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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: 2 hours 44 min ago

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution.

Fri, 08/17/2018 - 06:55
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Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution.

Genome Biol. 2018 02 28;19(1):26

Authors: Dylus DV, Czarkwiani A, Blowes LM, Elphick MR, Oliveri P

Abstract
BACKGROUND: Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm-the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ .
RESULTS: We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation.
CONCLUSIONS: Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms.

PMID: 29490679 [PubMed - indexed for MEDLINE]

Categories: pubmed

An optogenetic approach to control protein localization during embryogenesis of the sea urchin.

Thu, 08/09/2018 - 06:41
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An optogenetic approach to control protein localization during embryogenesis of the sea urchin.

Dev Biol. 2018 09 01;441(1):19-30

Authors: Uchida A, Yajima M

Abstract
Light inducible protein-protein interactions have been used to manipulate protein localization and function in the cell with utmost spatial and temporal precision. In this technical report, we use a recently developed optogenetic approach to manipulate protein localization in the developing sea urchin embryo. A photosensitive LOV domain from Avena sativa phototropin1 cages a small peptide that binds the engineered PDZ domain (ePDZ) upon blue light irradiation. Using this system, mCherry tagged proteins fused with the LOV domain were recruited to ectopic sub-cellular regions such as the membrane, microtubules, or actin by GFP tagged proteins fused with the ePDZ domain upon blue light irradiation within 1-3 min in the sea urchin embryo. The efficiency and speed of recruitment of each protein to its respective subcellular region appeared to be dependent on the power and duration of laser irradiation, as well as the respective level of affinity to the tagged location. Controlled laser irradiation allowed partial recruitment of the spindle to the membrane, and resulted in cell blebbing. Vasa, a cell cycle and germline factor that localizes on the spindle and enriches in the micromeres at 8-16 cell stage was recruited to ectopic sites, preventing normal enrichment. Continuous blue light activation with a regular blue aquarium light over two days of culture successfully induced LOV-ePDZ binding in the developing embryos, resulting in continued ectopic recruitment of Vasa and failure in gastrulation at Day 2. Although some cytotoxicity was observed with prolonged blue light irradiation, this optogenetic system provides a promising approach to test the sub-cellular activities of developmental factors, as well as to alter protein localization and development during embryogenesis.

PMID: 29958898 [PubMed - indexed for MEDLINE]

Categories: pubmed

Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms.

Tue, 08/07/2018 - 06:39
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Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms.

Elife. 2017 11 20;6:

Authors: Khor JM, Ettensohn CA

Abstract
Alx1 is a pivotal transcription factor in a gene regulatory network that controls skeletogenesis throughout the echinoderm phylum. We performed a structure-function analysis of sea urchin Alx1 using a rescue assay and identified a novel, conserved motif (Domain 2) essential for skeletogenic function. The paralogue of Alx1, Alx4, was not functionally interchangeable with Alx1, but insertion of Domain 2 conferred robust skeletogenic function on Alx4. We used cross-species expression experiments to show that Alx1 proteins from distantly related echinoderms are not interchangeable, although the sequence and function of Domain 2 are highly conserved. We also found that Domain 2 is subject to alternative splicing and provide evidence that this domain was originally gained through exonization. Our findings show that a gene duplication event permitted the functional specialization of a transcription factor through changes in exon-intron organization and thereby supported the evolution of a major morphological novelty.

PMID: 29154754 [PubMed - indexed for MEDLINE]

Categories: pubmed

Ocean acidification modulates the incorporation of radio-labeled heavy metals in the larvae of the Mediterranean sea urchin Paracentrotus lividus.

Sat, 08/04/2018 - 06:38
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Ocean acidification modulates the incorporation of radio-labeled heavy metals in the larvae of the Mediterranean sea urchin Paracentrotus lividus.

