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NCBI: db=pubmed; Term=(((((((((echinoderm) AND developmental biology) OR strongylocentrotus purpuratus) OR patiria miniata) OR lytechinus variegatus) OR eucidaris tribuloides) OR parastichopus parvimensis) OR ophiothrix apiculata) OR allocentrotus fragilis) OR strongylocentrotus franciscanus AND ( ( Humans[Mesh] OR Animals[Mesh:noexp] ) ) AND ("last 5 years"[PDat])
Updated: 11 hours 46 min ago

A Conserved Role for VEGF Signaling in Specification of Homologous Mesenchymal Cell Types Positioned at Spatially Distinct Developmental Addresses in Early Development of Sea Urchins.

Fri, 10/20/2017 - 12:53
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A Conserved Role for VEGF Signaling in Specification of Homologous Mesenchymal Cell Types Positioned at Spatially Distinct Developmental Addresses in Early Development of Sea Urchins.

J Exp Zool B Mol Dev Evol. 2017 Jul;328(5):423-432

Authors: Erkenbrack EM, Petsios E

Abstract
Comparative studies of early development in echinoderms are revealing the tempo and mode of alterations to developmental gene regulatory networks and to the cell types they specify. In euechinoid sea urchins, skeletogenic mesenchyme (SM) ingresses prior to gastrulation at the vegetal pole and aligns into a ring-like array with two bilateral pockets of cells, the sites where spiculogenesis will later occur. In cidaroid sea urchins, the anciently diverged sister clade to euechinoid sea urchins, a homologous SM cell type ingresses later in development, after gastrulation has commenced, and consequently at a distinct developmental address. Thus, a heterochronic shift of ingression of the SM cell type occurred in one of the echinoid lineages. In euechinoids, specification and migration of SM are facilitated by vascular endothelial growth factor (VEGF) signaling. We describe spatiotemporal expression of vegf and vegfr and experimental manipulations targeting VEGF signaling in the cidaroid Eucidaris tribuloides. Spatially, vegf and vegfr mRNA localizes similarly as in euechinoids, suggesting conserved deployment in echinoids despite their spatially distinct development addresses of ingression. Inhibition of VEGF signaling in E. tribuloides suggests its role in SM specification is conserved in echinoids. Temporal discrepancies between the onset of vegf expression and SM ingression likely result in previous observations of SM "random wandering" behavior. Our results indicate that, although the SM cell type in echinoids ingresses into distinct developmental landscapes, it retains a signaling mechanism that restricts their spatial localization to a conserved developmental address where spiculogenesis later occurs.

PMID: 28544452 [PubMed - indexed for MEDLINE]

Categories: pubmed

A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica.

Fri, 10/20/2017 - 12:53
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A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica.

Biol Bull. 2016 Dec;231(3):236-244

Authors: Pierce SK, Mahadevan P, Massey SE, Middlebrooks ML

Abstract
An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus. However, nucleotide BLAST analysis of the whole genome resulted in hits to only a few portions of the genome, indicating that the Elysia chlorotica retrovirus is novel, has not been previously sequenced, and does not have great genetic similarity to other known viral species. When more invertebrate retroviral genomes are examined, a more precise phylogenetic placement of the Elysia chlorotica retrovirus can be determined.

PMID: 28048954 [PubMed - indexed for MEDLINE]

Categories: pubmed

De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus.

Tue, 10/17/2017 - 12:46
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De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus.

