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Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids.

Latest Publications - Tue, 04/09/2019 - 15:27
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Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids.

Development. 2018 12 18;145(24):

Authors: Erkenbrack EM, Davidson EH, Peter IS

Abstract
Evolution of the animal body plan is driven by changes in developmental gene regulatory networks (GRNs), but how networks change to control novel developmental phenotypes remains, in most cases, unresolved. Here, we address GRN evolution by comparing the endomesoderm GRN in two echinoid sea urchins, Strongylocentrotus purpuratus and Eucidaris tribuloides, with at least 268 million years of independent evolution. We first analyzed the expression of twelve transcription factors and signaling molecules of the S. purpuratus GRN in E. tribuloides embryos, showing that orthologous regulatory genes are expressed in corresponding endomesodermal cell fates in the two species. However, perturbation of regulatory genes revealed that important regulatory circuits of the S. purpuratus GRN are significantly different in E. tribuloides For example, mesodermal Delta/Notch signaling controls exclusion of alternative cell fates in E. tribuloides but controls mesoderm induction and activation of a positive feedback circuit in S. purpuratus These results indicate that the architecture of the sea urchin endomesoderm GRN evolved by extensive gain and loss of regulatory interactions between a conserved set of regulatory factors that control endomesodermal cell fate specification.

PMID: 30470703 [PubMed - indexed for MEDLINE]

Categories: pubmed

Inhibition of microRNA suppression of Dishevelled results in Wnt pathway-associated developmental defects in sea urchin.

Latest Publications - Tue, 04/09/2019 - 15:27
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Inhibition of microRNA suppression of Dishevelled results in Wnt pathway-associated developmental defects in sea urchin.

Development. 2018 11 30;145(23):

Authors: Sampilo NF, Stepicheva NA, Zaidi SAM, Wang L, Wu W, Wikramanayake A, Song JL

Abstract
MicroRNAs (miRNAs) are highly conserved, small non-coding RNAs that regulate gene expressions by binding to the 3' untranslated region of target mRNAs thereby silencing translation. Some miRNAs are key regulators of the Wnt signaling pathways, which impact developmental processes. This study investigates miRNA regulation of different isoforms of Dishevelled (Dvl/Dsh), which encode a key component in the Wnt signaling pathway. The sea urchin Dvl mRNA isoforms have similar spatial distribution in early development, but one isoform is distinctively expressed in the larval ciliary band. We demonstrated that Dvl isoforms are directly suppressed by miRNAs. By blocking miRNA suppression of Dvl isoforms, we observed dose-dependent defects in spicule length, patterning of the primary mesenchyme cells, gut morphology, and cilia. These defects likely result from increased Dvl protein levels, leading to perturbation of Wnt-dependent signaling pathways and additional Dvl-mediated processes. We further demonstrated that overexpression of Dvl isoforms recapitulated some of the Dvl miRNATP-induced phenotypes. Overall, our results indicate that miRNA suppression of Dvl isoforms plays an important role in ensuring proper development and function of primary mesenchyme cells and cilia.

PMID: 30389855 [PubMed - indexed for MEDLINE]

Categories: pubmed

Transcriptomics reveal transgenerational effects in purple sea urchin embryos: Adult acclimation to upwelling conditions alters the response of their progeny to differential pCO2 levels.

Latest Publications - Thu, 04/04/2019 - 15:03
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Transcriptomics reveal transgenerational effects in purple sea urchin embryos: Adult acclimation to upwelling conditions alters the response of their progeny to differential pCO2 levels.

