scholarly journals Galactose-Binding C-Type Lectin Promotes Cellular Aggregation of Coelomocytes in Sea Cucumber

2021 ◽  
Vol 12 ◽  
Author(s):  
Mizuki Taguchi ◽  
Chikaya Tanaka ◽  
Shigeyuki Tsutsui ◽  
Osamu Nakamura
Keyword(s):  
Sea Cucumber ◽  
De Novo ◽  
Apostichopus Japonicus ◽  
Glass Slide ◽  
Coelomic Fluid ◽  
Rna Seq ◽  
Coelomic Cavity ◽  
Cellular Aggregation ◽  
First Time ◽  
Cellular Movement

Echinoderms have a large coelomic cavity containing coelomocytes. When the coelomic fluid is removed from the cavity, the cells aggregate immediately. We found that a fraction or an extract of the intestine of the sea cucumber, Apostichopus japonicus, markedly accelerated cellular movement and aggregation on a glass slide, and this effect was clearly inhibited by galactose. We successfully purified the aggregation-promoting factor, a 16 kDa protein, from the intestine. TOF-MS analysis followed by de novo sequencing revealed that the protein is a C-type lectin. RNA-seq data and cDNA cloning demonstrated the factor to be a novel lectin, named AjGBCL, consisting of 158 aa residues in the mature form. Microscopic observation revealed that most of the aggregating cells moved toward aggregates and not to an intestinal fragment, suggesting that AjGBCL is not a chemoattractant but a cellular aggregation-inducing factor that may induce aggregates to release chemoattractant. We report, for the first time, an endogenous molecule that promotes coelomocyte aggregation in echinoderms.

Antioxidant enzymes in sea cucumber Apostichopus japonicus (Selenka) during aestivation

2010 ◽  
Vol 91 (1) ◽  
pp. 209-214 ◽  
Author(s):  
Wang Fangyu ◽  
Yang Hongsheng Yang ◽  
Wang Xiaoyu ◽  
Xing Kun ◽  
Gao Fei
Keyword(s):  
Oxygen Consumption ◽  
Glutathione Peroxidase ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Sampling Period ◽  
Coelomic Fluid ◽  
Sharp Change ◽  
Antioxidant Defence ◽  
Antioxidant Defences ◽  
And Function

To evaluate the effect of antioxidant defence in coelomic fluid of sea cucumber, Apostichopus japonicus in aestivation was studied in the field from July to November 2006 in Qingdao. During the sampling period, activities of superoxide dismutase and catalase increased significantly in August and November. Activities of glutathione reductase and glutathione decreased significantly in August and increased significantly in November and activities of Se-glutathione peroxidase increased significantly in August. There were no significant differences in total glutathione peroxidase. In relation to the water temperature in the field, it is known that the oxygen consumption rate dropped and antioxidant defence was enhanced in August. The structure and function of respiratory trees of A. japonicus were completely vivified as normal in November, and it is suggested that antioxidant defence was enhanced because of the sharp change of oxygen consumption. Data indicate that both enzymatic and metabolite antioxidant defences in sea cucumber are adaptable systems that are modulated during pre-aestivating stage and arousing stage.

scholarly journals Transcriptomic and Lipidomic Analysis of Lipids in Forsythia suspensa

2021 ◽  
Vol 12 ◽  
Author(s):  
Bei Wu ◽  
Yinping Li ◽  
Wenjia Zhao ◽  
Zhiqiang Meng ◽  
Wen Ji ◽  
...  
Keyword(s):  
De Novo ◽  
Growth Stages ◽  
Rna Seq ◽  
Dynamic Regulation ◽  
Kegg Pathways ◽  
Reference Information ◽  
Forsythia Suspensa ◽  
First Time ◽  
Differential Genes ◽  
Lipid Components