PLoS One. 2017;12(9):e0184090

Authors: Musacchia F, Vasilev F, Borra M, Biffali E, Sanges R, Santella L, Chun JT

Abstract
Starfish have been instrumental in many fields of biological and ecological research. Oocytes of Astropecten aranciacus, a common species native to the Mediterranean Sea and the East Atlantic, have long been used as an experimental model to study meiotic maturation, fertilization, intracellular Ca2+ signaling, and cell cycle controls. However, investigation of the underlying molecular mechanisms has often been hampered by the overall lack of DNA or protein sequences for the species. In this study, we have assembled a transcriptome for this species from the oocytes, eggs, zygotes, and early embryos, which are known to have the highest RNA sequence complexity. Annotation of the transcriptome identified over 32,000 transcripts including the ones that encode 13 distinct cyclins and as many cyclin-dependent kinases (CDK), as well as the expected components of intracellular Ca2+ signaling toolkit. Although the mRNAs of cyclin and CDK families did not undergo significant abundance changes through the stages from oocyte to early embryo, as judged by real-time PCR, the transcript encoding Mos, a negative regulator of mitotic cell cycle, was drastically reduced during the period of rapid cleavages. Molecular phylogenetic analysis using the homologous amino acid sequences of cytochrome oxidase subunit I from A. aranciacus and 30 other starfish species indicated that Paxillosida, to which A. aranciacus belongs, is not likely to be the most basal order in Asteroidea. Taken together, the first transcriptome we assembled in this species is expected to enable us to perform comparative studies and to design gene-specific molecular tools with which to tackle long-standing biological questions.

PMID: 28873438 [PubMed - indexed for MEDLINE]

Categories: pubmed

Endocytosis in primary mesenchyme cells during sea urchin larval skeletogenesis.

Tue, 10/17/2017 - 12:46
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Endocytosis in primary mesenchyme cells during sea urchin larval skeletogenesis.

Exp Cell Res. 2017 Oct 01;359(1):205-214

Authors: Killian CE, Wilt FH

Abstract
The sea urchin larval embryo elaborates two calcitic endoskeletal elements called spicules. Spicules are synthesized by the primary mesenchyme cells (PMCs) and begin to form at early gastrula stage. It is known that the calcium comprising the spicules comes from the seawater and we wish to further consider the mode of calcium transport from the extracellular seawater to the PMCs and then onto the forming spicules. We used PMC in vitro cultures, calcein, fluorescently labeled dextran, and fluorescently labeled Wheat Germ Agglutinin (WGA) to track calcium transport from the seawater into PMCs and spicules and to determine how molecules from the surface of PMCs interact with the incoming calcium. Labeling of PMC endocytic vesicles and forming spicules by both calcein and fluorescently tagged dextran indicate that calcium is taken up from the seawater by endocytosis and directly incorporated into spicules. Calcein labeling studies also indicate that calcium from the extracellular seawater begins to be incorporated into spicules within 30min of uptake. In addition, we demonstrate that fluorescently labeled WGA and calcein are taken up by many of the same endocytic vesicles and are incorporated into growing spicules. These findings suggest that PMC specific surface molecules accompany calcium ions as they enter PMCs via endocytosis and are incorporated together in the growing spicule. Using anti-spicule matrix protein antibodies, we pinpoint a subset of spicule matrix proteins that may accompany calcium ions from the surface of the PMCs until they are incorporated into spicules. Msp130 is identified as one of these spicule matrix proteins.

PMID: 28782554 [PubMed - indexed for MEDLINE]

Categories: pubmed

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

Fri, 10/13/2017 - 12:42
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The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms.

BMC Evol Biol. 2017 Jun 05;17(1):125

Authors: Flores RL, Livingston BT

Abstract
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. A comparative study of the brittle star Ophiocoma wendtii skeletal proteome revealed an order of magnitude fewer proteins containing C-type lectin domains. A number of other proteins conserved in the skeletons of the two groups were identified. Here we report the complete skeletal proteome of the sea star Patiria miniata and compare it to that of the other echinoderm groups.
RESULTS: We have identified eighty-five proteins in the P. miniata skeletal proteome. Forty-two percent of the proteins were determined to be homologous to proteins found in the S. purpuratus skeletal proteomes. An additional 34 % were from similar functional classes as proteins in the urchin proteomes. Thirteen percent of the P. miniata proteins had homologues in the O. wendtii skeletal proteome with an additional 29% showing similarity to brittle star skeletal proteins. The P. miniata skeletal proteome did not contain any proteins with C-lectin domains or with acidic repetitive regions similar to the sea urchin or brittle star spicule matrix proteins. MSP130 proteins were also not found. We did identify a number of proteins homologous between the three groups. Some of the highly conserved proteins found in echinoderm skeletons have also been identified in vertebrate skeletons.
CONCLUSIONS: The presence of proteins conserved in the skeleton in three different echinoderm groups indicates these proteins are important in skeleton formation. That a number of these proteins are involved in skeleton formation in vertebrates suggests a common origin for some of the fundamental processes co-opted for skeleton formation in deuterostomes. The proteins we identify suggest transport of proteins and calcium via endosomes was co-opted to this function in a convergent fashion. Our data also indicate that modifications to the process of skeleton formation can occur through independent co-option of proteins following species divergence as well as through domain shuffling.