Mol Ecol. 2018 03;27(5):1120-1137

Authors: Wong JM, Johnson KM, Kelly MW, Hofmann GE

Abstract
Understanding the mechanisms with which organisms can respond to a rapidly changing ocean is an important research priority in marine sciences, especially in the light of recent predictions regarding the pace of ocean change in the coming decades. Transgenerational effects, in which the experience of the parental generation can shape the phenotype of their offspring, may serve as such a mechanism. In this study, adult purple sea urchins, Strongylocentrotus purpuratus, were conditioned to regionally and ecologically relevant pCO2 levels and temperatures representative of upwelling (colder temperature and high pCO2 ) and nonupwelling (average temperature and low pCO2 ) conditions typical of coastal upwelling regions in the California Current System. Following 4.5 months of conditioning, adults were spawned and offspring were raised under either high or low pCO2 levels, to examine the role of maternal effects. Using RNA-seq and comparative transcriptomics, our results indicate that differential conditioning of the adults had an effect on the gene expression patterns of the progeny during the gastrula stage of early development. For example, maternal conditioning under upwelling conditions intensified the transcriptomic response of the progeny when they were raised under high versus low pCO2 conditions. Additionally, mothers that experienced upwelling conditions produced larger progeny. The overall findings of this study are complex, but do suggest that transgenerational plasticity in situ could act as an important mechanism by which populations might keep pace with rapid environmental change.

PMID: 29411447 [PubMed - indexed for MEDLINE]

Categories: pubmed

Neurogenesis in the sea urchin embryo is initiated uniquely in three domains.

Latest Publications - Tue, 04/02/2019 - 14:46
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Neurogenesis in the sea urchin embryo is initiated uniquely in three domains.

Development. 2018 11 09;145(21):

Authors: McClay DR, Miranda E, Feinberg SL

Abstract
Many marine larvae begin feeding within a day of fertilization, thus requiring rapid development of a nervous system to coordinate feeding activities. Here, we examine the patterning and specification of early neurogenesis in sea urchin embryos. Lineage analysis indicates that neurons arise locally in three regions of the embryo. Perturbation analyses showed that when patterning is disrupted, neurogenesis in the three regions is differentially affected, indicating distinct patterning requirements for each neural domain. Six transcription factors that function during proneural specification were identified and studied in detail. Perturbations of these proneural transcription factors showed that specification occurs differently in each neural domain prior to the Delta-Notch restriction signal. Though gene regulatory network state changes beyond the proneural restriction are largely unresolved, the data here show that the three neural regions already differ from each other significantly early in specification. Future studies that define the larval nervous system in the sea urchin must therefore separately characterize the three populations of neurons that enable the larva to feed, to navigate, and to move food particles through the gut.

PMID: 30413529 [PubMed - indexed for MEDLINE]

Categories: pubmed

Transcriptome profiling reveals key roles of phagosome and NOD-like receptor pathway in spotting diseased Strongylocentrotus intermedius.

Latest Publications - Sat, 03/23/2019 - 14:27
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Transcriptome profiling reveals key roles of phagosome and NOD-like receptor pathway in spotting diseased Strongylocentrotus intermedius.

Fish Shellfish Immunol. 2019 Jan;84:521-531

Authors: Zhang W, Lv Z, Li C, Sun Y, Jiang H, Zhao M, Zhao X, Shao Y, Chang Y

Abstract
Spotting disease is a common disease in the process of aquaculture and restocking of the sea urchin Strongylocentrotus intermedius and leads to mass mortality. To characterize the molecular processes and candidate genes related to spotting disease in S. intermedius, we conducted next-generation sequencing to assess the key genes/pathways in spotting diseased sea urchin (DUG) compared to healthy ones (HUG). A total of 321.1 million clean reads were obtained and assembled into 93,877 Unigenes with an N50 of 1185 bp, in which 86.48% of them matched to the genome sequence of the sea urchin S. purpuratus and 27,456 Unigenes mapped to Nr database. Salmon expression analysis revealed 1557 significantly differently expressed genes (DEGs) between DUG and HUG. These DEGs were enriched into 151 KEGG pathways including a core set of immune correlated pathways notably in phagosome and NOD-like receptor signaling. DUG displayed an obvious downregulation in these immune pathways. The expression patterns of six DEGs were confirmed by RT-qPCR, and the expressions were consistent with the results of RNA-seq. Furthermore, 15,990 SSRs were identified and a total of 235,249 and 295,567 candidate SNPs were identified from DUG and HUG, respectively. All these results provided basic information for our understanding of spotting disease outbreak in sea urchin.

PMID: 30342081 [PubMed - indexed for MEDLINE]

Categories: pubmed

Identification of Cell Death Genes in Sea Urchin Paracentrotus lividus and Their Expression Patterns during Embryonic Development.

Latest Publications - Fri, 03/22/2019 - 14:27
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Identification of Cell Death Genes in Sea Urchin Paracentrotus lividus and Their Expression Patterns during Embryonic Development.

Genome Biol Evol. 2019 02 01;11(2):586-596

Authors: Galasso C, D'Aniello S, Sansone C, Ianora A, Romano G

Abstract
Apoptosis and autophagy are fundamental mechanisms of programed cell death activated during protostome and deuterostome embryonic development, contributing to the creation and remodeling of different anatomical structures. Programed cell death has been investigated at morphological and biochemical levels, but there is a lack of information concerning gene expression of death factors during deuterostome embryonic development. In this study, we analyze the expression patterns of 13 genes involved in autophagy, extrinsic and intrinsic apoptosis during blastula, gastrula, and pluteus stages of the sea urchin Paracentrotus lividus embryonic development. Results suggested the occurrence of all death mechanisms investigated, highlighting the simultaneous involvement of apoptosis and autophagy during embryonic development. In particular, gastrula was the developmental stage where the majority of death genes were highly expressed. During gastrulation apoptotic processes are fundamental for tissue remodeling, such as cavity formation and removal of inner ectodermal cells. This is the first report that identifies a panel of cell death genes in the P. lividus genome and analyzes their expression variations during ontogenesis.

PMID: 30698765 [PubMed - indexed for MEDLINE]

Categories: pubmed

Soil pollution and toxicity in an area affected by emissions from a bauxite processing plant and a power plant in Gardanne (southern France).

Latest Publications - Thu, 03/21/2019 - 14:24
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Soil pollution and toxicity in an area affected by emissions from a bauxite processing plant and a power plant in Gardanne (southern France).

Ecotoxicol Environ Saf. 2019 Apr 15;170:55-61

Authors: Oral R, Pagano G, Siciliano A, Toscanesi M, Gravina M, Di Nunzio A, Palumbo A, Thomas PJ, Tommasi F, Burić P, Lyons DM, Guida M, Trifuoggi M

Abstract
Soil pollution and toxicity have been investigated in the Gardanne area (southern France) at a range of sites around a recognized pollution source, a bauxite processing plant (BPP), and a power plant (PP). Soil samples were submitted to inorganic and organic analyses and tested for toxicity in two invertebrate models. Inorganic analysis was based on determining elemental concentrations by ICP-MS, encompassing a total of 26 elements including 13 rare earth elements (REEs), of the soil samples and their leachates after 24 or 48 h in seawater. Organic analyses were performed by measuring the sums of 16 polycyclic aromatic hydrocarbons (PAHs) and of total hydrocarbons (C-10 to C-40). Bioassays were carried out on the early life stages of three sea urchin species (Arbacia lixula, Paracentrotus lividus and Sphaerechinus granularis), and on a nematode (Caenorhabditis elegans). Sea urchin bioassays were evaluated by the effects of soil samples (0.1-0.5% dry wt/vol) on developing embryos and on sperm, and scored as: a) % developmental defects, b) inhibition of sperm fertilization success and offspring damage, and c) frequencies of mitotic aberrations. C. elegans 24 h-mortality assay showed significant toxicity associated with soil samples. The effects of soil samples showed heightened toxicity at two groups of sites, close to the BPP main entrance and around the PP, which was consistent with the highest concentrations found for metals and PAHs, respectively. Total hydrocarbon concentrations displayed high concentrations both close to BPP main entrance and to the PP. Further studies of the health effects of such materials in Gardanne are warranted.

PMID: 30529620 [PubMed - indexed for MEDLINE]

Categories: pubmed

Theoretical tool bridging cell polarities with development of robust morphologies.

Latest Publications - Fri, 03/15/2019 - 14:13
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Theoretical tool bridging cell polarities with development of robust morphologies.

Elife. 2018 11 27;7:

Authors: Nissen SB, Rønhild S, Trusina A, Sneppen K

Abstract
Despite continual renewal and damages, a multicellular organism is able to maintain its complex morphology. How is this stability compatible with the complexity and diversity of living forms? Looking for answers at protein level may be limiting as diverging protein sequences can result in similar morphologies. Inspired by the progressive role of apical-basal and planar cell polarity in development, we propose that stability, complexity, and diversity are emergent properties in populations of proliferating polarized cells. We support our hypothesis by a theoretical approach, developed to effectively capture both types of polar cell adhesions. When applied to specific cases of development - gastrulation and the origins of folds and tubes - our theoretical tool suggests experimentally testable predictions pointing to the strength of polar adhesion, restricted directions of cell polarities, and the rate of cell proliferation to be major determinants of morphological diversity and stability.

