ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos.

Cis-regulatory elements (CREs) and transcription factors (TFs) associated with them determine temporal and spatial domains of gene expression. Therefore, identification of these CREs and TFs is crucial to elucidating transcriptional programs across taxa. With chromatin accessibility facilitating transcription factor access to DNA, the identification of regions of open chromatin sheds light both on the function of the regulatory elements and their evolution, thus allowing the recognition of potential CREs. Buenrostro and colleagues have developed a novel method for exploring chromatin accessibility: assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), which can be used for the purpose of identifying putative CREs. This method was shown to have considerable advantages when compared to traditional methods such as sequence conservation analyses or functional assays. Here we present the adaptation of the ATAC-seq method to echinoderm species and discuss how it can be used for CRE discovery.

Extremely stable high molecular mass soluble multiprotein complex from eggs of sea urchin Strongylocentrotus intermedius with phosphatase activity.

It was proposed that most biological processes are performed by different protein complexes. In contrast to individual proteins and enzymes, their complexes usually have other biological functions, and their formation may be important system process for the expansion of diversity and biological functions of different molecules. Identification and characterization of embryonic components including proteins and their multiprotein complexes seem to be very important for an understanding of embryo function. We have isolated and analyzed for the first time a very stable multiprotein complex (SPC; approximately 1100 kDa) from the soluble fraction of extracts of the sea urchin embryos. By fast protein liquid chromatography (FPLC) gel filtration the SPC was well separated from other extract proteins. Stable multiprotein complex is stable in different drastic conditions but dissociates moderately in the presence of 8M urea + 1.0M NaCl. According to sodium dodecyl sulfate polyacrylamide gel electrophoresis data, this complex contains many major, moderate and minor proteins with molecular masses from 10 to 95 kDa. The SPC was destroyed by 8M urea or SDS, and its components were separated using thin layer chromatography, ion-exchange chromatography, gel filtration, and reverse phase chromatography. Using matrix-assisted laser desorption/ionization mass spectrometry of partially dissociated SPC, it was shown that the complex contains not only proteins (10-95 kDa) but also few dozens of peptides with molecular masses from 2 to 9.5 kDa. Short peptides form very strong complexes, which at the treatment of SPC with urea or SDS can be partially break down into smaller complexes having different peptide compositions. Reverse phase chromatography of these complexes after all type of abovementioned chromatographies led to detection from 6 to 11 distinct peaks corresponding to new complexes containing up to a few dozens of peptides. The SPCs possess alkaline phosphatase activity. Progress in the study of embryos protein complexes can help to understand their biological functions.

Low-dose action of tryptanthrin and its derivatives against developing embryos of the sea urchin Strongylocentrotus intermedius.

Nine tryptanthrin derivatives, including tryptanthrin itself, were synthesized using different methods, including oxidation of the corresponding isatins to obtain 1-4, the reaction of tryptanthrin 1 with hydrazine and its derivatives to obtain 5-7, and aldol condensation of 1 with acetone and methylethylketone to obtain 8 and 9. The action of 1-9 in doses corresponding to the IC50 against developing embryos of the sea urchin Strongylocentrotus intermedius and in the sperm test allowed us to estimate to potency of all the compounds and to determine which were cytotoxic. In addition, these studies showed that compounds 3, 4, 8, and 9 had a stimulatory effect at lower doses. In particular, the tryptanthrin derivatives stimulated the larval stages of development in surviving embryos at concentrations lower than the IC50.

Parental exposure to heavy fuel oil induces developmental toxicity in offspring of the sea urchin Strongylocentrotus intermedius.

The present study investigated the toxic effects of parental (maternal/paternal) exposure to heavy fuel oil (HFO) on the adult reproductive state, gamete quality and development of the offspring of the sea urchin Strongylocentrotus intermedius. Adult sea urchins were exposed to effluents from HFO-oiled gravel columns for 7 days to simulate an oil-contaminated gravel shore, and then gametes of adult sea urchins were used to produce embryos to determine developmental toxicity. For adult sea urchins, no significant difference in the somatic size and weight was found between the various oil loadings tested, while the gonad weight and gonad index were significantly decreased at higher oil loadings. The spawning ability of adults and fecundity of females significantly decreased. For gametes, no effect was observed on the egg size and fertilization success in any of the groups. However, a significant increase in the percentage of anomalies in the offspring was observed and then quantified by an integrative toxicity index (ITI) at 24 and 48 h post fertilization. The offspring from exposed parents showed higher ITI values with more malformed embryos. The results confirmed that parental exposure to HFO can cause adverse effects on the offspring and consequently affect the recruitment and population maintenance of sea urchins.