PMID: 28583083 [PubMed - indexed for MEDLINE]

Categories: pubmed

Parallel embryonic transcriptional programs evolve under distinct constraints and may enable morphological conservation amidst adaptation.

Wed, 10/04/2017 - 12:25
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Parallel embryonic transcriptional programs evolve under distinct constraints and may enable morphological conservation amidst adaptation.

Dev Biol. 2017 Oct 01;430(1):202-213

Authors: Malik A, Gildor T, Sher N, Layous M, Ben-Tabou de-Leon S

Abstract
Embryonic development evolves by balancing stringent morphological constraints with genetic and environmental variation. The design principle that allows developmental transcriptional programs to conserve embryonic morphology while adapting to environmental changes is still not fully understood. To address this fundamental challenge, we compare developmental transcriptomes of two sea urchin species, Paracentrotus lividus and Strongylocentrotus purpuratus, that shared a common ancestor about 40 million years ago and are geographically distant yet show similar morphology. We find that both developmental and housekeeping genes show highly dynamic and strongly conserved temporal expression patterns. The expression of other gene sets, including homeostasis and response genes, show divergent expression which could result from either evolutionary drift or adaptation to local environmental conditions. The interspecies correlations of developmental gene expressions are highest between morphologically similar developmental time points whereas the interspecies correlations of housekeeping gene expression are high between all the late zygotic time points. Relatedly, the position of the phylotypic stage varies between these two groups of genes: developmental gene expression shows highest conservation at mid-developmental stage, in agreement with the hourglass model while the conservation of housekeeping genes keeps increasing with developmental time. When all genes are combined, the relationship between conservation of gene expression and morphological similarity is partially masked by housekeeping genes and genes with diverged expression. Our study illustrates various transcriptional programs that coexist in the developing embryo and evolve under different constraints. Apparently, morphological constraints underlie the conservation of developmental gene expression while embryonic fitness requires the conservation of housekeeping gene expression and the species-specific adjustments of homeostasis gene expression. The distinct evolutionary forces acting on these transcriptional programs enable the conservation of similar body plans while allowing adaption.

PMID: 28780048 [PubMed - indexed for MEDLINE]

Categories: pubmed

A key role for foxQ2 in anterior head and central brain patterning in insects.

Tue, 10/03/2017 - 12:24
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A key role for foxQ2 in anterior head and central brain patterning in insects.

Development. 2017 Aug 15;144(16):2969-2981

Authors: Kitzmann P, Weißkopf M, Schacht MI, Bucher G

Abstract
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression. Surprisingly, Tc-foxQ2 and Tc-six3 mutually activate each other, forming a novel regulatory module at the top of the aGRN. Comparisons of our results with those of sea urchins and cnidarians suggest that foxQ2 has acquired more upstream functions in the aGRN during protostome evolution. Our findings expand the knowledge on foxQ2 gene function to include essential roles in epidermal development and central brain patterning.

PMID: 28811313 [PubMed - indexed for MEDLINE]

Categories: pubmed

Asymmetric distribution of hypoxia-inducible factor α regulates dorsoventral axis establishment in the early sea urchin embryo.

Tue, 10/03/2017 - 12:24
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Asymmetric distribution of hypoxia-inducible factor α regulates dorsoventral axis establishment in the early sea urchin embryo.