J Environ Radioact. 2018 Oct;190-191:20-30

Authors: Dorey N, Martin S, Oberhänsli F, Teyssié JL, Jeffree R, Lacoue-Labarthe T

Abstract
The marine organisms which inhabit the coastline are exposed to a number of anthropogenic pressures that may interact. For instance, the accumulation of toxic metals present in coastal waters is expected to be modified by ocean acidification through e.g. changes in physiological performance and/or elements availability. Changes in bioaccumulation due to lowering pH are likely to be differently affected depending on the nature (essential vs. non-essential) and speciation of each element. The Mediterranean is of high concern for possible cumulative effects due to strong human influences on the coastline. The aim of this study was to determine the effect of ocean acidification (from pH 8.1 down to -1.0 pH units) on the incorporation kinetics of six trace metals (Mn, Co, Zn, Se, Ag, Cd, Cs) and one radionuclide (241Am) in the larvae of an economically- and ecologically-relevant sea urchin of the Mediterranean coastline: Paracentrotus lividus. The radiolabelled metals and radionuclides added in trace concentrations allowed precise tracing of their incorporation in larvae during the first 74 h of their development. Independently of the expected indirect effect of pH on larval size/developmental rates, Paracentrotus lividus larvae exposed to decreasing pHs incorporated significantly more Mn and Ag and slightly less Cd. The incorporation of Co, Cs and 241Am was unchanged, and Zn and Se exhibited complex incorporation behaviors. Studies such as this are necessary prerequisites to the implementation of metal toxicity mitigation policies for the future ocean. We discuss possible reasons and mechanisms for the specific effect of pH on each metals.

PMID: 29738950 [PubMed - indexed for MEDLINE]

Categories: pubmed

SpTransformer proteins from the purple sea urchin opsonize bacteria, augment phagocytosis, and retard bacterial growth.

Fri, 08/03/2018 - 06:33
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SpTransformer proteins from the purple sea urchin opsonize bacteria, augment phagocytosis, and retard bacterial growth.

PLoS One. 2018;13(5):e0196890

Authors: Chou HY, Lun CM, Smith LC

Abstract
The purple sea urchin, Strongylocentrotus purpuratus, has a complex and robust immune system that is mediated by a number of multi-gene families including the SpTransformer (SpTrf) gene family (formerly Sp185/333). In response to immune challenge from bacteria and various pathogen-associated molecular patterns, the SpTrf genes are up-regulated in sea urchin phagocytes and express a diverse array of SpTrf proteins. We show here that SpTrf proteins from coelomocytes and isolated by nickel affinity (cNi-SpTrf) bind to Gram-positive and Gram-negative bacteria and to Baker's yeast, Saccharomyces cerevisiae, with saturable kinetics and specificity. cNi-SpTrf opsonization of the marine bacteria, Vibrio diazotrophicus, augments phagocytosis, however, opsonization by the recombinant protein, rSpTrf-E1, does not. Binding by cNi-SpTrf proteins retards growth rates significantly for several species of bacteria. SpTrf proteins, previously thought to be strictly membrane-associated, are secreted from phagocytes in short term cultures and bind V. diazotrophicus that are located both outside of and within phagocytes. Our results demonstrate anti-microbial activities of native SpTrf proteins and suggest variable functions among different SpTrf isoforms. Multiple isoforms may act synergistically to detect a wide array of pathogens and provide flexible and efficient host immunity.

PMID: 29738524 [PubMed - indexed for MEDLINE]

Categories: pubmed

An empirical model of Onecut binding activity at the sea urchin SM50 C-element gene regulatory region.

Tue, 07/31/2018 - 06:31
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An empirical model of Onecut binding activity at the sea urchin SM50 C-element gene regulatory region.

Int J Dev Biol. 2017;61(8-9):537-543

Authors: Otim O

Abstract
Studying the formation of endoskeleton in many species is complex and difficult. The sea urchin embryo offers an unparalleled platform for understanding this process because of the ease with which its skeletogenic mesenchyme cells can be manipulated. In this study, preliminary evidence from biochemical studies towards understanding the role of the Onecut transcription factor during sea urchin skeletogenic mesenchyme cell specification is presented. Based on the evidence, an empirical model is proposed showing how Onecut, together with associated co-factors, may be using the C-element of the SM50 gene regulatory region in advance of the sea urchin Strongylocentrotus purpuratus spicule development. In the model, Onecut recognizes and binds the DNA sequence CATCGATCTC in the C-element without temporal restriction. Onecut then utilizes different sets of co-factors to switch from its unknown function early in development (four cell stage to the mesenchyme blastula stage), to its known role in the oral-aboral boundary thereafter. At the writing of this report, definitive evidence as to whether the "early" factors are expressed in all cells except the micromere lineages, or whether the "late" factors are expressed in micromere descendants or ectodermal precursors only are lacking. The former would suggest a possible Onecut repression function for the early co-factors outside the micromere lineages; the latter scenario would suggest a Onecut activation function for the late co-factors in the presumptive ciliary band.

