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Analyses of transcriptomic responses to heavy metal exposure in Manila clam collected in Venice lagoon areas characterized by different anthropogenic impact

ABSTRACT: A Ruditapes philippinarum microarray platform was developed to assess variations on transcritpomic response to copper exposures in Manila clam colelctted in Venice lagoon areas subjected to different anthropogenic impact

ORGANISM(S): Ruditapes philippinarum

PROVIDER: GSE69811 | GEO | 2016/09/22

SECONDARY ACCESSION(S): PRJNA286852

REPOSITORIES: GEO

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Which role for genomics in environmental risk assessment? A case study in Venice Lagoon.

Project description:DNA microarray analyses of Ruditapes philippinarum sampled in Venice lagoon areas subjected to different anthropogenic impact. A comparative analysis of gene expression was conducted between Manila clam from lowly-polluted Chioggia and Colmata area and polluted Marghera site.

2013-10-01 | E-GEOD-50062 | biostudies-arrayexpress

Manila clam - Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites [Manila clam]

Project description:The Manila clam (Ruditapes philippinarum) is the bivalve species with the highest world production from both fisheries and aquaculture, but its production is seriously threatened by perkinsosis, a disease caused by the protozoan parasite Perkinsus olseni. To understand the molecular mechanisms underlying R. philippinarum–P. olseni interaction, we analyzed the gene expression profiles of in vitro challenged clam hemocytes and P. olseni trophozoites, using two oligo-microarray platforms, one previously validated for R. philippinarum hemocytes and a new one developed and validated in this study for P. olseni. Manila clam hemocytes were in vitro challenged with trophozoites, zoospores, and extracellular products from P. olseni in vitro cultures, while P. olseni trophozoites were in vitro challenged with Manila clam plasma along the same time-series (1 h, 8 h, and 24 h). The hemocytes showed a fast activation of the innate immune response, particularly associated with hemocyte recruitment, in the three types of challenges. Nevertheless, different immune-related pathways were activated in response to the different parasite stages, suggesting specific recognition mechanisms. Furthermore, the analyses provided useful complementary data to previous in vivo challenges, and confirmed the potential of some proposed biomarkers. The combined analysis of gene expression in host and parasite identified several processes in both the clam and P. olseni, such as redox and glucose metabolism, protease activity, apoptosis and iron metabolism, whose modulation suggests cross-talk between parasite and host. This information might be critical to determine the outcome of the infection, thus highlighting potential therapeutic targets. Altogether, the results of this study aid to understand the response and interaction between R. philippinarum–P. olseni and will contribute for developing effective control strategies for this threatening parasitosis.

2019-12-18 | GSE142172 | GEO

Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray

Project description:The Manila clam (Ruditapes philippinarum) is a cultured bivalve species with high worldwide commercial importance. Nevertheless, diseases can cause high economical losses. For this reason, the study of immune genes in bivalve mollusks has increased in the last years. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application for the study of the gene transcription profiles of hemocytes from clams challenged with Vibrio alginolyticus through a time course.

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New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

2019-12-27 | GSE142666 | GEO

Ruditapes philippinarum cultivar:manila clam

Project description:Ruditapes philippinarum cultivar:manila clam Raw sequence reads

| PRJNA579230 | ENA

New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges [Perkinsus olseni]

2019-12-27 | GSE142665 | GEO

Gene expression profile of hemocytes from Manila clam (Venerupis philippinarum) after a Perkinsus olseni challenge using an immune-enriched oligo-microarray

Project description:Parasites of the genus Perkinsus spp. cause high mortalities and economic losses to the most noticeable bivalves produced in the worldwide aquaculture. In this study, we analyze how P. olseni influences the gene expression profiles of hemocytes from Manila clam (Venerupis philippinarum) using experimental infections along a temporal series and a Manila clam immune-enriched DNA microarray.

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Which role for genomics in environmental risk assessment? A case study in Venice Lagoon.

Project description:DNA microarray analyses of Ruditapes philippinarum sampled in Venice lagoon areas subjected to different anthropogenic impact.

2013-10-01 | GSE50062 | GEO

Transcriptome analysis of Manila clam (Ruditapes philippinarum) digestive gland after exposure to different concentrations of ibuprofen.

Project description:A Ruditapes philippinarum microarray platform was developed to identify digestive gland gene expression profiles in response to 100 Âµg /l and 1000 Âµg/l ibuprofen exposure. A comparative analysis of gene expression was conducted in Manila clam R.philippinarum exposed to ibuprofen.Clams were exposed for 1, 3, 5 and 7 days to 0, 100 and 1000 Âµg IBU/l, and digestive gland gene expression were measured. Gene expression profiling was performed using an Manila clam-specific oligo-DNA microarray of 14,156 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

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Ruditapes philippinarum strain:wild population | cultivar:manila clam

Project description:Ruditapes philippinarum strain:wild population | cultivar:manila clam Raw sequence reads

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