Development. 2017 Aug 15;144(16):2940-2950

Authors: Chang WL, Chang YC, Lin KT, Li HR, Pai CY, Chen JH, Su YH

Abstract
Hypoxia signaling is an ancient pathway by which animals can respond to low oxygen. Malfunction of this pathway disturbs hypoxic acclimation and can result in various diseases, including cancers. The role of hypoxia signaling in early embryogenesis remains unclear. Here, we show that in the blastula of the sea urchin Strongylocentrotus purpuratus, hypoxia-inducible factor α (HIFα), the downstream transcription factor of the hypoxia pathway, is localized and transcriptionally active on the future dorsal side. This asymmetric distribution is attributable to its oxygen-sensing ability. Manipulations of the HIFα level entrained the dorsoventral axis, as the side with the higher level of HIFα tends to develop into the dorsal side. Gene expression analyses revealed that HIFα restricts the expression of nodal to the ventral side and activates several genes encoding transcription factors on the dorsal side. We also observed that intrinsic hypoxic signals in the early embryos formed a gradient, which was disrupted under hypoxic conditions. Our results reveal an unprecedented role of the hypoxia pathway in animal development.

PMID: 28705895 [PubMed - indexed for MEDLINE]

Categories: pubmed

Warmer temperatures reduce the influence of an important keystone predator.

Fri, 09/29/2017 - 12:17
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Warmer temperatures reduce the influence of an important keystone predator.

J Anim Ecol. 2017 May;86(3):490-500

Authors: Bonaviri C, Graham M, Gianguzza P, Shears NT

Abstract
Predator-prey interactions may be strongly influenced by temperature variations in marine ecosystems. Consequently, climate change may alter the importance of predators with repercussions for ecosystem functioning and structure. In North-eastern Pacific kelp forests, the starfish Pycnopodia helianthoides is known to be an important predator of the purple sea urchin Strongylocentrotus purpuratus. Here we investigated the influence of water temperature on this predator-prey interaction by: (i) assessing the spatial distribution and temporal dynamics of both species across a temperature gradient in the northern Channel Islands, California, and (ii) investigating how the feeding rate of P. helianthoides on S. purpuratus is affected by temperature in laboratory tests. On average, at sites where mean annual temperatures were <14 °C, P. helianthoides were common, S. purpuratus was rare and kelp was persistent, whereas where mean annual temperatures exceeded 14 °C, P. helianthoides and kelp were rare and S. purpuratus abundant. Temperature was found to be the primary environmental factor influencing P. helianthoides abundance, and in turn P. helianthoides was the primary determinant of S. purpuratus abundance. In the laboratory, temperatures >16 °C (equivalent to summer temperatures at sites where P. helianthoides were rare) reduced predation rates regardless of predator and prey sizes, although larger sea urchins were consumed only by large starfishes. These results clearly demonstrate that the effect of P. helianthoides on S. purpuratus is strongly mediated by temperature, and that the local abundance and predation rate of P. helianthoides on sea urchins will likely decrease with future warming. A reduction in top-down control on sea urchins, combined with other expected impacts of climate change on kelp, poses significant risks for the persistence of kelp forests in the future.

PMID: 28075025 [PubMed - indexed for MEDLINE]

Categories: pubmed

An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo.

Wed, 09/20/2017 - 12:09
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An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo.