Base excision DNA repair in the embryonic development of the sea urchin, Strongylocentrotus intermedius.

In actively proliferating cells, such as the cells of the developing embryo, DNA repair is crucial for preventing the accumulation of mutations and synchronizing cell division. Sea urchin embryo growth was analyzed and extracts were prepared. The relative activity of DNA polymerase, apurinic/apyrimidinic (AP) endonuclease, uracil-DNA glycosylase, 8-oxoguanine-DNA glycosylase, and other glycosylases was analyzed using specific oligonucleotide substrates of these enzymes; the reaction products were resolved by denaturing 20% polyacrylamide gel electrophoresis. We have characterized the profile of several key base excision repair activities in the developing embryos (2 blastomers to mid-pluteus) of the grey sea urchin, Strongylocentrotus intermedius. The uracil-DNA glycosylase specific activity sharply increased after blastula hatching, whereas the specific activity of 8-oxoguanine-DNA glycosylase steadily decreased over the course of the development. The AP-endonuclease activity gradually increased but dropped at the last sampled stage (mid-pluteus 2). The DNA polymerase activity was high at the first cleavage division and then quickly decreased, showing a transient peak at blastula hatching. It seems that the developing sea urchin embryo encounters different DNA-damaging factors early in development within the protective envelope and later as a free-floating larva, with hatching necessitating adaptation to the shift in genotoxic stress conditions. No correlation was observed between the dynamics of the enzyme activities and published gene expression data from developing congeneric species, S. purpuratus. The results suggest that base excision repair enzymes may be regulated in the sea urchin embryos at the level of covalent modification or protein stability.

Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin.

Early in embryogenesis, maternally deposited transcripts are degraded and new zygotic transcripts are generated during the maternal to zygotic transition. Recent works have shown that early zygotic transcripts are short compared to maternal transcripts, in zebrafish and Drosophila species. The reduced zygotic transcript length was attributed to the short cell cycle in these organisms that prevents the transcription of long primary transcripts (intron delay). Here we study the length of maternal mRNAs and their degradation kinetics in two sea urchin species to further the understanding of maternal gene usage and processing. Early zygotic primary transcripts and mRNAs are shorter than maternal ones in the sea urchin, Strongylocentrotus purpuratus. Yet, while primary transcripts length increases when cell cycle lengthens, typical for intron delay, the relatively short length of zygotic mRNAs is consistent. The enhanced mRNA length is due to significantly longer maternal open reading frames and 3'UTRs compared to the zygotic lengths, a ratio that does not change with developmental time. This implies unique usage of both coding sequences and regulatory information in the maternal stage compared to the zygotic stages. We extracted the half-lifetimes due to maternal and zygotic degradation mechanisms from high-density time course of a set of maternal mRNAs in Paracentrotus lividus. The degradation rates due to maternal and zygotic degradation mechanisms are not correlated, indicating that these mechanisms are independent and relay on different regulatory information. Our studies illuminate specific structural and kinetic properties of sea urchin maternal mRNAs that might be broadly shared by other organisms.

[BIOLOGICAL ACTIVITY OF YERSINIA PSEUDOTUBERCULOSIS TOXINS].

AIM: Study of effect of heat-labile (HLT) and thermostable (HST) lethal toxins of Yersinia pseudotuberculosis on the development of embryos of sea urchin Strongylocentrotus intermedius, processes of biosynthesis of nucleic acids and protein in embryo cells and activity of nucleoside- kinases of sea urchin. Materials-and methods. Y pseudotuberculosis strains 2517 (pYV-) and 512 (pYV48MD, pYV82MD) were used for isolation of HLT and HST Gametes and embryos of sea urchin S. intermediuswere used to carry out the experiments and isolate nucleoside-kinases. RESULTS: , Both of the studied toxins of Y pseudotuberculosis possessed, spermiotoxic effect and reduced fertilizing ability of sea urchin spermies. HLT LD50 was 1 µg/ml, and HST - 2 µg/ml. Toxins affected the development of embryos of sea urchin resulting in severe morphologic damages, cessation ofthe development of embryos at early stages of embryogenesis, destruction of cells and death of embryos. Wherein; damaging effect of HLT was observed at lower concentrations compared with HST HLT inhibited DNA and RNA biosynthesis at concentrations of 1-2 µg/ml. HST did not affect biosynthesis of nucleic acids even at high concentrations, but inhibited protein biosynthesis in sea urchin embryos. HLT did not reduce the level of inclusion of labeled amino acids into embryo cells. HLT had inhibiting effect on the activity of thymidine- and uridine-kinase of sea urchin, whereas HST did not affect these enzymes. CONCLUSION: Both of Y pseudotuberculosis protein toxins affect the development of sea urchin embryos, however, mechanisms of action of HLT and HST on embryos and processes occurring in them differ.

