Latest Publications

Selective 2-desulfation of tetrasaccharide-repeating sulfated fucans during oligosaccharide production by mild acid hydrolysis

Sun, 11/27/2022 - 03:00

Carbohydr Polym. 2023 Feb 1;301(Pt A):120316. doi: 10.1016/j.carbpol.2022.120316. Epub 2022 Nov 9.

ABSTRACT

Sulfated fucans (SFs) from echinoderms, such as sea cucumbers and sea urchins, present linear and regular sulfation patterns within defined oligosaccharide building blocks. The high molecular weights of these polymers pose a problem in advanced structure-activity relationship studies for which derived oligosaccharides are more appropriate tools for investigation. However, enzymes capable of specifically depolymerizing SFs, fucanases, are not very common. Scarce abundance and unknown catalytic activities are additional barriers to exploiting fucanases. Oligosaccharide production by controlled chemical reactions such as mild acid hydrolysis then becomes a convenient strategy. As a consequence, physicochemical studies are necessary to understand the structural modifications caused on SFs by this chemical hydrolysis. Hence, in this work, we subjected three tetrasaccharide-repeating SFs from sea cucumbers, Isostichopus badionotus (IbSF), Holothuria floridana (HfSF), and Lytechinus variegatus (LvSF) to mild acid hydrolysis for oligosaccharide production. Interestingly, selective 2-desulfation reaction was observed in all three SFs. Through our study, we indicate that selective 2-desulfation is a common and expected phenomenon in oligosaccharide production by mild acid hydrolysis of SFs, including those composed of tetrasaccharide-repeating units.

PMID:36436858 | DOI:10.1016/j.carbpol.2022.120316

Categories: pubmed

Thyroid hormone-induced cell death in sea urchin metamorphic development

Tue, 11/22/2022 - 03:00

J Exp Biol. 2022 Dec 1;225(23):jeb244560. doi: 10.1242/jeb.244560. Epub 2022 Dec 1.

NO ABSTRACT

PMID:36412991 | DOI:10.1242/jeb.244560

Categories: pubmed

An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes

Fri, 11/18/2022 - 03:00

Nat Ecol Evol. 2022 Dec;6(12):1921-1939. doi: 10.1038/s41559-022-01905-w. Epub 2022 Nov 17.

NO ABSTRACT

PMID:36396969 | DOI:10.1038/s41559-022-01905-w

Categories: pubmed

Single-cell RNA-sequencing analysis of early sea star development

Fri, 11/18/2022 - 03:00

Development. 2022 Nov 15;149(22):dev200982. doi: 10.1242/dev.200982. Epub 2022 Nov 18.

ABSTRACT

Echinoderms represent a broad phylum with many tractable features to test evolutionary changes and constraints. Here, we present a single-cell RNA-sequencing analysis of early development in the sea star Patiria miniata, to complement the recent analysis of two sea urchin species. We identified 20 cell states across six developmental stages from 8 hpf to mid-gastrula stage, using the analysis of 25,703 cells. The clusters were assigned cell states based on known marker gene expression and by in situ RNA hybridization. We found that early (morula, 8-14 hpf) and late (blastula-to-mid-gastrula) cell states are transcriptionally distinct. Cells surrounding the blastopore undergo rapid cell state changes that include endomesoderm diversification. Of particular import to understanding germ cell specification is that we never see Nodal pathway members within Nanos/Vasa-positive cells in the region known to give rise to the primordial germ cells (PGCs). The results from this work contrast the results of PGC specification in the sea urchin, and the dataset presented here enables deeper comparative studies in tractable developmental models for testing a variety of developmental mechanisms.

PMID:36399063 | DOI:10.1242/dev.200982

Categories: pubmed

Oocyte quality assessment in marine invertebrates: a novel approach by fluorescence spectroscopy

Sat, 11/12/2022 - 03:00

Biol Res. 2022 Nov 12;55(1):34. doi: 10.1186/s40659-022-00403-4.

ABSTRACT

BACKGROUND: The assessment of oocyte quality is, nowadays, a major challenge in aquaculture, oocyte cryopreservation, and environmental science. Oocyte quality is a determining factor in fertilization and embryo development; however, there is still a lack of rapid and sensitive cellular markers for its assessment. Currently, its estimation is predominantly based on morphological analysis, which is subjective and does not consistently reflect the developmental competence of the oocytes. Despite several recent studies investigating molecular markers related to oocyte quality, methods currently available for their determination pose various technical challenges and limitations. In this study, we developed a novel approach based on fluorescence spectroscopy to assess different intrinsic physiological parameters that can be employed to evaluate egg quality in marine invertebrates that are widely used as animal models such as sea urchins and mussels.

