Morphological Plasticity in the Tropical Sponge Anthosigmella Varians: Responses to Predators and Wave Energy.

The goal of the research presented here was to examine phenotypic plasticity exhibited by three morphotypes of the common Caribbean sponge Anthosigmella varians (Duchassaing & Michelotti). We were interested in examining the biotic (and, to a lesser extent, abiotic) factors responsible for branch production in this species. We also tested the hypothesis that the skeleton may serve an antipredator function in this sponge, focusing on vertebrate fish predators (i.e., angelfish) in this work. In transplant and caging experiments, unprotected forma varians replicates were immediately consumed by angelfish, while caged replicates persisted on the reef for several months. These findings support the hypothesis that predators (and not wave energy) restrict forma varians to lagoonal habitats. Branch production was not observed in A. varians forma incrustans when sponges were protected from predators or placed in predator-free, low-wave-energy environments. It is not clear from our work whether forma incrustans is capable of producing branches (i.e., whether branch production is a plastic trait in this morph). Additional field experiments demonstrated that A. varians forma varians increased spicule concentrations, compared to uninjured sponges, in response to artificial predation events, and A. varians forma rigida reduced spicule concentrations, compared to uncaged controls, when protected from predators. These findings indicate that spicule concentration is a plastic morphological trait that can be induced by damage, and that A. varians may be able to reduce spicule concentrations when environmental conditions change (e.g., in the absence of predators). The potential significance of inducible defenses and structural anti-predator defenses in sponges is discussed in relation to recent work on sponge chemical defenses

Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A wellsupported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets

RNA Interference in Marine and Freshwater Sponges: Actin Knockdown in \u3cem\u3eTethya wilhelma\u3c/em\u3e and \u3cem\u3eEphydatia muelleri\u3c/em\u3e by Ingested dsRNA Expressing Bacteria

Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from \u27knocking down\u27 expression of the actin gene. Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals

RNA interference in marine and freshwater sponges

Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from ‘knocking down’ expression of the actin gene. Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals

Assignment of Fragile Site 8E (FRA8E) to Human Chromosome Band 8q24.11 Adjacent to the Hereditary Multiple Exostoses 1 Gene and Two Overlapping Langer-Giedion Syndrome Deletion Endpoints

The distamycin A inducible fragile site, FRA8E, Fra(8) (q24.11) has been previously mapped to 8q24.11, proximal to the MYC gene, by fluorescent in situ hybridization (Takahasi et al., 1991). This fragile site has been shown to be present in about 1 out of every 140 healthy Japanese individuals (Takahasi et al., 1988). To more precisely map FRA8E, we have used cosmids isolated from the Langer-Giedion chromosomal region (LGCR) for FISH analysis. Langer-Giedion syndrome (LGS) is a contiguous gene syndrome characterized by chromosome deletions in Sq24.11 (Ludecke et al., 1991). One of the genes known to be involved in the etiology of LGS is hereditary multiple exostosis type 1 (EXTl). In addition to being associated with LGS, hereditary multiple exostosis is an independent disorder characterized by cartilage capped exostoses on the juxtaepiphyseal regions of the enchondral bones (Hennekam, 1991)

Challenging Disciplinary Boundaries in the First Year: A New Introductory Integrated Science Course for STEM Majors

To help undergraduates make connections among disciplines so they are able to approach, evaluate, and contribute to the solutions of important global problems, our campus has been focused on interdisciplinary research and education opportunities across the science, technology, engineering, and mathematics (STEM) disciplines. This paper describes the mobilization, planning, and implementation of a first-year interdisciplinary course for STEM majors that integrates key concepts found in traditional first-semester biology, chemistry, computer science, mathematics, and physics courses. This team-taught course, Integrated Quantitative Science (IQS), is half of a first-year student’s schedule in both semesters and is composed of a double lecture and a weekly lab and workshop. Features of this first-year course, including themes and concepts covered each semester, some of the materials developed, lessons learned, challenges, and preliminary measures of success are described

Challenging Disciplinary Boundaries in the First Year: A New Introductory Integrated Science Course for STEM Majors

To help undergraduates make connections among disciplines so they are able to approach, evaluate, and contribute to the solutions of important global problems, our campus has been focused on interdisciplinary research and education opportunities across the science, technology, engineering, and mathematics (STEM) disciplines. This paper describes the mobilization, planning, and implementation of a first-year interdisciplinary course for STEM majors that integrates key concepts found in traditional first-semester biology, chemistry, computer science, mathematics, and physics courses. This team-taught course, Integrated Quantitative Science (IQS), is half of a first-year student’s schedule in both semesters and is composed of a double lecture and a weekly lab and workshop. Features of this first-year course, including themes and concepts covered each semester, some of the materials developed, lessons learned, challenges, and preliminary measures of success are described

RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria

Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from `knocking down' expression of the actin gene. Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals

Methylation specific targeting of a chromatin remodeling complex from sponges to humans

DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution

Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets