High-quality RNA extraction from the sea urchin Paracentrotus lividus embryos

Ruocco, Nadia; Costantini, Susan; Zupo, Valerio; Romano, Giovanna; Ianora, Adrianna; Fontana, Angelo; Costantini, Maria

doi:10.1371/journal.pone.0172171

Cited by 22 publications

(15 citation statements)

References 40 publications

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“…It has shown that the use of sea urchin shells confers certain beneficial advantages, including antioxidant and pharmaceutical effects (Shankarlal et al, 2011). The sea urchin, Paracentrotus lividus (Dincer and Cakli, 2007) is a keystone herbivore in the Mediterranean Sea (Ruocco et al, 2017). It has special substances, such as quinonoid pigments which called echinochromes (Mohamed et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Protective effect of Echinochrome against intrahepatic cholestasis induced by alpha-naphthylisothiocyanate in rats

et al. 2020

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Abstract The present study was designed to evaluate the protective effects of echinochrome (Ech) on intrahepatic cholestasis in rats induced by a single (i.p.) injection of alpha-naphthylisothiocyanate (ANIT) (75 mg/kg body weight). The rats were pre-treated orally for 48hr (one dose / 24hr) with Ech (1, 5 and 10 mg/kg body weight) or ursodeoxycholic acid (UDCA) 80 mg/kg body weight drug then, injected with ANIT. ANIT markedly increased serum activities of alanine amino transaminase (ALT), aspartate amino transaminase (AST) and alkaline phosphatase (ALP), which was accompanied by a massive inflammation of epithelial cells on bile duct at 24h after ANIT injection. ANIT also increased the levels of total protein (TP), total bilirubin (TB), direct bilirubin (DB), indirect bilirubin (IB), however decrease albumin content (ALB). In addition ANIT increased hepatic MDA and NO level and decreased GSH level and GST activity. The Ech exerted hepatoprotective and anticholestatic effects as assessed by a significant decrease in the activities of serum AST, ALT and ALP, and the levels of TP, TB, DB and IB as well as liver MDA level and NO level. In conclusion, Ech was found to possess hepatoprotective effect against intrahepatic cholestasis induced by hepatotoxin such as ANIT.

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Section: Discussionmentioning

confidence: 99%

Protective effect of Echinochrome against intrahepatic cholestasis induced by alpha-naphthylisothiocyanate in rats

et al. 2020

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“…The application of RNA‐Seq in embryos is limited by the low RNA content of a single pre‐hatching bovine embryo (200–2,300 pg) depending on the stage of the development (Gilbert et al., ). To ensure sufficient quantity and integrity of RNA for RNA‐Seq, we used RNeasy ® Micro Kit (Ruocco et al., ) to extract RNA from yak embryos and Smart‐seq2 (Picelli et al., ) to generate sequencing libraries from embryos. In this way, we successfully provide the first comprehensive description of gene activities during in vitro yak embryonic development in this study.…”

Section: Discussionmentioning

confidence: 99%

“…Total RNA was extracted from pooled embryos of each stage using RNeasy ® Micro Kit (Qiagen, Austin, TX, US) as previously described by Ruocco et al (2017). Full-length single-cell RNAseq libraries were prepared using the Smart-seq2 protocol (Picelli et al, 2013) with minor modifications.…”

Section: Library Preparation and Sequencingmentioning

confidence: 99%

Characterization of transcriptional complexity during pre‐implantation development of the yak (Bos grunniens) using RNA‐Seq

Xia

et al. 2018

Reprod Domestic Animals

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The objective of this study was to investigate the mechanism that regulates pre-implantation development of the yak (Bos grunniens). We determined the transcriptomes of in vitro-produced yak embryos at two-cell, four-cell, eight-cell stages, and morula and blastocyst using the Illumina RNA-seq for the first time. We obtained 47.36-50.86 million clean reads for each stage, of which, 85.65%-90.02% reads were covered in the reference genome. A total of 17,368 genes were expressed during the two-cell stage to blastocyst of the yak, of which 7,236 genes were co-expressed at all stages, whereas 10,132 genes were stage-specific expression. Transcripts from 9,827 to 14,893 different genes were detected in various developmental stages. When |log ratio| ≥ 1 and q-value <0.05 were set as thresholds for identifying differentially expressed genes (DEGs), we detected a total of 6,922-10,555 DEGs between any two consecutive stages. The GO distributions of these DEGs were classified into three categories: biological processes (23 terms), cellular components (22 terms) and molecular functions (22 terms). Pathway analysis revealed 310 pathways of the DEGs that were operative in early pre-implantation yak development, of which 32 were the significantly enriched pathways. In conclusion, this is the first report to investigate the mechanism that regulates yak embryonic development using high-throughput sequencing, which provides a comprehensive framework of transcriptome landscapes of yak pre-implantation embryos.

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“…Total RNA was extracted using Aurum ™ Total RNA Mini Kit (Bio-Rad, Hercules, CA, USA), according to the manufacturer’s instructions 53 for RNA-seq experiments. Total RNA was extracted using RNAqueous Micro Kit (Ambion from Life Technologies), according to the manufacturer’s instructions for Real Time qPCR experiments 53 . Samples were stored at −80 °C.…”

Section: Methodsmentioning

confidence: 99%

Toxigenic effects of two benthic diatoms upon grazing activity of the sea urchin: morphological, metabolomic and de novo transcriptomic analysis

Ruocco

Costantini

Zupo

et al. 2018

Sci Rep

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Diatoms are unicellular algae playing a key role as photosynthetic organisms in the world’s ocean food webs. The chemical ecology of planktonic diatoms is well documented, but few studies have reported on the effects of benthic diatoms on their consumers, also due to difficulties in the collection, quantification and massive culturing of benthic species. Here for the first time we investigate the effects of feeding on two abundantly occurring benthic diatoms, Nanofrustulum shiloi and Cylindrotheca closterium, isolated from the leaves of the seagrass Posidonia oceanica, on the sea urchin Paracentrotus lividus. Adult P. lividus were fed for one month on diets of either one of the two diatoms and on the green alga Ulva rigida, used as a feeding control. By combining morphological, metabolomic and de novo transcriptomic approaches, we demonstrate toxigenic effect on embryos generated by females fed with these benthic diatoms. Furthermore, chemical analysis reveal the presence of polyunsaturated aldehydes only for N. shiloi, and a high production of other oxylipins (cytotoxic compounds on their grazers and on cancer cell lines) for both diatoms, including some additional peaks not correlated to the canonic oxylipins commonly observed in planktonic diatoms. These findings open new perspectives in the study of diatom secondary metabolites influencing their grazers.

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High-quality RNA extraction from the sea urchin Paracentrotus lividus embryos

Cited by 22 publications

References 40 publications

Protective effect of Echinochrome against intrahepatic cholestasis induced by alpha-naphthylisothiocyanate in rats

Protective effect of Echinochrome against intrahepatic cholestasis induced by alpha-naphthylisothiocyanate in rats

Characterization of transcriptional complexity during pre‐implantation development of the yak (Bos grunniens) using RNA‐Seq

Toxigenic effects of two benthic diatoms upon grazing activity of the sea urchin: morphological, metabolomic and de novo transcriptomic analysis

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