RESULTS: Different physiological parameters, such as viability, mitochondrial activity, intracellular ROS levels, plasma membrane lipid peroxidation, and intracellular pH, for egg quality evaluation have been successfully assessed in sea urchins and mussels by using specific fluorescent dyes and detecting the fluorescent signals in eggs through fluorescence spectroscopy.

CONCLUSIONS: Based on our findings, we propose these physiological markers as useful predictors of egg quality in marine invertebrates; they can be estimated rapidly, selectively, and sensitively by employing this novel approach, which, due to the speed of analysis, the low cost, and easy use can be considered a powerful analytical tool for the egg quality assessment.

PMID:36371313 | DOI:10.1186/s40659-022-00403-4

Categories: pubmed

Ethanol exposure perturbs sea urchin development and disrupts developmental timing

Fri, 11/11/2022 - 03:00

Dev Biol. 2023 Jan;493:89-102. doi: 10.1016/j.ydbio.2022.11.001. Epub 2022 Nov 8.

NO ABSTRACT

PMID:36368523 | DOI:10.1016/j.ydbio.2022.11.001

Categories: pubmed

The complex set of internal repeats in SpTransformer protein sequences result in multiple but limited alternative alignments

Fri, 11/04/2022 - 03:00

Front Immunol. 2022 Oct 18;13:1000177. doi: 10.3389/fimmu.2022.1000177. eCollection 2022.

ABSTRACT

The SpTransformer (SpTrf) gene family encodes a set of proteins that function in the sea urchin immune system. The gene sequences have a series of internal repeats in a mosaic pattern that is characteristic of this family. This mosaic pattern necessitates the insertion of large gaps, which has made alignments of the deduced protein sequences computationally difficult such that only manual alignments have been reported previously. Because manual alignments are time consuming for evaluating newly available SpTrf sequences, computational approaches were evaluated for the sequences reported previously. Furthermore, because two different manual alignments of the SpTrf sequences are feasible because of the multiple internal repeats, it is not known whether additional alternative alignments can be identified using different approaches. The bioinformatic program, PRANK, was used because it was designed to align sequences with large gaps and indels. The results from PRANK show that the alignments of the internal repeats are similar to those done manually, suggesting multiple feasible alignments for some regions. GUIDANCE based analysis of the alignments identified regions that were excellent and other regions that failed to align. This suggests that computational approaches have limits for aligning the SpTrf sequences that include multiple repeats and that require inserted gaps. Furthermore, it is unlikely that alternative alignments for the full-length SpTrf sequences will be identified.

PMID:36330505 | PMC:PMC9623053 | DOI:10.3389/fimmu.2022.1000177

Categories: pubmed

EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

Mon, 10/24/2022 - 03:00

BMC Genom Data. 2022 Oct 23;23(1):75. doi: 10.1186/s12863-022-01090-6.

ABSTRACT

BACKGROUND: Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity.

RESULTS: The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling.

CONCLUSION: EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.

PMID:36274129 | DOI:10.1186/s12863-022-01090-6

Categories: pubmed

Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins

Thu, 10/20/2022 - 03:00

Nat Ecol Evol. 2022 Dec;6(12):1907-1920. doi: 10.1038/s41559-022-01906-9. Epub 2022 Oct 20.

NO ABSTRACT

PMID:36266460 | DOI:10.1038/s41559-022-01906-9

Categories: pubmed

Mechanism underlying retinoic acid-dependent metamorphosis in the starfish

Fri, 10/14/2022 - 03:00

Dev Biol. 2022 Dec;492:119-125. doi: 10.1016/j.ydbio.2022.10.002. Epub 2022 Oct 12.

ABSTRACT

The evolution of the biphasic life cycle in marine invertebrates has attracted considerable interest in zoology. We recently provided evidence that retinoic acid (RA) is involved in the regulation of metamorphosis in starfish. It also functions in life cycle transitions of jellyfish (cnidaria). Thus, documenting the evolutionarily conserved role of RA in such transitions will help to trace the life cycle evolution of bilaterians and cnidarians. In this study, we examined the molecular mechanisms by which RA signaling is involved in the commencement of metamorphosis in starfish. First, we measured RA levels during the larval and metamorphosis stages by liquid chromatography-tandem mass spectrometry. We found that all-trans RA levels in the larval body are high before larvae acquire competence for metamorphosis, suggesting that the commencement of metamorphosis is not controlled by increased RA synthesis. Furthermore, the suppression of rar gene expression by TALEN-mediated gene knockout revealed that RA receptor (RAR) is essential for metamorphosis. These observations suggest that the initiation of metamorphosis is regulated at the level of synthesized RA to activate RAR. We discuss the divergence of ligand molecules and receptors during the evolution of life cycle regulation.

PMID:36240875 | DOI:10.1016/j.ydbio.2022.10.002

Categories: pubmed