Forsythiae Fructus (Lianqiao in Chinese) is widely used in traditional Chinese medicine. The lipid components in Forsythiae Fructus are the basis of plant growth and active metabolism. Samples were collected at two growth stages for a comprehensive study. Transcriptome and lipidomics were performed by using the RNA-seq and UPLC-Q-TOF-MS techniques separately. For the first time, it was reported that there were 5802 lipid components in Lianqiao comprised of 31.7% glycerolipids, 16.57% phospholipids, 13.18% sphingolipids, and 10.54% fatty acids. Lipid components such as terpenes and flavonoids have pharmacological activity, but their content was low. Among these lipids which were isolated from Forsythiae Fructus, 139 showed significant differences from the May and July harvest periods. The lipids of natural products are mainly concentrated in pregnenolones and polyvinyl lipids. RNA-Seq analysis revealed 92,294 unigenes, and 1533 of these were differentially expressed. There were 551 differential genes enriched in 119 KEGG pathways. The de novo synthesis pathways of terpenoids and flavonoids were explored. Combined with the results of lipidomics and transcriptomics, it is hypothesized that in the synthesis of abscisic acid, a terpenoid, may be under the dynamic regulation of genes EC: 1.1.1.288, EC: 1.14.14.137 and EC: 1.13.11.51 in balanced state. In the synthesis of gibberellin, GA20-oxidase (GA20ox, EC: 1.14.11.12), and GA3-oxidase (GA3ox, EC: 1.14.11.15) catalyze the production of active GAs, and EC: 1.14.11.13 is the metabolic enzymes of active GAs. In the synthesis of flavonoids, MF (multifunctional), PAL (phenylalanine ammonia-lyase), CHS (chalcone synthase), ANS (anthocyanidin synthase), FLS (flavonol synthase) are all key enzymes. The results of the present study provide valuable reference information for further research on the metabolic pathways of the secondary metabolites of Forsythia suspensa.

Seasonal variations of immune parameters in the coelomic fluid of sea cucumber Apostichopus japonicus cultured in pond

2016 ◽  
Vol 48 (4) ◽  
pp. 1677-1687 ◽  
Author(s):  
Jingwei Jiang ◽  
Zunchun Zhou ◽  
Ying Dong ◽  
Bei Jiang ◽  
Zhong Chen ◽  
...  
Keyword(s):  
Seasonal Variations ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Coelomic Fluid ◽  
Immune Parameters

scholarly journals Physiological and immunological responses of sea cucumber Apostichopus japonicus during desiccation and subsequent resubmersion

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7427 ◽  
Author(s):  
Shiying Hou ◽  
Zewei Jin ◽  
Wenwen Jiang ◽  
Liang Chi ◽  
Bin Xia ◽  
...  
Keyword(s):  
Oxidative Damage ◽  
Sea Cucumber ◽  
Health Management ◽  
Physiological Stress ◽  
Apostichopus Japonicus ◽  
Complement C3 ◽  
Coelomic Fluid ◽  
Control Group ◽  
Immunological Responses ◽  
Immune Parameters

Desiccation is one of the extremely stressful situations experienced by aquatic animals, and sea cucumber usually suffers from desiccation stress during transportation without water. The present study was conducted to evaluate the effect of desiccation and subsequent resubmersion on physiological stress, oxidative damage, antioxidant status and non-specific immune response of Apostichopus japonicus, providing valuable information on the health management of sea cucumber culturing. Control and desiccation groups were set up, and each group has three replicates. After 1, 3 and 6 h of desiccation, individuals were resubmersed in aerated seawater for a 24 h recovery in three batches, which were represented as D1, D3 and D6, respectively. The results showed that glucose level in coelomic fluid of sea cucumber significantly decreased after desiccation, whereas lactate, cortisol and osmolality showed remarkable ascending trends. Thereafter, all stress parameters gently recovered towards normal levels as control group during 24 h resubmersion. The prolonged desiccation at D6 treatment induced the significant increases of malondialdehyde (MDA) and reactive oxygen species (ROS) contents, as well as relatively lower superoxide dismutase (SOD) and catalase (CAT) activities. During the period of desiccation and subsequent resubmersion, sea cucumber adjusted antioxidant defense to reduce the concentrations of MDA and ROS as a strategy for protecting against oxidative damage. Desiccation also had significant effects on non-specific immune parameters (total coelomocytes counts, TCC; complement C3; total nitric oxide synthase, T-NOS; lysozyme, LSZ; alkaline phosphatase, AKP) of A. japonicus, which could be recovered to some extent during resubmersion. In conclusion, less than 6 h of desiccation did not induce irreparable damage to sea cucumber, and was recommended for handling and shipping live sea cucumbers.

scholarly journals De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates

Marine Drugs ◽  
2020 ◽  
Vol 18 (8) ◽  
pp. 386 ◽  
Author(s):  
Giorgio Maria Vingiani ◽  
Dārta Štālberga ◽  
Pasquale De Luca ◽  
Adrianna Ianora ◽  
Daniele De Luca ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
De Novo ◽  
Phosphate Starvation ◽  
Toxin Production ◽  
Rna Seq ◽  
Toxic Compounds ◽  
Gulf Of Naples ◽  
Potential Applications ◽  
In Silico Identification ◽  
First Time