Assessment of the toxic effect exerted by fluorescent pseudomonads on embryos and larvae of the sea urchin Strongylocentrotus nudus.

Strains of bacteria capable of growing on artificial culture media were isolated from the fouling of brass plates submerged in Nha Trang Bay, South China Sea, and from tissues of the seastar Distolasterias nipon, caught in Peter the Great Bay, Sea of Japan. According to the complex of data of genetic and physiological/biochemical analyzes, two strains of cultivated bacteria were identified by us as the species Pseudomonas aeruginosa, two strains as Pseudomonas fluorescens, and one strain as Ruegeria sp. It was shown that the cultivated strains of P. aeruginosa released exotoxins, particularly phenazine pigments, into the environment. Production of the toxins did not depend on presence of a target organism in the system and was aimed at regulation of interactions in the microbial community. The toxicity of the studied natural isolates of fluorescent pseudomonads was analyzed by using embryos and larvae of the sea urchin Strongylocentrotus nudus, which are the sensitive and dynamic toxicological sea-urchin embryo test (SET) system. As was established, exotoxins produced by the strains of P. aeruginosa inhibit activity of cilia in sea urchin larvae, as well as disturb processes of cell differentiation in embryos and larvae. Their toxic influence is accompanied by disturbances of protein synthesis and the disruptions of cytoskeleton in the course of zygote cleavage and larval development. Unlike P. aeruginosa, the strains of P. fluorescens and Ruegeria sp. did not exert the toxic effect on SET. The obtained data allow considering objects of the environment as the natural reservoir of opportunistic microorganisms posing a potential threat to human, whereas the use of SET for determination of toxicity of isolated bacteria provides an opportunity to study the mechanisms of their interactions with organisms in marine ecosystems.

Expression pattern of vascular endothelial growth factor 2 during sea urchin development.

The VEGF family in the sea urchin is comprised of three members designated Vegf1 through Vegf3. In this study, we found a high level of similarity between the PDGF/VEGF domain of the predicted gene Sp-Vegf2 in the sea urchin Strongylocentrotus purpuratus and the same domain of a gene that we found in a closely related sea urchin, Strongylocentrotus intermedius. The sequence of the Si-Vegf2 cDNA was determined, and the expression of the Si-Vegf2 mRNA throughout early sea urchin development was studied by RT-PCR and in situ hybridization. Also we analyzed phylogenetic relationships of Si-Vegf2 and other members of the PDGF and VEGF families. We have found that the Si-Vegf2 present during the time span from the egg to the 4-arm pluteus stage. This mRNA is uniformly distributed in eggs, cleaving embryos and early blastulae. At the gastrula stage, the Si-Vegf2 transcripts are localized in the ventrolateral clusters of primary mesenchyme cells, and later, at the prism stage, they are detected in the forming apex. At the early pluteus stage, Si-Vegf2 mRNAs are found in two groups of mesenchyme cells in the scheitel region on the apical pole. We have determined that Si-Vegf2 is a mesenchyme-expressed factor but its developmental function is unknown.

[Effect of exogenous factors on the induction of spicule formation in sea urchin embryonic cell cultures].

The effect of exogenous factors on the realization of the spicule formation program in two sea urchin species, Strongylocentrotus intermedius and S. nudus, has been studied in primary embryonic cell cultures derived from the blastula and gastrula stages. It has been shown that the process of spicule formation depends on the type of substrate and the composition of the medium. An original finding is that calf or horse serum necessary for spicule formation in vitro can be replaced by a complex of factors including insulin, transferrin, and lectins. Methods allowing control over the growth and differentiation of marine invertebrate embryonic cells in vitro open prospects for their application to practical problems such as the establishment of cell cultures producing certain mineral structures.

Influence of P-glycoprotein on embryotoxicity of the antifouling biocides to sea urchin (Strongylocentrotus intermedius).