Development. 2016 May 01;143(9):1523-33

Authors: Range RC, Wei Z

Abstract
Anterior signaling centers help specify and pattern the early anterior neuroectoderm (ANE) in many deuterostomes. In sea urchin the ANE is restricted to the anterior of the late blastula stage embryo, where it forms a simple neural territory comprising several types of neurons as well as the apical tuft. Here, we show that during early development, the sea urchin ANE territory separates into inner and outer regulatory domains that express the cardinal ANE transcriptional regulators FoxQ2 and Six3, respectively. FoxQ2 drives this patterning process, which is required to eliminate six3 expression from the inner domain and activate the expression of Dkk3 and sFRP1/5, two secreted Wnt modulators. Dkk3 and low expression levels of sFRP1/5 act additively to potentiate the Wnt/JNK signaling pathway governing the positioning of the ANE territory around the anterior pole, whereas high expression levels of sFRP1/5 antagonize Wnt/JNK signaling. sFRP1/5 and Dkk3 levels are rigidly maintained via autorepressive and cross-repressive interactions with Wnt signaling components and additional ANE transcription factors. Together, these data support a model in which FoxQ2 initiates an anterior patterning center that implements correct size and positions of ANE structures. Comparisons of functional and expression studies in sea urchin, hemichordate and chordate embryos reveal striking similarities among deuterostome ANE regulatory networks and the molecular mechanism that positions and defines ANE borders. These data strongly support the idea that the sea urchin embryo uses an ancient anterior patterning system that was present in the common ambulacrarian/chordate ancestor.

PMID: 26952978 [PubMed - indexed for MEDLINE]

Categories: pubmed

New inter-correlated genes targeted by diatom-derived polyunsaturated aldehydes in the sea urchin Paracentrotus lividus.

Tue, 09/19/2017 - 12:09
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New inter-correlated genes targeted by diatom-derived polyunsaturated aldehydes in the sea urchin Paracentrotus lividus.

Ecotoxicol Environ Saf. 2017 Aug;142:355-362

Authors: Ruocco N, Maria Fedele A, Costantini S, Romano G, Ianora A, Costantini M

Abstract
The marine environment is continually subjected to the action of stressors (including natural toxins), which represent a constant danger for benthic communities. In the present work using network analysis we identified ten genes on the basis of associated functions (FOXA, FoxG, GFI-1, nodal, JNK, OneCut/Hnf6, TAK1, tcf4, TCF7, VEGF) in the sea urchin Paracentrotus lividus, having key roles in different processes, such as embryonic development and asymmetry, cell fate specification, cell differentiation and morphogenesis, and skeletogenesis. These genes are correlated with three HUB genes, Foxo, Jun and HIF1A. Real Time qPCR revealed that during sea urchin embryonic development the expression levels of these genes were modulated by three diatom-derived polyunsaturated aldehydes (PUAs), decadienal, heptadienal and octadienal. Our findings show how changes in gene expression levels may be used as an early indicator of stressful conditions in the marine environment. The identification of key genes and the molecular pathways in which they are involved represents a fundamental tool in understanding how marine organisms try to afford protection against toxicants, to avoid deleterious consequences and irreversible damages. The genes identified in this work as targets for PUAs can be considered as possible biomarkers to detect exposure to different environmental pollutants.

PMID: 28437727 [PubMed - indexed for MEDLINE]

Categories: pubmed

Echinoderm development and evolution in the post-genomic era.

Wed, 09/13/2017 - 12:05
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Echinoderm development and evolution in the post-genomic era.

Dev Biol. 2017 Jul 15;427(2):203-211

Authors: Cary GA, Hinman VF

Abstract
The highly recognizable animals within the phylum Echinodermata encompass an enormous disparity of adult and larval body plans. The extensive knowledge of sea urchin development has culminated in the description of the exquisitely detailed gene regulatory network (GRN) that governs the specification of various embryonic territories. This information provides a unique opportunity for comparative studies in other echinoderm taxa to understand the evolution and developmental mechanisms underlying body plan change. This review focuses on recent work that has utilized new genomic resources and systems-level experiments to address questions of evolutionary developmental biology. In particular, we synthesize the results of several recent studies from various echinoderm classes that have explored the development and evolution of the larval skeleton, which is a major feature that distinguishes the two predominant larval subtypes within the Phylum. We specifically examine the ways in which GRNs can evolve, either through cis regulatory and/or protein-level changes in transcription factors. We also examine recent work comparing evolution across shorter time scales that occur within and between species of sea urchin, and highlight the kinds of questions that can be addressed by these comparisons. The advent of new genomic and transcriptomic datasets in additional species from all classes of echinoderm will continue to empower the use of these taxa for evolutionary developmental studies.