PMID: 29139539 [PubMed - indexed for MEDLINE]

Categories: pubmed

Expression of genes and proteins of the pax-six-eya-dach network in the metamorphic sea urchin: Insights into development of the enigmatic echinoderm body plan and sensory structures.

Sat, 07/28/2018 - 06:28
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Expression of genes and proteins of the pax-six-eya-dach network in the metamorphic sea urchin: Insights into development of the enigmatic echinoderm body plan and sensory structures.

Dev Dyn. 2018 Jan;247(1):239-249

Authors: Byrne M, Koop D, Morris VB, Chui J, Wray GA, Cisternas P

Abstract
BACKGROUND: Photoreception-associated genes of the Pax-Six-Eya-Dach network (PSEDN) are deployed for many roles in addition to photoreception development. In this first study of PSEDN genes during development of the pentameral body in sea urchins, we investigated their spatial expression in Heliocidaris erythrogramma.
RESULTS: Expression of PSEDN genes in the hydrocoele of early (Dach, Eya, Six1/2) and/or late (Pax6, Six3/6) larvae, and the five hydrocoele lobes, the first morphological expression of pentamery, supports a role in body plan development. Pax6, Six1/2, and Six3/6 were localized to the primary and/or secondary podia and putative sensory/neuronal cells. Six1/2 and Six3/6 were expressed in the neuropil region in the terminal disc of the podia. Dach was localized to spines. Sequential up-regulation of gene expression as new podia and spines formed was evident. Rhabdomeric opsin and pax6 protein were localized to cells in the primary podia and spines.
CONCLUSIONS: Our results support roles for PSEDN genes in development of the pentameral body plan, contributing to our understanding of how the most unusual body plan in the Bilateria may have evolved. Development of sensory cells within the Pax-Six expression field is consistent with the role of these genes in sensory cell development in diverse species. Developmental Dynamics 247:239-249, 2018. © 2017 Wiley Periodicals, Inc.

PMID: 28850769 [PubMed - indexed for MEDLINE]

Categories: pubmed

Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays.

Tue, 07/24/2018 - 06:24
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Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays.

Sci Rep. 2016 10 06;6:34808

Authors: Mishra LN, Pepenella S, Rogge R, Hansen JC, Hayes JJ

Abstract
The activation of a silent gene locus is thought to involve pioneering transcription factors that initiate changes in the local chromatin structure to increase promoter accessibility and binding of downstream effectors. To better understand the molecular requirements for the first steps of locus activation, we investigated whether acetylation of a single nucleosome is sufficient to alter DNA accessibility within a condensed 25-nucleosome array. We found that acetylation mimics within the histone H4 tail domain increased accessibility of the surrounding linker DNA, with the increased accessibility localized to the immediate vicinity of the modified nucleosome. In contrast, acetylation mimics within the H3 tail had little effect, but were able to synergize with H4 tail acetylation mimics to further increase accessibility. Moreover, replacement of the central nucleosome with a nucleosome free region also resulted in increased local, but not global DNA accessibility. Our results indicate that modification or disruption of only a single target nucleosome results in significant changes in local chromatin architecture and suggest that very localized chromatin modifications imparted by pioneer transcription factors are sufficient to initiate a cascade of events leading to promoter activation.

PMID: 27708426 [PubMed - indexed for MEDLINE]

Categories: pubmed

Single nucleotide editing without DNA cleavage using CRISPR/Cas9-deaminase in the sea urchin embryo.

Tue, 07/10/2018 - 06:06
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Single nucleotide editing without DNA cleavage using CRISPR/Cas9-deaminase in the sea urchin embryo.

