protecting their resource and reducing the damage to the hosts. We also demonstrate feeding on host tissues by sponge-associated shrimps of the genera Onycocaris, Periclimenaeus, and Thaumastocaris (Pontoniinae) and Synalpheus (Alpheidae). The parasitic mode of life appears to be widely distributed among sponge-inhabiting shrimps. However, it is possible that under some circumstances, the shrimps provide a service to the host sponge by preventing a penetration by potentially more damaging associated animals. The overall nature of interspecific shrimp-sponge relationships thus warrants further investigation.     

Macromolecular solvation energies derived from small molecule crystal morphology.

The morphology of small molecule crystals provides a model for evaluating surface solvation energies in a system with similar packing density to that observed for amino acid residues in proteins. The solvation energies associated with the transfer of methylene and carboxyl groups between vacuum and aqueous phases are estimated to be approx. $40 and -260 cal/A2, respectively, from an analysis of the morphology of succinic acid crystals. These solvation energies predict values for contact angles in reasonable agreement with measurements determined from macroscopic monolayer surfaces. Transfer free energies between vapor and water phases for a series of carboxylic acids are also predicted reasonably well by these solvation energies, provided the surface exposure of different groups is quantitated with the molecular surface area rather than the more traditional accessible surface area. In general, molecular surfaces and molecular surface areas are seen to have important advantages for characterizing the structure and energetics of macromolecular surfaces. Crystal faces of succinic acid with the lowest surface energies in aqueous solution are characteristically smooth. Increasing surface roughness and apolarity are associated with higher surface energies, which suggests an approach for modifying the surface properties of proteins and other macromolecules.     

Monogenic traits are not simple: lessons from phenylketonuria.

The classification of genetic disease into chromosomal, monogenic and multifactorial categories is an oversimplification. Phenylketonuria (PKU) is a classic 'monogenic' autosomal recessive disease in which mutation at the human PAH locus was deemed sufficient to explain the impaired function of the enzyme phenylalanine hydroxylase (enzymic phenotype), the attendant hyperphenylalaninemia (metabolic phenotype) and the resultant mental retardation (cognitive phenotype). In the era of molecular genetics, expectations for a consistently close correlation between the mutant genotype and variant phenotype have been somewhat disappointed, and PKU is used here to illustrate how and why this might be the case. So-called monogenic traits do, indeed, conform to long-accepted ideas about the expression of 'major' loci and their importance in determining parameters of phenotype, but the associated features are as complex, in their own ways, as those in so-called complex traits.     

Microorganisms in the gut of beetles: evidence from molecular cloning

We have regularly cultured yeasts from the gut of certain beetles in our ongoing research. In this study cloned PCR products amplified from the gut contents of certain mushroom-feeding and wood-ingesting beetles in four families (Erotylidae, Tenebrionidae, Ciidae, and Passalidae) were sequenced and compared with culture results. Cultural techniques detected some yeasts present in the gut of the beetles, including a Pichia stipitis-like yeast associated with wood-ingesting passalid beetles. Clone sequences similar to several ascomycete yeasts and Malassezia restricta, a fastidious basidiomycetous yeast requiring special growth media, however, were not detected by culturing. Unexpectedly, phylogenetic analysis of additional clone sequences discovered from passalid beetles showed similarity to members of the Parabasalia, protists known from other wood-ingesting insects, termites, and wood roaches. Examination of all gut regions of living passalids, however, failed to reveal parabasalids, and it is possible that they were parasites in the gut tissue present in low numbers.