PMID: 28185788 [PubMed - indexed for MEDLINE]

Categories: pubmed

Comparative studies on the skeletogenic mesenchyme of echinoids.

Wed, 09/13/2017 - 12:05
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Comparative studies on the skeletogenic mesenchyme of echinoids.

Dev Biol. 2017 Jul 15;427(2):212-218

Authors: Minokawa T

Abstract
Skeletogenic mesenchyme cells in echinoids are suitable for studying developmental mechanisms, and have been used extensively. Most of these studies have been performed on species in the order Camarodonta, which are modern echinoids (subclass Euechinoidea) and are considered "model" echinoid species. In contrast, species belonging to other orders are studied less frequently, especially investigations of their molecular developmental biology such as gene regulatory networks. Recent studies on mesenchyme development in non-camarodont species suggest that these species are potential sources of comparative information to elucidate the mechanisms underlying skeletogenic mesenchyme development. In this review, the importance of using comparative data to understand development and evolution is discussed.

PMID: 27856261 [PubMed - indexed for MEDLINE]

Categories: pubmed

Transient translational quiescence in primordial germ cells.

Tue, 09/12/2017 - 12:02
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Transient translational quiescence in primordial germ cells.

Development. 2017 Apr 01;144(7):1201-1210

Authors: Oulhen N, Swartz SZ, Laird J, Mascaro A, Wessel GM

Abstract
Stem cells in animals often exhibit a slow cell cycle and/or low transcriptional activity referred to as quiescence. Here, we report that the translational activity in the primordial germ cells (PGCs) of the sea urchin embryo (Strongylocentrotus purpuratus) is quiescent. We measured new protein synthesis with O-propargyl-puromycin and L-homopropargylglycine Click-iT technologies, and determined that these cells synthesize protein at only 6% the level of their adjacent somatic cells. Knockdown of translation of the RNA-binding protein Nanos2 by morpholino antisense oligonucleotides, or knockout of the Nanos2 gene by CRISPR/Cas9 resulted in a significant, but partial, increase (47%) in general translation specifically in the PGCs. We found that the mRNA of the translation factor eEF1A is excluded from the PGCs in a Nanos2-dependent manner, a consequence of a Nanos/Pumilio response element (PRE) in its 3'UTR. In addition to eEF1A, the cytoplasmic pH of the PGCs appears to repress translation and simply increasing the pH also significantly restores translation selectively in the PGCs. We conclude that the PGCs of this sea urchin institute parallel pathways to quiesce translation thoroughly but transiently.

PMID: 28235822 [PubMed - indexed for MEDLINE]

Categories: pubmed

An interview with David McClay.

Tue, 09/12/2017 - 12:02
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An interview with David McClay.

Development. 2016 Dec 01;143(23):4289-4290

Authors: Maartens A

Abstract
David McClay is the Arthur S. Pearse Professor of Biology at Trinity College of Arts and Sciences, Duke University, North Carolina. His lab works on the transcriptional control of morphogenesis in the sea urchin embryo. We caught up with David at the 2016 Society for Developmental Biology - International Society of Differentiation joint meeting in Boston, where he received the Lifetime Achievement Award.

PMID: 27899505 [PubMed - indexed for MEDLINE]

Categories: pubmed

RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.

Tue, 09/12/2017 - 12:02
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RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.

BMC Genomics. 2016 Jun 14;17:459

Authors: Yang A, Zhou Z, Pan Y, Jiang J, Dong Y, Guan X, Sun H, Gao S, Chen Z

Abstract
BACKGROUND: Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression.
RESULTS: RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches.
CONCLUSIONS: Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber.

PMID: 27296384 [PubMed - indexed for MEDLINE]

Categories: pubmed

Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos.

Fri, 09/08/2017 - 11:54
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Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos.