Dev Dyn. 2017 Dec;246(12):1036-1046

Authors: Shevidi S, Uchida A, Schudrowitz N, Wessel GM, Yajima M

Abstract
BACKGROUND: A single base pair mutation in the genome can result in many congenital disorders in humans. The recent gene editing approach using CRISPR/Cas9 has rapidly become a powerful tool to replicate or repair such mutations in the genome. These approaches rely on cleaving DNA, while presenting unexpected risks.
RESULTS: In this study, we demonstrate a modified CRISPR/Cas9 system fused to cytosine deaminase (Cas9-DA), which induces a single nucleotide conversion in the genome. Cas9-DA was introduced into sea urchin eggs with sgRNAs targeted for SpAlx1, SpDsh, or SpPks, each of which is critical for skeletogenesis, embryonic axis formation, or pigment formation, respectively. We found that both Cas9 and Cas9-DA edit the genome, and cause predicted phenotypic changes at a similar efficiency. Cas9, however, resulted in significant deletions in the genome centered on the gRNA target sequence, whereas Cas9-DA resulted in single or double nucleotide editing of C to T conversions within the gRNA target sequence.
CONCLUSIONS: These results suggest that the Cas9-DA approach may be useful for manipulating gene activity with decreased risks of genomic aberrations. Developmental Dynamics 246:1036-1046, 2017. © 2017 Wiley Periodicals, Inc.

PMID: 28857338 [PubMed - indexed for MEDLINE]

Categories: pubmed

New insights from a high-resolution look at gastrulation in the sea urchin, Lytechinus variegatus.

Tue, 07/10/2018 - 06:06
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New insights from a high-resolution look at gastrulation in the sea urchin, Lytechinus variegatus.

Mech Dev. 2017 Dec;148:3-10

Authors: Martik ML, McClay DR

Abstract
BACKGROUND: Gastrulation is a complex orchestration of movements by cells that are specified early in development. Until now, classical convergent extension was considered to be the main contributor to sea urchin archenteron extension, and the relative contributions of cell divisions were unknown. Active migration of cells along the axis of extension was also not considered as a major factor in invagination.
RESULTS: Cell transplantations plus live imaging were used to examine endoderm cell morphogenesis during gastrulation at high-resolution in the optically clear sea urchin embryo. The invagination sequence was imaged throughout gastrulation. One of the eight macromeres was replaced by a fluorescently labeled macromere at the 32 cell stage. At gastrulation those patches of fluorescent endoderm cell progeny initially about 4 cells wide, released a column of cells about 2 cells wide early in gastrulation and then often this column narrowed to one cell wide by the end of archenteron lengthening. The primary movement of the column of cells was in the direction of elongation of the archenteron with the narrowing (convergence) occurring as one of the two cells moved ahead of its neighbor. As the column narrowed, the labeled endoderm cells generally remained as a contiguous population of cells, rarely separated by intrusion of a lateral unlabeled cell. This longitudinal cell migration mechanism was assessed quantitatively and accounted for almost 90% of the elongation process. Much of the extension was the contribution of Veg2 endoderm with a minor contribution late in gastrulation by Veg1 endoderm cells. We also analyzed the contribution of cell divisions to elongation. Endoderm cells in Lytechinus variagatus were determined to go through approximately one cell doubling during gastrulation. That doubling occurs without a net increase in cell mass, but the question remained as to whether oriented divisions might contribute to archenteron elongation. We learned that indeed there was a biased orientation of cell divisions along the plane of archenteron elongation, but when the impact of that bias was analyzed quantitatively, it contributed a maximum 15% to the total elongation of the gut.
CONCLUSIONS: The major driver of archenteron elongation in the sea urchin, Lytechinus variagatus, is directed movement of Veg2 endoderm cells as a narrowing column along the plane of elongation. The narrowing occurs as cells in the column converge as they migrate, so that the combination of migration and the angular convergence provide the major component of the lengthening. A minor contributor to elongation is oriented cell divisions that contribute to the lengthening but no more than about 15%.

PMID: 28684256 [PubMed - indexed for MEDLINE]

Categories: pubmed

Comparative expression analysis of immune-related factors in the sea cucumber Apostichopus japonicus.