Many dinoflagellates species, especially of the Alexandrium genus, produce a series of toxins with tremendous impacts on human and environmental health, and tourism economies. Alexandrium tamutum was discovered for the first time in the Gulf of Naples, and it is not known to produce saxitoxins. However, a clone of A. tamutum from the same Gulf showed copepod reproduction impairment and antiproliferative activity. In this study, the full transcriptome of the dinoflagellate A. tamutum is presented in both control and phosphate starvation conditions. RNA-seq approach was used for in silico identification of transcripts that can be involved in the synthesis of toxic compounds. Phosphate starvation was selected because it is known to induce toxin production for other Alexandrium spp. Results showed the presence of three transcripts related to saxitoxin synthesis (sxtA, sxtG and sxtU), and others potentially related to the synthesis of additional toxic compounds (e.g., 44 transcripts annotated as “polyketide synthase”). These data suggest that even if this A. tamutum clone does not produce saxitoxins, it has the potential to produce toxic metabolites, in line with the previously observed activity. These data give new insights into toxic microalgae, toxin production and their potential applications for the treatment of human pathologies.

scholarly journals Integument transcriptome profile of the European sea cucumber Holothuria forskali (Holothuroidea, Echinodermata)

2021 ◽  
Author(s):  
Jérôme Delroisse ◽  
Marie Bonneel ◽  
Mélanie Demeuldre ◽  
Igor Eeckhaut ◽  
Patrick Flammang
Keyword(s):  
Sea Cucumber ◽  
De Novo ◽  
Model Organisms ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Purple Sea Urchin ◽  
New Genes ◽  
Illumina Hiseq Sequencing ◽  
Reference Databases ◽  
Next Generation Sequencing Ngs

AbstractIn non-model organisms, Next Generation Sequencing (NGS) technology improve our ability to analyze gene expression and identify new genes or transcripts of interest. In this research, paired-end Illumina HiSeq sequencing has been used to describe a composite transcriptome based on two libraries generated from dorsal and ventral integuments of the European sea cucumber Holothuria forskali (Holothuroidea, Echinodermata). A total of 43,044,977 million HQ reads were initially generated. After de novo assembly, a total of 111,194 unigenes were predicted. On all predicted unigenes, 32,569 show significant matches with genes/proteins present in the reference databases. Around 50% of annotated unigenes were significantly similar to sequences from the purple sea urchin Strongylocentrotus purpuratus genome. Annotation analyses were performed on predicted unigenes using public reference databases. These RNA-seq data provide an interesting resource for researchers with a broad interest in sea cucumber biology.

scholarly journals Baltica: integrated splice junction usage analysis

2021 ◽  
Author(s):  
Thiago Britto-Borges ◽  
Volker Boehm ◽  
Niels H Gehring ◽  
Christoph Dieterich
Keyword(s):  
Data Integration ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Splice Junction ◽  
Rna Seq ◽  
Oxford Nanopore ◽  
Single Method ◽  
Usage Analysis ◽  
First Time ◽  
Transcriptional Process

Alternative splicing is a tightly regulated co- and post-transcriptional process contributing to the transcriptome diversity observed in eukaryotes. Several methods for detecting differential junction usage (DJU) from RNA sequencing (RNA-seq) datasets exist. Yet, efforts to integrate the results from DJU methods are lacking. Here, we present Baltica, a framework that provides workflows for quality control, de novo transcriptome assembly with StringTie2, and currently 4 DJU methods: rMATS, JunctionSeq, Majiq, and LeafCutter. Baltica puts the results from different DJU methods into context by integrating the results at the junction level. We present Baltica using 2 datasets, one containing known artificial transcripts (SIRVs) and the second dataset of paired Illumina and Oxford Nanopore Technologies RNA-seq. The data integration allows the user to compare the performance of the tools and reveals that JunctionSeq outperforms the other methods, in terms of F1 score, for both datasets. Finally, we demonstrate for the first time that meta-classifiers trained on scores of multiple methods outperform classifiers trained on scores of a single method, emphasizing the application of our data integration approach for differential splicing identification. Baltica is available at https://github.com/dieterich-lab/Baltica under MIT license.

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