PLoS One. 2017;12(4):e0176479

Authors: Famiglietti AL, Wei Z, Beres TM, Milac AL, Tran DT, Patel D, Angerer RC, Angerer LM, Tabak LA

Abstract
Mucin-type O-glycosylation is a ubiquitous posttranslational modification in which N-Acetylgalactosamine (GalNAc) is added to the hydroxyl group of select serine or threonine residues of a protein by the family of UDP-GalNAc:Polypeptide N-Acetylgalactosaminyltransferases (GalNAc-Ts; EC 2.4.1.41). Previous studies demonstrate that O-glycosylation plays essential roles in protein function, cell-cell interactions, cell polarity and differentiation in developing mouse and Drosophila embryos. Although this type of protein modification is highly conserved among higher eukaryotes, little is known about this family of enzymes in echinoderms, basal deuterostome relatives of the chordates. To investigate the potential role of GalNAc-Ts in echinoderms, we have begun the characterization of this enzyme family in the purple sea urchin, S. purpuratus. We have fully or partially cloned a total of 13 genes (SpGalnts) encoding putative sea urchin SpGalNAc-Ts, and have confirmed enzymatic activity of five recombinant proteins. Amino acid alignments revealed high sequence similarity among sea urchin and mammalian glycosyltransferases, suggesting the presence of putative orthologues. Structural models underscored these similarities and helped reconcile some of the substrate preferences observed. Temporal and spatial expression of SpGalnt transcripts, was studied by whole-mount in situ hybridization. We found that many of these genes are transcribed early in developing embryos, often with restricted expression to the endomesodermal region. Multicolor fluorescent in situ hybridization (FISH) demonstrated that transcripts encoding SpGalnt7-2 co-localized with both Endo16 (a gene expressed in the endoderm), and Gcm (a gene expressed in secondary mesenchyme cells) at the early blastula stage, 20 hours post fertilization (hpf). At late blastula stage (28 hpf), SpGalnt7-2 message co-expresses with Gcm, suggesting that it may play a role in secondary mesenchyme development. We also discovered that morpholino-mediated knockdown of SpGalnt13 transcripts, results in a deficiency of embryonic skeleton and neurons, suggesting that mucin-type O-glycans play essential roles during embryonic development in S. purpuratus.

PMID: 28448610 [PubMed - indexed for MEDLINE]

Categories: pubmed

Experimental demonstration of a trophic cascade in the Galápagos rocky subtidal: Effects of consumer identity and behavior.

Fri, 09/08/2017 - 11:54
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Experimental demonstration of a trophic cascade in the Galápagos rocky subtidal: Effects of consumer identity and behavior.

PLoS One. 2017;12(4):e0175705

Authors: Witman JD, Smith F, Novak M

Abstract
In diverse tropical webs, trophic cascades are presumed to be rare, as species interactions may dampen top-down control and reduce their prevalence. To test this hypothesis, we used an open experimental design in the Galápagos rocky subtidal that enabled a diverse guild of fish species, in the presence of each other and top predators (sea lions and sharks), to attack two species of sea urchins grazing on benthic algae. Time-lapse photography of experiments on natural and experimental substrates revealed strong species identity effects: only two predator species-blunthead triggerfish (Pseudobalistes naufragium) and finescale triggerfish (Balistes polylepis)-drove a diurnal trophic cascade extending to algae, and they preferred large pencil urchins (Eucidaris galapagensis) over green urchins (Lytechinus semituberculatus). Triggerfish predation effects were strong, causing a 24-fold reduction of pencil urchin densities during the initial 21 hours of a trophic cascade experiment. A trophic cascade was demonstrated for pencil urchins, but not for green urchins, by significantly higher percent cover of urchin-grazed algae in cages that excluded predatory fish than in predator access (fence) treatments. Pencil urchins were more abundant at night when triggerfish were absent, suggesting that this species persists by exploiting a nocturnal predation refuge. Time-series of pencil urchin survivorship further demonstrated per capita interference effects of hogfish and top predators. These interference effects respectively weakened and extended the trophic cascade to a fourth trophic level through behavioral modifications of the triggerfish-urchin interaction. We conclude that interference behaviors capable of modifying interaction strength warrant greater attention as mechanisms for altering top-down control, particularly in speciose food webs.

