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ABSTRACT: The study of RNA viruses in endemic Baikal sponges

PROVIDER: PRJNA956241 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24184677_1.fastq.gz	Fastqsanger.gz
	SRR24184677_2.fastq.gz	Fastqsanger.gz
	SRR24184678_1.fastq.gz	Fastqsanger.gz
	SRR24184678_2.fastq.gz	Fastqsanger.gz
	SRR24184679_1.fastq.gz	Fastqsanger.gz

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Project description:Study of viral diversity in Baikal sponges

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Putative carotenoid-binding proteins from the hemolymph of endemic Lake Baikal amphipod Eulimnogammarus cyaneus and E. vittatus

Project description:Color is an important trait in nature, playing a role in selection and speciation. The most important colorants in crustaceans are carotenoids, which in complexes with carotenoid-binding proteins provide an astonishing variety of colors from red to violet. Over 350 species and subspecies of amphipods (Crustacea: Amphipoda) endemic to Lake Baikal exhibit an impressive variability of colors and coloration patterns. However, the mechanisms forming this diversity are underexplored. In this work, we analyze the coloration of two species of endemic Lake Baikal amphipods, Eulimnogammarus cyaneus and E. vittatus. These species are brightly colored and, even more importantly, characterized by intraspecific color variability. We showed that the color of either species strongly correlated with the abundance of two putative carotenoid-binding proteins (the relative abundance of these proteins was higher in blue or teal-colored animals than in the orange- or yellow-colored ones.). With LC-MS/MS, we were able to identifiy these proteins, which turned out to be similar to the pheromone/odorant-binding protein family.

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Proteomic response to heat shock in males and females of a Baikal endemic amphipod Eulimnogammarus cyaneus (Dyb. 1874) (Crustacea: Amphipoda)

Project description:In this project we aimed to establish a proteome-based pipeline for a non-model Baikal endemic amphipod species Eulimnogammarus cyaneus (Dybowsky, 1874). We used next-generation transcriptome sequencing to create a database for protein identification and investigated the proteome of E. cyaneus with LC-MS with particular emphasis on sexual dimorphism and response to acute thermal stress. We were able to characterize ca. 1000 protein groups and found male- and female-specific proteins, as well as proteins specific for thermal stress conditions.

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Synthetic circular RNA functions as a miR-21 sponge to suppress gastric carcinoma cell proliferation

Project description:MicroRNA (miRNA) sponges containing miRNA complementary binding sites constitute a potentially useful strategy for miRNA-inhibition therapeutics in cancer patients. Recently, naturally occurring circular RNAs (circRNAs) have been revealed to function as efficient microRNA sponges. We hypothesized that synthetic circRNA sponges targeting oncomiRs could be constructed and used to achieve potentially therapeutic microRNA loss of function. In this study, linear RNA molecules containing five miR-21 binding sites were transcribed in vitro. After dephosphorylation by calf intestinal phosphatase and phosphorylation by T4 polynucleotide kinase, circRNA sponges were circularized using 5’-3’ end ligation by T4 RNA ligase 1. Synthetic circular sponge stability was assayed in the presence of RNase R or fetal bovine serum. Luciferase reporter and cell proliferation assays were performed to assess competitive inhibition of miR-21 activity by circRNA sponges in NCI-N87 gastric cancer cells. Tandem Mass Tag (TMT) labeling proteomics analysis and Western blotting were performed to delineate effects of circRNA sponges on miR-21 downstream targeted proteins. Our experiments revealed that artificial circRNA sponges can be synthesized using enzymatic ligation. These synthetic circRNA sponges are more resistant than their linear RNA counterparts to nuclease degradation in vitro. They effectively suppress the activity of miR-21 on its downstream protein targets, including the important cancer protein DAXX. Finally, they also inhibit gastric cancer cell proliferation. Our results suggest that synthetic circRNA sponges represent a rapid, effective, convenient strategy to achieve loss of miRNA function in vitro, with potential future therapeutic application in vivo.

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Project description:Endemic lake Baikal amphipods Raw sequence reads

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Project description:Endemic lake Baikal amphipods Transcriptome Shotgun Assembly project

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The Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples - A Useful Panmicrobial Diagnostic Tool--Array Version 2f

Project description:Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travelling, climate changes and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. For many of them, the disease symptoms are similar to each other, as well as to other more common diseases, making them difficult to diagnose. A rapid identification will help to decide about specific treatment and appropriate case management. Real-time PCR is commonly used for specific virus detection in clinical samples. A diagnostic microarray containing probes for all human viruses, could replace hundreds of specific PCR-reactions and identify all viruses by one assay and thereby remove the need for a clear clinical hypothesis. We show that the Microbial Detection Array successfully identifies emerging viruses present in both non-clinical and clinical samples. Twenty-four clinical samples and 40 non-clinical samples (cell culture supernantants or purified viral DNA or RNA) were analyzed for presence of emerging viruses using the MDA microarray.

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