Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1264024 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR33619800_1.fastq.gz | Fastqsanger.gz | |||
| SRR33619800_2.fastq.gz | Fastqsanger.gz | |||
| SRR33619802_1.fastq.gz | Fastqsanger.gz | |||
| SRR33619802_2.fastq.gz | Fastqsanger.gz |
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Project description:Recently, we reported an emerging pathology named Brown Muscle Disease (BMD) affecting Asari clams inhabiting the most productive area for this species in France, the Arcachon Bay. The main macroscopic feature of the pathology relies on the atrophy of the posterior adductor muscle, affecting the ability of clams to burry. The research of the etiological agent of BMD privileged a viral infection. Contrary to healthy clams, infected animals are always found at the surface of the sediment and exhibit 30 nm virus-like particles in muscle, granulocytic and rectal cells. In order to get more insights on the etiology and impacts of the BMD on clams, we took advantage in the present study of next generation sequencing technologies. An RNA-Seq approach was used (i) to test whether viral RNA sequences can be specifically found in the transcriptome of diseased animals and (ii) to identify the genes that are differentially regulated between diseased and healthy clams. Contrary to healthy buried animals, in diseased clams one sequence showing extensive homologies with retroviridae-related genes was detected. Among the biological processes that were affected in diseased clams, the synaptic transmission process was the most represented. To deepen this result, a new sampling was carried out and the transcription level of genes involved in synaptic transmission was determined in healthy and diseased clams but also in clams with no visible sign of pathology but located at the surface of the sediment. Our findings suggest that muscle atrophy is a latter sign of the pathology and that nervous system could be instead a primary target of the BMD agent.
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Project description:Transcriptional profiling of different clam tissues (hemolymph, extrapallial fluid and mantle) in response to brown ring disease; Brown ring disease (BRD) is a bacterial infection affecting the economically-important clam Ruditapes philippinarum. The disease is caused by a bacterium, Vibrio tapetis, that colonizes the edge of the mantle, altering the biomineralization process and normal shell growth. Altered organic shell matrices accumulate on the inner face of the shell leading to the formation of the typical brown ring in the extrapallial space (between the mantle and the shell). Even though structural and functional changes have been described in solid (mantle) and fluid (hemolymph and extrapallial fluids) tissues from infected clams, the underlying molecular alterations and responses remain largely unknown. This study was designed to gather information on clam molecular responses to the disease and to compare focal responses at the site of the infection (mantle and extrapallial fluid) with systemic (hemolymph) responses. To do so, we designed and produced a Manila clam expression oligoarray (15K Agilent) using transcriptomic data available in public databases and used this platform to comparatively assess transcriptomic changes in mantle, hemolymph and extrapallial fluid of infected clams. Results showed significant regulation in diseased clams of molecules involved in pathogen recognition (e.g. lectins, C1q domain-containing proteins) and killing (defensin), apoptosis regulation (death-associated protein, bcl-2) and in biomineralization (shell matrix proteins, perlucin, galaxin, chitin- and calcium-binding proteins). While most changes in response to the disease were tissue-specific, systemic alterations included co-regulation in all 3 tested tissues of molecules involved in microbe recognition and killing (complement-related factors, defensin). These results provide a first glance at molecular alterations and responses caused by BRD and identify targets for future functional investigations.
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Project description:A C. gallina microarray platform was developed to assess variations on transcritpomic profiles between different seasons and sampling sites A comparative analysis of gene expression was conducted in Chamelea gallina collected in two different areas along Abruzzi coasts subjected to different mortality events. In particular sampling activities have been performed in collaboration with fishing cooperatives along Abruzzi coasts, Chamelea gallina clams have been collected from two sites (T4 and T7) at 0.25 mi (ca. 0.4 km) at commercial size (25 mm) and harvested by hydraulic dredge. The harvesting has been conducted in three periods of 2014 (July, August and September). The time of sampling has been obliged by a dramatic reduction of harvesting in T4 that has been reported by fishing cooperatives during spring. After sampling, clams have been kept with ice till their arrival in laboratory, within 6 hours. From each sampling site and each period, the digestive gland of 30 clams has been dissected and frozen at -21°C, for a total of 150 clams divided in 5 pools for each period and each site of sampling. During the clam sampling, from the same sites, the upper layer of bed sediments (0â10 cm) was collected by a small grab sampler in July and September. Composite sediment samples have been refrigerated during transport and stored at â 20 °C within a few hours from sampling, until analysis. Briefly, about 400 g of sediment have been suitably homogenized and dried in an oven at 40 ° C for 24 hours, then crushed, ground and sieved to 2 mm. A portion of about 100 g for each sample has been further ground and screened to 0.2 mm for heavy metal analysis. The content of cadmium (Cd), lead (Pb) and arsenic (As) have been performed, after extraction by aqua regia, by Inductively Coupled Plasma-Optical Emission Spectrometer ( ICP-OESâ¦..) the analysis have been recorded as means triplicate measurements. The determination of Hg have been done in Atomic Adsorption with Hydride System. Ten grams (accuracy ± 0.0001 g) of dry and homogenized sediment of 0.2 mm has been put into a clean centrifuge tube, and a 1:1 (v/v) acetone/n-hexane (5 mL), and surrogate standard mixture (2-fluorobiphenyl and 4-terphenyl-d14) solutions were then added, after extraction and clean-up processes, the samples were analyzed with a gas chromatographerâelectron capture detector (GM-ECD) to evaluate concentrations of Polycyclic aromatic hydrocarbons (PAHs) and organophosphate pesticides (OPPs). Organochloride pesticides (OCPs) have been analysed, after purification, with static headspace GC Gene expression profiling was performed using an Chamelea gallina-specific oligo-DNA microarray of15,019 probes representing 12,064 transcripts 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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