PMID: 28430794 [PubMed - indexed for MEDLINE]

Categories: pubmed

Extracellular matrix remodeling and matrix metalloproteinases (ajMMP-2 like and ajMMP-16 like) characterization during intestine regeneration of sea cucumber Apostichopus japonicus.

Thu, 09/07/2017 - 11:54
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Extracellular matrix remodeling and matrix metalloproteinases (ajMMP-2 like and ajMMP-16 like) characterization during intestine regeneration of sea cucumber Apostichopus japonicus.

Comp Biochem Physiol B Biochem Mol Biol. 2017 Oct;212:12-23

Authors: Miao T, Wan Z, Sun L, Li X, Xing L, Bai Y, Wang F, Yang H

Abstract
Remodeling of extracellular matrix (ECM) regulated by matrix metalloproteinases (MMPs) is essential for tissue regeneration. In the present study, we used immunohistochemistry (IHC) techniques against ECM components to reveal changes of ECM during intestine regeneration of Apostichopus japonicus. The expression of collagen I and laminin reduced apparently from the eviscerated intestine, while fibronectin exhibited continuous expression in all regeneration stages observed. Meanwhile, we cloned two MMP genes from A. japonicus by RACE PCR. The full-length cDNA of ajMMP-2 like is 2733bp and contains a predicted open reading frame (ORF) of 1716bp encoding 572 amino acids. The full-length cDNA of ajMMP-16 like is 2705bp and contains an ORF of 1452bp encoding 484 amino acids. The predicted protein sequences of each MMP contain two conserved domains, ZnMc_MMP and HX. Homology and phylogenetic analysis revealed that ajMMP-2 like and ajMMP-16 like share high sequence similarity with MMP-2 and MMP-16 from Strongylocentrotus purpuratus, respectively. Then we investigated spatio-temporal expression of ajMMP-2 like and ajMMP-16 like during different regeneration stages by qRT-PCR and IHC. The expression pattern of them showed a roughly opposite trend from that of ECM components. According to our results, a fibronectin-dominate temporary matrix is created in intestine regeneration, and it might provide structural integrity for matrix and promote cell movement. We also hypothesize that ajMMP-2 like and ajMMP-16 like could accelerate cell migration and regulate interaction between ECM components and growth factors. This work provides new evidence of ECM and MMPs involvement in sea cucumber regeneration.

PMID: 28687360 [PubMed - indexed for MEDLINE]

Categories: pubmed

Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family.

Sat, 09/02/2017 - 11:50
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Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family.

BMC Genomics. 2016 Nov 09;17(1):900

Authors: Oren M, Barela Hudgell MA, D'Allura B, Agronin J, Gross A, Podini D, Smith LC

Abstract
BACKGROUND: Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence. Consequently, we have resolved the structure of the family and profiled the members by sequencing selected BAC clones using Illumina and PacBio approaches.
RESULTS: BAC insert assemblies identified 15 predicted genes that are organized into three clusters. Two of the gene clusters have almost identical flanking regions, suggesting that they may be non-matching allelic clusters residing at the same genomic locus. GA STRs surround all genes and appear in large stretches at locations of putatively deleted genes. GAT STRs are positioned at the edges of segmental duplications that include a subset of the genes. The unique locations of the STRs suggest their involvement in gene deletions and segmental duplications. Genomic profiling of the Sp185/333 gene diversity in 10 sea urchins shows that no gene repertoires are shared among individuals indicating a very high gene diversification rate for this family.
CONCLUSIONS: The repetitive genomic structure of the Sp185/333 family that includes STRs in strategic locations may serve as platform for a controlled mechanism which regulates the processes of gene recombination, gene conversion, duplication and deletion. The outcome is genomic instability and allelic mismatches, which may further drive the swift diversification of the Sp185/333 gene family that may improve the immune fitness of the species.

PMID: 27829352 [PubMed - indexed for MEDLINE]

Categories: pubmed