Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1072075 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27834932_1.fastq.gz | Fastqsanger.gz | |||
| SRR27834933_1.fastq.gz | Fastqsanger.gz | |||
| SRR27834934_1.fastq.gz | Fastqsanger.gz | |||
| SRR27834935_1.fastq.gz | Fastqsanger.gz | |||
| SRR27834936_1.fastq.gz | Fastqsanger.gz |
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Project description:We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas were abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti were similar to those in the Americas and revealed the first wild example of dengue vsmRNAs. African Ae. aegypti displayed vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lacked viruses, yet two commercial strains were deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs revealed viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generated stably infected cell lines which produced vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can tolerate the persistence of viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.
2025-11-23 | GSE309873 | GEO
Project description:We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas were abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti were similar to those in the Americas and revealed the first wild example of dengue vsmRNAs. African Ae. aegypti displayed vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lacked viruses, yet two commercial strains were deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs revealed viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generated stably infected cell lines which produced vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can tolerate the persistence of viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.
2025-11-23 | GSE309876 | GEO
Project description:We performed a whole-genome transcriptomic analysis of pleometrotic queens infected by SINV-1, SINV-2 or co-infected with both viruses, to characterize patterns of gene expression associated with viral infection and identify genes responding differentially to the two viruses. We sampled fire ant queens in Gainesville, Florida, immediately after a mating flight. We arranged them in pairs based on having similar weights (range ±0.2 mg) to allow pleometrotic colony founding. We housed paired queens in nesting tubes in claustral conditions (no food or water) for one month. Thereafter, we collected queens in dry ice, we isolated total RNA from whole bodies and used it to quantify SINV-1 and SINV-2 viruses with real-time PCR. We selected 2 queens that were virus-free as controls, 3 SINV-1-infected, 4 SINV-2-infected and 11 co-infected by both viruses. These samples were processed for microarrays analysis.
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Project description:The samples used in this study originated from colonies of managed European honey bees (A. mellifera) that were at the epicenter of an AFB outbreak in 2020. The colonies were officially examined by the State Veterinary Administration of the Czech Republic. For our analyses, we targeted brood samples recognized as larvae before capping. Samples from two sites, namely, the villages Nevsova (denoted by N) and Tetcice (denoted by T), are included in this study.
We aimed to analyze samples of honey bee broods infected and affected by the pathogenic bacterium P. larvae. The colonies from which we collected samples had typical clinical signs of AFB. For our analysis, we selected larvae just before capping. We decided to analyze the samples using high-throughput proteomics, and to select an array of samples, it was necessary to confirm whether the samples were infected by P. larvae. Importantly, the presence/absence of P. larvae was confirmed using PCR before the proteomic analysis in the same individual sample.
The study was supported by project no. QK1710228 (NAZV) and RO0418 of the Ministry of Agriculture of the Czech Republic.
2022-04-11 | MSV000089235 | MassIVE
Project description:In the recent years, RNA silencing has been studied extensively to be a conserved regulatory process in plants. In the antiviral silencing, the intermediate double-stranded RNA form during the replication of RNA viruses were recognized and processed into abundant of overlapping viral siRNA (viRNAs). Accordingly, the cloned viRNAs could be conversely assembled into some contigs of viruses, which is recently exploited for identifying new viruses and their genome sequences.To obtain rapidly the complete genome sequence of BYSMV, we carried out deep sequencing of small RNAs from healthy and BYSMV infected wheat, respectively. Thirteen contigs were assembled from the overlapping viRNAs only present in the infected wheat but not in the healthy wheat. The results of BLAST showed that ten contigs shared about 96% identity with the reported L gene of BYSMV isolate Zanjan-1.
2015-09-15 | GSE61565 | GEO
Project description:COVID-19 is one of the deadliest respiratory diseases, and its emergence caught the pharmaceutical industry off guard. While vaccines have been rapidly developed, treatment options for infected people remain scarce, and COVID-19 poses a substantial global threat. This study presents a novel workflow to predict robust druggable targets against emerging RNA viruses using metabolic networks and information of the viral structure and its genome sequence. For this purpose, we implemented pymCADRE and PREDICATE to create tissue-specific metabolic models, construct viral biomass functions and predict host-based antiviral targets from more than one genome. We observed that pymCADRE reduces the computational time of flux variability analysis for internal optimizations. We applied these tools to create a new metabolic network of primary bronchial epithelial cells infected with SARS-CoV-2 and identified enzymatic reactions with inhibitory effects. The most promising reported targets were from the purine metabolism, while targeting the pyrimidine and carbohydrate metabolisms seemed to be promising approaches to enhance viral inhibition. Finally, we computationally tested the robustness of our targets in all known variants of concern, verifying our targets’ inhibitory effects. Since laboratory tests are time-consuming and involve complex readouts to track processes, our workflow focuses on metabolic fluxes within infected cells and is applicable for rapid hypothesis-driven identification of potentially exploitable antivirals concerning various viruses and host cell types.
Availability: https://github.com/draeger-lab/pymCADRE/.
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