P-glycoprotein (P-gp), as an ATP-binding cassette transporter, transports a wide variety of substrates varying from small molecules like steroids to large polypeptides across the cell membrane in human and animals, even in aquatic animals. Although P-gp protein has attracted much attention of research, its effect on the toxicity of environmental toxicants such as antifouling biocides is still poorly understood. The goal of this study is to evaluate whether copper pyrithione (CuPT), Sea-Nine 211, dichlofluanid and tolylfluanid, four widely used antifouling agents, can be transported by P-gp in embryos of sea urchin Strongylocentrotus intermedius in the presence and absence of the P-gp inhibitor verapamil. Cytotoxcicities of Sea-Nine 211 (EC50 = 99 nM, at 4-arm pluteus) and dichlofluanid (EC50 = 144 nM, at multi-cell) are enhanced by the addition of the P-gp inhibitor, indicating that the two biocides are potential P-gp substrates. Tolylfluanid and CuPT are not transported by P-gp out of the cell, since no obvious changes in the cytotoxicities of the two biocides are observed no matter whether verapamil is added or not. In addition, to understand the mechanisms of ligand binding and its interaction with P-gp, a three-dimensional model of the sea urchin P-gp is generated based on the mouse crystal structure by using homology modeling approach. With this model, a flexible docking is performed and the results indicate that Sea-Nine 211 and dichlofluanid share the same binding site with verapamil, composed of key residues Lys677, Lys753, Thr756, Ala780, Met1033 and Phe1037, whereas tolylfluanid and CuPT display totally different binding modes to P-gp. This further demonstrates that Sea-Nine 211 and dichlofluanid are P-gp substrates, which provides us with new insights into the interactions of P-gp with the antifouling contaminants in aquatic invertebrate embryos.

Assessment of toxic interactions of heavy metals in multi-component mixtures using sea urchin embryo-larval bioassay.

The toxicities of copper, lead, zinc and cadmium ions and various concentrations of mixtures of them were studied using sea urchin (Strongylocentyotus intermedius) embryo-larval bioassay. Toxic unit analysis was used to determine type of joint action for each mixture combination (binary, ternary and quaternary). For the majority of the binary combinations, the interactions were of synergistic nature, but in ternary or quaternary mixtures, the joint action was mainly concentration additive, while antagonism was only observed for two mixtures (Cu+Pb and Zn+Cd) among all the 11 combinations. Two prevailing theoretical models: the concentration addition (CA) model and the independent action (IA) model were used to predict the mixture toxicities. The weak correlation obtained (R≃0.55) indicated that the hypotheses of mode of action involved in the two models to some extent failed to describe the behavior of the mixture system. Then a novel bio-concentration factor-based model was developed and was successful to predict the toxicities of mixtures, with an obtained R of 0.92. This model indicated that in a mixture system of heavy metals, the joint toxicity was mainly determined by the combined action of bio-concentrations of metals other than the simply similar (CA) or dissimilar (IA) modes of action of the mixture components.

Characterization of steroid receptor coactivator in sea urchin, Strongylocentrotus nudus, and its involvement in embryonic development.

Ligand-bound nuclear receptors (NRs) recruit coactivators such as members of the p160 steroid receptor coactivator (SRC) family and cyclic AMP responsive element binding protein (CREB)-binding protein (CBP) to specific enhancer elements and activate target gene transcription. In the present study, we isolated a novel SRC from the sea urchin Strongylocentrotus nudus (SnSRC) by using the ligand-binding domain of retinoid X receptor as a bait in a yeast two-hybrid screening. The SnSRC and vertebrate SRCs are different in size but share the overall characteristic domains, such as NR interacting domain (NID), CBP-binding and glutamine-rich regions. SnSRC mRNA showed highest expression levels at the 32-cell, 64-cell and pluteus larval stages. Full-length SnSRC (1992 amino acids) interacted with several NRs, including sea urchin estrogen receptor-related receptor (ERR), human and masu salmon estrogen receptors (ERα), mouse ERRγ, rat glucocorticoid receptor α, and rat thyroid receptor ß. The SnSRC possesses two functional NIDs, both of which are dependent on their core LxxLL motifs. Furthermore, preferential interacting domains for ERα in the SnSRC are located in the central LxxLL motifs, revealed by the truncation and mutagenesis studies. Strikingly, the SnSRC has a single transcription activation domain, which interacts with CBP, a transcriptional integrator. In addition, transient knockdown of the SnSRC gene in the sea urchin embryo using morpholino antisense RNA induced abnormal phenotypes at gastrulation stage such as the lack of primary invagitation and exogastrulation. These results suggest that the SnSRC is a new member of the SRC family and plays an important role during early embryonic development.

Toxicity evaluation of single and mixed antifouling biocides using the Strongylocentrotus intermedius sea urchin embryo test.