Thu, 06/28/2018 - 05:52
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Comparative expression analysis of immune-related factors in the sea cucumber Apostichopus japonicus.

Fish Shellfish Immunol. 2018 Jan;72:342-347

Authors: Jiang J, Zhou Z, Dong Y, Zhao Z, Sun H, Wang B, Jiang B, Chen Z, Gao S

Abstract
In order to preliminarily explore the joint involvement of different immune-related factors during the same immune process in Apostichopus japonicus, the transcriptional expression of Cu/Zn superoxide dismutase (Cu/Zn-SOD), catalase (CAT), c-type lysozyme (c-LYZ), i-type lysozyme (i-LYZ), cathepsin D, melanotransferrin (MTF), Toll, c-type lectin (c-LCT) and complement 3 (C3) during the development from fertilized eggs to juveniles and after challenging the juveniles with Vibrio splendidus, Pseudoalteromonas nigrifaciens, Shewanella baltica and Bacillus cereus, respectively, was measured using the method of quantitative real-time PCR (qRT-PCR), and then the correlations among different immune-related factors were analyzed. The results showed that the selected immune-related factors were expressed at all of the determined developmental stages and significantly up-regulated at doliolaria stage, suggesting the selected factors are indispensable immune components and the immune system might be broadly activated at doliolaria stage in A. japonicus. After challenged with four pathogenic bacteria, Cu/Zn-SOD, CAT, i-LYZ, cathepsin D, MTF, Toll, C3 were all significantly down-regulated at 4 h, indicating that some components of A. japonicus immune system might be inhibited at the beginning of pathogenic bacteria invasion. The immune-responsive analysis also showed that the significant regulation in Toll after challenged with four tested bacteria, that in MTF after challenged with S. baltica and that in C3 after challenged with P. nigrifaciens were all minus, suggesting Toll, MTF and C3 are probably the primary targets of pathogenic bacteria attack. Furthermore, the correlation analysis indicated that, all of the selected immune-related factors except cathepsin D might be in the same immune regulatory network during A. japonicus development, while all of the selected immune-related factors except c-LYZ might be in the same responsive regulatory network after challenged with four pathogenic bacteria. Altogether, A. japonicus immune system exhibited high complexity in regulation during organism development and after bacterial challenges.

PMID: 29113862 [PubMed - indexed for MEDLINE]

Categories: pubmed

cDNA cloning, expression and immune function analysis of a novel Rac1 gene (AjRac1) in the sea cucumber Apostichopus japonicus.

Thu, 06/28/2018 - 05:52
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cDNA cloning, expression and immune function analysis of a novel Rac1 gene (AjRac1) in the sea cucumber Apostichopus japonicus.

Fish Shellfish Immunol. 2017 Oct;69:218-226

Authors: Li K, Liu L, Shang S, Wang Y, Zhan Y, Song J, Zhang X, Chang Y

Abstract
The ras-related C3 botulinum toxin substrate 1 (Rac1) belongs to Ras homolog (Rho) small GTPases subfamily. As an important molecular switch, Rac1 regulates various processes in the cell, especially in cellular immune response. With attempt to clarify characters and functions of Rac1 in sea cucumbers, full length cDNA of a Rac1 homolog in the sea cucumber Apostichopus japonicus (AjRac1) was cloned by transcriptome database mining and rapid amplification of cDNA ends (RACE) techniques. The open reading frame of AjRac1 is 579 bp encoding a protein with a length of 192 aa. Sequence analysis showed that AjRac1 is highly conserved as compared to those from other eukaryotic species. Phylogenetic analysis revealed that amino acid sequence of AjRac1 closely related to those from Strongylocentrotus purpuratus. Results of expression analysis showed that AjRac1 exhibited a relative high expression in blastula stage, adult coelomocytes and respiratory tree in A. japonicus. The transcription of AjRac1 in adult coelomocytes altered significantly at 4 h- and 12 h-after Vibrio splendidus infection, respectively, which indicated that AjRac1 involved in sea cucumber innate immunity. All data presented in this study will deepen our understanding of characterizations and immunological functions of Rac1 in sea cucumbers.

PMID: 28844967 [PubMed - indexed for MEDLINE]

Categories: pubmed