Mediterranean Holothurians
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB77360 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mytilus galloprovincialis (Lmk, 1819) is economically relevant bivalve specie. In Adriatic Sea, periodical temperatures increases define optimal growth conditions for Dinoflagellate spp which can reach high concentrations also in filter-feeding mussels, thus causing potential human health problems. The most commonly used methods for the detection of Diarrhoeic Shellfish Poisoning biotoxins have either a low sensitivity or are too expensive to be used for routine tests. Genomic tools, such as microarray platforms, provide a reliable and alternative solution to overcome these problems. In this study we used a mussel cDNA microarray for studying gene expression changes in mussels exposed to Okadaic acid. Mussels collected in the Gulf of Trieste, located in Northern Adriatic Sea, were fed with Okadaic acid-spiked invertebrates for five weeks. In a time course experiment we were able to describe an early acute response just from the first 4th day time point. Among the differentially expressed genes we found a general up-regulation of stress proteins and proteins involved in cellular synthesis. Overall, we identified 34 transcripts candidate as useful markers to monitor OA-induced stress in mussels. This study contributes to the characterization of many potential genetic markers that could be used in future environmental monitoring, and could lead to explore new mechanisms of stress tolerance in marine mollusc species. Keywords: Time course, stress response Loop Design experiment including 5 time points (T0 = control samples, T1 = 3 days post treatment, T2 = 1 week post treatment, T4 = 3 weeks post treatment, T6 = 5 weeks post treatment). 3 biological replicates were done for a total number of 15 samples
2010-05-05 | E-GEOD-14885 | biostudies-arrayexpress
Project description:Mytilus galloprovincialis (Lmk, 1819) is economically relevant bivalve specie. In Adriatic Sea, periodical temperatures increases define optimal growth conditions for Dinoflagellate spp which can reach high concentrations also in filter-feeding mussels, thus causing potential human health problems. The most commonly used methods for the detection of Diarrhoeic Shellfish Poisoning biotoxins have either a low sensitivity or are too expensive to be used for routine tests. Genomic tools, such as microarray platforms, provide a reliable and alternative solution to overcome these problems. In this study we used a mussel cDNA microarray for studying gene expression changes in mussels exposed to Okadaic acid. Mussels collected in the Gulf of Trieste, located in Northern Adriatic Sea, were fed with Okadaic acid-spiked invertebrates for five weeks. In a time course experiment we were able to describe an early acute response just from the first 4th day time point. Among the differentially expressed genes we found a general up-regulation of stress proteins and proteins involved in cellular synthesis. Overall, we identified 34 transcripts candidate as useful markers to monitor OA-induced stress in mussels. This study contributes to the characterization of many potential genetic markers that could be used in future environmental monitoring, and could lead to explore new mechanisms of stress tolerance in marine mollusc species. Keywords: Time course, stress response
2009-02-19 | GSE14885 | GEO
Project description:We wanted to explore the genomic regions 1p13, 1q41, 9p21 and 10q11, which are among the labeled âtop 12 golden lociâ linked to coronary artery disease (CAD) risk, in order to see whether their geographic variation could be explained by demographic effects. To do this, we have genotyped these risk regions in a set of Mediterranean populations. Genomic DNA was extracted from blood cells using a Blood Midi kit (Omega Biotek, USA) according to manufacturer's procedures. DNA samples were genotyped for a combined set of 366 SNPs using an Illumina Custom GoldenGate Panel. SNPs were selected as a representative set of the common variation in the four genomic regions, according to the following criteria: i) average coverage of 1 SNP every 1.5 kb, ii) minor allele frequency (MAF) higher than 0.05 in CEU and TSI HapMap populations, iii) given priority to markers not in linkage disequilibrium (LD) (r2<0.8) in European populations, and iv) prioritizing markers previously associated with CAD. These criteria were applied giving preference to tag SNPs.
2016-11-24 | E-MTAB-5265 | biostudies-arrayexpress
Project description:Deep-sea holothurian' hindgut metagenomic assembly
| PRJNA376231 | ENA
Project description:Groupers (Epinephelidae) are ecologically, commercially, and culturally important predatory fishes throughout their global distribution range in tropical, subtropical and occasionally temperate regions. They are key species for modern and ancient fisheries in the Mediterranean which have been heavily overfished in the past century leading to smaller catch sizes, lower CPUE, and decreased biomass. There are four species of grouper native to the Mediterranean within the Epinephelus genus.The abundance and distribution of grouper species prior to the 20th century in the Mediterranean remains poorly known. Using peptide mass fingerprinting, also known as Zooarchaeology by Mass Spectrometry (ZooMS), we investigated if ZooMS is a viable method for identifying intra-genus grouper bones to species level. Due to the lack of publicly available genomic sequences and for validation of ZooMS markers, we reconstructed collagen type I amino acid sequences using LC-MS/MS for four Epinephelus spp. Adequate variation between collagen sequences enabled the production of the best supported phylogenetic tree for Mediterranean Epinephelus spp. to date. We identified 23 previously undescribed ZooMS biomarkers capable of distinguishing groupers to the species level. Our novel biomarkers were applied to a case study of 23 grouper/comber fish bones from the Middle to Late Holocene archaeological site of Kinet Höyük, located along the coast of Iskenderun Bay, Turkey. ZooMS markers enabled species level identification of 19 bones with 18 identified as Epinephelus aeneus and 1 identified as Epinephelus marginatus. Combining ZooMS identifications with catch size reconstructions has revealed that E. aeneus is capable of growing ca. 30 cm larger than previously reported. This abundance and dominance of E. aeneus locally at Kinet Höyük is consistent with E. aeneus being the most prevalent grouper species in Iskenderun Bay today, testifying to several millennia of this species local population persistence despite fishing pressure, habitat degradation, and climatic changes.
2023-10-23 | PXD042430 | Pride
Project description:Aedes aegypti are vectors of several devastating arboviruses infecting hundreds of millions of people annually. Controlling mosquito populations by regulating their reproduction is important to minimize viral transmission in the absence of effective antiviral therapies or vaccines. Here, we demonstrate that leucine aminopeptidase1 (LAP1), screened from SWATH-MS-based proteomic data of female spermathecae, is a crucial determinant in mosquito population expansion. Mitochondrial defects and aberrant autophagy of sperm in LAP1 mutant males (LAP1-/-), prepared using CRISPR-Cas9 system, resulted in a reduction of reproduction in wild-type females that mated with them. Additionally, we found that the fitness of LAP1-/- males was strong enough to efficiently transmit genetic changes to mosquito populations through a low number of hatchable offspring, making it to be a promising opportunity to suppress mosquito populations using LAP1-/- males. Importantly, we provide a novel target gene for genetic drive, further amplifying the function of LAP1 in reducing mosquito populations.
2023-02-05 | PXD039869 |
Project description:Marine viromes from a depth profile at the Mediterranan sea
| PRJEB30684 | ENA
Project description:We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete. DNA isolated from approximately 10,000 single-cell Globobulimina pseudospinescens organisms
2011-06-20 | E-GEOD-26664 | biostudies-arrayexpress