The present study evaluated the single and mixed toxicities of commonly used antifouling biocides (copper pyrithione, Sea nine 211, dichlofluanid, tolylfluanid, and Irgarol 1051) on the early embryogenesis of sea urchin Strongylocentrotus intermedius. Their toxicities were quantified in terms of the median effective concentration (EC50) reducing the embryogenesis success by 50%. For individual biocides to the embryos, the toxicity was in order of copper pyrithione>Sea nine 211> tolylfluanid>dichlofluanid>Irgarol 1051. The toxicities of mixture (binary, ternary, quaternary, and quinary) of compounds, evaluated by toxic unit, additivity index, and mixture toxicity index, showed that the copper pyrithione-Sea nine 211 combination was the most toxic with the EC50 value of 7.87 nM in all mixtures. Synergistic enhancements of toxicity were observed for all mixtures except the combination of tolylfluanid-Sea nine 211, revealing antagonistic effect. Both the concentration addition and independent action concepts failed to accurately predict the mixture toxicities of the antifouling combinations; thus, a new log K(OW)-based model was developed to predict the combined toxicities of these antifouling chemicals, which were capable of predicting the mixture toxicities of antifouling biocides (R(2)=0.33).

Highly hydroxylated steroids of the starfish Archaster typicus from the Vietnamese waters.

Five new steroidal compounds, including an unusual glucoside, along with several known steroids were isolated from the starfish Archaster typicus collected in shallow waters of Quang Ninh province (Vietnam). Three new compounds are 27-nor-cholestane derivatives and the other two are 24,26-dihydroxycholestane derivatives. A biogenesis pathway for the unusual side chain of 27-nor-cholestane derivatives is proposed. Isolated compounds presented moderate toxic effects in the sperm- and 8-blastomere tests on embryonal development of the sea urchin Strongylocentrotusintermedius.

[O-glycosylhydrolases of embryos of the sea urchin Strongylocentrotus intermedius and effect of some natural substances on their biosynthesis].

Embryos of sea urchin Strongylocentrotus intermedius have been revealed to contain o-glycosylhydrolases: highly active 1,3-beta-D-glucanase and alpha-D-mannosidase as well as a lower activity of beta-D-glucosidase and beta-D-galactosidase. Dynamics of changes of the enzyme activities has been studied at various stages of the sea urchin embryo development. There also have been studied effects of some substances (natural fucoidans, beta-1,3; 1,6-glucans formed by enzymatic synthesis as well as a protein inhibitor of marine mollusc endo-1,3-beta-D-glucanases) on development of the embryos and biosynthesis of 1,3-beta-D-glucanase and alpha-D-mannosidase.

Effect of 1,3;1,6-beta-D-glucans on developing sea urchin embryos.

The effect of 1,3;1,6-beta-D-glucooligo- and polysaccharides with different structures (from 1 to 10 kDa of molecular mass; from 10-25% of beta-1,6-linked glucose residues content) on the developing embryos of sea urchin, Strongylocentrotus intermedius, was evaluated for the screening of potential positive stimulants. 1,3;1,6-beta-D-glucans with a molecular mass of between 6-10 kDa and at concentrations of 0.05-0.25 mg/ml shown the best modulator effect on the sea urchin embryos. 1,3;1,6-beta-D-glucans increased the survival of the sea urchin embryos up to 2.5-fold compared with the control animals.

[Influence of thermolabile lethal toxin of Yersinia pseudotuberculosis on development of sea urchin embryos and biosynthesis of DNA and RNA in embryonic cells].

Influence of thermolabile lethal toxin of Y. pseudotuberculosis on the development of embryos of sea urchin (Strongylocentrotus intermedius) and on biosynthesis of nucleic acids in embryonic cells was studied. Thermolabile lethal toxin affected metabolic processes of cells by inhibiting DNA and RNA synthesis. It had damaging action on developing embryos of sea urchin causing morphological changes and, as a consequence, death of embryos.

[New steroid glycosides from the starfish Fromia milleporella].

Two new steroid glycosides from the starfish Fromia milleporella collected in the Seychelles were isolated and characterized: milleporoside A, (20R, 24R)-29-O-[3-O-methyl-beta-D-xylopyranosyl-(1-->4)-3-O-methyl-beta-D-xylopyranosyl]-24-ethyl-5alpha-cholestane-3beta,4beta,6alpha,8,15beta,16beta,29-heptaol, and milleporoside B, (20R, 24R)-(22E)-28-O-[3-O-methyl-beta-D-xylopyranosyl-(1-->4)-3-O-methyl-beta-D-xylopyranosyl]-24-methyl-5alpha-cholest-22-ene-3beta,4beta,6alpha,8,15beta,16beta,28-heptaol. The structures of the glycosides were determined from their spectra and a comparison with spectral characteristics of known compounds. These compounds exhibit a moderate cytostatic activity toward the embryos of the sea urchin Strongylocentrotus intermedius.