Ontology highlight
ABSTRACT:
PROVIDER: PRJNA936818 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Lucinidae is a large family of marine bivalves. They occur in diverse habitats from shallow-water seagrass sediments to deep-sea hydrothermal vents. All members of this family so far investigated host intracellular sulfur-oxidizing symbionts that belong to the Gammaproteobacteria. We recently discovered the capability for nitrogen fixation in draft genomes of the symbionts of Loripes lucinalis from the Bay of Fetovaia, Elba, Italy. With proteomics, we investigated whether the genes for nitrogen fixation are expressed by the symbionts.
2016-08-19 | PXD004536 | Pride
Project description:The RNA interference (RNAi) pathway is found in most eukaryotic lineages but curiously is absent in others, including that of Saccharomyces cerevisiae. Here, we show that reconstituting RNAi in S. cerevisiae causes loss of a beneficial dsRNA virus, known as killer virus. Incompatibility between RNAi and killer viruses extends to other fungal species, in that RNAi is absent in all species known to possess dsRNA killer viruses, whereas killer viruses are absent in closely related species that retained RNAi. Thus, the advantage imparted by acquiring and retaining killer viruses explains the persistence of RNAi-deficient species during fungal evolution.
2011-08-10 | GSE31290 | GEO
Project description:Bats harbor highly virulent viruses that can infect other mammals, including humans, posing questions about their immune tolerance mechanisms. Bat cells employ multiple strategies to limit virus replication and virus-induced immunopathology, but the coexistence of bats and fatal viruses remains poorly understood. Here, we investigated the antiviral RNA interference (RNAi) pathway in bat cells and discovered that they have an enhanced antiviral RNAi response, producing canonical viral small interfering RNAs (vsiRNAs) upon Sindbis virus (SINV) infection that were missing in human cells. Disruption of Dicer function resulted in increased viral load for three different RNA viruses in bat cells, indicating an interferon-independent antiviral pathway. Furthermore, our findings reveal the simultaneous engagement of Dicer and pattern-recognition receptors (PRRs), such as retinoic acid-inducible gene I (RIG-I), with double-stranded RNA, suggesting that Dicer attenuates the interferon response initiation in bat cells. These insights advance our comprehension of the distinctive strategies bats employ to coexist with viruses.
2024-07-12 | GSE221607 | GEO
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.
2010-10-15 | E-GEOD-24626 | biostudies-arrayexpress
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.
2010-10-15 | E-GEOD-24699 | biostudies-arrayexpress
Project description:Bats harbor highly virulent viruses that can infect other mammals, including humans, posing questions about their immune tolerance mechanisms. Bat cells employ multiple strategies to limit virus replication and virus-induced immunopathology, but the coexistence of bats and fatal viruses remains poorly understood. Here, we investigated the antiviral RNA interference (RNAi) pathway in bat cells and discovered that they have an enhanced antiviral RNAi response, producing canonical viral small interfering RNAs (vsiRNAs) upon Sindbis virus (SINV) infection that were missing in human cells. Disruption of Dicer function resulted in increased viral load for three different RNA viruses in bat cells, indicating an interferon-independent antiviral pathway. Furthermore, our findings reveal the simultaneous engagement of Dicer and pattern-recognition receptors (PRRs), such as retinoic acid-inducible gene I (RIG-I), with double-stranded RNA, suggesting that Dicer attenuates the interferon response initiation in bat cells. These insights advance our comprehension of the distinctive strategies bats employ to coexist with viruses.
2024-07-12 | PXD053906 | Pride
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR.
2010-10-15 | GSE24699 | GEO
Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR.
2010-10-15 | GSE24626 | GEO
Project description:The RNA interference (RNAi) pathway is found in most eukaryotic lineages but curiously is absent in others, including that of Saccharomyces cerevisiae. Here, we show that reconstituting RNAi in S. cerevisiae causes loss of a beneficial dsRNA virus, known as killer virus. Incompatibility between RNAi and killer viruses extends to other fungal species, in that RNAi is absent in all species known to possess dsRNA killer viruses, whereas killer viruses are absent in closely related species that retained RNAi. Thus, the advantage imparted by acquiring and retaining killer viruses explains the persistence of RNAi-deficient species during fungal evolution.
2011-08-10 | GSE31288 | GEO