PMID: 30477635 [PubMed - indexed for MEDLINE]

Categories: pubmed

Differences in Larval Arm Movements Correlate with the Complexity of Musculature in Two Phylogenetically Distant Echinoids, Eucidaris tribuloides (Cidaroidea) and Lytechinus variegatus (Euechinoidea).

Latest Publications - Sat, 03/09/2019 - 13:04
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Differences in Larval Arm Movements Correlate with the Complexity of Musculature in Two Phylogenetically Distant Echinoids, Eucidaris tribuloides (Cidaroidea) and Lytechinus variegatus (Euechinoidea).

Biol Bull. 2017 10;233(2):111-122

Authors: MacNeil KEA, Scaros AT, Croll RP, Bishop CD

Abstract
Within a common body plan, echinoid planktotrophic larvae are morphologically diverse, with variations in overall size, the length, and number of arms and the presence or absence of epidermal structures. In this report, we are interested in variation in larval arm-flexing behavior and correlated differences in larval musculature. Larvae of the cidaroid Eucidaris tribuloides exhibit conspicuous and regular arm-flexing behavior. In contrast, Lytechinus variegatus, a representative of the euechinoid clade, does not exhibit this behavior. We hypothesized that there were differences in musculature that correlated with this behavioral contrast and compared the development and structure of larval muscles between these species. We report substantial differences in some aspects of larval musculature. In addition to previously described oral musculature, both larvae possessed polygon-shaped musculature at the basal end of the larva. However, larval musculature in E. tribuloides was larger and contained additional muscles not observed in larvae of L. variegatus. Therefore, a conspicuous larval behavior consisting of repeated flexing of the postoral and posterodorsal larval arms was correlated with a larger, more complex musculature. This simple contrast indicates that larval musculature not associated with endoderm evolves in a manner that relates to differences in larval behavior and that additional comparisons are warranted.

PMID: 29373065 [PubMed - indexed for MEDLINE]

Categories: pubmed

Developmental effector gene regulation: Multiplexed strategies for functional analysis.

Latest Publications - Tue, 03/05/2019 - 12:58
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Developmental effector gene regulation: Multiplexed strategies for functional analysis.

Dev Biol. 2019 01 01;445(1):68-79

Authors: Wang L, Koppitch K, Cutting A, Dong P, Kudtarkar P, Zeng J, Cameron RA, Davidson EH

Abstract
The staggering complexity of the genome controls for developmental processes is revealed through massively parallel cis-regulatory analysis using new methods of perturbation and readout. The choice of combinations of these new methods is tailored to the system, question and resources at hand. Our focus is on issues that include the necessity or sufficiency of given cis-regulatory modules, cis-regulatory function in the normal spatial genomic context, and easily accessible high throughput and multiplexed analysis methods. In the sea urchin embryonic model, recombineered BACs offer new opportunities for consecutive modes of cis-regulatory analyses that answer these requirements, as we here demonstrate on a diverse suite of previously unstudied sea urchin effector genes expressed in skeletogenic cells. Positively active cis-regulatory modules were located in single Nanostring experiments per BAC containing the gene of interest, by application of our previously reported "barcode" tag vectors of which> 100 can be analyzed at one time. Computational analysis of DNA sequences that drive expression, based on the known skeletogenic regulatory state, then permitted effective identification of functional target site clusters. Deletion of these sub-regions from the parent BACs revealed module necessity, as simultaneous tests of the same regions in short constructs revealed sufficiency. Predicted functional inputs were then confirmed by site mutations, all generated and tested in multiplex formats. There emerged the simple conclusion that each effector gene utilizes a small subset of inputs from the skeletogenic GRN. These inputs may function to only adjust expression levels or in some cases necessary for expression. Since we know the GRN architecture upstream of the effector genes, we could then conceptually isolate and compare the wiring of the effector gene driver sub-circuits and identify the inputs whose removal abolish expression.

PMID: 30392838 [PubMed - indexed for MEDLINE]

Categories: pubmed